+ * This class is exposed as a Spring Component via
+ * {@link AnnotationBrowserSidebarAutoConfiguration#annotationBrowserSidebarFactory}.
+ *
+ */
public class DiamSidebarFactory
extends AnnotationSidebarFactory_ImplBase
+ implements ClientSideUserPreferencesProvider
{
+ private WatchedResourceFile userPreferencesSchema;
+
+ public DiamSidebarFactory()
+ {
+ var userPreferencesSchemaFile = getClass()
+ .getResource("DiamSidebarFactoryUserPreferences.schema.json");
+ userPreferencesSchema = new WatchedResourceFile<>(userPreferencesSchemaFile,
+ JSONUtil::loadJsonSchema);
+ }
+
@Override
public String getDisplayName()
{
@@ -58,6 +82,21 @@ public AnnotationSidebar_ImplBase create(String aId, IModel aMod
AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
AnnotationPage aAnnotationPage)
{
- return new DiamSidebar(aId, aModel, aActionHandler, aCasProvider, aAnnotationPage);
+ return new DiamSidebar(aId, aModel, aActionHandler, aCasProvider, aAnnotationPage,
+ getUserPreferencesKey().get().getClientSideKey());
+ }
+
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ @Override
+ public Optional> getUserPreferencesKey()
+ {
+ return Optional.of(
+ new ClientSidePreferencesKey<>(Map.class, "annotation/annotation-browser-sidebar"));
+ }
+
+ @Override
+ public Optional getUserPreferencesSchema() throws IOException
+ {
+ return userPreferencesSchema.get();
}
}
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/DiamSidebarFactoryUserPreferences.schema.json b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/DiamSidebarFactoryUserPreferences.schema.json
new file mode 100644
index 00000000000..712bbd83d9b
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/DiamSidebarFactoryUserPreferences.schema.json
@@ -0,0 +1,18 @@
+{
+ "$schema": "http://json-schema.org/draft/2020-12/schema#",
+ "type": "object",
+ "properties": {
+ "mode": {
+ "type": "string",
+ "enum": ["by-label", "by-position"]
+ },
+ "sortByScore": {
+ "type": "boolean"
+ },
+ "recommendationsFirst": {
+ "type": "boolean"
+ }
+ },
+ "required": ["mode"],
+ "additionalProperties": false
+}
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/config/AnnotationBrowserSidebarAutoConfiguration.java b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/config/AnnotationBrowserSidebarAutoConfiguration.java
new file mode 100644
index 00000000000..b090e307b3e
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/config/AnnotationBrowserSidebarAutoConfiguration.java
@@ -0,0 +1,37 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.diam.sidebar.config;
+
+import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnWebApplication;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import de.tudarmstadt.ukp.inception.diam.sidebar.DiamSidebarFactory;
+
+@ConditionalOnWebApplication
+@Configuration
+public class AnnotationBrowserSidebarAutoConfiguration
+{
+ @ConditionalOnExpression("${websocket.enabled:true}")
+ @Bean
+ public DiamSidebarFactory annotationBrowserSidebarFactory()
+ {
+ return new DiamSidebarFactory();
+ }
+}
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.html b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.html
new file mode 100644
index 00000000000..438b5dda341
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.html
@@ -0,0 +1,39 @@
+
+
+
+
+
+
+
+
+
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.java b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.java
new file mode 100644
index 00000000000..3c5f0c5de07
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.java
@@ -0,0 +1,79 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.diam.sidebar.preferences;
+
+import static de.tudarmstadt.ukp.inception.diam.sidebar.preferences.DiamSidebarManagerPrefs.KEY_DIAM_SIDEBAR_MANAGER_PREFS;
+
+import org.apache.wicket.ajax.AjaxRequestTarget;
+import org.apache.wicket.markup.html.form.Form;
+import org.apache.wicket.markup.html.panel.Panel;
+import org.apache.wicket.model.CompoundPropertyModel;
+import org.apache.wicket.model.IModel;
+import org.apache.wicket.spring.injection.annot.SpringBean;
+
+import de.tudarmstadt.ukp.clarin.webanno.api.ProjectService;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaForm;
+import de.tudarmstadt.ukp.inception.editor.AnnotationEditorRegistry;
+import de.tudarmstadt.ukp.inception.preferences.PreferencesService;
+
+public class DiamSidebarManagerPrefPanel
+ extends Panel
+{
+ private static final long serialVersionUID = 3635729182772294488L;
+
+ private @SpringBean AnnotationEditorRegistry annotationEditorRegistry;
+ private @SpringBean PreferencesService preferencesService;
+ private @SpringBean ProjectService projectService;
+
+ private CompoundPropertyModel sidebarPreferences;
+
+ public DiamSidebarManagerPrefPanel(String aId, IModel aProjectModel)
+ {
+ super(aId, aProjectModel);
+ setOutputMarkupPlaceholderTag(true);
+
+ sidebarPreferences = CompoundPropertyModel.of(actionLoad());
+
+ LambdaForm form = new LambdaForm<>("form", sidebarPreferences);
+
+ form.add(new PinnedGroupsPanel("pinnedGroups", sidebarPreferences.bind("pinnedGroups")));
+
+ form.onSubmit(this::actionSave);
+
+ add(form);
+ }
+
+ @SuppressWarnings("unchecked")
+ public IModel getModel()
+ {
+ return (IModel) getDefaultModel();
+ }
+
+ private DiamSidebarManagerPrefs actionLoad()
+ {
+ return preferencesService.loadDefaultTraitsForProject(KEY_DIAM_SIDEBAR_MANAGER_PREFS,
+ getModel().getObject());
+ }
+
+ private void actionSave(AjaxRequestTarget aTarget, Form aForm)
+ {
+ preferencesService.saveDefaultTraitsForProject(KEY_DIAM_SIDEBAR_MANAGER_PREFS,
+ getModel().getObject(), aForm.getModelObject());
+ }
+}
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.properties b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.properties
new file mode 100755
index 00000000000..80316b0580a
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefPanel.properties
@@ -0,0 +1,18 @@
+# Licensed to the Technische Universität Darmstadt under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The Technische Universität Darmstadt
+# licenses this file to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+title=Annotation sidebar
+pinnedGroups=Pinned groups
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefs.java b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefs.java
new file mode 100644
index 00000000000..e86fea044fa
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/DiamSidebarManagerPrefs.java
@@ -0,0 +1,48 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.diam.sidebar.preferences;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import de.tudarmstadt.ukp.inception.preferences.Key;
+
+public class DiamSidebarManagerPrefs
+ implements Serializable
+{
+ private static final long serialVersionUID = 8420554954400084375L;
+
+ public static final Key KEY_DIAM_SIDEBAR_MANAGER_PREFS = new Key<>(
+ DiamSidebarManagerPrefs.class, "annotation/editor/annotation-sidebar/manager");
+
+ private final List pinnedGroups = new ArrayList<>();
+
+ public List getPinnedGroups()
+ {
+ return pinnedGroups;
+ }
+
+ public void setPinnedGroups(List aPinnedGroups)
+ {
+ pinnedGroups.clear();
+ if (aPinnedGroups != null) {
+ pinnedGroups.addAll(aPinnedGroups);
+ }
+ }
+}
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/PinnedGroupsPanel.html b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/PinnedGroupsPanel.html
new file mode 100644
index 00000000000..e7867bee885
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/PinnedGroupsPanel.html
@@ -0,0 +1,51 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/PinnedGroupsPanel.java b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/PinnedGroupsPanel.java
new file mode 100644
index 00000000000..f0167fbd71d
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/preferences/PinnedGroupsPanel.java
@@ -0,0 +1,137 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.diam.sidebar.preferences;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.enabledWhen;
+import static java.util.Collections.swap;
+
+import java.util.List;
+
+import org.apache.wicket.ajax.AjaxRequestTarget;
+import org.apache.wicket.markup.html.form.Form;
+import org.apache.wicket.markup.html.form.TextField;
+import org.apache.wicket.markup.html.list.ListItem;
+import org.apache.wicket.markup.html.list.ListView;
+import org.apache.wicket.markup.html.panel.Panel;
+import org.apache.wicket.model.IModel;
+import org.apache.wicket.model.Model;
+
+import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaAjaxFormComponentUpdatingBehavior;
+import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaAjaxLink;
+
+public class PinnedGroupsPanel
+ extends Panel
+{
+ private static final long serialVersionUID = 5606608290992666303L;
+
+ private final IModel newItemName = Model.of();
+
+ public PinnedGroupsPanel(String id, IModel> aModel)
+ {
+ super(id, aModel);
+
+ setOutputMarkupId(true);
+
+ ListView additionalMatchingPropertiesListView = new ListView("items",
+ getModel())
+ {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void populateItem(ListItem item)
+ {
+ var itemForm = new Form("itemForm");
+ itemForm.add(buildTextField("textField", item.getModel()));
+ itemForm.add(new LambdaAjaxLink("removeItem", t -> PinnedGroupsPanel.this
+ .actionRemoveProperty(t, item.getModelObject())));
+ itemForm.add(new LambdaAjaxLink("moveUp",
+ t -> PinnedGroupsPanel.this.actionMoveUp(t, item.getModelObject()))
+ .add(enabledWhen(() -> item.getIndex() > 0)));
+ itemForm.add(new LambdaAjaxLink("moveDown",
+ t -> PinnedGroupsPanel.this.actionMoveDown(t, item.getModelObject())).add(
+ enabledWhen(() -> item.getIndex() < getModelObject().size() - 1)));
+ item.add(itemForm);
+ }
+
+ };
+ additionalMatchingPropertiesListView.setOutputMarkupId(true);
+ add(additionalMatchingPropertiesListView);
+
+ TextField newPropertyField = new TextField<>("newItemName", newItemName);
+ newPropertyField.add(new LambdaAjaxFormComponentUpdatingBehavior("change"));
+ add(newPropertyField);
+
+ LambdaAjaxLink addPropertyButton = new LambdaAjaxLink("addItem",
+ PinnedGroupsPanel.this::actionAddProperty);
+ add(addPropertyButton);
+ }
+
+ @SuppressWarnings("unchecked")
+ public IModel> getModel()
+ {
+ return (IModel>) getDefaultModel();
+ }
+
+ private TextField buildTextField(String id, IModel model)
+ {
+ TextField iriTextfield = new TextField<>(id, model);
+ iriTextfield.setOutputMarkupId(true);
+ iriTextfield.add(new LambdaAjaxFormComponentUpdatingBehavior("change", t -> {
+ // Do nothing just update the model values
+ }));
+ iriTextfield.setEnabled(false);
+ return iriTextfield;
+ }
+
+ private void actionAddProperty(AjaxRequestTarget aTarget)
+ {
+ var item = newItemName.getObject();
+ var items = getModel().getObject();
+ if (!items.contains(item)) {
+ items.add(item);
+ }
+ newItemName.setObject(null);
+ aTarget.add(this);
+ }
+
+ private void actionRemoveProperty(AjaxRequestTarget aTarget, String aItem)
+ {
+ getModel().getObject().remove(aItem);
+ aTarget.add(this);
+ }
+
+ private void actionMoveUp(AjaxRequestTarget aTarget, String aItem)
+ {
+ var items = getModel().getObject();
+ int index = items.indexOf(aItem);
+ if (index > 0) {
+ swap(items, index - 1, index);
+ }
+ aTarget.add(this);
+ }
+
+ private void actionMoveDown(AjaxRequestTarget aTarget, String aItem)
+ {
+ var items = getModel().getObject();
+ int index = items.indexOf(aItem);
+ if (index < items.size() - 1) {
+ swap(items, index, index + 1);
+ }
+ aTarget.add(this);
+ }
+}
diff --git a/inception/inception-diam-editor/src/main/resources/META-INF/asciidoc/user-guide/annotation-sidebar.adoc b/inception/inception-diam-editor/src/main/resources/META-INF/asciidoc/user-guide/annotation-sidebar.adoc
new file mode 100644
index 00000000000..e7731a007f5
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/resources/META-INF/asciidoc/user-guide/annotation-sidebar.adoc
@@ -0,0 +1,40 @@
+// Licensed to the Technische Universität Darmstadt under one
+// or more contributor license agreements. See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership. The Technische Universität Darmstadt
+// licenses this file to you under the Apache License, Version 2.0 (the
+// "License"); you may not use this file except in compliance
+// with the License.
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+[[sect_annotation_sidebar]]
+= Annotation Sidebar
+
+The annotation sidebar provides an overview over all annotations in the current document. It is located in the left sidebar panel.
+
+The sidebar supports two modes of displaying annotations:
+
+* **Grouped by label (default)**: Annotations are grouped by label. Every annotation is represented
+ by its text. If the same text is annotated multiple times, there will be multiple items with the
+ same text. To help disambiguating between the same text occurring in different contexts, each item
+ also shows a bit of trailing context in a lighter font. Additionally, there is a small badge in
+ every annotation item which allows selecting the annotation or deleting it. Clicking on the text
+ itself will scroll to the annotation in the editor window, but it will not select the annotation.
+ If an item represents an annotation suggestion from a recommender, the badge instead has buttons
+ for accepting or rejecting the suggestion. Again, clicking on the text will scroll the editor
+ window to the suggestion without accepting or rejecting it. Within each group, annotations are
+ sorted alphabetically by their text. If the option **sort by score** is enabled, then
+ suggestions are sorted by score.
+* **Grouped by position**: In this mode, the items are ordered by their position in the text.
+ Relation annotations are grouped under their respective source span annotation. If there are
+ multiple annotations at the same position, then there are multiple badges in the respective item.
+ Each of these badges shows the label of an annotation present at this position and allows
+ selecting or deleting it. Clicking on the text will will scroll to the respective position in the
+ editor window.
diff --git a/inception/inception-diam-editor/src/main/resources/META-INF/asciidoc/user-guide/projects_annotation_sidebar.adoc b/inception/inception-diam-editor/src/main/resources/META-INF/asciidoc/user-guide/projects_annotation_sidebar.adoc
new file mode 100644
index 00000000000..0e4e8465fa3
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/resources/META-INF/asciidoc/user-guide/projects_annotation_sidebar.adoc
@@ -0,0 +1,35 @@
+// Licensed to the Technische Universität Darmstadt under one
+// or more contributor license agreements. See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership. The Technische Universität Darmstadt
+// licenses this file to you under the Apache License, Version 2.0 (the
+// "License"); you may not use this file except in compliance
+// with the License.
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+[[sect_projects_annotation_sidebar]]
+= Annotation sidebar
+
+.Pinned Groups
+This setting allows configuring groups which are always visible in the annotation sidebar on the
+annotation page when the sidebar is in **group by label** mode.
+
+Consider a situation where annotators should always locate one or more mentions of a particular
+concept in every document. Configuring the labels of these concepts as pinned groups will show
+them in the sidebar, even if the annotator has not yet created an annotation for them. This can
+help the annotator to see which concepts still need to be located and annotated in the text.
+
+This functionality can also be used to enforce a particular order of groups if the automatic alphabetic sorting is not convenient.
+
+Note that groups are formed by the label of an annotation which consists of the concatenated feature
+values. Thus, for annotations that have multiple features included in their labels, you need to pay
+close attention to exactly match the rendered labels in your pinned groups (wildcards are not
+supported!). You might consider excluding non-essential features from the label by unchecking the
+option **Visible** in the settings for the respective feature.
diff --git a/inception/inception-diam-editor/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports b/inception/inception-diam-editor/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports
new file mode 100644
index 00000000000..40459cc991a
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports
@@ -0,0 +1 @@
+de.tudarmstadt.ukp.inception.diam.sidebar.config.AnnotationBrowserSidebarAutoConfiguration
diff --git a/inception/inception-diam-editor/src/main/ts/src/AnnotationBrowserState.ts b/inception/inception-diam-editor/src/main/ts/src/AnnotationBrowserState.ts
new file mode 100644
index 00000000000..3d55a9228ed
--- /dev/null
+++ b/inception/inception-diam-editor/src/main/ts/src/AnnotationBrowserState.ts
@@ -0,0 +1,25 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { writable } from 'svelte/store'
+
+export const groupingMode = writable('by-label')
+
+export const sortByScore = writable(true)
+
+export const recommendationsFirst = writable(false)
diff --git a/inception/inception-diam-editor/src/main/ts/src/AnnotationsByLabelList.svelte b/inception/inception-diam-editor/src/main/ts/src/AnnotationsByLabelList.svelte
index f8a248c051a..0944425651b 100644
--- a/inception/inception-diam-editor/src/main/ts/src/AnnotationsByLabelList.svelte
+++ b/inception/inception-diam-editor/src/main/ts/src/AnnotationsByLabelList.svelte
@@ -27,23 +27,26 @@
import { compareOffsets } from "@inception-project/inception-js-api/src/model/Offsets";
import LabelBadge from "./LabelBadge.svelte";
import SpanText from "./SpanText.svelte";
- import { compareSpanText, groupBy, uniqueLabels } from "./Utils";
+ import { compareSpanText, groupBy, renderLabel, uniqueLabels } from "./Utils";
+ import { sortByScore, recommendationsFirst } from "./AnnotationBrowserState"
export let ajaxClient: DiamAjax;
export let data: AnnotatedText;
+ export let pinnedGroups: string[];
let groupedAnnotations: Record;
let sortedLabels: string[];
- let sortByScore: boolean = false;
- $: sortedLabels = uniqueLabels(data);
$: {
- const relations = data?.relations.values() || [];
- const spans = data?.spans.values() || [];
+ sortedLabels = [...pinnedGroups, ...uniqueLabels(data).filter(v => !pinnedGroups.includes(v))]
+
+ const relations = data?.relations.values() || []
+ const spans = data?.spans.values() || []
groupedAnnotations = groupBy(
[...spans, ...relations],
- (s) => s.label || ""
- );
+ (s) => renderLabel(s)
+ )
+
for (const items of Object.values(groupedAnnotations)) {
items.sort((a, b) => {
if (a instanceof Span && !(b instanceof Span)) {
@@ -54,12 +57,14 @@
return 1;
}
- if (sortByScore && a.vid.toString().startsWith("rec:") && !b.vid.toString().startsWith("rec:")) {
- return -1;
+ const aIsRec = a.vid.toString().startsWith("rec:")
+ const bIsRec = b.vid.toString().startsWith("rec:")
+ if ($sortByScore && aIsRec && !bIsRec) {
+ return $recommendationsFirst ? -1 : 1;
}
if (a instanceof Span && b instanceof Span) {
- if (sortByScore) {
+ if ($sortByScore && aIsRec && bIsRec) {
return b.score - a.score;
}
return (
@@ -69,7 +74,7 @@
}
if (a instanceof Relation && b instanceof Relation) {
- if (sortByScore) {
+ if ($sortByScore && aIsRec && bIsRec) {
return b.score - a.score;
}
return compareOffsets(
@@ -97,19 +102,31 @@
@@ -60,9 +56,14 @@ public String getCommand()
public DefaultAjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
{
try {
- AnnotationPageBase page = getPage();
- CAS cas = page.getEditorCas();
- actionSpan(aTarget, aRequest.getRequestParameters(), cas);
+ var page = getPage();
+ var cas = page.getEditorCas();
+ var state = getAnnotatorState();
+ var range = getRangeFromRequest(state, aRequest.getRequestParameters(), cas);
+
+ state.getSelection().selectSpan(cas, range.getBegin(), range.getEnd());
+ page.getAnnotationActionHandler().actionCreateOrUpdate(aTarget, cas);
+
return new DefaultAjaxResponse(getAction(aRequest));
}
catch (Exception e) {
@@ -70,43 +71,17 @@ public DefaultAjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
}
}
- private void actionSpan(AjaxRequestTarget aTarget, IRequestParameters aRequestParameters,
- CAS aCas)
- throws IOException, AnnotationException
- {
- AnnotationPageBase page = (AnnotationPageBase) aTarget.getPage();
- AnnotatorState state = getAnnotatorState();
-
- // This is the span the user has marked in the browser in order to create a new slot-filler
- // annotation OR the span of an existing annotation which the user has selected.
- var userSelectedSpan = getOffsetsFromRequest(state, aRequestParameters, aCas);
-
- if (state.isSlotArmed()) {
- // When filling a slot, the current selection is *NOT* changed. The
- // Span annotation which owns the slot that is being filled remains
- // selected!
- page.getAnnotationActionHandler().actionFillSlot(aTarget, aCas,
- userSelectedSpan.getBegin(), userSelectedSpan.getEnd(), VID.NONE_ID);
- return;
- }
-
- Selection selection = state.getSelection();
- selection.selectSpan(aCas, userSelectedSpan.getBegin(), userSelectedSpan.getEnd());
- page.getAnnotationActionHandler().actionCreateOrUpdate(aTarget, aCas);
- }
-
/**
* Extract offset information from the current request. These are either offsets of an existing
* selected annotations or offsets contained in the request for the creation of a new
* annotation.
*/
- static Range getOffsetsFromRequest(AnnotatorState aState, IRequestParameters request, CAS aCas)
+ static Range getRangeFromRequest(AnnotatorState aState, IRequestParameters request, CAS aCas)
throws IOException
{
- String offsets = request.getParameterValue(PARAM_OFFSETS).toString();
+ var offsets = request.getParameterValue(PARAM_OFFSETS).toString();
- CompactRangeList offsetLists = JSONUtil.getObjectMapper().readValue(offsets,
- CompactRangeList.class);
+ var offsetLists = JSONUtil.getObjectMapper().readValue(offsets, CompactRangeList.class);
int annotationBegin = aState.getWindowBeginOffset() + offsetLists.get(0).getBegin();
int annotationEnd = aState.getWindowBeginOffset()
diff --git a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithExistingAnnotationHandler.java b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithExistingAnnotationHandler.java
index 1c9f9af380e..ff7aed02ee6 100644
--- a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithExistingAnnotationHandler.java
+++ b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithExistingAnnotationHandler.java
@@ -17,12 +17,10 @@
*/
package de.tudarmstadt.ukp.inception.diam.editor.actions;
-import org.apache.uima.cas.CAS;
import org.apache.wicket.ajax.AjaxRequestTarget;
import org.apache.wicket.request.Request;
import org.springframework.core.annotation.Order;
-import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
import de.tudarmstadt.ukp.inception.diam.editor.config.DiamAutoConfig;
import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
@@ -48,13 +46,12 @@ public String getCommand()
public DefaultAjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
{
try {
- AnnotationPageBase page = getPage();
- CAS cas = page.getEditorCas();
-
- // When filling a slot, the current selection is *NOT* changed. The
- // Span annotation which owns the slot that is being filled remains
- // selected!
- page.getAnnotationActionHandler().actionFillSlot(aTarget, cas, 0, 0, getVid(aRequest));
+ var page = getPage();
+ var cas = page.getEditorCas();
+ var slotFillerId = getVid(aRequest);
+ // When filling a slot, the current selection is *NOT* changed. The Span annotation
+ // which owns the slot that is being filled remains selected!
+ page.getAnnotationActionHandler().actionFillSlot(aTarget, cas, slotFillerId);
return new DefaultAjaxResponse(getAction(aRequest));
}
@@ -66,6 +63,7 @@ public DefaultAjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
@Override
public boolean accepts(Request aRequest)
{
- return super.accepts(aRequest) && getAnnotatorState().isSlotArmed();
+ return super.accepts(aRequest) && getAnnotatorState().isSlotArmed()
+ && getVid(aRequest).isSet();
}
}
diff --git a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithNewAnnotationHandler.java b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithNewAnnotationHandler.java
index aefe6d378f5..89164f24f02 100644
--- a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithNewAnnotationHandler.java
+++ b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/FillSlotWithNewAnnotationHandler.java
@@ -31,8 +31,6 @@
import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
import de.tudarmstadt.ukp.inception.diam.model.compact.CompactRange;
import de.tudarmstadt.ukp.inception.diam.model.compact.CompactRangeList;
-import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
-import de.tudarmstadt.ukp.inception.rendering.vmodel.VID;
import de.tudarmstadt.ukp.inception.schema.adapter.AnnotationException;
/**
@@ -77,17 +75,14 @@ private void actionSpan(AjaxRequestTarget aTarget, IRequestParameters aRequestPa
CAS aCas)
throws IOException, AnnotationException
{
- AnnotationPageBase page = (AnnotationPageBase) aTarget.getPage();
-
// This is the span the user has marked in the browser in order to create a new slot-filler
// annotation OR the span of an existing annotation which the user has selected.
- CompactRange userSelectedSpan = getOffsetsFromRequest(aTarget, aRequestParameters, aCas);
+ var range = getRangeFromRequest(aTarget, aRequestParameters, aCas);
- // When filling a slot, the current selection is *NOT* changed. The
- // Span annotation which owns the slot that is being filled remains
- // selected!
- page.getAnnotationActionHandler().actionFillSlot(aTarget, aCas, userSelectedSpan.getBegin(),
- userSelectedSpan.getEnd(), VID.NONE_ID);
+ // When filling a slot, the current selection is *NOT* changed. The Span annotation which
+ // owns the slot that is being filled remains selected!
+ getPage().getAnnotationActionHandler().actionFillSlot(aTarget, aCas, range.getBegin(),
+ range.getEnd());
}
/**
@@ -95,18 +90,17 @@ private void actionSpan(AjaxRequestTarget aTarget, IRequestParameters aRequestPa
* selected annotations or offsets contained in the request for the creation of a new
* annotation.
*/
- private CompactRange getOffsetsFromRequest(AjaxRequestTarget aTarget,
- IRequestParameters request, CAS aCas)
+ private CompactRange getRangeFromRequest(AjaxRequestTarget aTarget, IRequestParameters request,
+ CAS aCas)
throws IOException
{
// Create new span annotation - in this case we get the offset information from the
// request
- String offsets = request.getParameterValue(PARAM_OFFSETS).toString();
+ var offsets = request.getParameterValue(PARAM_OFFSETS).toString();
- CompactRangeList offsetLists = JSONUtil.getObjectMapper().readValue(offsets,
- CompactRangeList.class);
+ var offsetLists = JSONUtil.getObjectMapper().readValue(offsets, CompactRangeList.class);
- AnnotatorState state = getAnnotatorState();
+ var state = getAnnotatorState();
int annotationBegin = state.getWindowBeginOffset() + offsetLists.get(0).getBegin();
int annotationEnd = state.getWindowBeginOffset()
+ offsetLists.get(offsetLists.size() - 1).getEnd();
diff --git a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LazyDetailsHandler.java b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LazyDetailsHandler.java
index d3faa9c1879..b22f7530900 100644
--- a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LazyDetailsHandler.java
+++ b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LazyDetailsHandler.java
@@ -67,9 +67,9 @@ public AjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
final VID paramId = getVid(aRequest);
AnnotatorState state = page.getModelObject();
- var result = lazyDetailsLookupService.lookupLazyDetails(
- aRequest.getRequestParameters(), paramId, casProvider, state.getDocument(),
- state.getUser(), state.getWindowBeginOffset(), state.getWindowEndOffset());
+ var result = lazyDetailsLookupService.lookupLazyDetails(aRequest.getRequestParameters(),
+ paramId, casProvider, state.getDocument(), state.getUser(),
+ state.getWindowBeginOffset(), state.getWindowEndOffset());
attachResponse(aTarget, aRequest, toInterpretableJsonString(result));
return result;
}
diff --git a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LoadAnnotationsHandler.java b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LoadAnnotationsHandler.java
index 8e89a293f94..0534af7211c 100644
--- a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LoadAnnotationsHandler.java
+++ b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LoadAnnotationsHandler.java
@@ -25,6 +25,7 @@
import org.apache.wicket.request.Request;
import org.springframework.core.annotation.Order;
+import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
import de.tudarmstadt.ukp.inception.diam.editor.config.DiamAutoConfig;
import de.tudarmstadt.ukp.inception.diam.model.ajax.AjaxResponse;
import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
@@ -55,12 +56,15 @@ public class LoadAnnotationsHandler
private final RenderingPipeline renderingPipeline;
private final VDocumentSerializerExtensionPoint vDocumentSerializerExtensionPoint;
+ private final UserDao userService;
public LoadAnnotationsHandler(RenderingPipeline aRenderingPipeline,
- VDocumentSerializerExtensionPoint aVDocumentSerializerExtensionPoint)
+ VDocumentSerializerExtensionPoint aVDocumentSerializerExtensionPoint,
+ UserDao aUserService)
{
renderingPipeline = aRenderingPipeline;
vDocumentSerializerExtensionPoint = aVDocumentSerializerExtensionPoint;
+ userService = aUserService;
}
@Override
@@ -100,6 +104,7 @@ private RenderRequest prepareRenderRequest(Request aRequest) throws IOException
RenderRequest request = RenderRequest.builder() //
.withState(state) //
+ .withSessionOwner(userService.getCurrentUser()) //
.withCas(page.getEditorCas()) //
.withWindow(begin, end) //
.withText(includeText) //
diff --git a/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LoadPreferences.java b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LoadPreferences.java
new file mode 100644
index 00000000000..da10ea025ff
--- /dev/null
+++ b/inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/editor/actions/LoadPreferences.java
@@ -0,0 +1,79 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.diam.editor.actions;
+
+import java.util.Map;
+
+import org.apache.wicket.ajax.AjaxRequestTarget;
+import org.apache.wicket.request.Request;
+import org.springframework.core.annotation.Order;
+
+import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
+import de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil;
+import de.tudarmstadt.ukp.inception.diam.editor.config.DiamAutoConfig;
+import de.tudarmstadt.ukp.inception.diam.model.ajax.AjaxResponse;
+import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
+import de.tudarmstadt.ukp.inception.preferences.ClientSidePreferencesKey;
+import de.tudarmstadt.ukp.inception.preferences.PreferencesService;
+
+/**
+ *
+ * This class is exposed as a Spring Component via {@link DiamAutoConfig#loadPreferences}.
+ *
+ */
+@Order(EditorAjaxRequestHandler.PRIO_RENDER_HANDLER)
+public class LoadPreferences
+ extends EditorAjaxRequestHandlerBase
+{
+ public static final String COMMAND = "loadPreferences";
+
+ public static final String PARAM_KEY = "key";
+
+ private final PreferencesService preferencesService;
+ private final UserDao userService;
+
+ public LoadPreferences(UserDao aUserService, PreferencesService aPreferencesService)
+ {
+ userService = aUserService;
+ preferencesService = aPreferencesService;
+ }
+
+ @Override
+ public String getCommand()
+ {
+ return COMMAND;
+ }
+
+ @Override
+ public AjaxResponse handle(AjaxRequestTarget aTarget, Request aRequest)
+ {
+ try {
+ var key = new ClientSidePreferencesKey
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/installation_docker.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/installation_docker.adoc
index 2218c210c8b..481ab6ce1f3 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/installation_docker.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/installation_docker.adoc
@@ -27,10 +27,10 @@ If you have Docker installed, you can run {product-name} using
[source,shell,subs="+attributes"]
----
-$ docker run -it --name inception -p8080:8080 inceptionproject/inception:{revnumber}
+$ docker run -it --name inception -p8080:8080 ghcr.io/inception-project/inception:{revnumber}
----
-The command downloads {product-name} from Dockerhub and starts it on port 8080. If this port is not
+The command downloads {product-name} from GitHub and starts it on port 8080. If this port is not
available on your machine, you should provide another port to the `-p` parameter.
The logs will be printed to the console. To stop the container, press `CTRL-C`.
@@ -39,7 +39,7 @@ To run the {product-name} docker in the background use
[source,shell,subs="+attributes"]
----
-$ docker run -d --name inception -p8080:8080 inceptionproject/inception:{revnumber}
+$ docker run -d --name inception -p8080:8080 ghcr.io/inception-project/inception:{revnumber}
----
Logs are accessible by typing
@@ -86,7 +86,7 @@ When you run {product-name} via Docker, you then mount this folder into the cont
[source,shell,subs="+attributes"]
----
-$ docker run -it --name inception -v /srv/inception:/export -p8080:8080 inceptionproject/inception:{revnumber}
+$ docker run -it --name inception -v /srv/inception:/export -p8080:8080 ghcr.io/inception-project/inception:{revnumber}
----
== Settings file
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/logging.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/logging.adoc
index d7c99beda72..c0cef03991f 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/logging.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/logging.adoc
@@ -39,15 +39,15 @@ logging.level.de.tudarmstadt.ukp.inception.security=TRACE
== Custom logging
A custom logging configuration can be specified when starting up {product-name} using the parameter
-`-Dlog4j.configurationFile=/path/to/your/log4.xml`. This should be a standard Log4J configuration file.
-A good starting point is the default configuration used by {product-name} which can be found in link:https://github.com/inception-project/inception/blob/main/inception/inception-app-webapp/src/main/resources/log4j2.xml[our code repository].
+`-Dlogging.config=/path/to/your/log4.xml`. This should be a standard Log4J2 configuration file.
+A good starting point is the default configuration used by {product-name} which can be found in link:https://github.com/inception-project/inception/blob/main/inception/inception-app-webapp/src/main/resources/log4j2-spring.xml[our code repository].
== Logging in JSON format
If you would like to integrate the logging output of {product-name} with something like LogStash and
Kibana, you may want log output to be in a properly interpretable JSON format, instead of the usual
plain text format. {product-name} comes with several JSON configurations that are compatible with
-popular tools like LogStash and others. You can activate it by adding the following sections to a custom `log4j.xml` file in the `Appenders` sections and in the `Root` logger.
+popular tools like LogStash and others. You can activate it by adding the following sections to a custom `log4j2.xml` file in the `Appenders` sections and in the `Root` logger.
[source,text]
----
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose-mysql8.yml b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose-mysql8.yml
index 79af4291aa6..9aa9ed18c44 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose-mysql8.yml
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose-mysql8.yml
@@ -28,7 +28,7 @@ services:
inception-net:
app:
- image: "${INCEPTION_IMAGE:-inceptionproject/inception}:${INCEPTION_VERSION:-{revnumber}"
+ image: "${INCEPTION_IMAGE:-ghcr.io/inception-project/inception}:${INCEPTION_VERSION:-{revnumber}}"
ports:
- "${INCEPTION_PORT:-8080}:8080"
environment:
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose.yml b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose.yml
index e64e66cc0c5..3f94f582937 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose.yml
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose.yml
@@ -28,7 +28,7 @@ services:
inception-net:
app:
- image: "${INCEPTION_IMAGE:-inceptionproject/inception}:${INCEPTION_VERSION:-{revnumber}}"
+ image: "${INCEPTION_IMAGE:-ghcr.io/inception-project/inception}:${INCEPTION_VERSION:-{revnumber}}"
ports:
- "${INCEPTION_PORT:-8080}:8080"
environment:
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/settings_cas-storage.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/settings_cas-storage.adoc
index 6b0a2ce6d38..71063ea77a9 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/settings_cas-storage.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/settings_cas-storage.adoc
@@ -26,10 +26,16 @@ This section describes settings related to the storage of CAS data objects (i.e.
| Default
| Example
-| cas-storage.compressed-cas-serialization
+| `cas-storage.compressed-cas-serialization`
| Whether to compress annotation files
-| true
-| false
+| `true`
+| `false`
+
+| `cas-storage.file-system-timestamp-accuracy`
+| For file systems where timestamps are not exact, this can be used to configure some leniency. This setting should be used with extreme caution. If an editor accesses an annotation file that is out-of-sync with the editor, this can lead to unexpected behavior. However, when deploying {product-name} e.g. on certain cloud storage facilitites, the file system timestamps may not be exact down to the millisecond,
+this it may be helpful to configure a slight leniency here.
+| `0`
+| `500ms`
|===
The compression setting takes effect whenever a CAS is written to disk. Changing it does not
@@ -49,19 +55,19 @@ This cache can be tuned using the following properties:
| Default
| Example
-| cas-storage.cache.shared-cas-cache-size
+| `cas-storage.cache.shared-cas-cache-size`
| Number of shared read-only CASes to keep in memory
-| 10-5000 _(depending on heap size)_
-| 20000
+| `10`-`5000` _(depending on heap size)_
+| `20000`
-| cas-storage.cache.idle-cas-eviction-delay
+| `cas-storage.cache.idle-cas-eviction-delay`
| Time a CAS is retained in the caches after the last access
-| 5m
-| 1h
+| `5m`
+| `1h`
-| cas-storage.cache.cas-borrow-wait-timeout
+| `cas-storage.cache.cas-borrow-wait-timeout`
| Time for an exclusive action to wait for another exclusive action to finish
-| 3m
-| 5m
+| `3m`
+| `5m`
|===
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade.adoc
index a02283487c6..d85a086ab6d 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade.adoc
@@ -17,9 +17,53 @@
[[sect_upgrade]]
= Upgrading
+== Upgrade paths
-In general, it is possible to perform an in-place upgrade of the application. However, before doing
-an upgrade, it is recommender to create a backup of the application and data to allow coming back
-to a working system if case of a problem during the upgrade. Mind that the upgrade is only completed
-once the new version has successfully started because during startup, the application may make
-changes to the database schema or to the data on disk.
+There are in principle three ways to upgrade {product-name} to a new version:
+
+* **In-place update** - in this scenario, you simply stop the application, replace the existing
+ {product-name} JAR file with the new version, and then start the application again. The benefit
+ of this approach is, that is is very fast. The downside is, that in case anything goes wrong, you
+ cannot simply go back to using the old version. You need to make sure that you have a proper
+ backup of the application home folder and the database (if you use an external database) because
+ the in-place update might migrate your data and after you might no longer be able to use it with
+ an older version (e.g. if you replace the JAR again with an older version). The steps for
+ performing an in-place upgrade are specifed in the respective section below.
+
+* **Migrating to a fresh installation** - in this scenario, you would set up a fresh installation
+ of the new {product-name} version using a different application home folder and a different database
+ than your existing installation. After that, you would move the data of the old installation over
+ to the new installation, e.g. by copying the contents of the old application home/database over
+ into the new ones. When you start the fresh installation then, it will find the data you just
+ copied over, automatically perform a database migration if there were any changes in the database
+ schema, and then start up. The benefit of this approach is that in case anything does wrong during
+ the upgrade or in case there is a critical problem with the new version, you can always go back
+ to using the old installation and e.g. retry the update again at a later time. The steps for
+ setting up a new instance are specified in the installation instructions. The steps for copying
+ the data over to the new instance are the same as for performing a backup.
+
+* **Copying projects to a fresh installation** - in this scenario, you would export all projects
+ from your existing installation. Then you would set up a new installation using a fresh
+ application home folder/database. Finally, you would import all the exported projects into this
+ new installation. The only situation where this type of upgrade procedure is necessary is, when
+ you want to change the database backend, e.g. if you want to switch from an embedded database to
+ an external database. Otherwise, there is typically no benefit in following this approach.
+ It would only be necessary if a new {product-name} release would completely break its database
+ schema and not offer an automatic migration. This typically does never happen since {product-name}
+ has support for automatic database migrations these days. Also note that none of the user's
+ passwords are migrated in this way. When you import the projects in the new installation, you need
+ to enable the **import missing users** option and after all projects have been imported, you need
+ to go through each of the users, enable them, set their roles and set a new password for them.
+ Or alternatively, you could copy the contents of the database tables `users` and `authorities`
+ from the old database into the new one.
+
+The release notes generally indicate that it is possible to perform an in-place upgrade of the
+application. However, before doing an upgrade, it is recommended to create a backup of the
+application and data to allow coming back to a working system if case of a problem during the
+upgrade. Mind that the upgrade is only completed once the new version has successfully started
+because during startup, the application may make changes to the database schema or to the data on
+disk.
+
+Also, for certain versions there might be special considerations to be aware of when performing the
+upgrade. Always be sure to check the section below **as well as the release notes** of every version
+between the version you are upgrading from up to and including the version you are upgrading to.
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_backup.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_backup.adoc
index aa245ed037e..48a3a67bedd 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_backup.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_backup.adoc
@@ -16,5 +16,12 @@
= Backup your data
-* Make a copy of your {product-name} home folder
-* If you are using MySQL, make a backup of your {product-name} database, e.g. using the link:http://dev.mysql.com/doc/refman/5.0/en/mysqldump.html[mysqldump] command.
+* Make a copy of your {product-name} application home folder
+* If you are using an external database like MariaDB, make a backup of your {product-name} database,
+ e.g. using the link:https://mariadb.com/kb/en/making-backups-with-mysqldump/[mysqldump] command.
+
+NOTE: Make sure that you can actually re-create a working installation by restoring your backup.
+ I.e. restore your database export into a fresh database and point a new {product-name} installation
+ at using your home folder copy and the restored database and then start the application and check
+ that everything is there and working. A backup which cannot be successfully restored is worthless.
+
\ No newline at end of file
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_imexport.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_imexport.adoc
deleted file mode 100644
index 30e17806445..00000000000
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_imexport.adoc
+++ /dev/null
@@ -1,33 +0,0 @@
-// Licensed to the Technische Universität Darmstadt under one
-// or more contributor license agreements. See the NOTICE file
-// distributed with this work for additional information
-// regarding copyright ownership. The Technische Universität Darmstadt
-// licenses this file to you under the Apache License, Version 2.0 (the
-// "License"); you may not use this file except in compliance
-// with the License.
-//
-// http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-= Upgrading via export/import
-
-This option can be used when performing an upgrade by exporting all data from once instance of
-the application into another instance which may potentially reside on a different machine. It
-is a very tedious approach because there is no option to bulk-export all projects.
-
-* Log into WebAnno and export all the projects that you wish to migrate using the *Export* pane in the project settings
-* Move your WebAnno home folder to a safe location so that WebAnno and create a new home folder in the old location
-* Copy the *settings.properties* back from your moved folder
-* Start the new WebAnno version to initialize the database
-* Recreate the users
-** If you are using MySQL
-*** create a new database for the new WebAnno version and update the *settings.properties* accordingly
-*** use link:http://dev.mysql.com/doc/refman/5.0/en/mysqldump.html[mysqldump] to dump the tables `users` and `authorities` from the old database and load it back into the new database
-** If you are not using MySQL, you have to recreate the users manually
-* When upgrading to WebAnno 2.x from a pre 2.x version, remove the *format.properties* file from the WebAnno home folder
-* Restart WebAnno and import the previously exported projects
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_jar.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_jar.adoc
index f50654b7321..0c4dd9f4d50 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_jar.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_jar.adoc
@@ -18,7 +18,7 @@
// See the License for the specific language governing permissions and
// limitations under the License.
-= Upgrading with embedded Tomcat
+= Performing an in-place upgrade
* Stop the {product-name} service
* Replace the `inception.jar` file with the new version
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_notes.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_notes.adoc
index 89741feffc4..1f5ac22ce5c 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_notes.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/upgrade_notes.adoc
@@ -18,7 +18,9 @@
This section summarizes important upgrade notes from the release history of INCEpTION. If you upgrade from any version `X`, carefully read all the upgrade notes for versions later than `X`. In particular, if any of the upgrade notes mentions that an intermediate upgrade to that version must be made before going to a higher version, then first perform all required intermediate upgrades in order.
-NOTE: It is a good idea to back up your installation and data before an upgrade.
+NOTE: It is a good idea to back up your installation and data before an upgrade. Also make sure that
+ you can actually re-create a working installation by restoring your backup. A backup which cannot be
+ successfully restored is worthless.
== INCEpTION 25.0
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/release.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/release.adoc
index a49a705c01f..db9a8e21916 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/release.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/release.adoc
@@ -105,7 +105,7 @@ version folder under `releases/{version}/docs` in the documentation
repository. Also update the `_data/releases.yml` file. Create a pull
request for this as well.
-== Publish to DockerHub
+== Publish to GitHub Packages
Make sure that you configured your docker user in your Maven settings:
@@ -118,7 +118,7 @@ Make sure that you configured your docker user in your Maven settings:
----
-Also, your user needs to have push rights to the `inceptionproject` Dockerhub group.
+Also, your user needs to have push rights to the `ghcr.io/inception-project` GitHub package repository.
If you have just made a release, change to `target/checkout/inception-docker`. Otherwise check out the release
tag e.g. via `git checkout tags/inception-app-0.18.0`.
Make sure that in the top-level POM, the version is set to a release version (no snapshot suffix).
@@ -126,11 +126,12 @@ Then go to the `inception-docker` module folder and there run the following comm
[source,xml]
----
-mvn -Pdocker clean docker:build -Ddocker.image.name="inceptionproject/inception"
-mvn -Pdocker docker:push -Ddocker.image.name="inceptionproject/inception"
+mvn -Pdocker clean docker:build -Ddocker.image.name="ghcr.io/inception-project/inception"
+mvn -Pdocker docker:push -Ddocker.image.name="ghcr.io/inception-project/inception"
----
-After successfully publishing to DockerHub, the DockerHub repository will show your released version as the latest version.
+After successfully publishing, the GitHub package repository will show your released
+version as the latest version.
== Aborting and re-running a release
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/setup_eclipse.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/setup_eclipse.adoc
index 01943dc9244..fe39be2151a 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/setup_eclipse.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/developer-guide/setup_eclipse.adoc
@@ -26,8 +26,8 @@ We recommend you start from a *Eclipse IDE for Java Developers* package.
== Use a JDK
-On Linux or OS X, the following setting is not necessary. Having a full JDK installed on your
-system is generally sufficient. You can skip on to the next section.
+On Linux or OS X, having a full JDK installed on your system is generally sufficient. You can skip
+on to the next section.
On Windows, you need to edit the `eclipse.ini` file and directly before the `-vmargs` line, you
have to add the following two lines. Mind to replace `C:/Program Files/Java/jdk11` with the actual
@@ -59,8 +59,9 @@ C:/Program Files/Java/jdk11/jre/bin/server/jvm.dll
== Eclipse Workspace Settings
-* You should check that Text file encoding is UTF-8 in *Preferences -> General -> Workspace* of
- your Eclipse install.
+* You should check that Text file encoding is `UTF-8` in *Preferences -> General -> Workspace*.
+* You need to enable Java annotation preprocessors. Go to *Preferences -> Maven -> Annotation Processing*
+ and set the *Annotation Processing Mode* to *Automatic*.
== Importing {product-name} into the Workspace
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide.adoc
index 5a747d70bca..affc5182045 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide.adoc
@@ -50,8 +50,6 @@ include::{include-dir}annotation_open.adoc[leveloffset=+2]
include::{include-dir}annotation_navigation.adoc[leveloffset=+2]
-include::{include-dir}annotation_undo.adoc[leveloffset=+2]
-
include::{include-dir}annotation_create-annotations.adoc[leveloffset=+2]
include::{include-dir}annotation_create-annotations_span.adoc[leveloffset=+3]
@@ -70,6 +68,10 @@ include::{include-dir}annotation_create-annotations_image-features.adoc[leveloff
include::{include-dir}annotation_create-annotations_concept-features.adoc[leveloffset=+3]
+include::{include-dir}annotation-sidebar.adoc[leveloffset=+2]
+
+include::{include-dir}annotation_undo.adoc[leveloffset=+2]
+
include::{include-dir}annotation_settings.adoc[leveloffset=+2]
include::{include-dir}annotation_export.adoc[leveloffset=+2]
@@ -131,6 +133,8 @@ include::{include-dir}projects_layers_feature_lookup.adoc[leveloffset=+4]
include::{include-dir}projects_annotation.adoc[leveloffset=+2]
+include::{include-dir}projects_annotation_sidebar.adoc[leveloffset=+3]
+
include::{include-dir}projects_knowledge-base.adoc[leveloffset=+2]
include::{include-dir}projects_recommendation.adoc[leveloffset=+2]
@@ -185,6 +189,8 @@ include::{include-dir}external-search-repos-solr.adoc[leveloffset=+3]
include::{include-dir}external-search-repos-pubannotation.adoc[leveloffset=+3]
+include::{include-dir}external-search-repos-pmc.adoc[leveloffset=+3]
+
<<<
include::{include-dir}constraints.adoc[leveloffset=+1]
@@ -235,6 +241,11 @@ data in a particular format. The **feature flag** column shows which flags you c
|====
| Format | Remote API format ID | Feature flag
+| <>
+| `bioc`
+| `format.bioc.enabled`
+
+
| <>
| `conll2000`
| `format.conll2000.enabled`
@@ -357,6 +368,8 @@ data in a particular format. The **feature flag** column shows which flags you c
|====
+include::{include-dir}formats-bioc.adoc[leveloffset=+2]
+
include::{include-dir}formats-conll2000.adoc[leveloffset=+2]
include::{include-dir}formats-conll2002.adoc[leveloffset=+2]
diff --git a/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide/getting-started.adoc b/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide/getting-started.adoc
index 04dfceade56..c8c474c4a5f 100644
--- a/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide/getting-started.adoc
+++ b/inception/inception-doc/src/main/resources/META-INF/asciidoc/user-guide/getting-started.adoc
@@ -575,8 +575,11 @@ You can modify and create tagsets in the project settings.
See section xref:tagsets_in_getting_started[Tagsets] in _Getting Started_ or check the main documentation for <>.
You have almost finished the _Getting Started_.
-One word about the left *Annotation Sidebar*.
-It folds out when clicking on the little arrow on top. Then you get detailed information about the currently chosen feature of the sidebar.
+One word can still be said about the *Sidebars* on the left. These offer access to various
+additional functionalities such as an annotation overview, search, recommenders, etc. Which
+functionalities are available to you is determined by the project settings. The sidebars can be
+opened by clicking on one of the sidebar icons and they can be closed by clicking on the arrow icon at the top.
+
image::getting_started_Sidebar_closed.png[align="center"]
diff --git a/inception/inception-docker/README.md b/inception/inception-docker/README.md
index edf14f6afa1..9a1823dfb26 100644
--- a/inception/inception-docker/README.md
+++ b/inception/inception-docker/README.md
@@ -13,20 +13,20 @@ To create a SNAPSHOT build:
To run the latest SNAPSHOT build, use:
- docker run -p8080:8080 -v inception-data:/export -it inceptionproject/inception-snapshots
+ docker run -p8080:8080 -v inception-data:/export -it ghcr.io/inception-project/inception-snapshots
To run the latest SNAPSHOT build with Docker Compose, use:
- INCEPTION_IMAGE=inceptionproject/inception-snapshots INCEPTION_VERSION=latest docker-compose -f ../inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose.yml -p inception up
+ INCEPTION_IMAGE=ghcr.io/inception-project/inception-snapshots INCEPTION_VERSION=latest docker-compose -f ../inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/scripts/docker-compose.yml -p inception up
## Release builds
For a release build:
- mvn -Pdocker clean docker:build -Ddocker.image.name="inceptionproject/inception"
- mvn -Pdocker docker:push -Ddocker.image.name="inceptionproject/inception"
+ mvn -Pdocker clean docker:build -Ddocker.image.name="ghcr.io/inception-project/inception"
+ mvn -Pdocker docker:push -Ddocker.image.name="ghcr.io/inception-project/inception"
- docker run -p8080:8080 -v inception-data:/export -it inceptionproject/inception
+ docker run -p8080:8080 -v inception-data:/export -it ghcr.io/inception-project/inception
## Multi-platform build for ARM46 and AMD64
@@ -35,7 +35,7 @@ To build a docker images which runs on AMD64 as well as ARM64 machines, use:
docker buildx create --use (need to do this only once!)
mvn -Pdocker-buildx clean package (will be pushed immediately!)
-Mind that you may have to log in to DockerHub before being able to publish. This can be done e.g.
+Mind that you may have to log in to GitHub before being able to publish. This can be done e.g.
via Docker Desktop or on the command line via `docker login`.
## Options
@@ -55,7 +55,7 @@ In the folder where the **inception-doc/src/main/resources/META-INF/asciidoc/adm
docker-compose -p inception up -d
-This starts an INCEpTION instance together with a MySQL database.
+This starts an INCEpTION instance together with a MariaDB database.
To stop, call
diff --git a/inception/inception-docker/pom.xml b/inception/inception-docker/pom.xml
index 01495e66e18..b63f244c96d 100644
--- a/inception/inception-docker/pom.xml
+++ b/inception/inception-docker/pom.xml
@@ -20,14 +20,14 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOT..inception-dockerINCEpTION - Docker Imagepom
- inceptionproject/inception-snapshots
+ ghcr.io/inception-project/inception-snapshots
diff --git a/inception/inception-docker/src/main/docker/Dockerfile b/inception/inception-docker/src/main/docker/Dockerfile
index 4971cf0cffe..279a1a24473 100644
--- a/inception/inception-docker/src/main/docker/Dockerfile
+++ b/inception/inception-docker/src/main/docker/Dockerfile
@@ -4,7 +4,7 @@
#
############################################################
-FROM openjdk:11
+FROM openjdk:17
MAINTAINER INCEpTION Team
@@ -12,7 +12,8 @@ MAINTAINER INCEpTION Team
RUN set -ex \
&& DEBIAN_FRONTEND=noninteractive \
&& apt-get update \
- && apt-get install -y --no-install-recommends locales
+ && apt-get install -y --no-install-recommends locales \
+ && apt-get upgrade -y
RUN set -ex \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
@@ -31,4 +32,4 @@ EXPOSE 8080
ENV JAVA_OPTS="-Xmx750m"
-CMD java ${JAVA_OPTS} -Djava.awt.headless=true -Dinception.home=/export -jar inception-app-standalone.jar
\ No newline at end of file
+CMD java ${JAVA_OPTS} -Djava.awt.headless=true -Dinception.home=/export -jar inception-app-standalone.jar
diff --git a/inception/inception-documents/pom.xml b/inception/inception-documents/pom.xml
index 7d124d5b94d..90aabc01c1f 100644
--- a/inception/inception-documents/pom.xml
+++ b/inception/inception-documents/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-documentsINCEpTION - Core - Persistence API
@@ -117,6 +117,16 @@
+
+ de.tudarmstadt.ukp.inception.app
+ inception-diag
+ test
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-api-schema
+ test
+ org.apache.uimauimafit-core
diff --git a/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccess.java b/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccess.java
index c74dd75e085..353ea22808f 100644
--- a/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccess.java
+++ b/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccess.java
@@ -17,7 +17,9 @@
*/
package de.tudarmstadt.ukp.inception.documents;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.security.AccessCheckingBean;
+import de.tudarmstadt.ukp.clarin.webanno.security.model.User;
import de.tudarmstadt.ukp.inception.documents.config.DocumentServiceAutoConfiguration;
/**
@@ -36,4 +38,6 @@ boolean canViewAnnotationDocument(String aUser, String aProjectId, long aDocumen
boolean canEditAnnotationDocument(String aUser, String aProjectId, long aDocumentId,
String aAnnotator);
+
+ boolean canExportAnnotationDocument(User aUser, Project aProject);
}
diff --git a/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccessImpl.java b/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccessImpl.java
index 039d1566084..e4a1eaece5e 100644
--- a/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccessImpl.java
+++ b/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentAccessImpl.java
@@ -17,9 +17,9 @@
*/
package de.tudarmstadt.ukp.inception.documents;
+import static de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel.ANNOTATOR;
import static de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel.CURATOR;
import static de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel.MANAGER;
-import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.CURATION_USER;
import static org.apache.commons.collections4.CollectionUtils.containsAny;
import java.util.List;
@@ -72,15 +72,16 @@ public boolean canViewAnnotationDocument(String aProjectId, String aDocumentId,
}
@Override
- public boolean canViewAnnotationDocument(String aUser, String aProjectId, long aDocumentId,
- String aAnnotator)
+ public boolean canViewAnnotationDocument(String aSessionOwner, String aProjectId,
+ long aDocumentId, String aAnnotator)
{
log.trace(
- "Permission check: canViewAnnotationDocument [user: {}] [project: {}] [document: {}] [annotator: {}]",
- aUser, aProjectId, aDocumentId, aAnnotator);
+ "Permission check: canViewAnnotationDocument [aSessionOwner: {}] [project: {}] "
+ + "[document: {}] [annotator: {}]",
+ aSessionOwner, aProjectId, aDocumentId, aAnnotator);
try {
- User user = getUser(aUser);
+ User user = getUser(aSessionOwner);
Project project = getProject(aProjectId);
List permissionLevels = projectService.listRoles(project, user);
@@ -90,15 +91,17 @@ public boolean canViewAnnotationDocument(String aUser, String aProjectId, long a
return false;
}
- // Annotators can see their own annotations and manager/curators can see annotations of
- // all users
- if (!aUser.equals(aAnnotator) && !permissionLevels.contains(MANAGER)
- && !(CURATION_USER.equals(aUser)
- && containsAny(permissionLevels, MANAGER, CURATOR))) {
+ // Managers and curators can see anything
+ if (containsAny(permissionLevels, MANAGER, CURATOR)) {
+ return true;
+ }
+
+ // Annotators can only see their own documents
+ if (!aSessionOwner.equals(aAnnotator)) {
return false;
}
- // Blocked documents cannot be viewed
+ // Annotators cannot view blocked documents
SourceDocument doc = documentService.getSourceDocument(project.getId(), aDocumentId);
if (documentService.existsAnnotationDocument(doc, aAnnotator)) {
AnnotationDocument aDoc = documentService.getAnnotationDocument(doc, aAnnotator);
@@ -116,24 +119,25 @@ && containsAny(permissionLevels, MANAGER, CURATOR))) {
}
@Override
- public boolean canEditAnnotationDocument(String aUser, String aProjectId, long aDocumentId,
- String aAnnotator)
+ public boolean canEditAnnotationDocument(String aSessionOwner, String aProjectId,
+ long aDocumentId, String aAnnotator)
{
log.trace(
- "Permission check: canEditAnnotationDocument [user: {}] [project: {}] [document: {}] [annotator: {}]",
- aUser, aProjectId, aDocumentId, aAnnotator);
+ "Permission check: canEditAnnotationDocument [aSessionOwner: {}] [project: {}] "
+ + "[document: {}] [annotator: {}]",
+ aSessionOwner, aProjectId, aDocumentId, aAnnotator);
try {
- User user = getUser(aUser);
+ User user = getUser(aSessionOwner);
Project project = getProject(aProjectId);
// Does the user have the permission to access the project at all?
- if (!projectService.hasRole(user, project, PermissionLevel.ANNOTATOR)) {
+ if (!projectService.hasRole(user, project, ANNOTATOR)) {
return false;
}
// Users can edit their own annotations
- if (!aUser.equals(aAnnotator)) {
+ if (!aSessionOwner.equals(aAnnotator)) {
return false;
}
@@ -154,6 +158,20 @@ public boolean canEditAnnotationDocument(String aUser, String aProjectId, long a
}
}
+ @Override
+ public boolean canExportAnnotationDocument(User aSessionOwner, Project aProject)
+ {
+ if (aProject == null) {
+ return false;
+ }
+
+ if (projectService.hasRole(aSessionOwner, aProject, MANAGER)) {
+ return true;
+ }
+
+ return !aProject.isDisableExport();
+ }
+
private Project getProject(String aProjectId)
{
try {
diff --git a/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentServiceImpl.java b/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentServiceImpl.java
index 54962b203f1..42184519ae7 100644
--- a/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentServiceImpl.java
+++ b/inception/inception-documents/src/main/java/de/tudarmstadt/ukp/inception/documents/DocumentServiceImpl.java
@@ -70,7 +70,6 @@
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@@ -1214,9 +1213,9 @@ public List listAllAnnotationDocuments(SourceDocument aDocum
public Map listAnnotatableDocuments(Project aProject,
User aUser)
{
- Map map = listAllDocuments(aProject, aUser);
+ var map = listAllDocuments(aProject, aUser.getUsername());
- Iterator> i = map.entrySet().iterator();
+ var i = map.entrySet().iterator();
while (i.hasNext()) {
Entry e = i.next();
if (e.getValue() != null && IGNORE == e.getValue().getState()) {
@@ -1229,7 +1228,7 @@ public Map listAnnotatableDocuments(Project
@Override
@Transactional(noRollbackFor = NoResultException.class)
- public Map listAllDocuments(Project aProject, User aUser)
+ public Map listAllDocuments(Project aProject, String aUser)
{
// First get the source documents
var sourceDocsQuery = "FROM SourceDocument WHERE project = (:project)";
@@ -1242,8 +1241,7 @@ public Map listAllDocuments(Project aProject
// documents which are IGNOREed for given users.
var annDocsQuery = "FROM AnnotationDocument WHERE user = (:username) AND project = (:project)";
List annotationDocuments = entityManager
- .createQuery(annDocsQuery, AnnotationDocument.class)
- .setParameter("username", aUser.getUsername()) //
+ .createQuery(annDocsQuery, AnnotationDocument.class).setParameter("username", aUser) //
.setParameter("project", aProject) //
.getResultList();
diff --git a/inception/inception-example-imls-data-majority/pom.xml b/inception/inception-example-imls-data-majority/pom.xml
index f6fad56f3da..49c5fdc0520 100644
--- a/inception/inception-example-imls-data-majority/pom.xml
+++ b/inception/inception-example-imls-data-majority/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-plugin-parent
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOT../inception-plugin-parentinception-example-imls-data-majority
diff --git a/inception/inception-export/pom.xml b/inception/inception-export/pom.xml
index 4f9bd816376..fe09ec4ecd7 100644
--- a/inception/inception-export/pom.xml
+++ b/inception/inception-export/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-exportINCEpTION - Core - Export
@@ -87,6 +87,10 @@
commons-iocommons-io
+
+ it.unimi.dsi
+ fastutil
+ org.springframework
diff --git a/inception/inception-export/src/main/java/de/tudarmstadt/ukp/inception/export/DocumentImportExportServiceImpl.java b/inception/inception-export/src/main/java/de/tudarmstadt/ukp/inception/export/DocumentImportExportServiceImpl.java
index 6e861ccb688..df59c506df5 100644
--- a/inception/inception-export/src/main/java/de/tudarmstadt/ukp/inception/export/DocumentImportExportServiceImpl.java
+++ b/inception/inception-export/src/main/java/de/tudarmstadt/ukp/inception/export/DocumentImportExportServiceImpl.java
@@ -100,6 +100,7 @@
import de.tudarmstadt.ukp.inception.export.config.DocumentImportExportServiceProperties;
import de.tudarmstadt.ukp.inception.export.config.DocumentImportExportServiceProperties.CasDoctorOnImportPolicy;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
+import it.unimi.dsi.fastutil.ints.IntArrayList;
/**
*
@@ -308,7 +309,7 @@ public CAS importCasFromFile(File aFile, SourceDocument aDocument, String aForma
// Prepare a CAS with the project type system
CAS cas = WebAnnoCasUtil.createCas(tsd);
- format.read(WebAnnoCasUtil.getRealCas(cas), aFile);
+ format.read(aDocument.getProject(), WebAnnoCasUtil.getRealCas(cas), aFile);
// Create sentence / token annotations if they are missing - sentences first because
// tokens are then generated inside the sentences
@@ -394,23 +395,56 @@ private void splitSenencesIfNecssaryAndCheckQuota(CAS cas, FormatSupport aFormat
public static void splitSentences(CAS aCas)
{
- BreakIterator bi = BreakIterator.getSentenceInstance(Locale.US);
- bi.setText(aCas.getDocumentText());
- int last = bi.first();
- int cur = bi.next();
- while (cur != BreakIterator.DONE) {
- int[] span = new int[] { last, cur };
- trim(aCas.getDocumentText(), span);
- if (!isEmpty(span[0], span[1])) {
- aCas.addFsToIndexes(createSentence(aCas, span[0], span[1]));
+ splitSentences(aCas, null);
+ }
+
+ public static void splitSentences(CAS aCas, Iterable aZones)
+ {
+ if (aCas.getDocumentText() == null) {
+ return;
+ }
+
+ int[] sortedZoneBoundaries = null;
+
+ if (aZones != null) {
+ var zoneBoundaries = new IntArrayList();
+ for (var zone : aZones) {
+ zoneBoundaries.add(zone.getBegin());
+ zoneBoundaries.add(zone.getEnd());
+ }
+
+ sortedZoneBoundaries = zoneBoundaries.intStream().distinct().sorted().toArray();
+ }
+
+ if (sortedZoneBoundaries == null || sortedZoneBoundaries.length < 2) {
+ sortedZoneBoundaries = new int[] { 0, aCas.getDocumentText().length() };
+ }
+
+ for (int i = 1; i < sortedZoneBoundaries.length; i++) {
+ var begin = sortedZoneBoundaries[i - 1];
+ var end = sortedZoneBoundaries[i];
+ BreakIterator bi = BreakIterator.getSentenceInstance(Locale.US);
+ bi.setText(aCas.getDocumentText().substring(begin, end));
+ int last = bi.first();
+ int cur = bi.next();
+ while (cur != BreakIterator.DONE) {
+ int[] span = new int[] { last + begin, cur + begin };
+ trim(aCas.getDocumentText(), span);
+ if (!isEmpty(span[0], span[1])) {
+ aCas.addFsToIndexes(createSentence(aCas, span[0], span[1]));
+ }
+ last = cur;
+ cur = bi.next();
}
- last = cur;
- cur = bi.next();
}
}
public static void tokenize(CAS aCas)
{
+ if (aCas.getDocumentText() == null) {
+ return;
+ }
+
BreakIterator bi = BreakIterator.getWordInstance(Locale.US);
for (AnnotationFS s : selectSentences(aCas)) {
bi.setText(s.getCoveredText());
diff --git a/inception/inception-export/src/test/java/de/tudarmstadt/ukp/inception/export/SegmentationTest.java b/inception/inception-export/src/test/java/de/tudarmstadt/ukp/inception/export/SegmentationTest.java
index 2cd4993ef52..88af663c2d4 100644
--- a/inception/inception-export/src/test/java/de/tudarmstadt/ukp/inception/export/SegmentationTest.java
+++ b/inception/inception-export/src/test/java/de/tudarmstadt/ukp/inception/export/SegmentationTest.java
@@ -17,15 +17,17 @@
*/
package de.tudarmstadt.ukp.inception.export;
-import static java.util.Arrays.asList;
import static org.apache.uima.fit.util.CasUtil.toText;
import static org.apache.uima.fit.util.JCasUtil.select;
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.assertj.core.api.Assertions.assertThat;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.jcas.JCas;
import org.junit.jupiter.api.Test;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Div;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Heading;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Paragraph;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
@@ -38,7 +40,21 @@ public void testSplitSentences() throws Exception
DocumentImportExportServiceImpl.splitSentences(jcas.getCas());
- assertEquals(asList("I am one.", "I am two."), toText(select(jcas, Sentence.class)));
+ assertThat(toText(select(jcas, Sentence.class))) //
+ .containsExactly("I am one.", "I am two.");
+ }
+
+ @Test
+ public void testSplitSentencesWithZones() throws Exception
+ {
+ JCas jcas = JCasFactory.createText("Heading I am two.", "en");
+ new Heading(jcas, 0, 7).addToIndexes();
+ new Paragraph(jcas, 8, 17).addToIndexes();
+
+ DocumentImportExportServiceImpl.splitSentences(jcas.getCas(), jcas.select(Div.class));
+
+ assertThat(toText(select(jcas, Sentence.class))) //
+ .containsExactly("Heading", "I am two.");
}
@Test
@@ -46,13 +62,14 @@ public void testTokenize() throws Exception
{
JCas jcas = JCasFactory.createText("i am one.i am two.", "en");
new Sentence(jcas, 0, 9).addToIndexes();
- ;
new Sentence(jcas, 9, 18).addToIndexes();
DocumentImportExportServiceImpl.tokenize(jcas.getCas());
- assertEquals(asList("i am one.", "i am two."), toText(select(jcas, Sentence.class)));
- assertEquals(asList("i", "am", "one", ".", "i", "am", "two", "."),
- toText(select(jcas, Token.class)));
+ assertThat(toText(select(jcas, Sentence.class))) //
+ .containsExactly("i am one.", "i am two.");
+
+ assertThat(toText(select(jcas, Token.class))) //
+ .containsExactly("i", "am", "one", ".", "i", "am", "two", ".");
}
}
diff --git a/inception/inception-external-editor/pom.xml b/inception/inception-external-editor/pom.xml
index c226288a2e5..e462d53fef9 100644
--- a/inception/inception-external-editor/pom.xml
+++ b/inception/inception-external-editor/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-external-editorINCEpTION - Editor - External editor
@@ -69,6 +69,10 @@
de.tudarmstadt.ukp.inception.appinception-diam
+
+ de.tudarmstadt.ukp.inception.app
+ inception-preferences
+ de.tudarmstadt.ukp.inception.appinception-websocket
@@ -125,6 +129,10 @@
com.fasterxml.jackson.corejackson-annotations
+
+ com.networknt
+ json-schema-validator
+ org.apache.wicket
@@ -146,6 +154,10 @@
com.googlecode.wicket-jquery-uiwicket-jquery-ui
+
+ org.danekja
+ jdk-serializable-functional
+ org.slf4j
diff --git a/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditor.java b/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditor.java
index 2d3471e8100..ce268afd50c 100644
--- a/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditor.java
+++ b/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditor.java
@@ -33,8 +33,6 @@
import de.tudarmstadt.ukp.clarin.webanno.api.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
-import de.tudarmstadt.ukp.inception.editor.AnnotationEditorRegistry;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
import de.tudarmstadt.ukp.inception.editor.view.DocumentViewExtensionPoint;
import de.tudarmstadt.ukp.inception.externaleditor.config.ExternalEditorPluginDescripion;
@@ -51,18 +49,13 @@ public class ExternalAnnotationEditor
private @SpringBean DocumentViewExtensionPoint documentViewExtensionPoint;
private @SpringBean DocumentService documentService;
- private @SpringBean AnnotationEditorRegistry annotationEditorRegistry;
private @SpringBean ServletContext context;
- private final String editorFactoryId;
-
public ExternalAnnotationEditor(String aId, IModel aModel,
AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
String aEditorFactoryId)
{
- super(aId, aModel, aActionHandler, aCasProvider);
-
- editorFactoryId = aEditorFactoryId;
+ super(aId, aModel, aActionHandler, aCasProvider, aEditorFactoryId);
}
@Override
@@ -76,20 +69,22 @@ protected Component makeView()
AnnotatorState state = getModelObject();
- AnnotationDocument annDoc = documentService.getAnnotationDocument(state.getDocument(),
- state.getUser());
-
return documentViewExtensionPoint.getExtension(getDescription().getView()) //
- .map(ext -> ext.createView(CID_VIS, Model.of(annDoc), editorFactoryId)) //
+ .map(ext -> ext.createView(CID_VIS, Model.of(state.getDocument()),
+ getFactory().getBeanName())) //
.orElseGet(() -> new Label(CID_VIS,
"Unsupported view: [" + getDescription().getView() + "]"));
}
+ @Override
+ protected ExternalAnnotationEditorFactory getFactory()
+ {
+ return (ExternalAnnotationEditorFactory) super.getFactory();
+ }
+
private ExternalEditorPluginDescripion getDescription()
{
- ExternalAnnotationEditorFactory factory = (ExternalAnnotationEditorFactory) annotationEditorRegistry
- .getEditorFactory(editorFactoryId);
- return factory.getDescription();
+ return getFactory().getDescription();
}
private String getUrlForPluginAsset(String aAssetPath)
@@ -107,7 +102,7 @@ public static String getUrlForPluginAsset(ServletContext aContext,
@Override
protected AnnotationEditorProperties getProperties()
{
- AnnotationEditorProperties props = new AnnotationEditorProperties();
+ var props = new AnnotationEditorProperties();
ExternalEditorPluginDescripion pluginDesc = getDescription();
props.setEditorFactory(pluginDesc.getFactory());
props.setDiamAjaxCallbackUrl(getDiamBehavior().getCallbackUrl().toString());
@@ -118,6 +113,7 @@ protected AnnotationEditorProperties getProperties()
props.setScriptSources(pluginDesc.getScripts().stream() //
.map(this::getUrlForPluginAsset) //
.collect(toList()));
+ props.setEditorFactoryId(getFactory().getBeanName());
return props;
}
diff --git a/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorBase.java b/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorBase.java
index 7ce3c5e88ce..15d56f8f4f5 100644
--- a/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorBase.java
+++ b/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorBase.java
@@ -46,6 +46,7 @@
import de.tudarmstadt.ukp.clarin.webanno.api.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
+import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
import de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaMenuItem;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.ContextMenu;
@@ -56,6 +57,7 @@
import de.tudarmstadt.ukp.inception.diam.model.ajax.DefaultAjaxResponse;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorBase;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorExtensionRegistry;
+import de.tudarmstadt.ukp.inception.editor.AnnotationEditorFactory;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorRegistry;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
import de.tudarmstadt.ukp.inception.editor.view.DocumentViewExtensionPoint;
@@ -66,6 +68,7 @@
import de.tudarmstadt.ukp.inception.externaleditor.command.ScrollToCommand;
import de.tudarmstadt.ukp.inception.externaleditor.model.AnnotationEditorProperties;
import de.tudarmstadt.ukp.inception.externaleditor.resources.ExternalEditorJavascriptResourceReference;
+import de.tudarmstadt.ukp.inception.preferences.PreferencesService;
import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
import de.tudarmstadt.ukp.inception.rendering.selection.ScrollToEvent;
import de.tudarmstadt.ukp.inception.rendering.selection.Selection;
@@ -82,21 +85,28 @@ public abstract class ExternalAnnotationEditorBase
protected static final String CID_VIS = "vis";
+ private @SpringBean PreferencesService preferencesService;
private @SpringBean DocumentViewExtensionPoint documentViewExtensionPoint;
private @SpringBean DocumentService documentService;
private @SpringBean AnnotationEditorRegistry annotationEditorRegistry;
private @SpringBean AnnotationEditorExtensionRegistry extensionRegistry;
private @SpringBean ServletContext context;
+ private @SpringBean UserDao userService;
+
+ private final String editorFactoryId;
private DiamAjaxBehavior diamBehavior;
private Component vis;
private ContextMenu contextMenu;
public ExternalAnnotationEditorBase(String aId, IModel aModel,
- AnnotationActionHandler aActionHandler, CasProvider aCasProvider)
+ AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
+ String aEditorFactoryId)
{
super(aId, aModel, aActionHandler, aCasProvider);
+ editorFactoryId = aEditorFactoryId;
+
setOutputMarkupPlaceholderTag(true);
add(visibleWhen(getModel().map(AnnotatorState::getProject).isPresent()));
}
@@ -119,6 +129,11 @@ protected void onInitialize()
LOG.trace("[{}][{}] {}", getMarkupId(), vis.getMarkupId(), getClass().getSimpleName());
}
+ protected AnnotationEditorFactory getFactory()
+ {
+ return annotationEditorRegistry.getEditorFactory(editorFactoryId);
+ }
+
protected DiamAjaxBehavior createDiamBehavior()
{
var diam = new DiamAjaxBehavior();
diff --git a/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorFactory.java b/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorFactory.java
index 4fa0426b55b..424ac1002d2 100644
--- a/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorFactory.java
+++ b/inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorFactory.java
@@ -18,31 +18,40 @@
package de.tudarmstadt.ukp.inception.externaleditor;
import java.io.IOException;
+import java.util.Map;
import java.util.Optional;
import org.apache.wicket.model.IModel;
+import com.networknt.schema.JsonSchema;
+
import de.tudarmstadt.ukp.clarin.webanno.api.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.paging.NoPagingStrategy;
+import de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil;
import de.tudarmstadt.ukp.clarin.webanno.support.WatchedResourceFile;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorBase;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorFactoryImplBase;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
import de.tudarmstadt.ukp.inception.externaleditor.config.ExternalEditorPluginDescripion;
+import de.tudarmstadt.ukp.inception.preferences.ClientSidePreferencesKey;
+import de.tudarmstadt.ukp.inception.preferences.ClientSideUserPreferencesProvider;
import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
import de.tudarmstadt.ukp.inception.support.xml.sanitizer.PolicyCollection;
import de.tudarmstadt.ukp.inception.support.xml.sanitizer.PolicyCollectionIOUtils;
public class ExternalAnnotationEditorFactory
extends AnnotationEditorFactoryImplBase
+ implements ClientSideUserPreferencesProvider
{
private final ExternalEditorPluginDescripion description;
private WatchedResourceFile policyResource;
+ private WatchedResourceFile userPreferencesSchema;
public ExternalAnnotationEditorFactory(ExternalEditorPluginDescripion aDescription)
{
description = aDescription;
+
var policyFile = getDescription().getBasePath().resolve("policy.yaml");
try {
policyResource = new WatchedResourceFile<>(policyFile,
@@ -51,6 +60,16 @@ public ExternalAnnotationEditorFactory(ExternalEditorPluginDescripion aDescripti
catch (IOException e) {
throw new IllegalStateException(e);
}
+
+ var userPreferencesSchemaFile = getDescription().getBasePath()
+ .resolve("userPreferences.schema.json");
+ try {
+ userPreferencesSchema = new WatchedResourceFile<>(userPreferencesSchemaFile,
+ JSONUtil::loadJsonSchema);
+ }
+ catch (IOException e) {
+ throw new IllegalStateException(e);
+ }
}
@Override
@@ -78,8 +97,23 @@ public AnnotationEditorBase create(String aId, IModel aModel,
getBeanName());
}
+ @Override
public Optional getPolicy() throws IOException
{
return policyResource.get();
}
+
+ @Override
+ public Optional getUserPreferencesSchema() throws IOException
+ {
+ return userPreferencesSchema.get();
+ }
+
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ @Override
+ public Optional> getUserPreferencesKey()
+ {
+ return (Optional) Optional
+ .of(new ClientSidePreferencesKey
+
+ org.danekja
+ jdk-serializable-functional
+ org.slf4jslf4j-api
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ test
+
diff --git a/inception/inception-external-search-opensearch/pom.xml b/inception/inception-external-search-opensearch/pom.xml
index fcb5ccdfaf0..d880e4f2f1c 100644
--- a/inception/inception-external-search-opensearch/pom.xml
+++ b/inception/inception-external-search-opensearch/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-external-search-opensearchINCEpTION - External Search - OpenSearch
@@ -136,6 +136,10 @@
org.apache.wicketwicket-spring
+
+ org.danekja
+ jdk-serializable-functional
+
@@ -148,5 +152,10 @@
opensearch-runnertest
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ test
+
-
+
diff --git a/inception/inception-external-search-opensearch/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/opensearch/OpenSearchProviderTest.java b/inception/inception-external-search-opensearch/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/opensearch/OpenSearchProviderTest.java
index 116695d0052..5e6a1642f09 100644
--- a/inception/inception-external-search-opensearch/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/opensearch/OpenSearchProviderTest.java
+++ b/inception/inception-external-search-opensearch/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/opensearch/OpenSearchProviderTest.java
@@ -29,6 +29,7 @@
import org.junit.jupiter.api.Test;
import org.opensearch.LegacyESVersion;
import org.opensearch.common.settings.Settings;
+import org.opensearch.common.settings.Settings.Builder;
import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchResult;
import de.tudarmstadt.ukp.inception.externalsearch.model.DocumentRepository;
@@ -52,7 +53,16 @@ public class OpenSearchProviderTest
public void setup()
{
osRunner = new OpenSearchRunner();
- osRunner.build(newConfigs());
+ osRunner.onBuild(new OpenSearchRunner.Builder()
+ {
+ @Override
+ public void build(int aIndex, Builder aBuilder)
+ {
+ // This should hopefully allow running tests on machines with less than the
+ // default 90% high watermark disk space free (e.g on a 1TB drive less than 100 GB).
+ aBuilder.put("cluster.routing.allocation.disk.threshold_enabled", false);
+ }
+ }).build(newConfigs());
var port = osRunner.client().settings().get("http.port");
osRunner.ensureYellow();
diff --git a/inception/inception-external-search-pubannotation/pom.xml b/inception/inception-external-search-pubannotation/pom.xml
index b9373bfb134..88fc1f63e80 100644
--- a/inception/inception-external-search-pubannotation/pom.xml
+++ b/inception/inception-external-search-pubannotation/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-external-search-pubannotationINCEpTION - External Search - PubAnnotation
@@ -38,6 +38,14 @@
de.tudarmstadt.ukp.inception.appinception-api-formats
+
+ de.tudarmstadt.ukp.inception.app
+ inception-external-search-pubmed
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ org.dkpro.core
@@ -65,6 +73,10 @@
commons-iocommons-io
+
+ org.apache.commons
+ commons-lang3
+ org.springframework
diff --git a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProvider.java b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProvider.java
index 33919d331c9..7394473049a 100644
--- a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProvider.java
+++ b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProvider.java
@@ -17,8 +17,14 @@
*/
package de.tudarmstadt.ukp.inception.externalsearch.pubannotation;
+import static de.tudarmstadt.ukp.inception.externalsearch.pubannotation.model.PubAnnotationDocumentSection.SPRING_LIST_TYPE_REF;
+import static java.lang.Integer.parseInt;
import static java.nio.charset.StandardCharsets.UTF_8;
import static java.util.Arrays.asList;
+import static java.util.function.Function.identity;
+import static java.util.stream.Collectors.groupingBy;
+import static java.util.stream.Collectors.toMap;
+import static org.springframework.http.HttpMethod.GET;
import java.io.IOException;
import java.io.InputStream;
@@ -29,8 +35,7 @@
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
-import org.springframework.core.ParameterizedTypeReference;
-import org.springframework.http.HttpMethod;
+import org.apache.commons.lang3.tuple.Pair;
import org.springframework.http.ResponseEntity;
import org.springframework.web.client.RestClientException;
import org.springframework.web.client.RestTemplate;
@@ -44,37 +49,59 @@
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.model.PubAnnotationDocumentHandle;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.model.PubAnnotationDocumentSection;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.traits.PubAnnotationProviderTraits;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.model.DocSum;
public class PubAnnotationProvider
implements ExternalSearchProvider
{
- public List query(PubAnnotationProviderTraits aTraits,
- String aQuery)
+ private static final String EXT_JSON = ".json";
+
+ private final EntrezClient entrezClient;
+
+ public PubAnnotationProvider(EntrezClient aEntrezClient)
+ {
+ entrezClient = aEntrezClient;
+ }
+
+ List query(PubAnnotationProviderTraits aTraits, String aQuery,
+ int aPage, int aPageSize)
{
Map variables = new HashMap<>();
variables.put("keywords", aQuery);
+ variables.put("page", Integer.toString(aPage));
+ variables.put("per", Integer.toString(aPageSize));
RestTemplate restTemplate = new RestTemplate();
- ResponseEntity> response = restTemplate.exchange(
- aTraits.getUrl() + "/docs.json?keywords={keywords}", HttpMethod.GET, null,
- new DocumentHandleList(), variables);
+ ResponseEntity response = restTemplate.exchange(
+ aTraits.getUrl() + "/docs.json?keywords={keywords}&page={page}&per={per}", GET,
+ null, PubAnnotationDocumentHandle[].class, variables);
- return response.getBody();
+ return asList(response.getBody());
}
@Override
public List executeQuery(DocumentRepository aDocumentRepository,
PubAnnotationProviderTraits aTraits, String aQuery)
{
- List response = query(aTraits, aQuery);
+ List response = query(aTraits, aQuery, 1, 100);
+
+ var documentSummaries = lookupDocumentSummaries(response);
List results = new ArrayList<>();
for (PubAnnotationDocumentHandle handle : response) {
- ExternalSearchResult result = new ExternalSearchResult(aDocumentRepository,
- handle.getSourceDb(), handle.getSourceId() + ".json");
- result.setOriginalSource(handle.getSourceDb());
- result.setDocumentTitle(handle.getUrl());
- result.setHighlights(handle.getHighlights().stream().map(ExternalSearchHighlight::new)
+ var summary = documentSummaries
+ .get(Pair.of(handle.getSourceDb(), parseInt(handle.getSourceId())));
+ var result = new ExternalSearchResult(aDocumentRepository, handle.getSourceDb(),
+ handle.getSourceId() + EXT_JSON);
+ result.setOriginalSource(summary != null ? summary.source() : handle.getSourceDb());
+ result.setDocumentTitle(
+ summary != null ? summary.title() : handle.getSourceId() + EXT_JSON);
+ if (summary != null) {
+ result.setTimestamp(summary.date());
+ }
+ result.setHighlights(handle.getHighlights().stream() //
+ .map(ExternalSearchHighlight::new) //
.collect(Collectors.toList()));
results.add(result);
}
@@ -82,6 +109,25 @@ public List executeQuery(DocumentRepository aDocumentRepos
return results;
}
+ private Map, DocSum> lookupDocumentSummaries(
+ List response)
+ {
+ Map, DocSum> documentDetails = new HashMap<>();
+ var groupedByDb = response.stream()
+ .collect(groupingBy(PubAnnotationDocumentHandle::getSourceDb));
+ for (var group : groupedByDb.entrySet()) {
+ var db = group.getKey();
+ var ids = group.getValue().stream() //
+ .map(PubAnnotationDocumentHandle::getSourceId) //
+ .mapToInt(Integer::parseInt).toArray();
+ var summaries = entrezClient.esummary(db, ids).getDocSumaries();
+ documentDetails.putAll(summaries.stream()
+ .collect(toMap(summary -> Pair.of(db, summary.getId()), identity())));
+ }
+ return documentDetails;
+ }
+
+ @Deprecated
@Override
public ExternalSearchResult getDocumentResult(DocumentRepository aRepository,
PubAnnotationProviderTraits aTraits, String aCollectionId, String aDocumentId)
@@ -120,19 +166,17 @@ private List getSections(DocumentRepository aDocum
RestTemplate restTemplate = new RestTemplate();
+ var url = aTraits.getUrl() + "/docs/sourcedb/{collectionId}/sourceid/{documentId}.json";
try {
// If the document has multiple sections, a list is returned...
- ResponseEntity> response = restTemplate.exchange(
- aTraits.getUrl() + "/docs/sourcedb/{collectionId}/sourceid/{documentId}",
- HttpMethod.GET, null, PubAnnotationDocumentSection.SPRING_LIST_TYPE_REF,
- variables);
+ ResponseEntity> response = restTemplate.exchange(url,
+ GET, null, SPRING_LIST_TYPE_REF, variables);
return response.getBody();
}
catch (RestClientException e) {
// If the document has as single section, an object is returned...
- PubAnnotationDocumentSection section = restTemplate.getForObject(
- aTraits.getUrl() + "/docs/sourcedb/{collectionId}/sourceid/{documentId}",
+ PubAnnotationDocumentSection section = restTemplate.getForObject(url,
PubAnnotationDocumentSection.class, variables);
return asList(section);
@@ -146,10 +190,4 @@ public String getDocumentFormat(DocumentRepository aRepository,
{
return PubAnnotationSectionsFormatSupport.ID;
}
-
- private static class DocumentHandleList
- extends ParameterizedTypeReference>
- {
- // Just a type reference
- }
}
diff --git a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderFactory.java b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderFactory.java
index af0b0579611..8cb37ba0a52 100644
--- a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderFactory.java
+++ b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderFactory.java
@@ -35,6 +35,7 @@
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.config.PubAnnotationDocumentRepositoryAutoConfiguration;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.traits.PubAnnotationProviderTraits;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.traits.PubAnnotationProviderTraitsEditor;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
/**
* Support for PubAnnotation.
@@ -49,8 +50,15 @@ public class PubAnnotationProviderFactory
{
private final Logger log = LoggerFactory.getLogger(getClass());
+ private final EntrezClient entrezClient;
+
private String beanName;
+ public PubAnnotationProviderFactory(EntrezClient aEntrezClient)
+ {
+ entrezClient = aEntrezClient;
+ }
+
@Override
public void setBeanName(String aName)
{
@@ -72,7 +80,7 @@ public String getDisplayName()
@Override
public ExternalSearchProvider getNewExternalSearchProvider()
{
- return new PubAnnotationProvider();
+ return new PubAnnotationProvider(entrezClient);
}
@Override
diff --git a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/config/PubAnnotationDocumentRepositoryAutoConfiguration.java b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/config/PubAnnotationDocumentRepositoryAutoConfiguration.java
index 37f8bbaf4ae..b1ed29990f8 100644
--- a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/config/PubAnnotationDocumentRepositoryAutoConfiguration.java
+++ b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/config/PubAnnotationDocumentRepositoryAutoConfiguration.java
@@ -27,21 +27,21 @@
import de.tudarmstadt.ukp.inception.externalsearch.config.ExternalSearchAutoConfiguration;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.PubAnnotationProviderFactory;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.format.PubAnnotationSectionsFormatSupport;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.config.PubMedServicesAutoConfiguration;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
-/**
- * Provides support for ElasticSearch-based document repositories.
- */
@Configuration
-@AutoConfigureAfter(ExternalSearchAutoConfiguration.class)
+@AutoConfigureAfter({ ExternalSearchAutoConfiguration.class,
+ PubMedServicesAutoConfiguration.class })
@ConditionalOnProperty(prefix = "external-search.pub-annotation", //
name = "enabled", havingValue = "true", matchIfMissing = true)
@ConditionalOnBean(ExternalSearchService.class)
public class PubAnnotationDocumentRepositoryAutoConfiguration
{
@Bean
- public PubAnnotationProviderFactory pubAnnotationProviderFactory()
+ public PubAnnotationProviderFactory pubAnnotationProviderFactory(EntrezClient aEntrezClient)
{
- return new PubAnnotationProviderFactory();
+ return new PubAnnotationProviderFactory(aEntrezClient);
}
@Bean
diff --git a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/format/PubAnnotationSectionsFormatSupport.java b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/format/PubAnnotationSectionsFormatSupport.java
index 770b2d32ae7..5da2412b255 100644
--- a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/format/PubAnnotationSectionsFormatSupport.java
+++ b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/format/PubAnnotationSectionsFormatSupport.java
@@ -24,6 +24,7 @@
import org.apache.uima.resource.metadata.TypeSystemDescription;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.config.PubAnnotationDocumentRepositoryAutoConfiguration;
/**
@@ -58,7 +59,8 @@ public boolean isReadable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(PubAnnotationSectionsReader.class, aTSD);
diff --git a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/model/PubAnnotationDocumentSection.java b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/model/PubAnnotationDocumentSection.java
index ce27fd08c98..adc8844e9db 100644
--- a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/model/PubAnnotationDocumentSection.java
+++ b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/model/PubAnnotationDocumentSection.java
@@ -109,12 +109,14 @@ public void setSourceUrl(String aSourceUrl)
sourceUrl = aSourceUrl;
}
- public static final TypeReference> JACKSON_LIST_TYPE_REF = //
+ public static final TypeReference> //
+ JACKSON_LIST_TYPE_REF = //
new TypeReference>()
{
};
- public static ParameterizedTypeReference> SPRING_LIST_TYPE_REF = //
+ public static final ParameterizedTypeReference> //
+ SPRING_LIST_TYPE_REF = //
new ParameterizedTypeReference>()
{
};
diff --git a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/traits/PubAnnotationProviderTraits.java b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/traits/PubAnnotationProviderTraits.java
index 86049def64c..902e79757f5 100644
--- a/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/traits/PubAnnotationProviderTraits.java
+++ b/inception/inception-external-search-pubannotation/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/traits/PubAnnotationProviderTraits.java
@@ -24,7 +24,7 @@ public class PubAnnotationProviderTraits
{
private static final long serialVersionUID = -9198473282184073984L;
- private String url = "http://pubannotation.org";
+ private String url = "https://pubannotation.org";
public String getUrl()
{
diff --git a/inception/inception-external-search-pubannotation/src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pubannotation.adoc b/inception/inception-external-search-pubannotation/src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pubannotation.adoc
index a7ab93e639e..6624e9d15aa 100644
--- a/inception/inception-external-search-pubannotation/src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pubannotation.adoc
+++ b/inception/inception-external-search-pubannotation/src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pubannotation.adoc
@@ -1,3 +1,19 @@
+// Licensed to the Technische Universität Darmstadt under one
+// or more contributor license agreements. See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership. The Technische Universität Darmstadt
+// licenses this file to you under the Apache License, Version 2.0 (the
+// "License"); you may not use this file except in compliance
+// with the License.
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
[[sect_external-search-repos-pubannotation]]
= PubAnnotation
diff --git a/inception/inception-external-search-pubannotation/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderTest.java b/inception/inception-external-search-pubannotation/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderTest.java
index a95f4753c75..ea19d361507 100644
--- a/inception/inception-external-search-pubannotation/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderTest.java
+++ b/inception/inception-external-search-pubannotation/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubannotation/PubAnnotationProviderTest.java
@@ -19,28 +19,33 @@
import static org.assertj.core.api.Assertions.assertThat;
+import java.nio.charset.StandardCharsets;
import java.util.List;
+import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Tag;
import org.junit.jupiter.api.Test;
import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchResult;
import de.tudarmstadt.ukp.inception.externalsearch.model.DocumentRepository;
-import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.model.PubAnnotationDocumentHandle;
import de.tudarmstadt.ukp.inception.externalsearch.pubannotation.traits.PubAnnotationProviderTraits;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
@Tag("slow")
public class PubAnnotationProviderTest
{
+ private EntrezClient entrezClient = new EntrezClient();
private PubAnnotationProvider sut;
private DocumentRepository repo;
private PubAnnotationProviderTraits traits;
@BeforeEach
- public void setup()
+ public void setup() throws Exception
{
- sut = new PubAnnotationProvider();
+ Thread.sleep(1000); // Get around API rate limiting
+
+ sut = new PubAnnotationProvider(entrezClient);
repo = new DocumentRepository("dummy", null);
@@ -50,7 +55,7 @@ public void setup()
@Test
public void thatQueryWorks() throws Exception
{
- List results = sut.query(traits, "binding");
+ var results = sut.query(traits, "binding", 1, 10);
// System.out.println(results);
@@ -70,10 +75,25 @@ public void thatExecuteQueryWorks() throws Exception
@Test
public void thatDocumentTextCanBeRetrieved() throws Exception
{
- String text = sut.getDocumentText(repo, traits, "PMC", "1064873");
+ var text = sut.getDocumentText(repo, traits, "PMC", "1064873");
// System.out.println(text);
- assertThat(text).isNotEmpty();
+ assertThat(text)
+ .startsWith("Resistance to IL-10 inhibition of interferon gamma production");
+ }
+
+ @Test
+ public void thatDocumentStreamCanBeRetrieved() throws Exception
+ {
+ String data;
+ try (var is = sut.getDocumentAsStream(repo, traits, "PMC", "1064873")) {
+ data = IOUtils.toString(is, StandardCharsets.UTF_8);
+ }
+
+ // System.out.println(data);
+
+ assertThat(data).startsWith(
+ "[{\"text\":\"Resistance to IL-10 inhibition of interferon gamma production");
}
}
diff --git a/inception/inception-external-search-pubmed/LICENSE.txt b/inception/inception-external-search-pubmed/LICENSE.txt
new file mode 100644
index 00000000000..d6456956733
--- /dev/null
+++ b/inception/inception-external-search-pubmed/LICENSE.txt
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
+ and distribution as defined by Sections 1 through 9 of this document.
+
+ "Licensor" shall mean the copyright owner or entity authorized by
+ the copyright owner that is granting the License.
+
+ "Legal Entity" shall mean the union of the acting entity and all
+ other entities that control, are controlled by, or are under common
+ control with that entity. For the purposes of this definition,
+ "control" means (i) the power, direct or indirect, to cause the
+ direction or management of such entity, whether by contract or
+ otherwise, or (ii) ownership of fifty percent (50%) or more of the
+ outstanding shares, or (iii) beneficial ownership of such entity.
+
+ "You" (or "Your") shall mean an individual or Legal Entity
+ exercising permissions granted by this License.
+
+ "Source" form shall mean the preferred form for making modifications,
+ including but not limited to software source code, documentation
+ source, and configuration files.
+
+ "Object" form shall mean any form resulting from mechanical
+ transformation or translation of a Source form, including but
+ not limited to compiled object code, generated documentation,
+ and conversions to other media types.
+
+ "Work" shall mean the work of authorship, whether in Source or
+ Object form, made available under the License, as indicated by a
+ copyright notice that is included in or attached to the work
+ (an example is provided in the Appendix below).
+
+ "Derivative Works" shall mean any work, whether in Source or Object
+ form, that is based on (or derived from) the Work and for which the
+ editorial revisions, annotations, elaborations, or other modifications
+ represent, as a whole, an original work of authorship. For the purposes
+ of this License, Derivative Works shall not include works that remain
+ separable from, or merely link (or bind by name) to the interfaces of,
+ the Work and Derivative Works thereof.
+
+ "Contribution" shall mean any work of authorship, including
+ the original version of the Work and any modifications or additions
+ to that Work or Derivative Works thereof, that is intentionally
+ submitted to Licensor for inclusion in the Work by the copyright owner
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+ "Contributor" shall mean Licensor and any individual or Legal Entity
+ on behalf of whom a Contribution has been received by Licensor and
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+ 2. Grant of Copyright License. Subject to the terms and conditions of
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+ 3. Grant of Patent License. Subject to the terms and conditions of
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+ 5. Submission of Contributions. Unless You explicitly state otherwise,
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+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
+ except as required for reasonable and customary use in describing the
+ origin of the Work and reproducing the content of the NOTICE file.
+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+ implied, including, without limitation, any warranties or conditions
+ of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+ PARTICULAR PURPOSE. You are solely responsible for determining the
+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
+ Work (including but not limited to damages for loss of goodwill,
+ work stoppage, computer failure or malfunction, or any and all
+ other commercial damages or losses), even if such Contributor
+ has been advised of the possibility of such damages.
+
+ 9. Accepting Warranty or Additional Liability. While redistributing
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+ and charge a fee for, acceptance of support, warranty, indemnity,
+ or other liability obligations and/or rights consistent with this
+ License. However, in accepting such obligations, You may act only
+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
+ same "printed page" as the copyright notice for easier
+ identification within third-party archives.
+
+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
diff --git a/inception/inception-external-search-pubmed/marker-wicket-module b/inception/inception-external-search-pubmed/marker-wicket-module
new file mode 100644
index 00000000000..44dcaf8bea4
--- /dev/null
+++ b/inception/inception-external-search-pubmed/marker-wicket-module
@@ -0,0 +1 @@
+Marker file which activates the profile "wicket-module" from the parent POM.
diff --git a/inception/inception-external-search-pubmed/pom.xml b/inception/inception-external-search-pubmed/pom.xml
new file mode 100644
index 00000000000..affb66b34a6
--- /dev/null
+++ b/inception/inception-external-search-pubmed/pom.xml
@@ -0,0 +1,109 @@
+
+
+ 4.0.0
+
+ de.tudarmstadt.ukp.inception.app
+ inception-app
+ 29.0-SNAPSHOT
+
+ inception-external-search-pubmed
+ INCEpTION - External Search - PubMed
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-external-search-core
+
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-support
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-io-bioc
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-api-annotation
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-api-schema
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+
+
+
+ org.apache.uima
+ uimaj-core
+
+
+
+ org.springframework
+ spring-core
+
+
+ org.springframework
+ spring-beans
+
+
+ org.springframework
+ spring-context
+
+
+ org.springframework
+ spring-web
+
+
+ org.springframework.boot
+ spring-boot-autoconfigure
+
+
+
+ org.apache.wicket
+ wicket-core
+
+
+ org.apache.wicket
+ wicket-spring
+
+
+
+ com.fasterxml.jackson.core
+ jackson-annotations
+
+
+ com.fasterxml.jackson.dataformat
+ jackson-dataformat-xml
+
+
+
+ org.slf4j
+ slf4j-api
+
+
+
+ org.apache.uima
+ uimafit-core
+ test
+
+
+
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProvider.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProvider.java
new file mode 100644
index 00000000000..3c373d21ecf
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProvider.java
@@ -0,0 +1,153 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed;
+
+import static java.time.temporal.ChronoField.DAY_OF_MONTH;
+import static java.time.temporal.ChronoField.MONTH_OF_YEAR;
+import static java.time.temporal.ChronoField.YEAR;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.time.Duration;
+import java.time.Instant;
+import java.time.ZoneOffset;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.uima.UIMAException;
+
+import de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchProvider;
+import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchResult;
+import de.tudarmstadt.ukp.inception.externalsearch.model.DocumentRepository;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa.PmcOaClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraits;
+import de.tudarmstadt.ukp.inception.io.bioc.BioCFormatSupport;
+import de.tudarmstadt.ukp.inception.io.bioc.model.BioCToCas;
+import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
+
+public class PubMedCentralProvider
+ implements ExternalSearchProvider
+{
+ private static final String PMCID_PREFIX = "PMC";
+
+ public static final String DB_PUB_MED_CENTRAL = "pmc";
+
+ private static final String EXT_XML = ".xml";
+
+ private final PmcOaClient pmcoaClient;
+ private final EntrezClient entrezClient;
+ private final AnnotationSchemaService schemaService;
+
+ public PubMedCentralProvider(EntrezClient aEntrezClient, PmcOaClient aPmcoaClient,
+ AnnotationSchemaService aSchemaService)
+ {
+ pmcoaClient = aPmcoaClient;
+ entrezClient = aEntrezClient;
+ schemaService = aSchemaService;
+ }
+
+ @Override
+ public List executeQuery(DocumentRepository aDocumentRepository,
+ PubMedProviderTraits aTraits, String aQuery)
+ {
+ var date = Instant.now().atZone(ZoneOffset.UTC).minus(Duration.ofHours(24));
+ var query = aQuery + " AND \"free full text\"[filter] AND (\"0001/01/01\"[PubDate] : \""
+ + date.get(YEAR) + "/" + date.get(MONTH_OF_YEAR) + "/" + date.get(DAY_OF_MONTH)
+ + "\"[PubDate])";
+
+ var searchResponse = entrezClient.esearch(DB_PUB_MED_CENTRAL, query, 0, 100);
+ var summaryResponse = entrezClient.esummary(DB_PUB_MED_CENTRAL,
+ searchResponse.getIdList().stream().mapToInt(i -> i).toArray());
+
+ List results = new ArrayList<>();
+ for (var summary : summaryResponse.getDocSumaries()) {
+ ExternalSearchResult result = new ExternalSearchResult(aDocumentRepository,
+ DB_PUB_MED_CENTRAL, summary.getId() + EXT_XML);
+ result.setOriginalUri(
+ "https://www.ncbi.nlm.nih.gov/pmc/articles/" + PMCID_PREFIX + summary.getId());
+ result.setOriginalSource(summary.source());
+ result.setDocumentTitle(summary.title());
+ result.setTimestamp(summary.date());
+ results.add(result);
+ }
+
+ return results;
+ }
+
+ private String stripExtension(String aDocumentId)
+ {
+ if (aDocumentId != null && aDocumentId.endsWith(EXT_XML)) {
+ return aDocumentId.substring(0, aDocumentId.length() - EXT_XML.length());
+ }
+ return aDocumentId;
+ }
+
+ @Deprecated
+ @Override
+ public ExternalSearchResult getDocumentResult(DocumentRepository aRepository,
+ PubMedProviderTraits aTraits, String aCollectionId, String aDocumentId)
+ throws IOException
+ {
+ ExternalSearchResult result = new ExternalSearchResult(aRepository, aCollectionId,
+ aDocumentId);
+ return result;
+ }
+
+ @Override
+ public String getDocumentText(DocumentRepository aDocumentRepository,
+ PubMedProviderTraits aTraits, String aCollectionId, String aDocumentId)
+ throws IOException
+ {
+ var biocXml = pmcoaClient.bioc(aTraits, PMCID_PREFIX + stripExtension(aDocumentId));
+
+ try {
+ Project project = aDocumentRepository.getProject();
+ var cas = WebAnnoCasUtil.createCas(schemaService.getFullProjectTypeSystem(project));
+ new BioCToCas().parseXml(new ByteArrayInputStream(biocXml), cas.getJCas());
+ return cas.getDocumentText();
+ }
+ catch (UIMAException | JAXBException | XMLStreamException e) {
+ throw new IOException(e);
+ }
+ }
+
+ @Override
+ public InputStream getDocumentAsStream(DocumentRepository aDocumentRepository,
+ PubMedProviderTraits aTraits, String aCollectionId, String aDocumentId)
+ throws IOException
+ {
+ var biocXml = pmcoaClient.bioc(aTraits, PMCID_PREFIX + stripExtension(aDocumentId));
+
+ return new ByteArrayInputStream(biocXml);
+ }
+
+ @Override
+ public String getDocumentFormat(DocumentRepository aRepository, PubMedProviderTraits aTraits,
+ String aCollectionId, String aDocumentId)
+ throws IOException
+ {
+ return BioCFormatSupport.ID;
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProviderFactory.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProviderFactory.java
new file mode 100644
index 00000000000..49f6e0d3c29
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedCentralProviderFactory.java
@@ -0,0 +1,130 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil.fromJsonString;
+import static de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil.toJsonString;
+
+import java.io.IOException;
+
+import org.apache.wicket.markup.html.panel.Panel;
+import org.apache.wicket.model.IModel;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.BeanNameAware;
+import org.springframework.core.annotation.Order;
+
+import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchProvider;
+import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchProviderFactory;
+import de.tudarmstadt.ukp.inception.externalsearch.model.DocumentRepository;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.config.PubMedDocumentRepositoryAutoConfiguration;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa.PmcOaClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraits;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraitsEditor;
+import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
+
+/**
+ * Support for PubAnnotation.
+ *
+ * This class is exposed as a Spring Component via
+ * {@link PubMedDocumentRepositoryAutoConfiguration#pubMedCentralProviderFactory}.
+ *
+ */
+@Order(100)
+public class PubMedCentralProviderFactory
+ implements BeanNameAware, ExternalSearchProviderFactory
+{
+ private final Logger log = LoggerFactory.getLogger(getClass());
+
+ private final EntrezClient entrezClient;
+ private final PmcOaClient pmcOaClient;
+ private final AnnotationSchemaService schemaService;
+
+ private String beanName;
+
+ public PubMedCentralProviderFactory(EntrezClient aEntrezClient, PmcOaClient aPmcOaClient,
+ AnnotationSchemaService aSchemaService)
+ {
+ entrezClient = aEntrezClient;
+ pmcOaClient = aPmcOaClient;
+ schemaService = aSchemaService;
+ }
+
+ @Override
+ public void setBeanName(String aName)
+ {
+ beanName = aName;
+ }
+
+ @Override
+ public String getBeanName()
+ {
+ return beanName;
+ }
+
+ @Override
+ public String getDisplayName()
+ {
+ return "PubMed Central (experimental)";
+ }
+
+ @Override
+ public ExternalSearchProvider getNewExternalSearchProvider()
+ {
+ return new PubMedCentralProvider(entrezClient, pmcOaClient, schemaService);
+ }
+
+ @Override
+ public Panel createTraitsEditor(String aId, IModel aDocumentRepository)
+ {
+ return new PubMedProviderTraitsEditor(aId, aDocumentRepository);
+ }
+
+ @Override
+ public PubMedProviderTraits readTraits(DocumentRepository aDocumentRepository)
+ {
+ PubMedProviderTraits traits = null;
+ try {
+ traits = fromJsonString(PubMedProviderTraits.class,
+ aDocumentRepository.getProperties());
+ }
+ catch (IOException e) {
+ log.error("Error while reading traits", e);
+ }
+
+ if (traits == null) {
+ traits = new PubMedProviderTraits();
+ }
+
+ return traits;
+ }
+
+ @Override
+ public void writeTraits(DocumentRepository aDocumentRepository,
+ PubMedProviderTraits aProperties)
+ {
+ try {
+ String json = toJsonString(aProperties);
+ aDocumentRepository.setProperties(json);
+ }
+ catch (IOException e) {
+ log.error("Error while writing traits", e);
+ }
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/config/PubMedDocumentRepositoryAutoConfiguration.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/config/PubMedDocumentRepositoryAutoConfiguration.java
new file mode 100644
index 00000000000..3af31c28c5a
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/config/PubMedDocumentRepositoryAutoConfiguration.java
@@ -0,0 +1,49 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.config;
+
+import org.springframework.boot.autoconfigure.AutoConfigureAfter;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnBean;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchService;
+import de.tudarmstadt.ukp.inception.externalsearch.config.ExternalSearchAutoConfiguration;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.PubMedCentralProviderFactory;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa.PmcOaClient;
+import de.tudarmstadt.ukp.inception.io.bioc.BioCFormatSupport;
+import de.tudarmstadt.ukp.inception.io.bioc.config.BioCAutoConfiguration;
+import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
+
+@Configuration
+@AutoConfigureAfter({ ExternalSearchAutoConfiguration.class, BioCAutoConfiguration.class,
+ PubMedServicesAutoConfiguration.class })
+@ConditionalOnProperty(prefix = "external-search.pmc", //
+ name = "enabled", havingValue = "true", matchIfMissing = false)
+@ConditionalOnBean({ ExternalSearchService.class, BioCFormatSupport.class })
+public class PubMedDocumentRepositoryAutoConfiguration
+{
+ @Bean
+ public PubMedCentralProviderFactory pubMedCentralProviderFactory(EntrezClient aEntrezClient,
+ PmcOaClient aPmcOaClient, AnnotationSchemaService aSchemaService)
+ {
+ return new PubMedCentralProviderFactory(aEntrezClient, aPmcOaClient, aSchemaService);
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/config/PubMedServicesAutoConfiguration.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/config/PubMedServicesAutoConfiguration.java
new file mode 100644
index 00000000000..dbe51945f94
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/config/PubMedServicesAutoConfiguration.java
@@ -0,0 +1,40 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.config;
+
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa.PmcOaClient;
+
+@Configuration
+public class PubMedServicesAutoConfiguration
+{
+ @Bean
+ public EntrezClient entrezClient()
+ {
+ return new EntrezClient();
+ }
+
+ @Bean
+ public PmcOaClient pmcOaClient()
+ {
+ return new PmcOaClient();
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/EntrezClient.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/EntrezClient.java
new file mode 100644
index 00000000000..06f5d6f1136
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/EntrezClient.java
@@ -0,0 +1,95 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez;
+
+import static java.util.stream.Collectors.joining;
+
+import java.util.Map;
+import java.util.stream.IntStream;
+
+import org.springframework.http.HttpMethod;
+import org.springframework.http.converter.xml.MappingJackson2XmlHttpMessageConverter;
+import org.springframework.web.client.RestTemplate;
+
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.model.ESearchResult;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.model.ESummaryResult;
+
+public class EntrezClient
+{
+ private static final String PARAM_ID = "id";
+ private static final String PARAM_TERM = "term";
+ private static final String PARAM_RETSTART = "retstart";
+ private static final String PARAM_DB = "db";
+ private static final String PARAM_RETMAX = "retmax";
+ private static final String PARAM_SORT = "sort";
+
+ private static final String EUTILS_BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";
+ private static final String ESEARCH_URL = EUTILS_BASE_URL
+ + "/esearch.fcgi?db={db}&retstart={retstart}&retmax={retmax}&term={term}&sort={sort}";
+ private static final String ESUMMARY_URL = EUTILS_BASE_URL + "/esummary.fcgi?db={db}&id={id}";
+ private static final String EFETCH_URL = EUTILS_BASE_URL + "/efetch.fcgi?db={db}&id={id}";
+
+ private final RestTemplate restTemplate;
+
+ public EntrezClient()
+ {
+ restTemplate = new RestTemplate();
+ restTemplate.getMessageConverters().add(new MappingJackson2XmlHttpMessageConverter());
+ }
+
+ // https://www.ncbi.nlm.nih.gov/books/NBK25499/
+ public ESearchResult esearch(String aDb, String aQuery, int aOffset, int aPageSize)
+ {
+ var variables = Map.of( //
+ PARAM_DB, aDb, //
+ PARAM_RETSTART, Integer.toString(aOffset), //
+ PARAM_RETMAX, Integer.toString(aPageSize), //
+ PARAM_TERM, aQuery, //
+ PARAM_SORT, "relevance");
+
+ var response = restTemplate.exchange(ESEARCH_URL, HttpMethod.GET, null, ESearchResult.class,
+ variables);
+
+ return response.getBody();
+ }
+
+ public ESummaryResult esummary(String aDb, int... aIDs)
+ {
+ var variables = Map.of( //
+ PARAM_DB, aDb, //
+ PARAM_RETMAX, Integer.toString(aIDs.length), //
+ PARAM_ID, IntStream.of(aIDs).mapToObj(Integer::toString).collect(joining(",")));
+
+ var response = restTemplate.exchange(ESUMMARY_URL, HttpMethod.GET, null,
+ ESummaryResult.class, variables);
+
+ return response.getBody();
+ }
+
+ public String efetch(String aDb, String aID)
+ {
+ var variables = Map.of( //
+ PARAM_DB, aDb, //
+ PARAM_ID, aID);
+
+ var response = restTemplate.exchange(EFETCH_URL, HttpMethod.GET, null, String.class,
+ variables);
+
+ return response.getBody();
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/DocSum.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/DocSum.java
new file mode 100644
index 00000000000..7e75e51e731
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/DocSum.java
@@ -0,0 +1,91 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
+
+public class DocSum
+{
+ private static final String ITEM_SOURCE = "Source";
+ private static final String ITEM_PUB_DATE = "PubDate";
+ private static final String ITEM_TITLE = "Title";
+
+ @JacksonXmlProperty(localName = "Id")
+ @JsonProperty("Id")
+ private int id;
+
+ @JacksonXmlElementWrapper(useWrapping = false)
+ @JacksonXmlProperty(localName = "Item")
+ @JsonProperty("Item")
+ private final List items = new ArrayList<>();
+
+ public int getId()
+ {
+ return id;
+ }
+
+ public void setId(int aId)
+ {
+ id = aId;
+ }
+
+ public List getItems()
+ {
+ return items;
+ }
+
+ public void setItems(List aItems)
+ {
+ items.clear();
+ if (aItems != null) {
+ items.addAll(aItems);
+ }
+ }
+
+ public String source()
+ {
+ return getItems().stream() //
+ .filter(i -> ITEM_SOURCE.equals(i.getName())) //
+ .findFirst() //
+ .map(Item::getValue) //
+ .orElse(null);
+ }
+
+ public String title()
+ {
+ return getItems().stream() //
+ .filter(i -> ITEM_TITLE.equals(i.getName())) //
+ .findFirst() //
+ .map(Item::getValue) //
+ .orElse(Integer.toString(getId()));
+ }
+
+ public String date()
+ {
+ return getItems().stream() //
+ .filter(i -> ITEM_PUB_DATE.equals(i.getName())) //
+ .findFirst() //
+ .map(Item::getValue) //
+ .orElse(null);
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/ESearchResult.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/ESearchResult.java
new file mode 100644
index 00000000000..62cc7a87975
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/ESearchResult.java
@@ -0,0 +1,90 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+
+@JacksonXmlRootElement(localName = "eSearchResult")
+public class ESearchResult
+{
+ @JacksonXmlProperty(localName = "Count")
+ @JsonProperty("Count")
+ private int count;
+
+ @JacksonXmlProperty(localName = "RetMax")
+ @JsonProperty("RetMax")
+ private int retMax;
+
+ @JacksonXmlProperty(localName = "RetStart")
+ @JsonProperty("RetStart")
+ private int retStart;
+
+ @JacksonXmlElementWrapper(localName = "IdList")
+ @JacksonXmlProperty(localName = "ID")
+ @JsonProperty("IdList")
+ private final List idList = new ArrayList<>();
+
+ public int getCount()
+ {
+ return count;
+ }
+
+ public void setCount(int aCount)
+ {
+ this.count = aCount;
+ }
+
+ public int getRetMax()
+ {
+ return retMax;
+ }
+
+ public void setRetMax(int aRetMax)
+ {
+ this.retMax = aRetMax;
+ }
+
+ public int getRetStart()
+ {
+ return retStart;
+ }
+
+ public void setRetStart(int aRetStart)
+ {
+ this.retStart = aRetStart;
+ }
+
+ public List getIdList()
+ {
+ return idList;
+ }
+
+ public void setIdList(List aIdList)
+ {
+ idList.clear();
+ if (aIdList != null) {
+ idList.addAll(aIdList);
+ }
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/ESummaryResult.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/ESummaryResult.java
new file mode 100644
index 00000000000..d3553d19315
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/ESummaryResult.java
@@ -0,0 +1,48 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
+
+@JacksonXmlRootElement(localName = "eSummaryResult")
+public class ESummaryResult
+{
+ @JacksonXmlElementWrapper(useWrapping = false)
+ @JacksonXmlProperty(localName = "DocSum")
+ @JsonProperty("DocSum")
+ private final List docSum = new ArrayList<>();
+
+ public List getDocSumaries()
+ {
+ return docSum;
+ }
+
+ public void setDocSummaries(List aDocSum)
+ {
+ docSum.clear();
+ if (aDocSum != null) {
+ docSum.addAll(aDocSum);
+ }
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/Item.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/Item.java
new file mode 100644
index 00000000000..24bb27f9fe7
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/model/Item.java
@@ -0,0 +1,86 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlProperty;
+import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlText;
+
+public class Item
+{
+ @JacksonXmlProperty(localName = "Name", isAttribute = true)
+ private String name;
+
+ @JacksonXmlProperty(localName = "Type", isAttribute = true)
+ private String type;
+
+ @JacksonXmlText
+ private String value;
+
+ @JacksonXmlElementWrapper(useWrapping = false)
+ @JacksonXmlProperty(localName = "Item")
+ @JsonProperty("Item")
+ private final List items = new ArrayList<>();
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String aName)
+ {
+ name = aName;
+ }
+
+ public String getType()
+ {
+ return type;
+ }
+
+ public void setType(String aType)
+ {
+ type = aType;
+ }
+
+ public List getItems()
+ {
+ return items;
+ }
+
+ public void setItems(List aItems)
+ {
+ items.clear();
+ if (aItems != null) {
+ items.addAll(aItems);
+ }
+ }
+
+ public String getValue()
+ {
+ return value;
+ }
+
+ public void setValue(String aValue)
+ {
+ value = aValue;
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClient.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClient.java
new file mode 100644
index 00000000000..6a6ad19bae7
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClient.java
@@ -0,0 +1,53 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa;
+
+import java.util.Map;
+
+import org.springframework.http.HttpMethod;
+import org.springframework.http.converter.xml.MappingJackson2XmlHttpMessageConverter;
+import org.springframework.web.client.RestTemplate;
+
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraits;
+
+public class PmcOaClient
+{
+ private static final String PMCOA_BASE_URL = "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi";
+ private static final String BIOC_URL = PMCOA_BASE_URL + "/BioC_xml/{id}/unicode";
+
+ private static final String PARAM_ID = "id";
+
+ private final RestTemplate restTemplate;
+
+ public PmcOaClient()
+ {
+ restTemplate = new RestTemplate();
+ restTemplate.getMessageConverters().add(new MappingJackson2XmlHttpMessageConverter());
+ }
+
+ public byte[] bioc(PubMedProviderTraits aTraits, String aID)
+ {
+ var variables = Map.of( //
+ PARAM_ID, aID);
+
+ var response = restTemplate.exchange(BIOC_URL, HttpMethod.GET, null, byte[].class,
+ variables);
+
+ return response.getBody();
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraits.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraits.java
new file mode 100644
index 00000000000..c2a52c61449
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraits.java
@@ -0,0 +1,26 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits;
+
+import java.io.Serializable;
+
+public class PubMedProviderTraits
+ implements Serializable
+{
+ private static final long serialVersionUID = 2493476436227641544L;
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.html b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.html
new file mode 100644
index 00000000000..02f043450d8
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.html
@@ -0,0 +1,24 @@
+
+
+
+
+
+
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.java b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.java
new file mode 100644
index 00000000000..1dad380bac5
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.java
@@ -0,0 +1,62 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits;
+
+import org.apache.wicket.markup.html.form.Form;
+import org.apache.wicket.markup.html.panel.Panel;
+import org.apache.wicket.model.CompoundPropertyModel;
+import org.apache.wicket.model.IModel;
+import org.apache.wicket.model.Model;
+import org.apache.wicket.spring.injection.annot.SpringBean;
+
+import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchProviderFactory;
+import de.tudarmstadt.ukp.inception.externalsearch.model.DocumentRepository;
+
+public class PubMedProviderTraitsEditor
+ extends Panel
+{
+ private static final long serialVersionUID = 1677442652521110324L;
+
+ private static final String MID_FORM = "form";
+
+ private @SpringBean ExternalSearchProviderFactory externalSearchProviderFactory;
+ private final DocumentRepository documentRepository;
+ private final PubMedProviderTraits properties;
+
+ public PubMedProviderTraitsEditor(String aId, IModel aDocumentRepository)
+ {
+ super(aId, aDocumentRepository);
+ documentRepository = aDocumentRepository.getObject();
+ properties = externalSearchProviderFactory.readTraits(documentRepository);
+
+ Form form = new Form(MID_FORM,
+ CompoundPropertyModel.of(Model.of(properties)))
+ {
+ private static final long serialVersionUID = -3109239608742291123L;
+
+ @Override
+ protected void onSubmit()
+ {
+ super.onSubmit();
+ externalSearchProviderFactory.writeTraits(documentRepository, properties);
+ }
+ };
+
+ add(form);
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.properties b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.properties
new file mode 100644
index 00000000000..c1b1a3aaa88
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/traits/PubMedProviderTraitsEditor.properties
@@ -0,0 +1,15 @@
+# Licensed to the Technische Universität Darmstadt under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The Technische Universität Darmstadt
+# licenses this file to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
diff --git a/inception/inception-external-search-pubmed/src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pmc.adoc b/inception/inception-external-search-pubmed/src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pmc.adoc
new file mode 100644
index 00000000000..4a7dac56462
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/resources/META-INF/asciidoc/user-guide/external-search-repos-pmc.adoc
@@ -0,0 +1,31 @@
+// Licensed to the Technische Universität Darmstadt under one
+// or more contributor license agreements. See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership. The Technische Universität Darmstadt
+// licenses this file to you under the Apache License, Version 2.0 (the
+// "License"); you may not use this file except in compliance
+// with the License.
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+[[sect_external-search-repos-pmc]]
+= PubMed Central
+
+====
+CAUTION: Experimental feature. To use this functionality, you need to enable it first by adding `external-search.pmc.enabled=true` to the `settings.properties` file (see the <>). You should also add `format.bioc.enabled=true` to enable
+support for the BioC format used by this repository connector.
+====
+
+link:https://www.ncbi.nlm.nih.gov/pmc/[PubMed Central]® (PMC) is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). It can be added as an external document repository by
+selecting the **PubMed Central** repository type.
+
+NOTE: {product-name} uses the BioC version of the PMC documents for import. The search tries to
+ consider only documents that have full text available, but the BioC version of these texts may be
+ available only with a delay. Thus, if you cannot import a recently uploaded document from PMC into
+ {product-name}, you may try it again a day later and have more success.
diff --git a/inception/inception-external-search-pubmed/src/main/resources/META-INF/spring.factories b/inception/inception-external-search-pubmed/src/main/resources/META-INF/spring.factories
new file mode 100644
index 00000000000..0cdea788bbf
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/main/resources/META-INF/spring.factories
@@ -0,0 +1,2 @@
+org.springframework.boot.autoconfigure.EnableAutoConfiguration=\
+de.tudarmstadt.ukp.inception.externalsearch.pubmed.config.PubMedDocumentRepositoryAutoConfiguration
diff --git a/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedProviderTest.java b/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedProviderTest.java
new file mode 100644
index 00000000000..2166b47c695
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/PubMedProviderTest.java
@@ -0,0 +1,83 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed;
+
+import static org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.when;
+
+import java.util.List;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import de.tudarmstadt.ukp.inception.externalsearch.ExternalSearchResult;
+import de.tudarmstadt.ukp.inception.externalsearch.model.DocumentRepository;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez.EntrezClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa.PmcOaClient;
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraits;
+import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
+
+@ExtendWith(MockitoExtension.class)
+@Tag("slow")
+public class PubMedProviderTest
+{
+ protected @Mock AnnotationSchemaService annotationService;
+
+ private EntrezClient entrezClient = new EntrezClient();
+ private PmcOaClient pmcOaClient = new PmcOaClient();
+ private PubMedCentralProvider sut;
+ private DocumentRepository repo;
+ private PubMedProviderTraits traits = null;
+
+ @BeforeEach
+ public void setup() throws Exception
+ {
+ Thread.sleep(1000); // Get around API rate limiting
+ sut = new PubMedCentralProvider(entrezClient, pmcOaClient, annotationService);
+ repo = new DocumentRepository("dummy", null);
+ }
+
+ @Test
+ public void thatExecuteQueryWorks() throws Exception
+ {
+ List results = sut.executeQuery(repo, traits, "asthma");
+
+ // System.out.println(results);
+
+ assertThat(results).isNotEmpty();
+ }
+
+ @Test
+ public void thatGetDocumentTextWorks() throws Exception
+ {
+ when(annotationService.getFullProjectTypeSystem(any()))
+ .thenReturn(createTypeSystemDescription());
+
+ String results = sut.getDocumentText(repo, traits, "PMC", "PMC8222896");
+
+ // System.out.println(results);
+
+ assertThat(results).contains("Longitudinal symptoms in asthmatic COVIDâ€19 patients.");
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/EntrezClientTest.java b/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/EntrezClientTest.java
new file mode 100644
index 00000000000..5cf5d8dfab4
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/entrez/EntrezClientTest.java
@@ -0,0 +1,55 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.entrez;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
+
+@Tag("slow")
+class EntrezClientTest
+{
+ private EntrezClient sut;
+
+ @BeforeEach
+ public void setup() throws InterruptedException
+ {
+ Thread.sleep(1000); // Get around API rate limiting
+ sut = new EntrezClient();
+ }
+
+ @Test
+ public void thatESearchWorks() throws Exception
+ {
+ var results = sut.esearch("pmc", "asthma", 0, 10);
+
+ System.out.println(results);
+
+ // assertThat(results).isNotEmpty();
+ }
+
+ @Test
+ public void thatEsummaryWorks() throws Exception
+ {
+ var results = sut.esummary("pmc", 6678417, 9507199);
+
+ System.out.println(results);
+
+ // assertThat(results).isNotEmpty();
+ }
+}
diff --git a/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClientTest.java b/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClientTest.java
new file mode 100644
index 00000000000..79b048bf2f8
--- /dev/null
+++ b/inception/inception-external-search-pubmed/src/test/java/de/tudarmstadt/ukp/inception/externalsearch/pubmed/pmcoa/PmcOaClientTest.java
@@ -0,0 +1,51 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.externalsearch.pubmed.pmcoa;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.assertj.core.api.Assertions.assertThat;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
+
+import de.tudarmstadt.ukp.inception.externalsearch.pubmed.traits.PubMedProviderTraits;
+
+@Tag("slow")
+class PmcOaClientTest
+{
+ private PubMedProviderTraits traits;
+ private PmcOaClient sut;
+
+ @BeforeEach
+ public void setup() throws InterruptedException
+ {
+ Thread.sleep(1000); // Get around API rate limiting
+ sut = new PmcOaClient();
+ }
+
+ @Test
+ public void thatBiocWorks() throws Exception
+ {
+ String results = new String(sut.bioc(traits, "PMC8222896"), UTF_8);
+
+ // System.out.println(results);
+
+ assertThat(results).contains("Longitudinal symptoms in asthmatic COVIDâ€19 patients.");
+ }
+}
diff --git a/inception/inception-external-search-solr/pom.xml b/inception/inception-external-search-solr/pom.xml
index eaffdb1323c..c1332853d61 100644
--- a/inception/inception-external-search-solr/pom.xml
+++ b/inception/inception-external-search-solr/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-external-search-solrINCEpTION - External Search - Solr
@@ -77,6 +77,10 @@
org.apache.wicketwicket-spring
+
+ org.danekja
+ jdk-serializable-functional
+ org.springframework.boot
@@ -93,5 +97,10 @@
solr-coretest
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ test
+
diff --git a/inception/inception-feature-lookup/pom.xml b/inception/inception-feature-lookup/pom.xml
index 6db293fe73d..809aa57982c 100644
--- a/inception/inception-feature-lookup/pom.xml
+++ b/inception/inception-feature-lookup/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-feature-lookupINCEpTION - Lookup Feature Support
diff --git a/inception/inception-feature-lookup/src/main/java/de/tudarmstadt/ukp/inception/feature/lookup/LookupFeatureEditor.java b/inception/inception-feature-lookup/src/main/java/de/tudarmstadt/ukp/inception/feature/lookup/LookupFeatureEditor.java
index a1b1405906d..5339e1378cb 100644
--- a/inception/inception-feature-lookup/src/main/java/de/tudarmstadt/ukp/inception/feature/lookup/LookupFeatureEditor.java
+++ b/inception/inception-feature-lookup/src/main/java/de/tudarmstadt/ukp/inception/feature/lookup/LookupFeatureEditor.java
@@ -225,6 +225,7 @@ public void onConfigure(JQueryBehavior aBehavior)
// because onSelected does not tell us when the auto-complete field is CLEARED!
aBehavior.setOption("select", String.join(" ", //
"function (e) {", //
+ " e.sender.select(e.item);", //
" e.sender.element.trigger('change');", //
"}"));
}
@@ -263,11 +264,11 @@ public String[] getInputAsArray()
public String getIdentifierDynamicAttributeScript()
{
return String.join(" ", //
- "var item = $(attrs.event.target).data('kendoAutoComplete').dataItem();", //
+ "var item = $(attrs.event.target).data('kendoAutoComplete')?.dataItem();", //
"if (item) {", //
" return [{", //
" 'name': '" + getInputName() + ":identifier', ", //
- " 'value': $(attrs.event.target).data('kendoAutoComplete').dataItem().identifier", //
+ " 'value': item.identifier", //
" }]", //
"}", //
"return [];");
diff --git a/inception/inception-guidelines/pom.xml b/inception/inception-guidelines/pom.xml
index c2cf26dcff2..a567549a314 100644
--- a/inception/inception-guidelines/pom.xml
+++ b/inception/inception-guidelines/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-guidelinesINCEpTION - Core - Annotation Guidelines
@@ -90,6 +90,10 @@
de.agilecoders.wicketwicket-bootstrap-extensions
+
+ org.danekja
+ jdk-serializable-functional
+ org.apache.commons
diff --git a/inception/inception-html-editor/pom.xml b/inception/inception-html-editor/pom.xml
index 54af683308c..35616f95f23 100644
--- a/inception/inception-html-editor/pom.xml
+++ b/inception/inception-html-editor/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-html-editorINCEpTION - Editor - HTML + Annotator JS
@@ -54,62 +54,23 @@
de.tudarmstadt.ukp.inception.appinception-support
-
- de.tudarmstadt.ukp.inception.app
- inception-io-xml
- de.tudarmstadt.ukp.inception.appinception-diamde.tudarmstadt.ukp.inception.app
- inception-security
+ inception-external-editorde.tudarmstadt.ukp.inception.appinception-io-html
-
- de.tudarmstadt.ukp.inception.app
- inception-external-editor
-
-
-
- org.dkpro.core
- dkpro-core-api-segmentation-asl
-
-
-
- org.apache.commons
- commons-lang3
-
-
-
- org.apache.uima
- uimaj-core
-
-
- org.apache.uima
- uimafit-core
- org.springframeworkspring-context
-
- org.springframework
- spring-web
-
-
- org.springframework
- spring-beans
-
-
- org.springframework.security
- spring-security-core
- org.springframework.bootspring-boot-autoconfigure
@@ -123,10 +84,6 @@
org.apache.wicketwicket-spring
-
- org.apache.wicket
- wicket-util
- jakarta.servlet
@@ -138,6 +95,16 @@
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+
+
+
+ de.tudarmstadt.ukp.inception.app:inception-io-html
+
+
+ org.apache.ratapache-rat-plugin
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/AnnotatorJsHtmlAnnotationEditor.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/AnnotatorJsHtmlAnnotationEditor.java
similarity index 74%
rename from inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/AnnotatorJsHtmlAnnotationEditor.java
rename to inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/AnnotatorJsHtmlAnnotationEditor.java
index e28a83dc08e..538253fbdd8 100644
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/AnnotatorJsHtmlAnnotationEditor.java
+++ b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/AnnotatorJsHtmlAnnotationEditor.java
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package de.tudarmstadt.ukp.inception.htmleditor.annotatorjs;
+package de.tudarmstadt.ukp.inception.annotatorjs;
import static de.tudarmstadt.ukp.clarin.webanno.support.wicket.ServletContextUtils.referenceToUrl;
import static java.util.Arrays.asList;
@@ -27,14 +27,12 @@
import de.tudarmstadt.ukp.clarin.webanno.api.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
-import de.tudarmstadt.ukp.inception.editor.AnnotationEditorFactory;
+import de.tudarmstadt.ukp.inception.annotatorjs.resources.AnnotatorJsCssResourceReference;
+import de.tudarmstadt.ukp.inception.annotatorjs.resources.AnnotatorJsJavascriptResourceReference;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
-import de.tudarmstadt.ukp.inception.editor.view.DocumentViewFactory;
import de.tudarmstadt.ukp.inception.externaleditor.ExternalAnnotationEditorBase;
import de.tudarmstadt.ukp.inception.externaleditor.model.AnnotationEditorProperties;
-import de.tudarmstadt.ukp.inception.htmleditor.annotatorjs.resources.AnnotatorJsCssResourceReference;
-import de.tudarmstadt.ukp.inception.htmleditor.annotatorjs.resources.AnnotatorJsJavascriptResourceReference;
+import de.tudarmstadt.ukp.inception.externaleditor.xhtml.XHtmlXmlDocumentIFrameViewFactory;
import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
import jakarta.servlet.ServletContext;
@@ -43,15 +41,16 @@ public class AnnotatorJsHtmlAnnotationEditor
{
private static final long serialVersionUID = -3358207848681467993L;
- private @SpringBean(name = "htmlAnnotationEditorFactory") AnnotationEditorFactory editorFactory;
- private @SpringBean(name = "xHtmlXmlDocumentIFrameViewFactory") DocumentViewFactory viewFactory;
+ private @SpringBean AnnotatorJsHtmlAnnotationEditorFactory editorFactory;
+ private @SpringBean XHtmlXmlDocumentIFrameViewFactory viewFactory;
private @SpringBean DocumentService documentService;
private @SpringBean ServletContext servletContext;
public AnnotatorJsHtmlAnnotationEditor(String aId, IModel aModel,
- AnnotationActionHandler aActionHandler, CasProvider aCasProvider)
+ AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
+ String aEditorFactoryId)
{
- super(aId, aModel, aActionHandler, aCasProvider);
+ super(aId, aModel, aActionHandler, aCasProvider, aEditorFactoryId);
}
@Override
@@ -59,10 +58,8 @@ protected Component makeView()
{
AnnotatorState state = getModelObject();
- AnnotationDocument annDoc = documentService.getAnnotationDocument(state.getDocument(),
- state.getUser());
-
- return viewFactory.createView(CID_VIS, Model.of(annDoc), editorFactory.getBeanName());
+ return viewFactory.createView(CID_VIS, Model.of(state.getDocument()),
+ editorFactory.getBeanName());
}
@Override
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/AnnotatorJsHtmlAnnotationEditorFactory.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/AnnotatorJsHtmlAnnotationEditorFactory.java
similarity index 78%
rename from inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/AnnotatorJsHtmlAnnotationEditorFactory.java
rename to inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/AnnotatorJsHtmlAnnotationEditorFactory.java
index 0709a52ad78..1762cda2843 100644
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/AnnotatorJsHtmlAnnotationEditorFactory.java
+++ b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/AnnotatorJsHtmlAnnotationEditorFactory.java
@@ -15,17 +15,18 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package de.tudarmstadt.ukp.inception.htmleditor.annotatorjs;
+package de.tudarmstadt.ukp.inception.annotatorjs;
import org.apache.wicket.model.IModel;
import de.tudarmstadt.ukp.clarin.webanno.api.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.paging.NoPagingStrategy;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.clarin.webanno.support.wicket.resource.Strings;
+import de.tudarmstadt.ukp.inception.annotatorjs.config.AnnotatorJsAnnotationEditorSupportAutoConfiguration;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorBase;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorFactoryImplBase;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
-import de.tudarmstadt.ukp.inception.htmleditor.config.HtmlAnnotationEditorSupportAutoConfiguration;
import de.tudarmstadt.ukp.inception.io.html.HtmlFormatSupport;
import de.tudarmstadt.ukp.inception.io.html.LegacyHtmlFormatSupport;
import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
@@ -34,7 +35,7 @@
* Support for HTML-oriented editor component.
*
* This class is exposed as a Spring Component via
- * {@link HtmlAnnotationEditorSupportAutoConfiguration#htmlAnnotationEditorFactory()}.
+ * {@link AnnotatorJsAnnotationEditorSupportAutoConfiguration#annotatorJsHtmlAnnotationEditorFactory()}.
*
*/
public class AnnotatorJsHtmlAnnotationEditorFactory
@@ -43,7 +44,10 @@ public class AnnotatorJsHtmlAnnotationEditorFactory
@Override
public String getDisplayName()
{
- return "HTML (AnnotatorJS)";
+ // return Strings.getString(Messages_.ANNOTATORJS_EDITOR_NAME);
+ // FIXME: For some reason the annotation processor does not seem to work in Eclipse full
+ // builds. Needs to be debugged....
+ return Strings.getString("annotatorjs-editor.name");
}
@Override
@@ -62,7 +66,8 @@ public int accepts(Project aProject, String aFormat)
public AnnotationEditorBase create(String aId, IModel aModel,
AnnotationActionHandler aActionHandler, CasProvider aCasProvider)
{
- return new AnnotatorJsHtmlAnnotationEditor(aId, aModel, aActionHandler, aCasProvider);
+ return new AnnotatorJsHtmlAnnotationEditor(aId, aModel, aActionHandler, aCasProvider,
+ getBeanName());
}
@Override
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/config/HtmlAnnotationEditorSupportAutoConfiguration.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/config/AnnotatorJsAnnotationEditorSupportAutoConfiguration.java
similarity index 64%
rename from inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/config/HtmlAnnotationEditorSupportAutoConfiguration.java
rename to inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/config/AnnotatorJsAnnotationEditorSupportAutoConfiguration.java
index 1743ca68790..d78708ce4be 100644
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/config/HtmlAnnotationEditorSupportAutoConfiguration.java
+++ b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/config/AnnotatorJsAnnotationEditorSupportAutoConfiguration.java
@@ -15,37 +15,27 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package de.tudarmstadt.ukp.inception.htmleditor.config;
+package de.tudarmstadt.ukp.inception.annotatorjs.config;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.boot.autoconfigure.condition.ConditionalOnWebApplication;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
-import de.tudarmstadt.ukp.inception.htmleditor.annotatorjs.AnnotatorJsHtmlAnnotationEditorFactory;
-import de.tudarmstadt.ukp.inception.htmleditor.docview.HtmlDocumentIFrameViewFactory;
+import de.tudarmstadt.ukp.inception.annotatorjs.AnnotatorJsHtmlAnnotationEditorFactory;
/**
- * Provides support for an HTML-oriented annotation editor.
+ * Provides support for an AnnotatorJS-based HTML-oriented annotation editor.
*/
@ConditionalOnWebApplication
@Configuration
-public class HtmlAnnotationEditorSupportAutoConfiguration
+public class AnnotatorJsAnnotationEditorSupportAutoConfiguration
{
@ConditionalOnProperty(prefix = "ui.html-annotatorjs", name = "enabled", //
havingValue = "true", matchIfMissing = false)
@Bean
- public AnnotatorJsHtmlAnnotationEditorFactory htmlAnnotationEditorFactory()
+ public AnnotatorJsHtmlAnnotationEditorFactory annotatorJsHtmlAnnotationEditorFactory()
{
return new AnnotatorJsHtmlAnnotationEditorFactory();
}
-
- @ConditionalOnProperty(prefix = "ui.html.legacy-iframe-view", name = "enabled", //
- havingValue = "true", matchIfMissing = false)
- @Bean
- @Deprecated
- public HtmlDocumentIFrameViewFactory htmlDocumentIFrameViewFactory()
- {
- return new HtmlDocumentIFrameViewFactory();
- }
}
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/AnnotatorJsCssResourceReference.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/resources/AnnotatorJsCssResourceReference.java
similarity index 95%
rename from inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/AnnotatorJsCssResourceReference.java
rename to inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/resources/AnnotatorJsCssResourceReference.java
index e2f0cf22566..2acf2788b83 100644
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/AnnotatorJsCssResourceReference.java
+++ b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/resources/AnnotatorJsCssResourceReference.java
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package de.tudarmstadt.ukp.inception.htmleditor.annotatorjs.resources;
+package de.tudarmstadt.ukp.inception.annotatorjs.resources;
import org.apache.wicket.request.resource.CssResourceReference;
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/AnnotatorJsJavascriptResourceReference.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/resources/AnnotatorJsJavascriptResourceReference.java
similarity index 95%
rename from inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/AnnotatorJsJavascriptResourceReference.java
rename to inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/resources/AnnotatorJsJavascriptResourceReference.java
index 97d74b0c8a6..335de1f40bd 100644
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/annotatorjs/resources/AnnotatorJsJavascriptResourceReference.java
+++ b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/resources/AnnotatorJsJavascriptResourceReference.java
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package de.tudarmstadt.ukp.inception.htmleditor.annotatorjs.resources;
+package de.tudarmstadt.ukp.inception.annotatorjs.resources;
import org.apache.wicket.request.resource.JavaScriptResourceReference;
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/wicket-package.properties b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/wicket-package.properties
new file mode 100644
index 00000000000..2e90cf12daa
--- /dev/null
+++ b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/annotatorjs/wicket-package.properties
@@ -0,0 +1,16 @@
+# Licensed to the Technische Universität Darmstadt under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The Technische Universität Darmstadt
+# licenses this file to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+annotatorjs-editor.name=HTML (AnnotatorJS)
\ No newline at end of file
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentIFrameView.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentIFrameView.java
deleted file mode 100644
index 1d4e730809a..00000000000
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentIFrameView.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Licensed to the Technische Universität Darmstadt under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The Technische Universität Darmstadt
- * licenses this file to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.tudarmstadt.ukp.inception.htmleditor.docview;
-
-import org.apache.wicket.markup.ComponentTag;
-import org.apache.wicket.markup.html.WebMarkupContainer;
-import org.apache.wicket.model.IModel;
-import org.apache.wicket.spring.injection.annot.SpringBean;
-
-import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
-import de.tudarmstadt.ukp.inception.externaleditor.xhtml.XHtmlXmlDocumentIFrameView;
-
-/**
- * @deprecated Use {@link XHtmlXmlDocumentIFrameView} instead
- */
-@Deprecated
-public class HtmlDocumentIFrameView
- extends WebMarkupContainer
-{
- private static final long serialVersionUID = 4436249885266856565L;
-
- private @SpringBean DocumentService documentService;
- private @SpringBean HtmlDocumentViewController htmlDocumentViewController;
-
- private IModel document;
-
- public HtmlDocumentIFrameView(String aId, IModel aDoc)
- {
- super(aId);
-
- document = aDoc;
- }
-
- @Override
- protected void onComponentTag(ComponentTag aTag)
- {
- aTag.setName("iframe");
- aTag.put("src",
- htmlDocumentViewController.getDocumentUrl(document.getObject().getDocument()));
- super.onComponentTag(aTag);
- }
-}
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentIFrameViewFactory.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentIFrameViewFactory.java
deleted file mode 100644
index f164ec74a35..00000000000
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentIFrameViewFactory.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Licensed to the Technische Universität Darmstadt under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The Technische Universität Darmstadt
- * licenses this file to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.tudarmstadt.ukp.inception.htmleditor.docview;
-
-import org.apache.wicket.Component;
-import org.apache.wicket.model.IModel;
-
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
-import de.tudarmstadt.ukp.inception.editor.view.DocumentViewFactory;
-import de.tudarmstadt.ukp.inception.externaleditor.xhtml.XHtmlXmlDocumentIFrameViewFactory;
-import de.tudarmstadt.ukp.inception.htmleditor.config.HtmlAnnotationEditorSupportAutoConfiguration;
-import de.tudarmstadt.ukp.inception.io.html.HtmlFormatSupport;
-
-/**
- *
- * This class is exposed as a Spring Component via
- * {@link HtmlAnnotationEditorSupportAutoConfiguration#htmlDocumentIFrameViewFactory}.
- *
- *
- * @deprecated Use {@link XHtmlXmlDocumentIFrameViewFactory} instead
- */
-@Deprecated
-public class HtmlDocumentIFrameViewFactory
- implements DocumentViewFactory
-{
- public static final String ID = "iframe:cas+html";
-
- @Override
- public String getId()
- {
- return ID;
- }
-
- @Override
- public boolean accepts(AnnotationDocument aContext)
- {
- return HtmlFormatSupport.ID.equals(aContext.getDocument().getFormat());
- }
-
- @Override
- public Component createView(String aId, IModel aDoc,
- String aEditorFactoryId)
- {
- return new HtmlDocumentIFrameView(aId, aDoc);
- }
-}
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentRenderer.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentRenderer.java
deleted file mode 100644
index 9379a0c61ea..00000000000
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentRenderer.java
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- * Licensed to the Technische Universität Darmstadt under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The Technische Universität Darmstadt
- * licenses this file to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.tudarmstadt.ukp.inception.htmleditor.docview;
-
-import static javax.xml.transform.OutputKeys.INDENT;
-import static javax.xml.transform.OutputKeys.METHOD;
-import static javax.xml.transform.OutputKeys.OMIT_XML_DECLARATION;
-import static org.apache.commons.lang3.StringUtils.equalsIgnoreCase;
-import static org.apache.uima.fit.util.JCasUtil.selectSingle;
-
-import java.io.IOException;
-import java.io.StringWriter;
-import java.io.Writer;
-
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.sax.SAXTransformerFactory;
-import javax.xml.transform.sax.TransformerHandler;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.uima.cas.CAS;
-import org.apache.uima.cas.CASException;
-import org.apache.uima.fit.util.JCasUtil;
-import org.dkpro.core.api.xml.type.XmlDocument;
-import org.dkpro.core.api.xml.type.XmlElement;
-import org.xml.sax.ContentHandler;
-import org.xml.sax.SAXException;
-
-import de.tudarmstadt.ukp.clarin.webanno.support.xml.TextSanitizingContentHandler;
-import de.tudarmstadt.ukp.inception.externaleditor.policy.DefaultHtmlDocumentPolicy;
-import de.tudarmstadt.ukp.inception.externaleditor.xhtml.XHtmlXmlDocumentIFrameView;
-import de.tudarmstadt.ukp.inception.io.xml.dkprocore.Cas2SaxEvents;
-import de.tudarmstadt.ukp.inception.support.xml.XmlParserUtils;
-import de.tudarmstadt.ukp.inception.support.xml.sanitizer.SanitizingContentHandler;
-
-/**
- * @deprecated Use {@link XHtmlXmlDocumentIFrameView} instead
- */
-@Deprecated
-public class HtmlDocumentRenderer
-{
- private boolean renderOnlyBody = true;
-
- public void setRenderOnlyBody(boolean aRenderOnlyBody)
- {
- renderOnlyBody = aRenderOnlyBody;
- }
-
- public String render(CAS aCas)
- throws IOException, TransformerConfigurationException, CASException, SAXException
- {
- try (Writer out = new StringWriter()) {
- SAXTransformerFactory tf = XmlParserUtils.newTransformerFactory();
- TransformerHandler th = tf.newTransformerHandler();
- th.getTransformer().setOutputProperty(OMIT_XML_DECLARATION, "yes");
- th.getTransformer().setOutputProperty(METHOD, "xml");
- th.getTransformer().setOutputProperty(INDENT, "no");
- th.setResult(new StreamResult(out));
-
- ContentHandler ch = new TextSanitizingContentHandler(th);
- ch = new SanitizingContentHandler(ch, new DefaultHtmlDocumentPolicy().getPolicy());
-
- if (!JCasUtil.exists(aCas.getJCas(), XmlDocument.class)) {
- String text = aCas.getDocumentText();
-
- ch.startDocument();
- ch.characters(text.toCharArray(), 0, text.length());
- ch.endDocument();
- return out.toString();
- }
-
- // The HtmlDocumentReader only extracts text from the body. So here we need to limit
- // rendering to the body so that the text and the annotations align properly. Also,
- // we wouldn't want to render anything outside the body anyway.
- var rootElement = selectSingle(aCas.getJCas(), XmlDocument.class).getRoot();
-
- Cas2SaxEvents serializer = new Cas2SaxEvents(ch);
- if (renderOnlyBody) {
- XmlElement body = rootElement.getChildren().stream() //
- .filter(e -> e instanceof XmlElement) //
- .map(e -> (XmlElement) e) //
- .filter(e -> equalsIgnoreCase("body", e.getQName())) //
- .findFirst().orElseThrow();
- serializer.process(body);
- }
- else {
- serializer.process(rootElement);
- }
-
- return out.toString();
- }
- }
-}
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentViewControllerImpl.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentViewControllerImpl.java
deleted file mode 100644
index b8ab0f5acd3..00000000000
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentViewControllerImpl.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
- * Licensed to the Technische Universität Darmstadt under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The Technische Universität Darmstadt
- * licenses this file to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.tudarmstadt.ukp.inception.htmleditor.docview;
-
-import java.security.Principal;
-
-import org.apache.uima.cas.CAS;
-import org.dkpro.core.api.xml.type.XmlDocument;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnWebApplication;
-import org.springframework.http.MediaType;
-import org.springframework.http.ResponseEntity;
-import org.springframework.security.access.prepost.PreAuthorize;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RestController;
-
-import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
-import de.tudarmstadt.ukp.inception.externaleditor.xhtml.XHtmlXmlDocumentIFrameViewFactory;
-import jakarta.servlet.ServletContext;
-
-/**
- * @deprecated Use {@link XHtmlXmlDocumentIFrameViewFactory} instead
- */
-@Deprecated
-@ConditionalOnWebApplication
-@RestController
-@RequestMapping(HtmlDocumentViewController.BASE_URL)
-public class HtmlDocumentViewControllerImpl
- implements HtmlDocumentViewController
-{
- private static final String GET_DOCUMENT_PATH = "/p/{projectId}/raw/{documentId}";
-
- private final DocumentService documentService;
- private final ServletContext servletContext;
-
- @Autowired
- public HtmlDocumentViewControllerImpl(DocumentService aDocumentService,
- ServletContext aServletContext)
- {
- documentService = aDocumentService;
- servletContext = aServletContext;
- }
-
- @Override
- public String getDocumentUrl(SourceDocument aDoc)
- {
- return servletContext.getContextPath() + BASE_URL
- + GET_DOCUMENT_PATH
- .replace("{projectId}", String.valueOf(aDoc.getProject().getId()))
- .replace("{documentId}", String.valueOf(aDoc.getId()));
- }
-
- @PreAuthorize("@documentAccess.canViewAnnotationDocument(#aProjectId, #aDocumentId, #principal.name)")
- @Override
- @GetMapping(path = GET_DOCUMENT_PATH)
- public ResponseEntity getDocument(@PathVariable("projectId") long aProjectId,
- @PathVariable("documentId") long aDocumentId, Principal principal)
- throws Exception
- {
- SourceDocument doc = documentService.getSourceDocument(aProjectId, aDocumentId);
-
- CAS cas = documentService.createOrReadInitialCas(doc);
-
- if (cas.select(XmlDocument.class).isEmpty()) {
- return ResponseEntity.ok() //
- .contentType(MediaType.TEXT_PLAIN) //
- .body(cas.getDocumentText());
- }
-
- HtmlDocumentRenderer renderer = new HtmlDocumentRenderer();
- renderer.setRenderOnlyBody(false);
- String xml = renderer.render(cas);
- return ResponseEntity.ok() //
- .contentType(MediaType.TEXT_HTML) //
- .body(xml);
- }
-}
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/LegacyHtmlDocumentRenderer.java b/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/LegacyHtmlDocumentRenderer.java
deleted file mode 100644
index 627be3f913b..00000000000
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/LegacyHtmlDocumentRenderer.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
- * Licensed to the Technische Universität Darmstadt under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The Technische Universität Darmstadt
- * licenses this file to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.tudarmstadt.ukp.inception.htmleditor.docview;
-
-import static org.apache.uima.fit.util.CasUtil.getType;
-import static org.apache.uima.fit.util.CasUtil.select;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.transform.TransformerConfigurationException;
-
-import org.apache.uima.cas.CAS;
-import org.apache.uima.cas.CASException;
-import org.apache.uima.cas.text.AnnotationFS;
-import org.apache.wicket.util.string.Strings;
-import org.xml.sax.SAXException;
-
-import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Div;
-import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Heading;
-import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Paragraph;
-import de.tudarmstadt.ukp.inception.externaleditor.xhtml.XHtmlXmlDocumentIFrameViewFactory;
-
-/**
- * @deprecated Use {@link XHtmlXmlDocumentIFrameViewFactory} instead
- */
-@Deprecated
-public class LegacyHtmlDocumentRenderer
-{
- public String renderHtmlDocumentStructure(CAS aCas)
- throws IOException, TransformerConfigurationException, CASException, SAXException
- {
- StringBuilder buf = new StringBuilder(
- Strings.escapeMarkup(aCas.getDocumentText().replace('\r', ' ')));
-
- List nodes = new ArrayList<>();
- for (AnnotationFS div : select(aCas, getType(aCas, Div.class))) {
- if (div.getType().getName().equals(Paragraph.class.getName())) {
- Node startNode = new Node();
- startNode.position = div.getBegin();
- startNode.type = "
",
- " `",
- " $(warning).insertAfter(img);",
- "}",
- "var startTime = new Date().getTime();",
- "var colorThief = new ColorThief();",
- "$('#" + getMarkupId() + " .img-thumbnail').each((index, img) => {",
- // Make sure image data is actually available before trying to fetch it to calculate
- // the background color
- " if (img.complete) {",
- // Check if the image has been properly loaded and if not try without CORS
- " if (typeof img.naturalWidth != 'undefined' && img.naturalWidth == 0) {",
- " fallbackToNonCors(img);",
- " }",
- " else {",
- " updateImageBackground(img);",
- " }",
- " }",
- " else {",
- " img.addEventListener('load', () => updateImageBackground(img));",
- // If the image cannot be loaded it may be due to CORS - so try without
- " img.addEventListener('error', () => fallbackToNonCors(img));",
- " }",
- "});",
- "console.debug('Calculating image border color took ' + ",
- " (new Date().getTime() - startTime) + 'ms');");
- // @formatter:on
- }
-
private List listImageUrls()
{
AnnotatorState state = getModelObject();
@@ -260,7 +169,6 @@ private List listImageUrls()
public void onRenderRequested(RenderRequestedEvent aEvent)
{
aEvent.getRequestHandler().add(mainContainer);
- aEvent.getRequestHandler().appendJavaScript(colorScript());
}
public void actionJumpTo(AjaxRequestTarget aTarget, ImageHandle aHandle)
diff --git a/inception/inception-imls-elg/pom.xml b/inception/inception-imls-elg/pom.xml
index eb8ba4e7b2a..9f36062828b 100644
--- a/inception/inception-imls-elg/pom.xml
+++ b/inception/inception-imls-elg/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-imls-elg
@@ -92,6 +92,10 @@
com.googlecode.wicket-jquery-uiwicket-jquery-ui-core
+
+ org.danekja
+ jdk-serializable-functional
+ com.fasterxml.jackson.core
diff --git a/inception/inception-imls-external/pom.xml b/inception/inception-imls-external/pom.xml
index dfd891a5e0b..f8ca49a14c3 100644
--- a/inception/inception-imls-external/pom.xml
+++ b/inception/inception-imls-external/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-imls-external
@@ -69,6 +69,10 @@
org.apache.wicketwicket-spring
+
+ org.danekja
+ jdk-serializable-functional
+ org.apache.uima
diff --git a/inception/inception-imls-external/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommender.java b/inception/inception-imls-external/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommender.java
index 2de24b30bd6..3d5abe5c0af 100644
--- a/inception/inception-imls-external/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommender.java
+++ b/inception/inception-imls-external/src/main/java/de/tudarmstadt/ukp/inception/recommendation/imls/external/v1/ExternalRecommender.java
@@ -72,6 +72,7 @@
import de.tudarmstadt.ukp.inception.recommendation.imls.external.v1.model.Document;
import de.tudarmstadt.ukp.inception.recommendation.imls.external.v1.model.Metadata;
import de.tudarmstadt.ukp.inception.rendering.model.Range;
+import de.tudarmstadt.ukp.inception.support.xml.sanitizer.IllegalXmlCharacterSanitizingContentHandler;
public class ExternalRecommender
extends RecommendationEngine
@@ -194,7 +195,7 @@ public Range predict(RecommenderContext aContext, CAS aCas, int aBegin, int aEnd
throw new RecommendationException("Error while deserializing CAS!", e);
}
- return new Range(aCas);
+ return Range.rangeCoveringDocument(aCas);
}
private String serializeTypeSystem(CAS aCas) throws RecommendationException
@@ -210,13 +211,13 @@ private String serializeTypeSystem(CAS aCas) throws RecommendationException
private String serializeCas(CAS aCas) throws RecommendationException
{
- try (StringWriter out = new StringWriter()) {
+ try (var out = new StringWriter()) {
// Passing "null" as the type system to the XmiCasSerializer means that we want
// to serialize all types (i.e. no filtering for a specific target type system).
XmiCasSerializer xmiCasSerializer = new XmiCasSerializer(null);
- XMLSerializer sax2xml = new XMLSerializer(out, true);
- xmiCasSerializer.serialize(getRealCas(aCas), sax2xml.getContentHandler(), null, null,
- null);
+ var contentHandler = new XMLSerializer(out, true).getContentHandler();
+ contentHandler = new IllegalXmlCharacterSanitizingContentHandler(contentHandler);
+ xmiCasSerializer.serialize(getRealCas(aCas), contentHandler, null, null, null);
return out.toString();
}
catch (CASRuntimeException | SAXException | IOException e) {
diff --git a/inception/inception-imls-external/src/main/resources/META-INF/asciidoc/developer-guide/external_recommender.adoc b/inception/inception-imls-external/src/main/resources/META-INF/asciidoc/developer-guide/external_recommender.adoc
index f536d43bbca..e8ef881d93c 100644
--- a/inception/inception-imls-external/src/main/resources/META-INF/asciidoc/developer-guide/external_recommender.adoc
+++ b/inception/inception-imls-external/src/main/resources/META-INF/asciidoc/developer-guide/external_recommender.adoc
@@ -15,35 +15,16 @@ When making changes to the API, just copy the stuff from there over to this docu
[[_external_recommender_api_overview]]
== Overview
-This section describes the External Recommender API for INCEpTION. An external recommender is a
+This section describes the External Recommender API for {product-name}. An external recommender is a
classifier whose functionality is exposed via a HTTP web service. It can predict annotations for
given documents and optionally be trained on new data. This document describes the endpoints a web
-service needs to expose so it can be used with INCEpTION. The documents that are exchanged are in
+service needs to expose so it can be used with {product-name}. The documents that are exchanged are in
form of a UIMA CAS. For sending, they have to be serialized to CAS XMI. For receiving, it has to be
-deserialized back. There are two main libraries available that manage CAS handling, one is the UIMA
-Java SDK, the other one dkpro-cassis (Python).
-
-=== Version information
-[%hardbreaks]
-__Version__ : 1.0.0
-
-
-=== Contact information
-[%hardbreaks]
-__Contact Email__ : inception-users@googlegroups.com
-
-
-=== License information
-[%hardbreaks]
-__License__ : Apache 2.0
-__License URL__ : http://www.apache.org/licenses/LICENSE-2.0.html
-__Terms of service__ : https://inception-project.github.io
-
-
-
+deserialized back. There are two main libraries available that manage CAS handling, one is the
+link:https://uima.apache.org[Apache UIMA Java SDK], the other one link:https://github.com/dkpro/dkpro-cassis#dkpro-cassis[dkpro-cassis] (Python).
[[_external_recommender_api_paths]]
-== Paths
+== API Endpoints
[[_external_recommender_api_predictcas]]
=== Predict annotations for a single document
@@ -291,5 +272,16 @@ __required__|Type system XML of the CAS +
**Example** : `" uima.tcas.DocumentAnnotationuima.tcas.Annotationlanguageuima.cas.String"`|string
|===
+== Encoding annotation suggestions
+
+This section explains how annotation suggestions can be encoded in the response to a `predict` call.
+
+Note that a recommender can only produce suggestions for one feature on one layer. The name of the layer and feature are contained in the request to the `predict` call and only suggestions generated for that specific layer and feature will be processed by {product-name} when the call returns.
+For the purpose of producing annotation suggestions, this specific layer is extended with additional features that can be set. Some of these features start with the name of the feature (we use `` as a placeholder for the actual feature name below) to be predicted and then add a suffix:
+* `inception_internal_predicted`: this boolean feature indicates that an annotation was added by the external recommender. It allows the system to distinguish between annotations that already existed in the document and annotations that the recommender has created. Only annotations where this flag is set to `true` will be processed by {product-name}.
+* ``: this feature takes the label that the external recommender assigns.
+* `_score` (optional): this floating-point (double) feature can be used to indicate the score assigned to a predicted label.
+* `_score_explanation` (optional): this string feature can be used to provide an explanation for the score. This explanation is shown on the annotation page when the user inspects a particular suggestion (note that not all editors may support displaying explanations).
+* `_auto_accept` (optional): this feature can be set to `on-first-access` to force-accept an annotation into a document when an annotator accesses a document for the first time. This should only be used in conjunction with non-trainable recommenders and with the option **Wait for suggestions from non-trainable recommenders when opening document** in the recommender project settings. Thus, when an annotator opens a document for the first time, the system would wait for recommendations by non-trainable (pre-trained) recommenders and then directly accept any of the suggestions that the recommender has marked to uto-accept on-first-access. When the annotator resets a document via the action bar, this procedure is also followed. This provides a convenient way of "pre-annotating" documents with the help of external recommenders. Note though that an annotator has to actually open a document in order for this process to trigger.
diff --git a/inception/inception-imls-hf/pom.xml b/inception/inception-imls-hf/pom.xml
index c8c2aabf6d2..1b336474e25 100644
--- a/inception/inception-imls-hf/pom.xml
+++ b/inception/inception-imls-hf/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-imls-hf
@@ -85,6 +85,10 @@
com.googlecode.wicket-jquery-uiwicket-jquery-ui-core
+
+ org.danekja
+ jdk-serializable-functional
+ com.fasterxml.jackson.core
diff --git a/inception/inception-imls-lapps/pom.xml b/inception/inception-imls-lapps/pom.xml
index 2f2a060d26f..b42411dc35f 100644
--- a/inception/inception-imls-lapps/pom.xml
+++ b/inception/inception-imls-lapps/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-imls-lapps
@@ -112,6 +112,10 @@
org.apache.wicketwicket-spring
+
+ org.danekja
+ jdk-serializable-functional
+ com.fasterxml.jackson.core
diff --git a/inception/inception-imls-opennlp/pom.xml b/inception/inception-imls-opennlp/pom.xml
index 2a1ad7e4bbb..68be68d4c93 100644
--- a/inception/inception-imls-opennlp/pom.xml
+++ b/inception/inception-imls-opennlp/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-imls-opennlpINCEpTION - ML - OpenNLP (v ${opennlp.version})
diff --git a/inception/inception-imls-stringmatch/pom.xml b/inception/inception-imls-stringmatch/pom.xml
index 9aa4143de9d..b90b424957d 100644
--- a/inception/inception-imls-stringmatch/pom.xml
+++ b/inception/inception-imls-stringmatch/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-imls-stringmatchINCEpTION - ML - String Matching
@@ -114,6 +114,10 @@
de.agilecoders.wicketwicket-bootstrap-extensions
+
+ org.danekja
+ jdk-serializable-functional
+ org.hibernate.orm
diff --git a/inception/inception-imls-weblicht/pom.xml b/inception/inception-imls-weblicht/pom.xml
index d98239baa49..3f803caf317 100644
--- a/inception/inception-imls-weblicht/pom.xml
+++ b/inception/inception-imls-weblicht/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-imls-weblicht
@@ -144,6 +144,10 @@
de.agilecoders.wicketwicket-bootstrap-extensions
+
+ org.danekja
+ jdk-serializable-functional
+ com.fasterxml.jackson.core
diff --git a/inception/inception-io-bioc/LICENSE.txt b/inception/inception-io-bioc/LICENSE.txt
new file mode 100644
index 00000000000..d6456956733
--- /dev/null
+++ b/inception/inception-io-bioc/LICENSE.txt
@@ -0,0 +1,202 @@
+
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+ 1. Definitions.
+
+ "License" shall mean the terms and conditions for use, reproduction,
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+
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+
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+ the conditions stated in this License.
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+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+ any Contribution intentionally submitted for inclusion in the Work
+ by You to the Licensor shall be under the terms and conditions of
+ this License, without any additional terms or conditions.
+ Notwithstanding the above, nothing herein shall supersede or modify
+ the terms of any separate license agreement you may have executed
+ with Licensor regarding such Contributions.
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+ 6. Trademarks. This License does not grant permission to use the trade
+ names, trademarks, service marks, or product names of the Licensor,
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+
+ 7. Disclaimer of Warranty. Unless required by applicable law or
+ agreed to in writing, Licensor provides the Work (and each
+ Contributor provides its Contributions) on an "AS IS" BASIS,
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+ appropriateness of using or redistributing the Work and assume any
+ risks associated with Your exercise of permissions under this License.
+
+ 8. Limitation of Liability. In no event and under no legal theory,
+ whether in tort (including negligence), contract, or otherwise,
+ unless required by applicable law (such as deliberate and grossly
+ negligent acts) or agreed to in writing, shall any Contributor be
+ liable to You for damages, including any direct, indirect, special,
+ incidental, or consequential damages of any character arising as a
+ result of this License or out of the use or inability to use the
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+ has been advised of the possibility of such damages.
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+ 9. Accepting Warranty or Additional Liability. While redistributing
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+ on Your own behalf and on Your sole responsibility, not on behalf
+ of any other Contributor, and only if You agree to indemnify,
+ defend, and hold each Contributor harmless for any liability
+ incurred by, or claims asserted against, such Contributor by reason
+ of your accepting any such warranty or additional liability.
+
+ END OF TERMS AND CONDITIONS
+
+ APPENDIX: How to apply the Apache License to your work.
+
+ To apply the Apache License to your work, attach the following
+ boilerplate notice, with the fields enclosed by brackets "[]"
+ replaced with your own identifying information. (Don't include
+ the brackets!) The text should be enclosed in the appropriate
+ comment syntax for the file format. We also recommend that a
+ file or class name and description of purpose be included on the
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+ Copyright [yyyy] [name of copyright owner]
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
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diff --git a/inception/inception-io-bioc/pom.xml b/inception/inception-io-bioc/pom.xml
new file mode 100644
index 00000000000..86e3084cf8a
--- /dev/null
+++ b/inception/inception-io-bioc/pom.xml
@@ -0,0 +1,122 @@
+
+
+ 4.0.0
+
+ de.tudarmstadt.ukp.inception.app
+ inception-app
+ 29.0-SNAPSHOT
+
+ inception-io-bioc
+ INCEpTION - IO - BioC
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-api-formats
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-io-xml
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-support
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-project-initializers-basic
+
+
+ de.tudarmstadt.ukp.inception.app
+ inception-io-webanno-tsv
+
+
+
+ org.dkpro.core
+ dkpro-core-api-resources-asl
+
+
+ org.dkpro.core
+ dkpro-core-api-parameter-asl
+
+
+ org.dkpro.core
+ dkpro-core-api-io-asl
+
+
+ org.dkpro.core
+ dkpro-core-api-metadata-asl
+
+
+ org.dkpro.core
+ dkpro-core-api-segmentation-asl
+
+
+
+ org.slf4j
+ slf4j-api
+
+
+
+ org.springframework
+ spring-context
+
+
+ org.springframework.boot
+ spring-boot-autoconfigure
+
+
+
+ org.apache.uima
+ uimaj-core
+
+
+ org.apache.uima
+ uimafit-core
+
+
+
+ org.apache.commons
+ commons-collections4
+
+
+ org.apache.commons
+ commons-lang3
+
+
+
+ org.dkpro.core
+ dkpro-core-testing-asl
+ test
+
+
+ org.dkpro.core
+ dkpro-core-io-xmi-asl
+ test
+
+
+ xmlunit
+ xmlunit
+ test
+
+
+
\ No newline at end of file
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCComponent.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCComponent.java
new file mode 100644
index 00000000000..0d9cc813ea9
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCComponent.java
@@ -0,0 +1,180 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isRelationLayer;
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isSpanLayer;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicRelationLayerInitializer.BASIC_RELATION_LAYER_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LABEL_FEATURE_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LAYER_NAME;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_BEGIN;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_END;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_SOFA;
+
+import java.util.Map;
+import java.util.Optional;
+import java.util.Set;
+
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.Type;
+import org.apache.uima.cas.TypeSystem;
+import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.jcas.JCas;
+
+import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.MetaDataStringField;
+
+public interface BioCComponent
+{
+ Set EXCLUDED_FEATURES = Set.of(FEATURE_FULL_NAME_BEGIN, FEATURE_FULL_NAME_END,
+ FEATURE_FULL_NAME_SOFA);
+
+ String E_DOCUMENT = "document";
+ String E_COLLECTION = "collection";
+ String E_PASSAGE = "passage";
+ String E_SENTENCE = "sentence";
+ String E_ANNOTATION = "annotation";
+ String E_NODE = "node";
+ String E_RELATION = "relation";
+ String E_INFON = "infon";
+ String E_OFFSET = "offset";
+ String E_LOCATION = "location";
+ String E_KEY = "key";
+ String E_DATE = "date";
+ String E_ID = "id";
+ String E_SOURCE = "source";
+ String E_TEXT = "text";
+
+ String A_ID = "id";
+ String A_KEY = "key";
+ String A_OFFSET = "offset";
+ String A_LENGTH = "length";
+ String A_REFID = "refid";
+ String A_ROLE = "role";
+
+ // Well-known infon keys
+ String I_TYPE = "type";
+
+ // Well-known relation roles
+ String R_SOURCE = "source";
+ String R_TARGET = "target";
+
+ static void addCollectionMetadataField(JCas aJCas, String aKey, String aValue)
+ {
+ if (aValue == null) {
+ return;
+ }
+
+ var keyField = new MetaDataStringField(aJCas);
+ keyField.setKey(aKey);
+ keyField.setValue(aValue);
+ keyField.addToIndexes();
+ }
+
+ static Optional getCollectionMetadataField(CAS aCas, String aKey)
+ {
+ return aCas.select(MetaDataStringField.class) //
+ .filter(f -> aKey.equals(f.getKey())) //
+ .findFirst();
+ }
+
+ static Type guessBestRelationType(TypeSystem aTypeSystem, Map aInfons)
+ {
+ var type = guessBestType(aTypeSystem, aInfons);
+ if (type != null && isRelationLayer(type)) {
+ return type;
+ }
+
+ type = aTypeSystem.getType(BASIC_RELATION_LAYER_NAME);
+ if (type != null) {
+ return type;
+ }
+
+ return null;
+ }
+
+ static Type guessBestSpanType(TypeSystem aTypeSystem, Map aInfons)
+ {
+ var type = guessBestType(aTypeSystem, aInfons);
+ if (type != null && isSpanLayer(type)) {
+ return type;
+ }
+
+ type = aTypeSystem.getType(BASIC_SPAN_LAYER_NAME);
+ if (type != null) {
+ return type;
+ }
+
+ return null;
+ }
+
+ private static Type guessBestType(TypeSystem aTypeSystem, Map aInfons)
+ {
+ var typeInfon = aInfons.get(I_TYPE);
+ if (typeInfon != null) {
+ var type = aTypeSystem.getType(typeInfon);
+ if (type != null) {
+ return type;
+ }
+
+ type = findTypeByShortName(aTypeSystem, typeInfon);
+ if (type != null) {
+ return type;
+ }
+ }
+
+ return null;
+ }
+
+ private static Type findTypeByShortName(TypeSystem aTypeSystem, String aBaseName)
+ {
+ for (var t : aTypeSystem) {
+ if (aBaseName.equals(t.getShortName())) {
+ return t;
+ }
+ }
+
+ return null;
+ }
+
+ public static void transferFeatures(AnnotationFS aAnnotation, Map aInfons)
+ {
+ var anyFeatureSet = false;
+ for (var infon : aInfons.entrySet()) {
+ if (EXCLUDED_FEATURES.contains(infon.getKey())) {
+ continue;
+ }
+
+ var feature = aAnnotation.getType().getFeatureByBaseName(infon.getKey());
+ if (feature == null) {
+ continue;
+ }
+
+ if (feature.getRange().isPrimitive()) {
+ aAnnotation.setFeatureValueFromString(feature, infon.getValue());
+ anyFeatureSet = true;
+ }
+ }
+
+ // If there is only one infon, then we assume that it is the value
+ var valueFeature = aAnnotation.getType()
+ .getFeatureByBaseName(BASIC_SPAN_LABEL_FEATURE_NAME);
+ if (!anyFeatureSet && aInfons.size() == 1 && valueFeature != null) {
+ aAnnotation.setFeatureValueFromString(valueFeature, aInfons.values().iterator().next());
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCFormatSupport.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCFormatSupport.java
new file mode 100644
index 00000000000..a17b1ca2036
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCFormatSupport.java
@@ -0,0 +1,67 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription;
+
+import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+
+import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.inception.io.bioc.config.BioCAutoConfiguration;
+
+/**
+ * Support for BioC format.
+ *
+ * This class is exposed as a Spring Component via {@link BioCAutoConfiguration#bioCFormatSupport}.
+ *
+ */
+public class BioCFormatSupport
+ implements FormatSupport
+{
+ public static final String ID = "bioc";
+ public static final String NAME = "BioC XML (experimental)";
+
+ @Override
+ public String getId()
+ {
+ return ID;
+ }
+
+ @Override
+ public String getName()
+ {
+ return NAME;
+ }
+
+ @Override
+ public boolean isReadable()
+ {
+ return true;
+ }
+
+ @Override
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
+ throws ResourceInitializationException
+ {
+ return createReaderDescription(BioCReader.class, aTSD);
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReader.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReader.java
new file mode 100644
index 00000000000..866f31731b3
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReader.java
@@ -0,0 +1,149 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.addCollectionMetadataField;
+
+import java.io.IOException;
+import java.util.Optional;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.uima.UimaContext;
+import org.apache.uima.collection.CollectionException;
+import org.apache.uima.fit.factory.JCasBuilder;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+
+import de.tudarmstadt.ukp.inception.io.bioc.model.BioCDocument;
+import de.tudarmstadt.ukp.inception.io.bioc.model.BioCToCas;
+
+public class BioCReader
+ extends BioCReaderImplBase
+{
+ private JAXBContext context;
+ private Unmarshaller unmarshaller;
+ private Optional nextDocument;
+
+ @Override
+ public void initialize(UimaContext aContext) throws ResourceInitializationException
+ {
+ super.initialize(aContext);
+
+ try {
+ context = JAXBContext.newInstance(BioCDocument.class);
+ }
+ catch (JAXBException e) {
+ throw new ResourceInitializationException(e);
+ }
+
+ try {
+ nextDocument = nextBioCDocument();
+ }
+ catch (CollectionException | XMLStreamException | JAXBException | IOException e) {
+ throw new ResourceInitializationException(e);
+ }
+ }
+
+ @Override
+ public void getNext(JCas aJCas) throws IOException, CollectionException
+ {
+ initCas(aJCas, currentResource());
+
+ addCollectionMetadataField(aJCas, E_KEY, getCollectionKey());
+ addCollectionMetadataField(aJCas, E_SOURCE, getCollectionSource());
+ addCollectionMetadataField(aJCas, E_DATE, getCollectionDate());
+
+ var document = nextDocument.get();
+
+ // if (getCollectionSource() != null) {
+ // DocumentMetaData.get(aJCas).setDocumentId(getCollectionSource());
+ // }
+ //
+ // if (document.getId() != null) {
+ // DocumentMetaData.get(aJCas).setDocumentId(document.getId());
+ // }
+
+ JCasBuilder jb = new JCasBuilder(aJCas);
+ new BioCToCas().readDocument(jb, document);
+ jb.close();
+
+ try {
+ nextDocument = nextBioCDocument();
+ }
+ catch (XMLStreamException | JAXBException e) {
+ throw new IOException(e);
+ }
+ }
+
+ @Override
+ public boolean hasNext() throws IOException, CollectionException
+ {
+ return nextDocument.isPresent();
+ }
+
+ private Optional nextBioCDocument()
+ throws XMLStreamException, JAXBException, CollectionException, IOException
+ {
+ if (!isFileOpen()) {
+ openNextFile();
+ readCollectionMetdata();
+ }
+
+ if (isFileOpen()) {
+ return nextBioCDocumentInFile();
+ }
+
+ return Optional.empty();
+ }
+
+ @Override
+ protected void openNextFile() throws IOException, XMLStreamException, CollectionException
+ {
+ super.openNextFile();
+ try {
+ unmarshaller = context.createUnmarshaller();
+ }
+ catch (JAXBException e) {
+ new IOException(e);
+ }
+ }
+
+ @Override
+ protected void closeFile()
+ {
+ unmarshaller = null;
+ super.closeFile();
+ }
+
+ private Optional nextBioCDocumentInFile() throws XMLStreamException, JAXBException
+ {
+ if (seekNextBioCDocumentInFile()) {
+ var document = unmarshaller.unmarshal(getXmlEventReader(), BioCDocument.class)
+ .getValue();
+ return Optional.of(document);
+ }
+
+ closeFile();
+
+ return Optional.empty();
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderImplBase.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderImplBase.java
new file mode 100644
index 00000000000..888485047d0
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderImplBase.java
@@ -0,0 +1,170 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.inception.support.xml.XmlParserUtils.isStartElement;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import javax.xml.stream.XMLEventReader;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.events.XMLEvent;
+
+import org.apache.uima.UimaContext;
+import org.apache.uima.collection.CollectionException;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.dkpro.core.api.io.JCasResourceCollectionReader_ImplBase;
+import org.dkpro.core.api.resources.CompressionUtils;
+
+import de.tudarmstadt.ukp.inception.support.xml.XmlParserUtils;
+
+public abstract class BioCReaderImplBase
+ extends JCasResourceCollectionReader_ImplBase
+ implements BioCComponent
+{
+ private InputStream is;
+ private XMLInputFactory xmlInputFactory;
+ private XMLEventReader xmlEventReader;
+ private Resource res;
+
+ private String collectionSource;
+ private String collectionDate;
+ private String collectionKey;
+
+ @Override
+ public void initialize(UimaContext aContext) throws ResourceInitializationException
+ {
+ super.initialize(aContext);
+
+ xmlInputFactory = XmlParserUtils.newXmlInputFactory();
+ }
+
+ public String getCollectionSource()
+ {
+ return collectionSource;
+ }
+
+ public String getCollectionDate()
+ {
+ return collectionDate;
+ }
+
+ public String getCollectionKey()
+ {
+ return collectionKey;
+ }
+
+ @Override
+ public void destroy()
+ {
+ closeFile();
+ super.destroy();
+ }
+
+ public Resource currentResource()
+ {
+ return res;
+ }
+
+ public XMLEventReader getXmlEventReader()
+ {
+ return xmlEventReader;
+ }
+
+ protected boolean isFileOpen()
+ {
+ return is != null;
+ }
+
+ protected void openNextFile() throws IOException, XMLStreamException, CollectionException
+ {
+ if (!super.hasNext()) {
+ return;
+ }
+
+ res = nextFile();
+ is = CompressionUtils.getInputStream(res.getLocation(), res.getInputStream());
+ xmlEventReader = xmlInputFactory.createXMLEventReader(is);
+ }
+
+ protected boolean seekNextBioCDocumentInFile() throws XMLStreamException
+ {
+ XMLEvent e = null;
+ while ((e = xmlEventReader.peek()) != null) {
+ if (isStartElement(e, E_DOCUMENT)) {
+ return true;
+ }
+ else {
+ xmlEventReader.next();
+ }
+ }
+
+ closeFile();
+
+ return false;
+ }
+
+ protected void closeFile()
+ {
+ collectionKey = null;
+ collectionSource = null;
+ collectionDate = null;
+ res = null;
+ xmlEventReader = null;
+ if (is != null) {
+ try {
+ is.close();
+ }
+ catch (IOException e) {
+ // Ignore
+ }
+ }
+ }
+
+ protected void readCollectionMetdata() throws XMLStreamException
+ {
+ if (isFileOpen()) {
+ collectionSource = null;
+ collectionDate = null;
+ collectionKey = null;
+ while ((collectionSource == null || collectionDate == null || collectionKey == null)
+ && xmlEventReader.hasNext()) {
+ var event = xmlEventReader.nextEvent();
+ if (event.isStartElement()) {
+ if (event.asStartElement().getName().getLocalPart().equals(E_KEY)) {
+ event = xmlEventReader.nextEvent();
+ collectionKey = event.asCharacters().getData();
+ xmlEventReader.nextEvent(); // Reader closing element
+ }
+ else if (event.asStartElement().getName().getLocalPart().equals(E_SOURCE)) {
+ event = xmlEventReader.nextEvent();
+ collectionSource = event.asCharacters().getData();
+ xmlEventReader.nextEvent(); // Reader closing element
+ }
+ else if (event.asStartElement().getName().getLocalPart().equals(E_DATE)) {
+ event = xmlEventReader.nextEvent();
+ collectionDate = event.asCharacters().getData();
+ xmlEventReader.nextEvent(); // Reader closing element
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCWriter.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCWriter.java
new file mode 100644
index 00000000000..cb91b6d7897
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCWriter.java
@@ -0,0 +1,111 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.getCollectionMetadataField;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.dkpro.core.api.io.JCasFileWriter_ImplBase;
+import org.dkpro.core.api.parameter.ComponentParameters;
+
+import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData;
+import de.tudarmstadt.ukp.inception.io.bioc.model.BioCCollection;
+import de.tudarmstadt.ukp.inception.io.bioc.model.CasToBioC;
+
+public class BioCWriter
+ extends JCasFileWriter_ImplBase
+ implements BioCComponent
+{
+ /**
+ * Indent output.
+ */
+ public static final String PARAM_INDENT = "indent";
+ @ConfigurationParameter(name = PARAM_INDENT, mandatory = true, defaultValue = "true")
+ private boolean indent;
+
+ /**
+ * Specify the suffix of output files. Default value .xml. If the suffix is not
+ * needed, provide an empty string as value.
+ */
+ public static final String PARAM_FILENAME_EXTENSION = ComponentParameters.PARAM_FILENAME_EXTENSION;
+ @ConfigurationParameter(name = PARAM_FILENAME_EXTENSION, mandatory = true, defaultValue = ".xml")
+ private String filenameSuffix;
+
+ /**
+ * Character encoding of the output data.
+ */
+ public static final String PARAM_TARGET_ENCODING = ComponentParameters.PARAM_TARGET_ENCODING;
+ @ConfigurationParameter(name = PARAM_TARGET_ENCODING, mandatory = true, //
+ defaultValue = ComponentParameters.DEFAULT_ENCODING)
+ private String targetEncoding;
+
+ private JAXBContext context;
+
+ @Override
+ public void initialize(UimaContext aContext) throws ResourceInitializationException
+ {
+ super.initialize(aContext);
+
+ try {
+ context = JAXBContext.newInstance(BioCCollection.class);
+ }
+ catch (JAXBException e) {
+ throw new ResourceInitializationException(e);
+ }
+ }
+
+ @Override
+ public void process(JCas aJCas) throws AnalysisEngineProcessException
+ {
+ try (var docOS = getOutputStream(aJCas, filenameSuffix)) {
+ Marshaller marshaller = context.createMarshaller();
+ marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+ // Set to fragment mode to omit XML declaration
+ marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
+
+ var bioCCollection = new BioCCollection();
+
+ // Base-information - may be overwritten by the metadata fields below
+ var dmd = DocumentMetaData.get(aJCas);
+ bioCCollection.setSource(dmd.getCollectionId());
+
+ // Use BioC metadata fields if available
+ getCollectionMetadataField(aJCas.getCas(), E_SOURCE)
+ .ifPresent($ -> bioCCollection.setSource($.getValue()));
+ getCollectionMetadataField(aJCas.getCas(), E_KEY)
+ .ifPresent($ -> bioCCollection.setKey($.getValue()));
+ getCollectionMetadataField(aJCas.getCas(), E_DATE)
+ .ifPresent($ -> bioCCollection.setDate($.getValue()));
+
+ new CasToBioC().convert(aJCas, bioCCollection);
+
+ marshaller.marshal(bioCCollection, docOS);
+ }
+ catch (Exception e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentFormatSupport.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentFormatSupport.java
new file mode 100644
index 00000000000..ec9bf4536e1
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentFormatSupport.java
@@ -0,0 +1,85 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription;
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription;
+
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+
+import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.inception.io.bioc.config.BioCAutoConfiguration;
+
+/**
+ * Support for BioC format.
+ *
+ * This class is exposed as a Spring Component via
+ * {@link BioCAutoConfiguration#bioCXmlDocumentFormatSupport}.
+ *
+ */
+public class BioCXmlDocumentFormatSupport
+ implements FormatSupport
+{
+ public static final String ID = "bioc-xml";
+ public static final String NAME = "BioC XML Document (experimental)";
+
+ @Override
+ public String getId()
+ {
+ return ID;
+ }
+
+ @Override
+ public String getName()
+ {
+ return NAME;
+ }
+
+ @Override
+ public boolean isReadable()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isWritable()
+ {
+ return true;
+ }
+
+ @Override
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
+ throws ResourceInitializationException
+ {
+ return createReaderDescription(BioCXmlDocumentReader.class, aTSD);
+ }
+
+ @Override
+ public AnalysisEngineDescription getWriterDescription(Project aProject,
+ TypeSystemDescription aTSD, CAS aCAS)
+ throws ResourceInitializationException
+ {
+ return createEngineDescription(BioCXmlDocumentWriter.class, aTSD);
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReader.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReader.java
new file mode 100644
index 00000000000..1219a61bc72
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReader.java
@@ -0,0 +1,157 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.addCollectionMetadataField;
+import static de.tudarmstadt.ukp.inception.io.bioc.xml.DocumentWrappingXmlInputReader.wrapInDocument;
+
+import java.io.IOException;
+
+import javax.xml.stream.XMLStreamException;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.sax.SAXResult;
+import javax.xml.transform.stax.StAXSource;
+
+import org.apache.uima.UimaContext;
+import org.apache.uima.collection.CollectionException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.dkpro.core.api.xml.type.XmlDocument;
+import org.dkpro.core.api.xml.type.XmlElement;
+import org.xml.sax.SAXException;
+
+import de.tudarmstadt.ukp.inception.io.bioc.xml.BioC2XmlCas;
+import de.tudarmstadt.ukp.inception.io.xml.dkprocore.CasXmlHandler;
+import de.tudarmstadt.ukp.inception.io.xml.dkprocore.CasXmlHandler.ElementListener;
+import de.tudarmstadt.ukp.inception.support.xml.XmlParserUtils;
+
+public class BioCXmlDocumentReader
+ extends BioCReaderImplBase
+{
+ private Transformer transformer;
+ private boolean documentAvailable = false;
+
+ @Override
+ public void initialize(UimaContext aContext) throws ResourceInitializationException
+ {
+ super.initialize(aContext);
+
+ try {
+ transformer = XmlParserUtils.newTransformerFactory().newTransformer();
+ }
+ catch (TransformerConfigurationException e) {
+ throw new ResourceInitializationException(e);
+ }
+
+ try {
+ documentAvailable = seekNextBioCDocument();
+ }
+ catch (XMLStreamException | CollectionException | IOException e) {
+ throw new ResourceInitializationException(e);
+ }
+ }
+
+ @Override
+ public boolean hasNext() throws IOException, CollectionException
+ {
+ return documentAvailable;
+ }
+
+ @Override
+ public void getNext(JCas aJCas) throws IOException, CollectionException
+ {
+ initCas(aJCas, currentResource());
+
+ addCollectionMetadataField(aJCas, E_KEY, getCollectionKey());
+ addCollectionMetadataField(aJCas, E_SOURCE, getCollectionSource());
+ addCollectionMetadataField(aJCas, E_DATE, getCollectionDate());
+
+ CasXmlHandler handler = new CasXmlHandler(aJCas);
+ handler.addListener(newElementFilter(handler));
+
+ try {
+ transformer.transform(new StAXSource(wrapInDocument(getXmlEventReader())),
+ new SAXResult(handler));
+ }
+ catch (TransformerException | XMLStreamException e) {
+ throw new IOException(e);
+ }
+
+ new BioC2XmlCas().transferAnnotations(aJCas);
+
+ try {
+ documentAvailable = seekNextBioCDocument();
+ }
+ catch (XMLStreamException e) {
+ throw new IOException(e);
+ }
+ }
+
+ private ElementListener newElementFilter(CasXmlHandler handler)
+ {
+ return new ElementListener()
+ {
+ @Override
+ public void startDocument(XmlDocument aDocument) throws SAXException
+ {
+ handler.startElement(null, null, E_COLLECTION, null);
+ handler.captureText(false);
+ }
+
+ @Override
+ public void endDocument(XmlDocument aDocument) throws SAXException
+ {
+ handler.endElement(null, null, E_COLLECTION);
+ }
+
+ @Override
+ public void startElement(XmlElement aElement)
+ {
+ var parent = aElement.getParent();
+ if (parent != null
+ && (E_PASSAGE.equals(parent.getQName())
+ || E_SENTENCE.equals(parent.getQName()))
+ && E_TEXT.equals(aElement.getQName())) {
+ handler.captureText(true);
+ }
+ else {
+ handler.captureText(false);
+ }
+ }
+ };
+ }
+
+ private boolean seekNextBioCDocument()
+ throws XMLStreamException, CollectionException, IOException
+ {
+ if (!isFileOpen()) {
+ openNextFile();
+
+ readCollectionMetdata();
+ }
+
+ if (isFileOpen()) {
+ return seekNextBioCDocumentInFile();
+ }
+
+ return false;
+ }
+
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentWriter.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentWriter.java
new file mode 100644
index 00000000000..3bc07e09fd4
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentWriter.java
@@ -0,0 +1,100 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static javax.xml.transform.OutputKeys.INDENT;
+import static javax.xml.transform.OutputKeys.METHOD;
+import static javax.xml.transform.OutputKeys.OMIT_XML_DECLARATION;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.StringReader;
+import java.io.StringWriter;
+
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.jcas.JCas;
+import org.dkpro.core.api.io.JCasFileWriter_ImplBase;
+import org.xml.sax.SAXException;
+
+import de.tudarmstadt.ukp.inception.io.bioc.xml.Cas2BioCSaxEvents;
+import de.tudarmstadt.ukp.inception.support.xml.XmlParserUtils;
+
+public class BioCXmlDocumentWriter
+ extends JCasFileWriter_ImplBase
+{
+ /**
+ * Indent output .
+ */
+ public static final String PARAM_INDENT = "indent";
+ @ConfigurationParameter(name = PARAM_INDENT, mandatory = true, defaultValue = "false")
+ private boolean indent;
+
+ @Override
+ public void process(JCas aJCas) throws AnalysisEngineProcessException
+ {
+ if (indent) {
+ String xmlString;
+ try (var stringWriter = new StringWriter()) {
+ var tf = XmlParserUtils.newTransformerFactory();
+ var th = tf.newTransformerHandler();
+ th.setResult(new StreamResult(stringWriter));
+ var serializer = new Cas2BioCSaxEvents(th);
+ serializer.process(aJCas);
+ xmlString = stringWriter.toString();
+ }
+ catch (IOException | SAXException | TransformerConfigurationException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ try (OutputStream docOS = getOutputStream(aJCas, ".xml")) {
+ var tf = XmlParserUtils.newTransformerFactory();
+ tf.setAttribute("indent-number", 2);
+ var transformer = tf.newTransformer();
+ transformer.setOutputProperty(OMIT_XML_DECLARATION, "yes");
+ transformer.setOutputProperty(INDENT, "yes");
+ transformer.transform(new StreamSource(new StringReader(xmlString)),
+ new StreamResult(docOS));
+ }
+ catch (IOException | TransformerException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+ else {
+ try (OutputStream docOS = getOutputStream(aJCas, ".xml")) {
+ var tf = XmlParserUtils.newTransformerFactory();
+ var th = tf.newTransformerHandler();
+ th.getTransformer().setOutputProperty(OMIT_XML_DECLARATION, "yes");
+ th.getTransformer().setOutputProperty(METHOD, "xml");
+ th.getTransformer().setOutputProperty(INDENT, "no");
+ th.setResult(new StreamResult(docOS));
+
+ var serializer = new Cas2BioCSaxEvents(th);
+ serializer.process(aJCas);
+ }
+ catch (IOException | SAXException | TransformerConfigurationException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/config/BioCAutoConfiguration.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/config/BioCAutoConfiguration.java
new file mode 100644
index 00000000000..e23233b8cb2
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/config/BioCAutoConfiguration.java
@@ -0,0 +1,43 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.config;
+
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import de.tudarmstadt.ukp.inception.io.bioc.BioCFormatSupport;
+import de.tudarmstadt.ukp.inception.io.bioc.BioCXmlDocumentFormatSupport;
+
+@Configuration
+public class BioCAutoConfiguration
+{
+ @Bean
+ @ConditionalOnProperty(prefix = "format.bioc", name = "enabled", havingValue = "true", matchIfMissing = false)
+ public BioCFormatSupport bioCFormatSupport()
+ {
+ return new BioCFormatSupport();
+ }
+
+ @Bean
+ @ConditionalOnProperty(prefix = "format.bioc-xml", name = "enabled", havingValue = "true", matchIfMissing = false)
+ public BioCXmlDocumentFormatSupport bioCXmlDocumentFormatSupport()
+ {
+ return new BioCXmlDocumentFormatSupport();
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCAnnotation.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCAnnotation.java
new file mode 100644
index 00000000000..0c40f26458b
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCAnnotation.java
@@ -0,0 +1,64 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+
+public class BioCAnnotation
+ extends BioCObject
+{
+ private String id;
+ private String text;
+ private List locations;
+
+ public String getId()
+ {
+ return id;
+ }
+
+ @XmlAttribute(name = "id")
+ public void setId(String aId)
+ {
+ id = aId;
+ }
+
+ public String getText()
+ {
+ return text;
+ }
+
+ @XmlElement(name = "text")
+ public void setText(String aText)
+ {
+ text = aText;
+ }
+
+ public List getLocations()
+ {
+ return locations;
+ }
+
+ @XmlElement(name = "location")
+ public void setLocations(List aLocations)
+ {
+ locations = aLocations;
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCAnnotationContainer.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCAnnotationContainer.java
new file mode 100644
index 00000000000..7924c09596d
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCAnnotationContainer.java
@@ -0,0 +1,70 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlTransient;
+
+@XmlTransient
+public abstract class BioCAnnotationContainer
+ extends BioCObject
+{
+ private List annotations;
+ private List relations;
+
+ public List getAnnotations()
+ {
+ return annotations;
+ }
+
+ @XmlElement(name = "annotation")
+ public void setAnnotations(List aAnnotations)
+ {
+ annotations = aAnnotations;
+ }
+
+ public void addAnnotation(BioCAnnotation aAnnotation)
+ {
+ if (annotations == null) {
+ annotations = new ArrayList<>();
+ }
+ annotations.add(aAnnotation);
+ }
+
+ public List getRelations()
+ {
+ return relations;
+ }
+
+ @XmlElement(name = "relation")
+ public void setRelations(List aRelations)
+ {
+ relations = aRelations;
+ }
+
+ public void addRelation(BioCRelation aRelation)
+ {
+ if (relations == null) {
+ relations = new ArrayList<>();
+ }
+ relations.add(aRelation);
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCCollection.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCCollection.java
new file mode 100644
index 00000000000..4115336646c
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCCollection.java
@@ -0,0 +1,94 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_DATE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_DOCUMENT;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_KEY;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_SOURCE;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlRootElement(name = "collection")
+@XmlType(propOrder = { "source", "date", "key", "infons", "documents" })
+public class BioCCollection
+ extends BioCObject
+{
+ private String source;
+ private String date;
+ private String key;
+ private List documents;
+
+ public String getSource()
+ {
+ return source;
+ }
+
+ @XmlElement(name = E_SOURCE)
+ public void setSource(String aSource)
+ {
+ source = aSource;
+ }
+
+ public String getDate()
+ {
+ return date;
+ }
+
+ @XmlElement(name = E_DATE)
+ public void setDate(String aDate)
+ {
+ date = aDate;
+ }
+
+ public String getKey()
+ {
+ return key;
+ }
+
+ @XmlElement(name = E_KEY)
+ public void setKey(String aKey)
+ {
+ key = aKey;
+ }
+
+ public List getDocuments()
+ {
+ return documents;
+ }
+
+ @XmlElement(name = E_DOCUMENT)
+ public void setDocuments(List aDocuments)
+ {
+ documents = aDocuments;
+ }
+
+ public void addDocument(BioCDocument aDocument)
+ {
+ if (documents == null) {
+ documents = new ArrayList<>();
+ }
+
+ documents.add(aDocument);
+ }
+}
diff --git a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentViewController.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCDocument.java
similarity index 51%
rename from inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentViewController.java
rename to inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCDocument.java
index 6c489eac83d..4a21c4f9d06 100644
--- a/inception/inception-html-editor/src/main/java/de/tudarmstadt/ukp/inception/htmleditor/docview/HtmlDocumentViewController.java
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCDocument.java
@@ -15,27 +15,39 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package de.tudarmstadt.ukp.inception.htmleditor.docview;
+package de.tudarmstadt.ukp.inception.io.bioc.model;
-import static de.tudarmstadt.ukp.inception.security.config.InceptionSecurityWebUIApiAutoConfiguration.BASE_VIEW_URL;
+import java.util.List;
-import java.security.Principal;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
-import org.springframework.http.ResponseEntity;
+@XmlRootElement(name = "document")
+public class BioCDocument
+ extends BioCObject
+{
+ private String id;
+ private List passages;
-import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
-import de.tudarmstadt.ukp.inception.externaleditor.xhtml.XHtmlXmlDocumentIFrameViewFactory;
+ public String getId()
+ {
+ return id;
+ }
-/**
- * @deprecated Use {@link XHtmlXmlDocumentIFrameViewFactory} instead
- */
-@Deprecated
-public interface HtmlDocumentViewController
-{
- String BASE_URL = BASE_VIEW_URL + "/html";
+ @XmlElement(name = "id")
+ public void setId(String aId)
+ {
+ id = aId;
+ }
- String getDocumentUrl(SourceDocument aDoc);
+ public List getPassages()
+ {
+ return passages;
+ }
- ResponseEntity getDocument(long aProjectId, long aDocumentId, Principal aPrincipal)
- throws Exception;
+ @XmlElement(name = "passage")
+ public void setPassages(List aPassages)
+ {
+ passages = aPassages;
+ }
}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCInfon.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCInfon.java
new file mode 100644
index 00000000000..5fa82bb6dbb
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCInfon.java
@@ -0,0 +1,60 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlValue;
+
+public class BioCInfon
+{
+ private String key;
+ private String value;
+
+ public BioCInfon()
+ {
+ // Required for serialization
+ }
+
+ public BioCInfon(String aKey, String aValue)
+ {
+ key = aKey;
+ value = aValue;
+ }
+
+ public String getKey()
+ {
+ return key;
+ }
+
+ @XmlAttribute(name = "key")
+ public void setKey(String aKey)
+ {
+ key = aKey;
+ }
+
+ @XmlValue
+ public String getValue()
+ {
+ return value;
+ }
+
+ public void setValue(String aValue)
+ {
+ value = aValue;
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCLocation.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCLocation.java
new file mode 100644
index 00000000000..2ae83a058e5
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCLocation.java
@@ -0,0 +1,59 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import javax.xml.bind.annotation.XmlAttribute;
+
+public class BioCLocation
+{
+ private int offset;
+ private int length;
+
+ public BioCLocation()
+ {
+ // Needed for serialization
+ }
+
+ public BioCLocation(int aOffset, int aLength)
+ {
+ offset = aOffset;
+ length = aLength;
+ }
+
+ public int getOffset()
+ {
+ return offset;
+ }
+
+ @XmlAttribute(name = "offset")
+ public void setOffset(int aOffset)
+ {
+ offset = aOffset;
+ }
+
+ public int getLength()
+ {
+ return length;
+ }
+
+ @XmlAttribute(name = "length")
+ public void setLength(int aLength)
+ {
+ length = aLength;
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCNode.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCNode.java
new file mode 100644
index 00000000000..0f0f42d41d1
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCNode.java
@@ -0,0 +1,59 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import javax.xml.bind.annotation.XmlAttribute;
+
+public class BioCNode
+{
+ private String refId;
+ private String role;
+
+ public BioCNode()
+ {
+ // Needed for serialization
+ }
+
+ public BioCNode(String aRefId, String aRole)
+ {
+ refId = aRefId;
+ role = aRole;
+ }
+
+ public String getRefId()
+ {
+ return refId;
+ }
+
+ @XmlAttribute(name = "refid")
+ public void setRefId(String aRefId)
+ {
+ refId = aRefId;
+ }
+
+ public String getRole()
+ {
+ return role;
+ }
+
+ @XmlAttribute(name = "role")
+ public void setRole(String aRole)
+ {
+ role = aRole;
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCObject.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCObject.java
new file mode 100644
index 00000000000..55bb3cc562c
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCObject.java
@@ -0,0 +1,70 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import static java.util.stream.Collectors.toMap;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlTransient;
+
+@XmlTransient
+public abstract class BioCObject
+{
+ private List infons;
+
+ public List getInfons()
+ {
+ return infons;
+ }
+
+ @XmlElement(name = "infon")
+ public void setInfons(List aInfons)
+ {
+ infons = aInfons;
+ }
+
+ public void addInfon(String aKey, String aValue)
+ {
+ if (infons == null) {
+ infons = new ArrayList<>();
+ }
+ infons.add(new BioCInfon(aKey, aValue));
+ }
+
+ public Optional infon(String aKey)
+ {
+ if (infons == null) {
+ return Optional.empty();
+ }
+
+ return infons.stream() //
+ .filter(i -> i.getKey().equals(aKey)) //
+ .findFirst() //
+ .map(BioCInfon::getValue);
+ }
+
+ public Map infonMap()
+ {
+ return infons.stream().collect(toMap(BioCInfon::getKey, BioCInfon::getValue));
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCPassage.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCPassage.java
new file mode 100644
index 00000000000..9f7f2c1d662
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCPassage.java
@@ -0,0 +1,65 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlType(propOrder = { "infons", "offset", "text", "sentences", "annotations", "relations" })
+public class BioCPassage
+ extends BioCAnnotationContainer
+{
+ private int offset;
+ private String text;
+ private List sentences;
+
+ public int getOffset()
+ {
+ return offset;
+ }
+
+ @XmlElement(name = "offset")
+ public void setOffset(int aOffset)
+ {
+ offset = aOffset;
+ }
+
+ public String getText()
+ {
+ return text;
+ }
+
+ @XmlElement(name = "text")
+ public void setText(String aText)
+ {
+ text = aText;
+ }
+
+ public List getSentences()
+ {
+ return sentences;
+ }
+
+ @XmlElement(name = "sentence")
+ public void setSentences(List aSentences)
+ {
+ sentences = aSentences;
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCRelation.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCRelation.java
new file mode 100644
index 00000000000..55360a4375e
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCRelation.java
@@ -0,0 +1,69 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import static java.util.stream.Collectors.toMap;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+
+public class BioCRelation
+ extends BioCObject
+{
+ private String id;
+ private List nodes;
+
+ public String getId()
+ {
+ return id;
+ }
+
+ @XmlAttribute(name = "id")
+ public void setId(String aId)
+ {
+ id = aId;
+ }
+
+ public List getNodes()
+ {
+ return nodes;
+ }
+
+ @XmlElement(name = "node")
+ public void setNodes(List aNodes)
+ {
+ nodes = aNodes;
+ }
+
+ public void addNode(String aRole, String aRefId)
+ {
+ if (nodes == null) {
+ nodes = new ArrayList<>();
+ }
+ nodes.add(new BioCNode(aRefId, aRole));
+ }
+
+ public Map nodeMap()
+ {
+ return nodes.stream().collect(toMap(BioCNode::getRole, BioCNode::getRefId));
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCSentence.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCSentence.java
new file mode 100644
index 00000000000..3563adae9b9
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCSentence.java
@@ -0,0 +1,51 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlType(propOrder = { "infons", "offset", "text", "annotations", "relations" })
+public class BioCSentence
+ extends BioCAnnotationContainer
+{
+ private int offset;
+ private String text;
+
+ public int getOffset()
+ {
+ return offset;
+ }
+
+ @XmlElement(name = "offset")
+ public void setOffset(int aOffset)
+ {
+ offset = aOffset;
+ }
+
+ public String getText()
+ {
+ return text;
+ }
+
+ @XmlElement(name = "text")
+ public void setText(String aText)
+ {
+ text = aText;
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCToCas.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCToCas.java
new file mode 100644
index 00000000000..2f2ef90731b
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/BioCToCas.java
@@ -0,0 +1,251 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_SOURCE;
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_TARGET;
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isRelationLayer;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_ID;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.I_TYPE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_SOURCE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_TARGET;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.addCollectionMetadataField;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.guessBestRelationType;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.guessBestSpanType;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.transferFeatures;
+import static java.lang.invoke.MethodHandles.lookup;
+import static java.util.Collections.emptyMap;
+import static org.apache.commons.collections4.CollectionUtils.isNotEmpty;
+import static org.apache.commons.lang3.StringUtils.repeat;
+import static org.slf4j.LoggerFactory.getLogger;
+
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.uima.cas.Type;
+import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.fit.factory.JCasBuilder;
+import org.apache.uima.fit.util.FSUtil;
+import org.apache.uima.jcas.JCas;
+import org.slf4j.Logger;
+
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Div;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+import de.tudarmstadt.ukp.inception.support.xml.XmlParserUtils;
+
+public class BioCToCas
+{
+ private static final Logger LOG = getLogger(lookup().lookupClass());
+
+ public void parseXml(InputStream aReader, JCas aJCas) throws JAXBException, XMLStreamException
+ {
+ var collection = loadBioCCollection(aReader);
+
+ convert(collection, aJCas);
+ }
+
+ public void convert(BioCCollection collection, JCas aJCas)
+ {
+ var builder = new JCasBuilder(aJCas);
+ readDocument(builder, collection.getDocuments().get(0));
+ builder.close();
+ }
+
+ public BioCCollection loadBioCCollection(InputStream aReader)
+ throws XMLStreamException, JAXBException
+ {
+ var xmlInputFactory = XmlParserUtils.newXmlInputFactory();
+ var xmlEventReader = xmlInputFactory.createXMLEventReader(aReader);
+
+ var context = JAXBContext.newInstance(BioCCollection.class);
+ var unmarshaller = context.createUnmarshaller();
+
+ var collection = unmarshaller.unmarshal(xmlEventReader, BioCCollection.class).getValue();
+ return collection;
+ }
+
+ public void readDocument(JCasBuilder aBuilder, BioCDocument aDocument)
+ {
+ addCollectionMetadataField(aBuilder.getJCas(), E_ID, aDocument.getId());
+
+ if (isNotEmpty(aDocument.getInfons())) {
+ LOG.warn("Document-level infons not supported");
+ }
+
+ if (aDocument.getPassages() != null) {
+ for (var passage : aDocument.getPassages()) {
+ readPassage(aBuilder, passage);
+ }
+ }
+ }
+
+ void readPassage(JCasBuilder aBuilder, BioCPassage aPassage)
+ {
+ if (aPassage.getText() != null) {
+ readPassageWithoutSentences(aBuilder, aPassage);
+ }
+ else if (aPassage.getSentences() != null) {
+ readPassageWithSentences(aBuilder, aPassage);
+ }
+ else {
+ LOG.warn("Passage contains neither text nor sentence!");
+ }
+
+ var id2Span = readAnnotations(aBuilder, aPassage.getOffset(), aPassage.getAnnotations());
+ readRelations(aBuilder, aPassage.getRelations(), id2Span);
+ }
+
+ private void readPassageWithSentences(JCasBuilder aBuilder, BioCPassage aPassage)
+ {
+ int passageBegin = aBuilder.getPosition();
+
+ for (var sentence : aPassage.getSentences()) {
+ readSentence(aBuilder, sentence);
+ }
+
+ var div = aBuilder.add(passageBegin, Div.class);
+ div.trim();
+ aPassage.infon(I_TYPE).ifPresent(div::setDivType);
+ }
+
+ private void readPassageWithoutSentences(JCasBuilder aBuilder, BioCPassage aPassage)
+ {
+ if (isNotEmpty(aPassage.getInfons())) {
+ LOG.warn("Passage-level infons not supported");
+ }
+
+ // Add empty line after passage - if there is space.
+ if (aPassage.getOffset() - aBuilder.getPosition() >= 2) {
+ aBuilder.add("\n\n");
+ }
+
+ if (aBuilder.getPosition() < aPassage.getOffset()) {
+ aBuilder.add(repeat(" ", aPassage.getOffset() - aBuilder.getPosition()));
+ }
+
+ var div = aBuilder.add(aPassage.getText(), Div.class);
+ div.trim();
+ aPassage.infon(I_TYPE).ifPresent(div::setDivType);
+ }
+
+ void readSentence(JCasBuilder aBuilder, BioCSentence aSentence)
+ {
+ if (aSentence.getText() == null) {
+ LOG.warn("Sentence contains no text!");
+ }
+
+ // Add line-break after sentences - if there is space.
+ if (aSentence.getOffset() - aBuilder.getPosition() >= 1) {
+ aBuilder.add("\n");
+ }
+
+ if (aBuilder.getPosition() < aSentence.getOffset()) {
+ aBuilder.add(repeat(" ", aSentence.getOffset() - aBuilder.getPosition()));
+ }
+
+ var sentence = aBuilder.add(aSentence.getText(), Sentence.class);
+ sentence.trim();
+
+ if (isNotEmpty(aSentence.getInfons())) {
+ LOG.warn("Sentence-level infons not supported");
+ }
+
+ var id2Span = readAnnotations(aBuilder, sentence.getBegin(), aSentence.getAnnotations());
+ readRelations(aBuilder, aSentence.getRelations(), id2Span);
+ }
+
+ private Map readAnnotations(JCasBuilder aBuilder, int aContainerBegin,
+ List aBioCAnnotations)
+ {
+ if (aBioCAnnotations == null) {
+ return emptyMap();
+ }
+
+ var id2Span = new LinkedHashMap();
+ var cas = aBuilder.getJCas().getCas();
+ var typeSystem = aBuilder.getJCas().getTypeSystem();
+ for (var bioCAnnotation : aBioCAnnotations) {
+ var infons = bioCAnnotation.infonMap();
+ Type uimaType = guessBestSpanType(typeSystem, infons);
+ if (uimaType == null) {
+ LOG.debug("Unable to find suitable UIMA type for span annotation");
+ continue;
+ }
+
+ var firstLocation = bioCAnnotation.getLocations().get(0);
+ var begin = aContainerBegin + firstLocation.getOffset();
+ var end = begin + firstLocation.getLength();
+ var annotation = cas.createAnnotation(uimaType, begin, end);
+ transferFeatures(annotation, infons);
+ cas.addFsToIndexes(annotation);
+
+ if (bioCAnnotation.getId() != null) {
+ id2Span.put(bioCAnnotation.getId(), annotation);
+ }
+ }
+ return id2Span;
+ }
+
+ private void readRelations(JCasBuilder aBuilder, List aRelations,
+ Map aId2Span)
+ {
+ if (aRelations == null) {
+ return;
+ }
+
+ var cas = aBuilder.getJCas().getCas();
+
+ for (var bioCRelation : aRelations) {
+ var infons = bioCRelation.infonMap();
+ var nodes = bioCRelation.nodeMap();
+
+ Type uimaType = guessBestRelationType(cas.getTypeSystem(), infons);
+ if (uimaType == null || !isRelationLayer(uimaType)) {
+ LOG.debug("Unable to find suitable UIMA type for relation annotation");
+ continue;
+ }
+
+ var sourceId = nodes.get(R_SOURCE);
+ var targetId = nodes.get(R_TARGET);
+ if (sourceId == null || targetId == null) {
+ LOG.debug("Relation must have a source ID and a target ID");
+ continue;
+ }
+
+ var sourceSpan = aId2Span.get(sourceId);
+ var targetSpan = aId2Span.get(targetId);
+ if (sourceSpan == null || targetSpan == null) {
+ LOG.debug("Relation must have a source and a target");
+ continue;
+ }
+
+ var annotation = cas.createAnnotation(uimaType, targetSpan.getBegin(),
+ targetSpan.getEnd());
+ transferFeatures(annotation, infons);
+ FSUtil.setFeature(annotation, FEAT_REL_SOURCE, sourceSpan);
+ FSUtil.setFeature(annotation, FEAT_REL_TARGET, targetSpan);
+ cas.addFsToIndexes(annotation);
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/CasToBioC.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/CasToBioC.java
new file mode 100644
index 00000000000..4aa35a4a7c7
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/CasToBioC.java
@@ -0,0 +1,219 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.model;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_SOURCE;
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_TARGET;
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isRelationLayer;
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isSpanLayer;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.I_TYPE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_SOURCE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_TARGET;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.getCollectionMetadataField;
+import static java.util.Arrays.asList;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_BEGIN;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_END;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_SOFA;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.fit.util.FSUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.dkpro.core.api.xml.type.XmlElement;
+
+import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData;
+import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.MetaDataStringField;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Div;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
+import de.tudarmstadt.ukp.inception.io.bioc.BioCComponent;
+
+public class CasToBioC
+{
+ private static final Set EXCLUDED_TYPES = Set.of(DocumentMetaData._TypeName,
+ Sentence._TypeName, Token._TypeName, MetaDataStringField._TypeName, Div._TypeName);
+
+ private static final Set EXCLUDED_FEATURES = Set.of(FEATURE_FULL_NAME_BEGIN,
+ FEATURE_FULL_NAME_END, FEATURE_FULL_NAME_SOFA);
+
+ private Map annotationToId;
+
+ public void convert(JCas aJCas, BioCCollection aCollection)
+ {
+ annotationToId = new HashMap<>();
+
+ var bioCDocument = new BioCDocument();
+ bioCDocument.setId(DocumentMetaData.get(aJCas).getDocumentId());
+
+ // Overwrite with BioC metadata if available
+ getCollectionMetadataField(aJCas.getCas(), BioCComponent.E_ID)
+ .ifPresent($ -> bioCDocument.setId($.getValue()));
+
+ var passagesIndex = buildPassagesIndex(aJCas);
+
+ for (var passageEntry : passagesIndex.entrySet()) {
+ var bioCPassage = passageEntry.getKey();
+ var div = passageEntry.getValue();
+ if (div.getDivType() != null) {
+ bioCPassage.addInfon(I_TYPE, div.getDivType());
+ }
+
+ var sentences = aJCas.select(Sentence.class).coveredBy(div).asList();
+ if (sentences.isEmpty()) {
+ bioCPassage.setText(div.getCoveredText());
+ processAnnotations(bioCPassage, bioCPassage.getOffset(),
+ aJCas.select(Annotation.class).coveredBy(div));
+ }
+ else {
+ var bioCSentences = processSentences(div.getBegin(), sentences);
+ bioCPassage.setSentences(bioCSentences);
+ processAnnotations(bioCPassage, bioCPassage.getOffset(),
+ aJCas.select(Annotation.class).coveredBy(div)
+ .filter(a -> aJCas.select(Sentence.class).covering(a).isEmpty())
+ .collect(Collectors.toList()));
+ }
+ }
+
+ bioCDocument.setPassages(new ArrayList<>(passagesIndex.keySet()));
+ aCollection.addDocument(bioCDocument);
+ }
+
+ private LinkedHashMap buildPassagesIndex(JCas aJCas)
+ {
+ var passagesIndex = new LinkedHashMap();
+ var divs = aJCas.select(Div.class).asList();
+ if (divs.isEmpty()) {
+ var bioCPassage = new BioCPassage();
+ bioCPassage.setOffset(0);
+ passagesIndex.put(bioCPassage, new Div(aJCas, 0, aJCas.getDocumentText().length()));
+ }
+ else {
+ for (var div : divs) {
+ var bioCPassage = new BioCPassage();
+ bioCPassage.setOffset(0);
+ passagesIndex.put(bioCPassage, div);
+ }
+ }
+ return passagesIndex;
+ }
+
+ private List processSentences(int aPassageOffset, List sentences)
+ {
+ var bioCSentences = new ArrayList();
+ for (var sentence : sentences) {
+ var bioCSentence = new BioCSentence();
+ bioCSentence.setOffset(sentence.getBegin() - aPassageOffset);
+ bioCSentence.setText(sentence.getCoveredText());
+
+ processAnnotations(bioCSentence, sentence.getBegin(),
+ sentence.getCAS().select(Annotation.class).coveredBy(sentence));
+
+ bioCSentences.add(bioCSentence);
+ }
+ return bioCSentences;
+ }
+
+ private void processAnnotations(BioCAnnotationContainer aContainer, int aContainerOffset,
+ Iterable aAnnotations)
+ {
+ for (var annotation : aAnnotations) {
+ if (isExcludedType(annotation)) {
+ continue;
+ }
+
+ if (isSpanLayer(annotation.getType())) {
+ var span = processSpanAnnotation(aContainerOffset, annotation);
+ aContainer.addAnnotation(span);
+ }
+
+ if (isRelationLayer(annotation.getType())) {
+ var relation = processRelationAnnotation(annotation);
+ aContainer.addRelation(relation);
+ }
+ }
+ }
+
+ private BioCRelation processRelationAnnotation(Annotation aAnnotation)
+ {
+ var relation = new BioCRelation();
+ relation.setId(idOf(aAnnotation));
+ relation.addInfon(I_TYPE, aAnnotation.getType().getName());
+ relation.addNode(R_SOURCE,
+ idOf(FSUtil.getFeature(aAnnotation, FEAT_REL_SOURCE, Annotation.class)));
+ relation.addNode(R_TARGET,
+ idOf(FSUtil.getFeature(aAnnotation, FEAT_REL_TARGET, Annotation.class)));
+ serializeFeatures(aAnnotation, relation);
+ return relation;
+ }
+
+ private String idOf(Annotation aAnnotation)
+ {
+ return annotationToId.computeIfAbsent(aAnnotation,
+ $ -> Integer.toString(annotationToId.size() + 1));
+ }
+
+ private BioCAnnotation processSpanAnnotation(int aContainerOffset, Annotation aAnnotation)
+ {
+ var annotation = new BioCAnnotation();
+ annotation.setId(idOf(aAnnotation));
+ annotation.addInfon(I_TYPE, aAnnotation.getType().getName());
+ annotation.setLocations(asList(new BioCLocation(aAnnotation.getBegin() - aContainerOffset,
+ aAnnotation.getEnd() - aAnnotation.getBegin())));
+ annotation.setText(aAnnotation.getCoveredText());
+ serializeFeatures(aAnnotation, annotation);
+ return annotation;
+ }
+
+ private void serializeFeatures(Annotation aAnnotation, BioCObject aBioCAnnotation)
+ {
+ for (var feature : aAnnotation.getType().getFeatures()) {
+ if (EXCLUDED_FEATURES.contains(feature.getName())) {
+ continue;
+ }
+
+ if (feature.getRange().isPrimitive()) {
+ var value = aAnnotation.getFeatureValueAsString(feature);
+ if (value != null) {
+ aBioCAnnotation.addInfon(feature.getShortName(), value);
+ }
+ }
+ }
+ }
+
+ private boolean isExcludedType(AnnotationFS aAnnotation)
+ {
+ String typeName = aAnnotation.getType().getName();
+ if (typeName.startsWith(XmlElement.class.getPackageName())) {
+ return true;
+ }
+
+ if (EXCLUDED_TYPES.contains(typeName)) {
+ return true;
+ }
+
+ return false;
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/BioC2XmlCas.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/BioC2XmlCas.java
new file mode 100644
index 00000000000..d987c1f3453
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/BioC2XmlCas.java
@@ -0,0 +1,219 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.xml;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_SOURCE;
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_TARGET;
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isRelationLayer;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_ID;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_KEY;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_LENGTH;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_OFFSET;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_REFID;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_ROLE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_ANNOTATION;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_INFON;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_NODE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_RELATION;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_SENTENCE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_SOURCE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_TARGET;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.guessBestRelationType;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.guessBestSpanType;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.transferFeatures;
+import static de.tudarmstadt.ukp.inception.io.bioc.xml.BioCXmlUtils.getChildLocationElement;
+import static de.tudarmstadt.ukp.inception.io.bioc.xml.BioCXmlUtils.getChildTextElement;
+import static de.tudarmstadt.ukp.inception.io.xml.dkprocore.XmlNodeUtils.getAttributeValue;
+import static de.tudarmstadt.ukp.inception.io.xml.dkprocore.XmlNodeUtils.getMandatoryAttributeValue;
+import static java.lang.Integer.parseInt;
+import static java.util.Collections.emptyMap;
+import static java.util.stream.Collectors.toList;
+
+import java.lang.invoke.MethodHandles;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+import org.apache.uima.cas.Type;
+import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.fit.util.FSUtil;
+import org.apache.uima.jcas.JCas;
+import org.dkpro.core.api.xml.type.XmlElement;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+import de.tudarmstadt.ukp.inception.io.xml.dkprocore.XmlNodeUtils;
+
+public class BioC2XmlCas
+{
+ private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+
+ public void transferAnnotations(JCas aJCas)
+ {
+ transferSentences(aJCas);
+ var id2Span = transferSpanAnnotations(aJCas);
+ transferRelationAnnotations(aJCas, id2Span);
+ }
+
+ private void transferRelationAnnotations(JCas aJCas, Map aId2Span)
+ {
+ var relationElements = aJCas.select(XmlElement.class) //
+ .filter(e -> E_RELATION.equals(e.getQName())) //
+ .collect(toList());
+
+ var cas = aJCas.getCas();
+ for (var relationElement : relationElements) {
+ var infons = extractInfons(relationElement);
+ var nodes = extractNodes(relationElement);
+
+ Type uimaType = guessBestRelationType(aJCas.getTypeSystem(), infons);
+ if (uimaType == null || !isRelationLayer(uimaType)) {
+ LOG.debug("Unable to find suitable UIMA type for relation annotation");
+ continue;
+ }
+
+ var sourceId = nodes.get(R_SOURCE);
+ var targetId = nodes.get(R_TARGET);
+ if (sourceId == null || targetId == null) {
+ LOG.debug("Relation must have a source ID and a target ID");
+ continue;
+ }
+
+ var sourceSpan = aId2Span.get(sourceId);
+ var targetSpan = aId2Span.get(targetId);
+ if (sourceSpan == null || targetSpan == null) {
+ LOG.debug("Relation must have a source and a target");
+ continue;
+ }
+
+ var annotation = cas.createAnnotation(uimaType, targetSpan.getBegin(),
+ targetSpan.getEnd());
+ transferFeatures(annotation, infons);
+ FSUtil.setFeature(annotation, FEAT_REL_SOURCE, sourceSpan);
+ FSUtil.setFeature(annotation, FEAT_REL_TARGET, targetSpan);
+ cas.addFsToIndexes(annotation);
+ }
+
+ relationElements.forEach(XmlNodeUtils::removeWithDescendantsFromTree);
+ }
+
+ private Map transferSpanAnnotations(JCas aJCas)
+ {
+ var annotationElements = aJCas.select(XmlElement.class) //
+ .filter(e -> E_ANNOTATION.equals(e.getQName())) //
+ .collect(toList());
+
+ var id2Span = new LinkedHashMap();
+
+ var cas = aJCas.getCas();
+ for (var annotationElement : annotationElements) {
+ var containerElement = annotationElement.getParent();
+ var containerTextElement = getChildTextElement(containerElement);
+ var locationElement = getChildLocationElement(annotationElement);
+ var id = getAttributeValue(annotationElement, A_ID);
+ var offset = parseInt(getMandatoryAttributeValue(locationElement.get(), A_OFFSET));
+ var length = parseInt(getMandatoryAttributeValue(locationElement.get(), A_LENGTH));
+
+ var infons = extractInfons(annotationElement);
+ Type uimaType = guessBestSpanType(aJCas.getTypeSystem(), infons);
+ if (uimaType == null || !Tsv3XCasSchemaAnalyzer.isSpanLayer(uimaType)) {
+ LOG.debug("Unable to find suitable UIMA type for span annotation");
+ continue;
+ }
+
+ var begin = containerTextElement.get().getBegin() + offset;
+ var end = begin + length;
+ var annotation = cas.createAnnotation(uimaType, begin, end);
+ transferFeatures(annotation, infons);
+ cas.addFsToIndexes(annotation);
+
+ id.ifPresent($ -> id2Span.put($, annotation));
+ }
+
+ annotationElements.forEach(XmlNodeUtils::removeWithDescendantsFromTree);
+
+ return id2Span;
+ }
+
+ private Map extractInfons(XmlElement aElement)
+ {
+ var children = aElement.getChildren();
+
+ if (children == null) {
+ return emptyMap();
+ }
+
+ var infonChildren = children.select(XmlElement.class) //
+ .filter(e -> E_INFON.equals(e.getQName())) //
+ .collect(toList());
+
+ var infons = new LinkedHashMap();
+ for (var infonChild : infonChildren) {
+ var key = getMandatoryAttributeValue(infonChild, A_KEY);
+ var value = XmlNodeUtils.textContent(infonChild);
+ infons.put(key, value);
+ }
+
+ return infons;
+ }
+
+ private Map extractNodes(XmlElement aElement)
+ {
+ var children = aElement.getChildren();
+
+ if (children == null) {
+ return emptyMap();
+ }
+
+ var infonChildren = children.select(XmlElement.class) //
+ .filter(e -> E_NODE.equals(e.getQName())) //
+ .collect(toList());
+
+ var nodes = new LinkedHashMap();
+ for (var infonChild : infonChildren) {
+ var key = getMandatoryAttributeValue(infonChild, A_ROLE);
+ var value = getMandatoryAttributeValue(infonChild, A_REFID);
+ nodes.put(key, value);
+ }
+
+ return nodes;
+ }
+
+ private void transferSentences(JCas aJCas)
+ {
+ var sentenceElements = aJCas.select(XmlElement.class) //
+ .filter(e -> E_SENTENCE.equals(e.getQName()))//
+ .collect(toList());
+
+ for (var sentenceElement : sentenceElements) {
+ var sentence = new Sentence(aJCas, sentenceElement.getBegin(),
+ sentenceElement.getEnd());
+ sentence.trim();
+ sentence.addToIndexes();
+
+ // We do not remove the sentence elements from the XML tree. That way, we do not have to
+ // re-generated them on export. It means we cannot change the boundaries of sentences,
+ // but if we did that we would be running out-of-sync with the offsets referenced in
+ // the BioC file anyway. That is a potential drawback of the XML-based approach to
+ // handling BioC files.
+ // XmlNodeUtils.removeFromTree(sentenceElement);
+ }
+ }
+
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/BioCXmlUtils.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/BioCXmlUtils.java
new file mode 100644
index 00000000000..bae243a6e31
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/BioCXmlUtils.java
@@ -0,0 +1,42 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.xml;
+
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_LOCATION;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_TEXT;
+
+import java.util.Optional;
+
+import org.dkpro.core.api.xml.type.XmlElement;
+
+public class BioCXmlUtils
+{
+ public static Optional getChildTextElement(XmlElement aContainer)
+ {
+ return aContainer.getChildren().select(XmlElement.class) //
+ .filter(e -> E_TEXT.equals(e.getQName())) //
+ .findFirst();
+ }
+
+ public static Optional getChildLocationElement(XmlElement aContainer)
+ {
+ return aContainer.getChildren().select(XmlElement.class) //
+ .filter(e -> E_LOCATION.equals(e.getQName())) //
+ .findFirst();
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/Cas2BioCSaxEvents.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/Cas2BioCSaxEvents.java
new file mode 100644
index 00000000000..a97c4d815c0
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/Cas2BioCSaxEvents.java
@@ -0,0 +1,293 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.xml;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_SOURCE;
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_TARGET;
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isRelationLayer;
+import static de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XCasSchemaAnalyzer.isSpanLayer;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_ID;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_KEY;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_LENGTH;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_OFFSET;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_REFID;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.A_ROLE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_ANNOTATION;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_COLLECTION;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_DATE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_DOCUMENT;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_INFON;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_KEY;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_LOCATION;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_NODE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_PASSAGE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_RELATION;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_SENTENCE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_SOURCE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.E_TEXT;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.I_TYPE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_SOURCE;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.R_TARGET;
+import static de.tudarmstadt.ukp.inception.io.bioc.BioCComponent.getCollectionMetadataField;
+import static de.tudarmstadt.ukp.inception.io.bioc.xml.BioCXmlUtils.getChildTextElement;
+import static java.util.stream.Collectors.toList;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_BEGIN;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_END;
+import static org.apache.uima.cas.CAS.FEATURE_FULL_NAME_SOFA;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.fit.util.FSUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.dkpro.core.api.xml.type.XmlElement;
+import org.dkpro.core.api.xml.type.XmlTextNode;
+import org.xml.sax.ContentHandler;
+import org.xml.sax.SAXException;
+
+import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData;
+import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.MetaDataStringField;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
+import de.tudarmstadt.ukp.inception.io.xml.dkprocore.Cas2SaxEvents;
+
+public class Cas2BioCSaxEvents
+ extends Cas2SaxEvents
+{
+ private static final Set EXCLUDED_TYPES = Set.of(DocumentMetaData._TypeName,
+ Sentence._TypeName, Token._TypeName, MetaDataStringField._TypeName);
+ private static final Set EXCLUDED_FEATURES = Set.of(FEATURE_FULL_NAME_BEGIN,
+ FEATURE_FULL_NAME_END, FEATURE_FULL_NAME_SOFA);
+ private static final Set DATA_ELEMENTS = Set.of(E_COLLECTION, E_DOCUMENT, E_PASSAGE,
+ E_SENTENCE, E_ANNOTATION, E_RELATION);
+
+ private Map annotationToId;
+
+ public Cas2BioCSaxEvents(ContentHandler aHandler)
+ {
+ super(aHandler);
+ }
+
+ @Override
+ public void process(JCas aJCas) throws SAXException
+ {
+ annotationToId = new HashMap<>();
+
+ super.process(aJCas);
+ }
+
+ private String idOf(Annotation aAnnotation)
+ {
+ return annotationToId.computeIfAbsent(aAnnotation,
+ $ -> Integer.toString(annotationToId.size() + 1));
+ }
+
+ @Override
+ public void processChildren(XmlElement aElement) throws SAXException
+ {
+ if (E_COLLECTION.equals(aElement.getQName())) {
+ processCollectionElement(aElement);
+ }
+
+ super.processChildren(aElement);
+
+ if (E_SENTENCE.equals(aElement.getQName())) {
+ processSentenceElement(aElement);
+ }
+
+ if (E_PASSAGE.equals(aElement.getQName())) {
+ processPassageElement(aElement);
+ }
+ }
+
+ @Override
+ public void process(XmlTextNode aChild) throws SAXException
+ {
+ if (DATA_ELEMENTS.contains(aChild.getParent().getQName())) {
+ return;
+ }
+
+ super.process(aChild);
+ }
+
+ private void processSentenceElement(XmlElement aSentenceElement) throws SAXException
+ {
+ var sentenceTextElement = getChildTextElement(aSentenceElement);
+
+ if (sentenceTextElement.isEmpty()) {
+ // If the sentence has no text element, we cannot determine the offset...
+ return;
+ }
+
+ for (var annotation : aSentenceElement.getCAS().select(Annotation.class)
+ .coveredBy(aSentenceElement)) {
+ serializeAnnotation(sentenceTextElement.get().getBegin(), annotation);
+ }
+ }
+
+ private void processPassageElement(XmlElement aPassageElement) throws SAXException
+ {
+ CAS cas = aPassageElement.getCAS();
+ var sentencesInPassage = cas.select(Sentence.class) //
+ .filter(s -> s.overlapping(aPassageElement)) //
+ .collect(toList());
+
+ var passageTextElement = getChildTextElement(aPassageElement);
+
+ if (passageTextElement.isEmpty()) {
+ // If the passage has no text element, we cannot determine the offset...
+ return;
+ }
+
+ for (var annotation : cas.select(Annotation.class).coveredBy(aPassageElement)) {
+ if (isSentenceLevelAnnotation(sentencesInPassage, annotation)) {
+ // Already serialized as a sentence-level annotation
+ continue;
+ }
+ serializeAnnotation(passageTextElement.get().getBegin(), annotation);
+ }
+ }
+
+ private void serializeAnnotation(int aContainerOffset, Annotation aAnnotation)
+ throws SAXException
+ {
+ if (isExcludedType(aAnnotation)) {
+ return;
+ }
+
+ if (isSpanLayer(aAnnotation.getType())) {
+ serializeSpanAnnotation(aContainerOffset, aAnnotation);
+ }
+
+ if (isRelationLayer(aAnnotation.getType())) {
+ serializeRelationAnnotation(aContainerOffset, aAnnotation);
+ }
+ }
+
+ private void serializeRelationAnnotation(int aContainerOffset, Annotation aAnnotation)
+ throws SAXException
+ {
+ handler.startElement(E_RELATION, Map.of(A_ID, idOf(aAnnotation)));
+ infon(I_TYPE, aAnnotation.getType().getName());
+ featureInfons(aAnnotation);
+ node(R_SOURCE, FSUtil.getFeature(aAnnotation, FEAT_REL_SOURCE, Annotation.class));
+ node(R_TARGET, FSUtil.getFeature(aAnnotation, FEAT_REL_TARGET, Annotation.class));
+ handler.endElement(E_RELATION);
+ }
+
+ private void serializeSpanAnnotation(int aContainerOffset, Annotation aAnnotation)
+ throws SAXException
+ {
+ handler.startElement(E_ANNOTATION, Map.of(A_ID, idOf(aAnnotation)));
+ infon(I_TYPE, aAnnotation.getType().getName());
+ featureInfons(aAnnotation);
+ location(aContainerOffset, aAnnotation);
+ text(aAnnotation.getCoveredText());
+ handler.endElement(E_ANNOTATION);
+ }
+
+ private boolean isExcludedType(Annotation aAnnotation)
+ {
+ String typeName = aAnnotation.getType().getName();
+ if (typeName.startsWith(XmlElement.class.getPackageName())) {
+ return true;
+ }
+
+ if (EXCLUDED_TYPES.contains(typeName)) {
+ return true;
+ }
+
+ return false;
+ }
+
+ private void featureInfons(Annotation aAnnotation) throws SAXException
+ {
+ for (var feature : aAnnotation.getType().getFeatures()) {
+ if (EXCLUDED_FEATURES.contains(feature.getName())) {
+ continue;
+ }
+
+ if (feature.getRange().isPrimitive()) {
+ var value = aAnnotation.getFeatureValueAsString(feature);
+ if (value != null) {
+ infon(feature.getShortName(), value);
+ }
+ }
+ }
+ }
+
+ private void node(String aRole, Annotation aReference) throws SAXException
+ {
+ handler.startElement(E_NODE, Map.of( //
+ A_ROLE, aRole, //
+ A_REFID, idOf(aReference)));
+ handler.endElement(E_NODE);
+ }
+
+ private void text(String aCoveredText) throws SAXException
+ {
+ handler.startElement(E_TEXT);
+ handler.characters(aCoveredText);
+ handler.endElement(E_TEXT);
+ }
+
+ private void location(int aContainerOffset, Annotation aAnnotation) throws SAXException
+ {
+ handler.startElement(E_LOCATION, Map.of( //
+ A_OFFSET, Integer.toString(aAnnotation.getBegin() - aContainerOffset), //
+ A_LENGTH, Integer.toString(aAnnotation.getEnd() - aAnnotation.getBegin())));
+ handler.endElement(E_LOCATION);
+ }
+
+ private void infon(String aKey, String aValue) throws SAXException
+ {
+ handler.startElement(E_INFON, Map.of(A_KEY, aKey));
+ if (aValue != null) {
+ handler.characters(aValue);
+ }
+ handler.endElement(E_INFON);
+ }
+
+ private boolean isSentenceLevelAnnotation(List sentences, Annotation annotation)
+ {
+ return sentences.stream().anyMatch(s -> s.covering(annotation));
+ }
+
+ private void processCollectionElement(XmlElement aElement) throws SAXException
+ {
+ processMetaDataField(aElement.getCAS(), E_SOURCE);
+ processMetaDataField(aElement.getCAS(), E_DATE);
+ processMetaDataField(aElement.getCAS(), E_KEY);
+ }
+
+ private void processMetaDataField(CAS aCas, String aKey) throws SAXException
+ {
+ var field = getCollectionMetadataField(aCas, aKey);
+
+ if (field.isPresent()) {
+ handler.startElement(field.get().getKey());
+ handler.characters(field.get().getValue());
+ handler.endElement(field.get().getKey());
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/DocumentWrappingXmlInputReader.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/DocumentWrappingXmlInputReader.java
new file mode 100644
index 00000000000..585dc806b61
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/DocumentWrappingXmlInputReader.java
@@ -0,0 +1,138 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.xml;
+
+import java.util.NoSuchElementException;
+
+import javax.xml.stream.XMLEventFactory;
+import javax.xml.stream.XMLEventReader;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.events.XMLEvent;
+import javax.xml.stream.util.EventReaderDelegate;
+
+public class DocumentWrappingXmlInputReader
+ extends EventReaderDelegate
+{
+ // private static final Logger LOG =
+ // LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+
+ private boolean startDocumentRead = false;
+ private boolean endDocumentRead = false;
+ private final XMLEventFactory eventFactory = XMLEventFactory.newInstance();
+ private boolean locationSet = false;
+ private int depth = 0;
+ private boolean done = false;
+
+ public DocumentWrappingXmlInputReader(XMLEventReader reader)
+ {
+ super(reader);
+ }
+
+ @Override
+ public XMLEvent nextEvent() throws XMLStreamException
+ {
+ initLocationIfNecessary();
+
+ if (!startDocumentRead) {
+ startDocumentRead = true;
+ // LOG.info("GET startDocument");
+ return eventFactory.createStartDocument();
+ }
+
+ if (done) {
+ if (!endDocumentRead) {
+ endDocumentRead = true;
+ // LOG.info("GET endDocument");
+ return eventFactory.createEndDocument();
+ }
+
+ throw new NoSuchElementException("Event stream exhausted");
+ }
+
+ XMLEvent event = getParent().nextEvent();
+ if (event.isStartElement()) {
+ depth++;
+ }
+
+ if (event.isEndElement()) {
+ depth--;
+ if (depth == 0) {
+ done = true;
+ }
+ }
+
+ // LOG.info("GET pass-through {}", event);
+ return event;
+ }
+
+ private void initLocationIfNecessary() throws XMLStreamException
+ {
+ if (!locationSet) {
+ eventFactory.setLocation(getParent().peek().getLocation());
+ locationSet = true;
+ }
+ }
+
+ @Override
+ public XMLEvent peek() throws XMLStreamException
+ {
+ initLocationIfNecessary();
+
+ if (!startDocumentRead) {
+ // LOG.info("PEEK startDocument");
+ return eventFactory.createStartDocument();
+ }
+
+ XMLEvent event = getParent().nextEvent();
+
+ if (depth == 1 && !endDocumentRead) {
+ // LOG.info("PEEK endDocument");
+ return eventFactory.createEndDocument();
+ }
+
+ // LOG.info("PEEK pass-through {}", event);
+ return event;
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ if (!startDocumentRead && super.hasNext()) {
+ // LOG.info("HAS-NEXT data available and document not started yet");
+ return true;
+ }
+
+ if (!done) {
+ var v = super.hasNext();
+ // LOG.info("HAS-NEXT pass-through {}", v);
+ return v;
+ }
+
+ if (done && !endDocumentRead) {
+ // LOG.info("HAS-NEXT done but document not ended yet");
+ return true;
+ }
+
+ return false;
+ }
+
+ public static DocumentWrappingXmlInputReader wrapInDocument(XMLEventReader aDelegate)
+ {
+ return new DocumentWrappingXmlInputReader(aDelegate);
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/SplittingContentHandler.java b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/SplittingContentHandler.java
new file mode 100644
index 00000000000..09fff8966cf
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/SplittingContentHandler.java
@@ -0,0 +1,148 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc.xml;
+
+import org.xml.sax.Attributes;
+import org.xml.sax.ContentHandler;
+import org.xml.sax.Locator;
+import org.xml.sax.SAXException;
+
+public class SplittingContentHandler
+ implements ContentHandler
+{
+ private final ContentHandler delegate;
+ private final String splitQName;
+
+ private int depth = 0;
+ private int depthOpened = -1;
+ private boolean open = false;
+
+ public SplittingContentHandler(ContentHandler aDelegate, String aSplitQName)
+ {
+ delegate = aDelegate;
+ splitQName = aSplitQName;
+ }
+
+ @Override
+ public void setDocumentLocator(Locator aLocator)
+ {
+ delegate.setDocumentLocator(aLocator);
+ }
+
+ @Override
+ public void startDocument() throws SAXException
+ {
+ if (open) {
+ delegate.startDocument();
+ }
+ }
+
+ @Override
+ public void endDocument() throws SAXException
+ {
+ if (open) {
+ delegate.endDocument();
+ }
+ }
+
+ @Override
+ public void startPrefixMapping(String aPrefix, String aUri) throws SAXException
+ {
+ if (open) {
+ delegate.startPrefixMapping(aPrefix, aUri);
+ }
+ }
+
+ @Override
+ public void endPrefixMapping(String aPrefix) throws SAXException
+ {
+ if (open) {
+ delegate.endPrefixMapping(aPrefix);
+ }
+ }
+
+ @Override
+ public void startElement(String aUri, String aLocalName, String aQName, Attributes aAtts)
+ throws SAXException
+ {
+ depth++;
+
+ if (splitQName.equals(aQName)) {
+ depthOpened = depth;
+ delegate.startDocument();
+ // FIXME It would be reasonable to remember the prefix mappings and to send them to the
+ // delegate at this point.
+ }
+
+ if (open) {
+ delegate.startElement(aUri, aLocalName, aQName, aAtts);
+ }
+ }
+
+ @Override
+ public void endElement(String aUri, String aLocalName, String aQName) throws SAXException
+ {
+ if (open) {
+ delegate.endElement(aUri, aLocalName, aQName);
+ }
+
+ if (depthOpened == depth) {
+ delegate.endDocument();
+ depthOpened = -1;
+ }
+
+ depth--;
+
+ if (depth < 0) {
+ throw new SAXException("Illegal XML structure");
+ }
+ }
+
+ @Override
+ public void characters(char[] aCh, int aStart, int aLength) throws SAXException
+ {
+ if (open) {
+ delegate.characters(aCh, aStart, aLength);
+ }
+ }
+
+ @Override
+ public void ignorableWhitespace(char[] aCh, int aStart, int aLength) throws SAXException
+ {
+ if (open) {
+ delegate.ignorableWhitespace(aCh, aStart, aLength);
+ }
+
+ }
+
+ @Override
+ public void processingInstruction(String aTarget, String aData) throws SAXException
+ {
+ if (open) {
+ delegate.processingInstruction(aTarget, aData);
+ }
+ }
+
+ @Override
+ public void skippedEntity(String aName) throws SAXException
+ {
+ if (open) {
+ delegate.skippedEntity(aName);
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/main/resources/META-INF/asciidoc/user-guide/formats-bioc.adoc b/inception/inception-io-bioc/src/main/resources/META-INF/asciidoc/user-guide/formats-bioc.adoc
new file mode 100644
index 00000000000..2595acb63d7
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/resources/META-INF/asciidoc/user-guide/formats-bioc.adoc
@@ -0,0 +1,62 @@
+// Licensed to the Technische Universität Darmstadt under one
+// or more contributor license agreements. See the NOTICE file
+// distributed with this work for additional information
+// regarding copyright ownership. The Technische Universität Darmstadt
+// licenses this file to you under the Apache License, Version 2.0 (the
+// "License"); you may not use this file except in compliance
+// with the License.
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+[[sect_formats_bioc]]
+= BioC (experimental)
+
+====
+CAUTION: Experimental feature. To use this functionality, you need to enable it first by adding `format.bioc.enabled=true` to the `settings.properties` file (see the <>).
+====
+
+This is a new and still experimental BioC format.
+
+* Sentence information is supported
+ * If sentences are present in a BioC document, they are imported. Otherwise, {product-name} will
+ automatically try to determine sentence boundaries.
+ * On export, the BioC files are always created with sentence information.
+* Passages are imported as a `Div` annotations and the passage `type` infon is set as the `type`
+ feature on these `Div` annotations
+* When reading span or relation annotations, the `type` infon is used to look up a suitable
+ annotation layer. If a layer exists where either the full technical name of the layer or the
+ simple technical name (the part after the last dot) match the type, then an attempt will be made
+ to match the annotation to that layer. If the annotation has other infons that match features on
+ that layer, they will also be matched. If no layer matches but the default `SimpleSpan` layer is
+ present, annotations will be matched to that. Similarly, if only a single infon is present in an
+ annotation and no other feature matches, then the infon value may be matched to a potentially
+ existing `value` feature.
+* When exporting annotations, the `type` infon will always be set to the full layer name and
+ features will be serialized to infons matching their names.
+* If a document has not been imported from a BioC file containing passages and does not contain
+ `Div` annotations from any other source either, then on export a single passage containing the
+ entire document is created.
+* Cross-passage relations are not supported.
+* Sentence-level infons are not supported.
+* Passage-level infons are not supported.
+* Document-level infons are not supported.
+* The writer writes one BioC file per CAS (i.e. writing multiple documents to a single collection file is not supported).
+
+[cols="2,1,1,1,3"]
+|====
+| Format | Read | Write | Custom Layers | Description
+
+| link:https://raw.githubusercontent.com/2mh/PyBioC/master/BioC.dtd[BioC (experimental)] (`bioc`)
+| yes
+| yes
+| yes
+| BioC format
+
+|====
+
diff --git a/inception/inception-io-bioc/src/main/resources/META-INF/spring.factories b/inception/inception-io-bioc/src/main/resources/META-INF/spring.factories
new file mode 100644
index 00000000000..0b49c0c1c19
--- /dev/null
+++ b/inception/inception-io-bioc/src/main/resources/META-INF/spring.factories
@@ -0,0 +1,2 @@
+org.springframework.boot.autoconfigure.EnableAutoConfiguration=\
+de.tudarmstadt.ukp.inception.io.bioc.config.BioCAutoConfiguration
\ No newline at end of file
diff --git a/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderTest.java b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderTest.java
new file mode 100644
index 00000000000..2aed15738bd
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderTest.java
@@ -0,0 +1,118 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_SOURCE;
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_TARGET;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicRelationLayerInitializer.BASIC_RELATION_LABEL_FEATURE_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicRelationLayerInitializer.BASIC_RELATION_LAYER_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LABEL_FEATURE_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LAYER_NAME;
+import static java.util.Arrays.asList;
+import static org.apache.uima.cas.CAS.TYPE_NAME_ANNOTATION;
+import static org.apache.uima.cas.CAS.TYPE_NAME_STRING;
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReader;
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription;
+import static org.apache.uima.fit.pipeline.SimplePipeline.iteratePipeline;
+import static org.apache.uima.fit.util.FSUtil.getFeature;
+import static org.apache.uima.util.CasCreationUtils.mergeTypeSystems;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.tuple;
+
+import java.util.ArrayList;
+
+import org.apache.uima.UIMAFramework;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.fit.factory.CasFactory;
+import org.apache.uima.fit.factory.TypeSystemDescriptionFactory;
+import org.junit.jupiter.api.Test;
+
+import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.MetaDataStringField;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+
+public class BioCReaderTest
+{
+ @Test
+ void testRead() throws Exception
+ {
+ var tsd = UIMAFramework.getResourceSpecifierFactory().createTypeSystemDescription();
+ var basicSpanType = tsd.addType(BASIC_SPAN_LAYER_NAME, null, TYPE_NAME_ANNOTATION);
+ basicSpanType.addFeature(BASIC_SPAN_LABEL_FEATURE_NAME, null, TYPE_NAME_STRING);
+
+ var basicRelationType = tsd.addType(BASIC_RELATION_LAYER_NAME, null, TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(FEAT_REL_SOURCE, null, CAS.TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(FEAT_REL_TARGET, null, CAS.TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(BASIC_RELATION_LABEL_FEATURE_NAME, null, TYPE_NAME_STRING);
+
+ var fullTsd = mergeTypeSystems(
+ asList(TypeSystemDescriptionFactory.createTypeSystemDescription(), tsd));
+
+ var reader = createReader( //
+ BioCReader.class, //
+ BioCReader.PARAM_SOURCE_LOCATION,
+ "src/test/resources/bioc/example-with-sentences.xml");
+
+ assertThat(reader.hasNext()).isTrue();
+
+ var cas = CasFactory.createCas(fullTsd);
+ reader.getNext(cas);
+
+ assertThat(cas.getDocumentText()) //
+ .contains("Sentence 1.") //
+ .contains("Sentence 2.");
+
+ assertThat(cas.select(Sentence.class).asList()) //
+ .extracting(Sentence::getCoveredText) //
+ .containsExactly("Sentence 1.", "Sentence 2.");
+
+ assertThat(cas.select(MetaDataStringField.class).asList())
+ .extracting(MetaDataStringField::getKey, MetaDataStringField::getValue)
+ .containsExactlyInAnyOrder( //
+ tuple(BioCComponent.E_ID, "some-id-1234567"),
+ tuple(BioCComponent.E_SOURCE, "example-with-sentences"),
+ tuple(BioCComponent.E_KEY, "example-with-sentences.key"),
+ tuple(BioCComponent.E_DATE, "2023-01-01"));
+
+ assertThat(cas.select(cas.getTypeSystem().getType(BASIC_SPAN_LAYER_NAME)).asList())
+ .extracting( //
+ a -> getFeature(a, CAS.FEATURE_BASE_NAME_BEGIN, Integer.class),
+ a -> getFeature(a, CAS.FEATURE_BASE_NAME_END, Integer.class),
+ a -> getFeature(a, BASIC_RELATION_LABEL_FEATURE_NAME, String.class))
+ .containsExactlyInAnyOrder( //
+ tuple(10, 18, "span-annotation-value"), //
+ tuple(19, 20, "span-annotation-value"));
+
+ assertThat(cas.select(cas.getTypeSystem().getType(BASIC_RELATION_LAYER_NAME)).asList())
+ .hasSize(1);
+ }
+
+ @Test
+ void testReadMultipleFromOneFile() throws Exception
+ {
+ var reader = createReaderDescription( //
+ BioCReader.class, //
+ BioCReader.PARAM_SOURCE_LOCATION,
+ "src/test/resources/bioc/example-with-multiple-documents.xml");
+
+ var texts = new ArrayList();
+ iteratePipeline(reader).forEach(cas -> texts.add(cas.getDocumentText().trim()));
+
+ assertThat(texts) //
+ .containsExactly("Document 1 text.", "Document 2 text.", "Document 3 text.");
+ }
+}
diff --git a/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderWriterTest.java b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderWriterTest.java
new file mode 100644
index 00000000000..20f36b3885b
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCReaderWriterTest.java
@@ -0,0 +1,125 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_SOURCE;
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_TARGET;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicRelationLayerInitializer.BASIC_RELATION_LABEL_FEATURE_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicRelationLayerInitializer.BASIC_RELATION_LAYER_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LABEL_FEATURE_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LAYER_NAME;
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static java.util.Arrays.asList;
+import static org.apache.uima.cas.CAS.TYPE_NAME_ANNOTATION;
+import static org.apache.uima.cas.CAS.TYPE_NAME_STRING;
+import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription;
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription;
+import static org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription;
+import static org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath;
+import static org.apache.uima.util.CasCreationUtils.mergeTypeSystems;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.contentOf;
+
+import java.io.File;
+
+import org.apache.uima.UIMAFramework;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.collection.CollectionReaderDescription;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.apache.uima.resource.metadata.TypeSystemDescription;
+import org.dkpro.core.io.xmi.XmiWriter;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
+
+public class BioCReaderWriterTest
+{
+ private static final String TYPESYSTEM_XML = "typesystem.xml";
+ private static final String REFERENCE_XML = "reference.xml";
+ private static final String DATA_XML = "data.xml";
+
+ public static Iterable testSuiteFiles()
+ {
+ return asList(new File("src/test/resources/bioc-suite/").listFiles(File::isDirectory));
+ }
+
+ @ParameterizedTest(name = "{index}: running on file {0}")
+ @MethodSource("testSuiteFiles")
+ public void runTest(File aReferenceFolder) throws Exception
+ {
+ TypeSystemDescription merged = createTestTypeSystem(aReferenceFolder);
+
+ String targetFolder = "target/test-output/bioc-suite/" + aReferenceFolder.getName();
+
+ CollectionReaderDescription reader = createReaderDescription( //
+ BioCReader.class, merged, BioCReader.PARAM_SOURCE_LOCATION, aReferenceFolder, //
+ BioCReader.PARAM_PATTERNS, DATA_XML);
+
+ AnalysisEngineDescription writer = createEngineDescription( //
+ BioCWriter.class, merged, //
+ BioCWriter.PARAM_TARGET_LOCATION, targetFolder, //
+ BioCWriter.PARAM_STRIP_EXTENSION, true, //
+ BioCWriter.PARAM_OVERWRITE, true);
+
+ AnalysisEngineDescription xmiWriter = createEngineDescription( //
+ XmiWriter.class, merged, //
+ XmiWriter.PARAM_TARGET_LOCATION, targetFolder, //
+ XmiWriter.PARAM_STRIP_EXTENSION, true, //
+ XmiWriter.PARAM_OVERWRITE, true);
+
+ SimplePipeline.runPipeline(reader, writer, xmiWriter);
+
+ var reference = contentOf(new File(aReferenceFolder, REFERENCE_XML), UTF_8).trim();
+
+ var actual = contentOf(new File(targetFolder, DATA_XML), UTF_8).trim();
+
+ assertThat(actual).isEqualToNormalizingNewlines(reference);
+ }
+
+ private TypeSystemDescription createTestTypeSystem(File aReferenceFolder)
+ throws ResourceInitializationException
+ {
+ TypeSystemDescription global = createTypeSystemDescription();
+
+ TypeSystemDescription local;
+ if (new File(aReferenceFolder, TYPESYSTEM_XML).exists()) {
+ local = createTypeSystemDescriptionFromPath(
+ new File(aReferenceFolder, TYPESYSTEM_XML).toString());
+ }
+ else {
+ local = createTestTypeSystem();
+ }
+
+ return mergeTypeSystems(asList(global, local));
+ }
+
+ private TypeSystemDescription createTestTypeSystem() throws ResourceInitializationException
+ {
+ var tsd = UIMAFramework.getResourceSpecifierFactory().createTypeSystemDescription();
+ var basicSpanType = tsd.addType(BASIC_SPAN_LAYER_NAME, null, TYPE_NAME_ANNOTATION);
+ basicSpanType.addFeature(BASIC_SPAN_LABEL_FEATURE_NAME, null, TYPE_NAME_STRING);
+
+ var basicRelationType = tsd.addType(BASIC_RELATION_LAYER_NAME, null, TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(FEAT_REL_SOURCE, null, CAS.TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(FEAT_REL_TARGET, null, CAS.TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(BASIC_RELATION_LABEL_FEATURE_NAME, null, TYPE_NAME_STRING);
+
+ return mergeTypeSystems(asList(createTypeSystemDescription(), tsd));
+ }
+}
diff --git a/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReaderTest.java b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReaderTest.java
new file mode 100644
index 00000000000..a7364558310
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReaderTest.java
@@ -0,0 +1,72 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReader;
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription;
+import static org.apache.uima.fit.pipeline.SimplePipeline.iteratePipeline;
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.util.ArrayList;
+
+import org.apache.uima.fit.factory.CasFactory;
+import org.junit.jupiter.api.Test;
+
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
+
+public class BioCXmlDocumentReaderTest
+{
+ @Test
+ void testRead() throws Exception
+ {
+ var reader = createReader( //
+ BioCXmlDocumentReader.class, //
+ BioCXmlDocumentReader.PARAM_SOURCE_LOCATION,
+ "src/test/resources/bioc/example-with-sentences.xml");
+
+ assertThat(reader.hasNext()).isTrue();
+
+ var cas = CasFactory.createCas();
+ reader.getNext(cas);
+
+ // CasIOUtils.save(cas, System.out, XMI_PRETTY);
+
+ assertThat(cas.getDocumentText()) //
+ .contains("Sentence 1.") //
+ .contains("Sentence 2.");
+
+ assertThat(cas.select(Sentence.class).asList()) //
+ .extracting(Sentence::getCoveredText) //
+ .containsExactly("Sentence 1.", "Sentence 2.");
+ }
+
+ @Test
+ void testReadMultipleFromOneFile() throws Exception
+ {
+ var reader = createReaderDescription( //
+ BioCXmlDocumentReader.class, //
+ BioCXmlDocumentReader.PARAM_SOURCE_LOCATION,
+ "src/test/resources/bioc/example-with-multiple-documents.xml");
+
+ var texts = new ArrayList();
+ iteratePipeline(reader).forEach(cas -> texts.add(cas.getDocumentText().trim()));
+
+ assertThat(texts) //
+ .containsExactly("Document 1 text.", "Document 2 text.", "Document 3 text.");
+ }
+}
diff --git a/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReaderWriterTest.java b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReaderWriterTest.java
new file mode 100644
index 00000000000..70a71d2524b
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/java/de/tudarmstadt/ukp/inception/io/bioc/BioCXmlDocumentReaderWriterTest.java
@@ -0,0 +1,83 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.bioc;
+
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_SOURCE;
+import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.FEAT_REL_TARGET;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicRelationLayerInitializer.BASIC_RELATION_LABEL_FEATURE_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicRelationLayerInitializer.BASIC_RELATION_LAYER_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LABEL_FEATURE_NAME;
+import static de.tudarmstadt.ukp.inception.project.initializers.basic.BasicSpanLayerInitializer.BASIC_SPAN_LAYER_NAME;
+import static java.util.Arrays.asList;
+import static org.apache.uima.cas.CAS.TYPE_NAME_ANNOTATION;
+import static org.apache.uima.cas.CAS.TYPE_NAME_STRING;
+import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription;
+import static org.apache.uima.fit.factory.CollectionReaderFactory.createReaderDescription;
+import static org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription;
+import static org.apache.uima.util.CasCreationUtils.mergeTypeSystems;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.uima.UIMAFramework;
+import org.apache.uima.cas.CAS;
+import org.custommonkey.xmlunit.XMLAssert;
+import org.dkpro.core.testing.IOTestRunner;
+import org.dkpro.core.testing.TestOptions;
+import org.junit.jupiter.api.Test;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+public class BioCXmlDocumentReaderWriterTest
+{
+ @Test
+ public void testOneWay() throws Exception
+ {
+ var tsd = UIMAFramework.getResourceSpecifierFactory().createTypeSystemDescription();
+ var basicSpanType = tsd.addType(BASIC_SPAN_LAYER_NAME, null, TYPE_NAME_ANNOTATION);
+ basicSpanType.addFeature(BASIC_SPAN_LABEL_FEATURE_NAME, null, TYPE_NAME_STRING);
+
+ var basicRelationType = tsd.addType(BASIC_RELATION_LAYER_NAME, null, TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(FEAT_REL_SOURCE, null, CAS.TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(FEAT_REL_TARGET, null, CAS.TYPE_NAME_ANNOTATION);
+ basicRelationType.addFeature(BASIC_RELATION_LABEL_FEATURE_NAME, null, TYPE_NAME_STRING);
+
+ var fullTsd = mergeTypeSystems(asList(createTypeSystemDescription(), tsd));
+
+ IOTestRunner.testOneWay( //
+ createReaderDescription( //
+ BioCXmlDocumentReader.class, fullTsd), //
+ createEngineDescription( //
+ BioCXmlDocumentWriter.class, fullTsd, //
+ BioCXmlDocumentWriter.PARAM_INDENT, true),
+ "bioc/example-with-sentences-ref.xml", //
+ "bioc/example-with-sentences.xml", //
+ new TestOptions().resultAssertor(this::assertXmlEquals));
+ }
+
+ private void assertXmlEquals(File expected, File actual)
+ {
+ try {
+ XMLAssert.assertXMLEqual(new InputSource(expected.getPath()),
+ new InputSource(actual.getPath()));
+ }
+ catch (SAXException | IOException e) {
+ throw new RuntimeException(e);
+ }
+ }
+}
diff --git a/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-fallback/data.xml b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-fallback/data.xml
new file mode 100644
index 00000000000..6a1b075c8d4
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-fallback/data.xml
@@ -0,0 +1,21 @@
+
+ example
+ 2023-01-01
+ example.key
+
+ doc-1
+
+ abstract
+ 0
+
+ 0
+ Sentence 1.
+
+ span-annotation-value
+
+ Sentence
+
+
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-fallback/reference.xml b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-fallback/reference.xml
new file mode 100644
index 00000000000..575586ffa3d
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-fallback/reference.xml
@@ -0,0 +1,23 @@
+
+
+ example
+ 2023-01-01
+ example.key
+
+ doc-1
+
+ abstract
+ 0
+
+ 0
+ Sentence 1.
+
+ custom.Span
+ span-annotation-value
+
+ Sentence
+
+
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-typed/data.xml b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-typed/data.xml
new file mode 100644
index 00000000000..1c13c204746
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-typed/data.xml
@@ -0,0 +1,22 @@
+
+ example
+ 2023-01-01
+ example.key
+
+ doc-1
+
+ abstract
+ 0
+
+ 0
+ Sentence 1.
+
+ de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity
+ PER
+
+ Sentence
+
+
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-typed/reference.xml b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-typed/reference.xml
new file mode 100644
index 00000000000..4865f6c4231
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc-suite/annotation-with-single-feature-typed/reference.xml
@@ -0,0 +1,22 @@
+
+ example
+ 2023-01-01
+ example.key
+
+ doc-1
+
+ abstract
+ 0
+
+ 0
+ Sentence 1.
+
+ de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity
+ PER
+
+ Sentence
+
+
+
+
+
\ No newline at end of file
diff --git a/inception/inception-io-bioc/src/test/resources/bioc-suite/passage-without-sentences/data.xml b/inception/inception-io-bioc/src/test/resources/bioc-suite/passage-without-sentences/data.xml
new file mode 100644
index 00000000000..a4ff786bc2b
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc-suite/passage-without-sentences/data.xml
@@ -0,0 +1,28 @@
+
+ example-with-text-in-passage.xml
+ 2023-01-01
+ example-with-text-in-passage.key
+
+ 1
+
+ passage-infon-value
+ 0
+ Sentence 1.
+
+ span-annotation-value
+
+ annotation text
+
+
+ span-annotation-value
+
+ annotation text
+
+
+ relation-annotation-value
+
+
+
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/bioc-suite/passage-without-sentences/reference.xml b/inception/inception-io-bioc/src/test/resources/bioc-suite/passage-without-sentences/reference.xml
new file mode 100644
index 00000000000..49fb94d278c
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc-suite/passage-without-sentences/reference.xml
@@ -0,0 +1,30 @@
+
+ example-with-text-in-passage.xml
+ 2023-01-01
+ example-with-text-in-passage.key
+
+ 1
+
+ 0
+ Sentence 1.
+
+ custom.Span
+ span-annotation-value
+
+ Sentence
+
+
+ custom.Span
+ span-annotation-value
+
+ 1
+
+
+ custom.Relation
+ relation-annotation-value
+
+
+
+
+
+
\ No newline at end of file
diff --git a/inception/inception-io-bioc/src/test/resources/bioc/BioC.dtd b/inception/inception-io-bioc/src/test/resources/bioc/BioC.dtd
new file mode 100644
index 00000000000..02bc5346cbc
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc/BioC.dtd
@@ -0,0 +1,146 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/bioc/example-with-multiple-documents.xml b/inception/inception-io-bioc/src/test/resources/bioc/example-with-multiple-documents.xml
new file mode 100644
index 00000000000..c43a65f1ef3
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc/example-with-multiple-documents.xml
@@ -0,0 +1,26 @@
+
+ example-with-multiple-documents.xml
+ 2023-01-01
+ example-with-multiple-documents.key
+
+ 1
+
+ 0
+ Document 1 text.
+
+
+
+ 2
+
+ 0
+ Document 2 text.
+
+
+
+ 3
+
+ 0
+ Document 3 text.
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/bioc/example-with-sentences-ref.xml b/inception/inception-io-bioc/src/test/resources/bioc/example-with-sentences-ref.xml
new file mode 100644
index 00000000000..a6ebf504268
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc/example-with-sentences-ref.xml
@@ -0,0 +1,40 @@
+
+ example-with-sentences
+ 2023-01-01
+ example-with-sentences.key
+
+ some-id-1234567
+
+ abstract
+ 0
+
+ type 1
+ 10
+ Sentence 1.
+
+ custom.Span
+ span-annotation-value
+
+ Sentence
+
+
+ custom.Span
+ span-annotation-value
+
+ 1
+
+
+ custom.Relation
+ relation-annotation-value
+
+
+
+
+
+ type 2
+ 30
+ Sentence 2.
+
+
+
+
\ No newline at end of file
diff --git a/inception/inception-io-bioc/src/test/resources/bioc/example-with-sentences.xml b/inception/inception-io-bioc/src/test/resources/bioc/example-with-sentences.xml
new file mode 100644
index 00000000000..4fcd1a17690
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc/example-with-sentences.xml
@@ -0,0 +1,37 @@
+
+ example-with-sentences
+ 2023-01-01
+ example-with-sentences.key
+
+ some-id-1234567
+
+ abstract
+ 0
+
+ type 1
+ 10
+ Sentence 1.
+
+ span-annotation-value
+
+ annotation text
+
+
+ span-annotation-value
+
+ annotation text
+
+
+ relation-annotation-value
+
+
+
+
+
+ type 2
+ 30
+ Sentence 2.
+
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/bioc/example-with-text-in-passage.xml b/inception/inception-io-bioc/src/test/resources/bioc/example-with-text-in-passage.xml
new file mode 100644
index 00000000000..a4ff786bc2b
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/bioc/example-with-text-in-passage.xml
@@ -0,0 +1,28 @@
+
+ example-with-text-in-passage.xml
+ 2023-01-01
+ example-with-text-in-passage.key
+
+ 1
+
+ passage-infon-value
+ 0
+ Sentence 1.
+
+ span-annotation-value
+
+ annotation text
+
+
+ span-annotation-value
+
+ annotation text
+
+
+ relation-annotation-value
+
+
+
+
+
+
diff --git a/inception/inception-io-bioc/src/test/resources/log4j2-test.xml b/inception/inception-io-bioc/src/test/resources/log4j2-test.xml
new file mode 100644
index 00000000000..08e37e9adf6
--- /dev/null
+++ b/inception/inception-io-bioc/src/test/resources/log4j2-test.xml
@@ -0,0 +1,15 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/inception/inception-io-conll/pom.xml b/inception/inception-io-conll/pom.xml
index 6111b1c04a0..b93dcfa7a00 100644
--- a/inception/inception-io-conll/pom.xml
+++ b/inception/inception-io-conll/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-conllINCEpTION - IO - CONLL
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2000FormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2000FormatSupport.java
index cf4662f120c..fa3bc472124 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2000FormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2000FormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(Conll2000Reader.class, aTSD);
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2002FormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2002FormatSupport.java
index 1e664067b8f..b0d70d47496 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2002FormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2002FormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(Conll2002Reader.class, aTSD);
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2003FormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2003FormatSupport.java
index 592f9080f4a..c979bd43ddd 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2003FormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2003FormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(Conll2003Reader.class, aTSD);
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2006FormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2006FormatSupport.java
index 8d663d98471..b691fada3c7 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2006FormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2006FormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(Conll2006Reader.class, aTSD);
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2009FormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2009FormatSupport.java
index 8fa08a76f28..2e78e10c211 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2009FormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2009FormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(Conll2009Reader.class, aTSD);
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2012FormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2012FormatSupport.java
index 1bc10d4955e..20b505ef3f2 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2012FormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/Conll2012FormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(Conll2012Reader.class, aTSD,
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllCoreNlpFormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllCoreNlpFormatSupport.java
index 7e3c05c6000..da16c4ec043 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllCoreNlpFormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllCoreNlpFormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(ConllCoreNlpReader.class, aTSD);
diff --git a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllUFormatSupport.java b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllUFormatSupport.java
index e9186bd79dc..cbb2b0c65d5 100644
--- a/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllUFormatSupport.java
+++ b/inception/inception-io-conll/src/main/java/de/tudarmstadt/ukp/clarin/webanno/conll/ConllUFormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(ConllUReader.class, aTSD);
diff --git a/inception/inception-io-html/pom.xml b/inception/inception-io-html/pom.xml
index a83e71f0945..b46b9c02360 100644
--- a/inception/inception-io-html/pom.xml
+++ b/inception/inception-io-html/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-htmlINCEpTION - IO - HTML
@@ -33,6 +33,10 @@
de.tudarmstadt.ukp.inception.appinception-io-xml
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ commons-io
diff --git a/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/HtmlFormatSupport.java b/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/HtmlFormatSupport.java
index fbb74b63430..bac2c041552 100644
--- a/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/HtmlFormatSupport.java
+++ b/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/HtmlFormatSupport.java
@@ -24,6 +24,7 @@
import org.apache.uima.resource.metadata.TypeSystemDescription;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.inception.io.html.config.HtmlSupportAutoConfiguration;
import de.tudarmstadt.ukp.inception.io.html.dkprocore.HtmlDocumentReader;
@@ -59,7 +60,8 @@ public boolean isReadable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(HtmlDocumentReader.class, aTSD);
diff --git a/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/LegacyHtmlFormatSupport.java b/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/LegacyHtmlFormatSupport.java
index deb69c7dace..b2d28b4a215 100644
--- a/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/LegacyHtmlFormatSupport.java
+++ b/inception/inception-io-html/src/main/java/de/tudarmstadt/ukp/inception/io/html/LegacyHtmlFormatSupport.java
@@ -25,6 +25,7 @@
import org.dkpro.core.io.html.HtmlReader;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
/**
* Support for HTML format.
@@ -58,7 +59,8 @@ public boolean isReadable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(HtmlReader.class, aTSD);
diff --git a/inception/inception-io-imscwb/pom.xml b/inception/inception-io-imscwb/pom.xml
index 1070e6e9468..09043173f7d 100644
--- a/inception/inception-io-imscwb/pom.xml
+++ b/inception/inception-io-imscwb/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-imscwbINCEpTION - IO - IMS CWB
@@ -29,6 +29,10 @@
de.tudarmstadt.ukp.inception.appinception-api-formats
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ org.springframework
diff --git a/inception/inception-io-imscwb/src/main/java/de/tudarmstadt/ukp/inception/io/imscwb/ImsCwbFormatSupport.java b/inception/inception-io-imscwb/src/main/java/de/tudarmstadt/ukp/inception/io/imscwb/ImsCwbFormatSupport.java
index ce68dc09348..2d22f62a956 100644
--- a/inception/inception-io-imscwb/src/main/java/de/tudarmstadt/ukp/inception/io/imscwb/ImsCwbFormatSupport.java
+++ b/inception/inception-io-imscwb/src/main/java/de/tudarmstadt/ukp/inception/io/imscwb/ImsCwbFormatSupport.java
@@ -25,6 +25,7 @@
import org.dkpro.core.io.imscwb.ImsCwbReader;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.inception.io.imscwb.config.ImsCwbFormatSupportAutoConfiguration;
/**
@@ -64,7 +65,8 @@ public boolean isReadable()
// }
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(ImsCwbReader.class, aTSD);
diff --git a/inception/inception-io-intertext/pom.xml b/inception/inception-io-intertext/pom.xml
index e34382d5142..f3d8f6f3244 100644
--- a/inception/inception-io-intertext/pom.xml
+++ b/inception/inception-io-intertext/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-intertextINCEpTION - IO - InterText
@@ -33,6 +33,10 @@
de.tudarmstadt.ukp.inception.appinception-io-xml
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ org.springframework
diff --git a/inception/inception-io-intertext/src/main/java/de/tudarmstadt/ukp/inception/io/intertext/IntertextFormatSupport.java b/inception/inception-io-intertext/src/main/java/de/tudarmstadt/ukp/inception/io/intertext/IntertextFormatSupport.java
index 74e2bed9d8d..5768978cdb9 100644
--- a/inception/inception-io-intertext/src/main/java/de/tudarmstadt/ukp/inception/io/intertext/IntertextFormatSupport.java
+++ b/inception/inception-io-intertext/src/main/java/de/tudarmstadt/ukp/inception/io/intertext/IntertextFormatSupport.java
@@ -28,6 +28,7 @@
import org.apache.wicket.request.resource.CssResourceReference;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.inception.io.intertext.config.IntertextAutoConfiguration;
/**
@@ -67,7 +68,8 @@ public boolean isReadable()
// }
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(IntertextReader.class, aTSD);
diff --git a/inception/inception-io-json/pom.xml b/inception/inception-io-json/pom.xml
index e9071d6bea3..564aa96ddda 100644
--- a/inception/inception-io-json/pom.xml
+++ b/inception/inception-io-json/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-jsonINCEpTION - IO - JSON
@@ -50,6 +50,10 @@
org.springframeworkspring-beans
+
+ org.springframework.boot
+ spring-boot
+ org.springframework.bootspring-boot-autoconfigure
diff --git a/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/LegacyUimaJsonFormatSupport.java b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/LegacyUimaJsonFormatSupport.java
index 06684d9d259..ef073e48632 100644
--- a/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/LegacyUimaJsonFormatSupport.java
+++ b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/LegacyUimaJsonFormatSupport.java
@@ -27,6 +27,7 @@
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.inception.io.jsoncas.config.LegacyUimaJsonCasFormatProperties;
public class LegacyUimaJsonFormatSupport
implements FormatSupport
@@ -34,6 +35,13 @@ public class LegacyUimaJsonFormatSupport
public static final String ID = "json";
public static final String NAME = "UIMA CAS JSON (legacy)";
+ private final LegacyUimaJsonCasFormatProperties properties;
+
+ public LegacyUimaJsonFormatSupport(LegacyUimaJsonCasFormatProperties aProps)
+ {
+ properties = aProps;
+ }
+
@Override
public String getId()
{
@@ -57,6 +65,7 @@ public AnalysisEngineDescription getWriterDescription(Project aProject,
TypeSystemDescription aTSD, CAS aCAS)
throws ResourceInitializationException
{
- return createEngineDescription(JsonWriter.class, aTSD);
+ return createEngineDescription(JsonWriter.class, aTSD, //
+ JsonWriter.PARAM_OMIT_DEFAULT_VALUES, properties.isOmitDefaultValues());
}
}
diff --git a/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/UimaJsonCasFormatSupport.java b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/UimaJsonCasFormatSupport.java
index b4f3f676de4..6e05c8dad31 100644
--- a/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/UimaJsonCasFormatSupport.java
+++ b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/UimaJsonCasFormatSupport.java
@@ -92,11 +92,11 @@ public AnalysisEngineDescription getWriterDescription(Project aProject,
}
@Override
- public void read(CAS aCas, File aFile)
+ public void read(Project aProject, CAS aCas, File aFile)
throws ResourceInitializationException, IOException, CollectionException
{
// We need to perform a little hack here because the JSON CAS IO does not support lenient
- // deserialization yet. INCEpTION includes some types in exports that are specific only to
+ // de-serialization yet. INCEpTION includes some types in exports that are specific only to
// exports. They are usually discarded by the lenient XMI import, but here they bite us.
var tsd = mergeTypeSystems(asList( //
TypeSystemUtil.typeSystem2TypeSystemDescription(aCas.getTypeSystem()),
@@ -104,7 +104,7 @@ public void read(CAS aCas, File aFile)
upgradeCas(aCas, tsd);
- FormatSupport.super.read(aCas, aFile);
+ FormatSupport.super.read(aProject, aCas, aFile);
// No need to go back to the original CAS TS because another upgrade happens after
// project import anyway.
@@ -122,7 +122,8 @@ private void upgradeCas(CAS aCas, TypeSystemDescription tsd)
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(UimaJsonCasReader.class, aTSD);
diff --git a/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/LegacyUimaJsonCasFormatProperties.java b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/LegacyUimaJsonCasFormatProperties.java
new file mode 100644
index 00000000000..2ed7bd2eff7
--- /dev/null
+++ b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/LegacyUimaJsonCasFormatProperties.java
@@ -0,0 +1,36 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.io.jsoncas.config;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+@ConfigurationProperties("format.json-cas-legacy")
+public class LegacyUimaJsonCasFormatProperties
+{
+ private boolean omitDefaultValues = false;
+
+ public void setOmitDefaultValues(boolean aOmitDefaultValues)
+ {
+ omitDefaultValues = aOmitDefaultValues;
+ }
+
+ public boolean isOmitDefaultValues()
+ {
+ return omitDefaultValues;
+ }
+}
diff --git a/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/UimaJsonCasSupportAutoConfiguration.java b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/UimaJsonCasSupportAutoConfiguration.java
index a4c53297865..c4b3256f651 100644
--- a/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/UimaJsonCasSupportAutoConfiguration.java
+++ b/inception/inception-io-json/src/main/java/de/tudarmstadt/ukp/inception/io/jsoncas/config/UimaJsonCasSupportAutoConfiguration.java
@@ -18,6 +18,7 @@
package de.tudarmstadt.ukp.inception.io.jsoncas.config;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@@ -26,14 +27,16 @@
import de.tudarmstadt.ukp.inception.io.jsoncas.UimaJsonCasFormatSupport;
@Configuration
+@EnableConfigurationProperties(LegacyUimaJsonCasFormatProperties.class)
public class UimaJsonCasSupportAutoConfiguration
{
@ConditionalOnProperty(prefix = "format.json-cas-legacy", name = "enabled", //
havingValue = "true", matchIfMissing = false)
@Bean
- public LegacyUimaJsonFormatSupport legacyUimaJsonFormatSupport()
+ public LegacyUimaJsonFormatSupport legacyUimaJsonFormatSupport(
+ LegacyUimaJsonCasFormatProperties aProps)
{
- return new LegacyUimaJsonFormatSupport();
+ return new LegacyUimaJsonFormatSupport(aProps);
}
@ConditionalOnProperty(prefix = "format.json-cas", name = "enabled", //
diff --git a/inception/inception-io-json/src/main/resources/META-INF/asciidoc/user-guide/formats-uimajson-legacy.adoc b/inception/inception-io-json/src/main/resources/META-INF/asciidoc/user-guide/formats-uimajson-legacy.adoc
index 9c40a78afde..263356b2a72 100644
--- a/inception/inception-io-json/src/main/resources/META-INF/asciidoc/user-guide/formats-uimajson-legacy.adoc
+++ b/inception/inception-io-json/src/main/resources/META-INF/asciidoc/user-guide/formats-uimajson-legacy.adoc
@@ -18,12 +18,11 @@
= UIMA CAS JSON (legacy)
====
-CAUTION: Legacy feature. To use this functionality, you need to enable it first by adding `ui.json-cas-legacy.enabled=true` to the `settings.properties` file.
+CAUTION: Legacy feature. To use this functionality, you need to enable it first by adding `format.json-cas-legacy.enabled=true` to the `settings.properties` file.
Support for this feature will be removed in a future version. The replacement is <>.
====
-
This is an old and deprecated UIMA CAS JSON format which can be exported but not imported.
It should no longer be used. Instead, one should turn to <>.
@@ -31,6 +30,10 @@ The format does support custom layers.
For more details on this format, please refer to the link:https://uima.apache.org/d/uimaj-current/references.html#ugr.ref.json[UIMA Reference Guide].
+By default, the format writes all values to the JSON output, even if the values are the default values
+in JSON (e.g. `0` for numbers or `false` for booleans). You can configure this behavior by setting
+`format.json-cas-legacy.omit-default-values` to `true` or `false` (default) respectively.
+
[cols="2,1,1,1,3"]
|====
| Format | Read | Write | Custom Layers | Description
@@ -41,4 +44,3 @@ For more details on this format, please refer to the link:https://uima.apache.or
| yes
| UIMA CAS JSON (legacy)
|====
-
diff --git a/inception/inception-io-lif/pom.xml b/inception/inception-io-lif/pom.xml
index 6c9ab8d5139..8b4e6f4e356 100644
--- a/inception/inception-io-lif/pom.xml
+++ b/inception/inception-io-lif/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-lifINCEpTION - IO - LIF (deprecated)
@@ -38,6 +38,7 @@
de.tudarmstadt.ukp.inception.appinception-model
+
org.springframeworkspring-context
@@ -46,6 +47,7 @@
org.springframework.bootspring-boot-autoconfigure
+
org.apache.uimauimaj-core
@@ -54,6 +56,7 @@
org.apache.uimauimafit-core
+
org.dkpro.coredkpro-core-io-lif-asl
diff --git a/inception/inception-io-lif/src/main/java/de/tudarmstadt/ukp/inception/io/lif/LifFormatSupport.java b/inception/inception-io-lif/src/main/java/de/tudarmstadt/ukp/inception/io/lif/LifFormatSupport.java
index 5ca0e03d9e1..0a551967a98 100644
--- a/inception/inception-io-lif/src/main/java/de/tudarmstadt/ukp/inception/io/lif/LifFormatSupport.java
+++ b/inception/inception-io-lif/src/main/java/de/tudarmstadt/ukp/inception/io/lif/LifFormatSupport.java
@@ -70,7 +70,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(LifReader.class, aTSD);
diff --git a/inception/inception-io-nif/pom.xml b/inception/inception-io-nif/pom.xml
index 3d99192b791..d4253576612 100644
--- a/inception/inception-io-nif/pom.xml
+++ b/inception/inception-io-nif/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-nifINCEpTION - IO - NIF
diff --git a/inception/inception-io-nif/src/main/java/de/tudarmstadt/ukp/inception/io/nif/NifFormatSupport.java b/inception/inception-io-nif/src/main/java/de/tudarmstadt/ukp/inception/io/nif/NifFormatSupport.java
index 82457b7a7ad..1f271840942 100644
--- a/inception/inception-io-nif/src/main/java/de/tudarmstadt/ukp/inception/io/nif/NifFormatSupport.java
+++ b/inception/inception-io-nif/src/main/java/de/tudarmstadt/ukp/inception/io/nif/NifFormatSupport.java
@@ -70,7 +70,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(NifReader.class, aTSD);
diff --git a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifReader.java b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifReader.java
index 0ef5a3af866..353cdbabef5 100644
--- a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifReader.java
+++ b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifReader.java
@@ -54,18 +54,16 @@
*/
@ResourceMetaData(name = "NLP Interchange Format (NIF) Reader")
@DocumentationResource("${docbase}/format-reference.html#format-${command}")
-@MimeTypeCapability({MimeTypes.APPLICATION_X_NIF_TURTLE})
-@TypeCapability(
- outputs = {
- "de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Heading",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Paragraph",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token",
- "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Lemma",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Stem",
- "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity" })
+@MimeTypeCapability({ MimeTypes.APPLICATION_X_NIF_TURTLE })
+@TypeCapability(outputs = { "de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Heading",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Paragraph",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token",
+ "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Lemma",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Stem",
+ "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity" })
public class NifReader
extends JCasResourceCollectionReader_ImplBase
{
@@ -82,35 +80,33 @@ public class NifReader
* Enable/disable type mapping.
*/
public static final String PARAM_MAPPING_ENABLED = ComponentParameters.PARAM_MAPPING_ENABLED;
- @ConfigurationParameter(name = PARAM_MAPPING_ENABLED, mandatory = true, defaultValue =
- ComponentParameters.DEFAULT_MAPPING_ENABLED)
+ @ConfigurationParameter(name = PARAM_MAPPING_ENABLED, mandatory = true, //
+ defaultValue = ComponentParameters.DEFAULT_MAPPING_ENABLED)
protected boolean mappingEnabled;
/**
- * Load the part-of-speech tag to UIMA type mapping from this location instead of locating
- * the mapping automatically.
+ * Load the part-of-speech tag to UIMA type mapping from this location instead of locating the
+ * mapping automatically.
*/
- public static final String PARAM_POS_MAPPING_LOCATION =
- ComponentParameters.PARAM_POS_MAPPING_LOCATION;
+ public static final String PARAM_POS_MAPPING_LOCATION = ComponentParameters.PARAM_POS_MAPPING_LOCATION;
@ConfigurationParameter(name = PARAM_POS_MAPPING_LOCATION, mandatory = false)
private String posMappingLocation;
-
+
private MappingProvider posMappingProvider;
-
+
private Resource res;
private Model model;
private StmtIterator contextIterator;
private int inFileCount;
-
+
@Override
- public void initialize(UimaContext aContext)
- throws ResourceInitializationException
+ public void initialize(UimaContext aContext) throws ResourceInitializationException
{
super.initialize(aContext);
-
+
posMappingProvider = createPosMappingProvider(this, posMappingLocation, posTagset,
getLanguage());
-
+
// Seek first article
try {
step();
@@ -119,7 +115,7 @@ public void initialize(UimaContext aContext)
throw new ResourceInitializationException(e);
}
}
-
+
@Override
public void getNext(JCas aJCas) throws IOException, CollectionException
{
@@ -146,29 +142,28 @@ public void getNext(JCas aJCas) throws IOException, CollectionException
inFileCount++;
step();
}
-
+
private void closeAll()
{
res = null;
contextIterator = null;
}
-
+
@Override
public void destroy()
{
closeAll();
super.destroy();
}
-
+
@Override
- public boolean hasNext()
- throws IOException, CollectionException
+ public boolean hasNext() throws IOException, CollectionException
{
// If there is still an iterator, then there is still data. This requires that we call
// step() already during initialization.
return contextIterator != null;
}
-
+
/**
* Seek article in file. Stop once article element has been found without reading it.
*/
@@ -188,7 +183,7 @@ private void step() throws IOException
RDFDataMgr.read(model, is, RDFLanguages.filenameToLang(
CompressionUtils.stripCompressionExtension(res.getLocation())));
}
- contextIterator = model.listStatements(null, RDF.type,
+ contextIterator = model.listStatements(null, RDF.type,
model.createResource(NIF.TYPE_CONTEXT));
}
else {
@@ -196,11 +191,11 @@ private void step() throws IOException
return;
}
}
-
+
if (contextIterator.hasNext()) {
return;
}
-
+
// End of file reached
closeAll();
}
diff --git a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifWriter.java b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifWriter.java
index 0c6efce05f9..fcadaa31cec 100644
--- a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifWriter.java
+++ b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/NifWriter.java
@@ -14,7 +14,8 @@
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
- */package org.dkpro.core.io.nif;
+ */
+package org.dkpro.core.io.nif;
import java.io.OutputStream;
@@ -40,46 +41,43 @@
/**
* Writer for the NLP Interchange Format (NIF).
*
- * @see NIF 2.0 Core Ontology
+ * @see NIF
+ * 2.0 Core Ontology
*/
@ResourceMetaData(name = "NLP Interchange Format (NIF) Writer")
@DocumentationResource("${docbase}/format-reference.html#format-${command}")
-@MimeTypeCapability({MimeTypes.APPLICATION_X_NIF_TURTLE})
-@TypeCapability(
- inputs = {
- "de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Heading",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Paragraph",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token",
- "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Lemma",
- "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Stem",
- "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity" })
+@MimeTypeCapability({ MimeTypes.APPLICATION_X_NIF_TURTLE })
+@TypeCapability(inputs = { "de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Heading",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Paragraph",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token",
+ "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Lemma",
+ "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Stem",
+ "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity" })
public class NifWriter
extends JCasFileWriter_ImplBase
{
/**
* Specify the suffix of output files. Default value .ttl. The file format will be
- * chosen depending on the file suffice.
+ * chosen depending on the file suffice.
*
* @see RDFLanguages
*/
- public static final String PARAM_FILENAME_EXTENSION =
- ComponentParameters.PARAM_FILENAME_EXTENSION;
+ public static final String PARAM_FILENAME_EXTENSION = ComponentParameters.PARAM_FILENAME_EXTENSION;
@ConfigurationParameter(name = PARAM_FILENAME_EXTENSION, mandatory = true, defaultValue = ".ttl")
private String filenameSuffix;
@Override
- public void process(JCas aJCas)
- throws AnalysisEngineProcessException
+ public void process(JCas aJCas) throws AnalysisEngineProcessException
{
OntModel model = ModelFactory.createOntologyModel();
model.setNsPrefix(NIF.PREFIX_NIF, NIF.NS_NIF);
model.setNsPrefix(ITS.PREFIX_ITS, ITS.NS_ITS);
-
+
DKPro2Nif.convert(aJCas, model);
-
+
try (OutputStream docOS = getOutputStream(aJCas, filenameSuffix)) {
RDFDataMgr.write(docOS, model.getBaseModel(),
RDFLanguages.fileExtToLang(filenameSuffix));
diff --git a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/DKPro2Nif.java b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/DKPro2Nif.java
index ba9b16236db..2ebcf8bcb6b 100644
--- a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/DKPro2Nif.java
+++ b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/DKPro2Nif.java
@@ -51,7 +51,7 @@ public static void convert(JCas aJCas, OntModel aTarget)
final Resource tParagraph = m.createResource(NIF.TYPE_PARAGRAPH);
final Resource tEntityOccurrence = m.createResource(NIF.TYPE_ENTITY_OCCURRENCE);
final Resource tOffsetBasedString = m.createResource(NIF.TYPE_OFFSET_BASED_STRING);
-
+
final Property pReferenceContext = m.createProperty(NIF.PROP_REFERENCE_CONTEXT);
final Property pIsString = m.createProperty(NIF.PROP_IS_STRING);
final Property pAnchorOf = m.createProperty(NIF.PROP_ANCHOR_OF);
@@ -73,7 +73,7 @@ public static void convert(JCas aJCas, OntModel aTarget)
DocumentMetaData dmd = DocumentMetaData.get(aJCas);
String docuri = dmd.getDocumentUri() != null ? dmd.getDocumentUri()
: "urn:" + dmd.getDocumentId();
-
+
// Convert document -> context node
Individual context;
{
@@ -81,14 +81,12 @@ public static void convert(JCas aJCas, OntModel aTarget)
aJCas.getDocumentText().length());
context = m.createIndividual(uri, tContext);
context.addRDFType(tOffsetBasedString);
- context.addLiteral(pIsString,
- m.createTypedLiteral(aJCas.getDocumentText(), XSDstring));
- context.addLiteral(pBeginIndex,
- m.createTypedLiteral(0, XSDnonNegativeInteger));
+ context.addLiteral(pIsString, m.createTypedLiteral(aJCas.getDocumentText(), XSDstring));
+ context.addLiteral(pBeginIndex, m.createTypedLiteral(0, XSDnonNegativeInteger));
context.addLiteral(pEndIndex,
m.createTypedLiteral(aJCas.getDocumentText().length(), XSDnonNegativeInteger));
}
-
+
// Convert headings/titles
for (Heading uimaHeading : select(aJCas, Heading.class)) {
String headingUri = String.format("%s#offset_%d_%d", docuri, uimaHeading.getBegin(),
@@ -97,7 +95,7 @@ public static void convert(JCas aJCas, OntModel aTarget)
nifTitle.addRDFType(tOffsetBasedString);
nifTitle.addProperty(pReferenceContext, context);
nifTitle.addLiteral(pAnchorOf, uimaHeading.getCoveredText());
- nifTitle.addLiteral(pBeginIndex,
+ nifTitle.addLiteral(pBeginIndex,
m.createTypedLiteral(uimaHeading.getBegin(), XSDnonNegativeInteger));
nifTitle.addLiteral(pEndIndex,
m.createTypedLiteral(uimaHeading.getEnd(), XSDnonNegativeInteger));
@@ -111,12 +109,12 @@ public static void convert(JCas aJCas, OntModel aTarget)
nifParagraph.addRDFType(tOffsetBasedString);
nifParagraph.addProperty(pReferenceContext, context);
nifParagraph.addLiteral(pAnchorOf, uimaParagraph.getCoveredText());
- nifParagraph.addLiteral(pBeginIndex,
+ nifParagraph.addLiteral(pBeginIndex,
m.createTypedLiteral(uimaParagraph.getBegin(), XSDnonNegativeInteger));
nifParagraph.addLiteral(pEndIndex,
m.createTypedLiteral(uimaParagraph.getEnd(), XSDnonNegativeInteger));
}
-
+
// Convert sentences
Individual previousNifSentence = null;
for (Sentence uimaSentence : select(aJCas, Sentence.class)) {
@@ -126,18 +124,18 @@ public static void convert(JCas aJCas, OntModel aTarget)
nifSentence.addRDFType(tOffsetBasedString);
nifSentence.addProperty(pReferenceContext, context);
nifSentence.addLiteral(pAnchorOf, uimaSentence.getCoveredText());
- nifSentence.addLiteral(pBeginIndex,
+ nifSentence.addLiteral(pBeginIndex,
m.createTypedLiteral(uimaSentence.getBegin(), XSDnonNegativeInteger));
nifSentence.addLiteral(pEndIndex,
m.createTypedLiteral(uimaSentence.getEnd(), XSDnonNegativeInteger));
-
+
// Link word sequence
if (previousNifSentence != null) {
previousNifSentence.addProperty(pNextSentence, nifSentence);
nifSentence.addProperty(pPreviousSentence, previousNifSentence);
}
previousNifSentence = nifSentence;
-
+
// Convert tokens
Individual previousNifWord = null;
for (Token uimaToken : selectCovered(Token.class, uimaSentence)) {
@@ -147,39 +145,39 @@ public static void convert(JCas aJCas, OntModel aTarget)
nifWord.addRDFType(tOffsetBasedString);
nifWord.addProperty(pReferenceContext, context);
nifWord.addLiteral(pAnchorOf, uimaToken.getText());
- nifWord.addLiteral(pBeginIndex,
+ nifWord.addLiteral(pBeginIndex,
m.createTypedLiteral(uimaToken.getBegin(), XSDnonNegativeInteger));
nifWord.addLiteral(pEndIndex,
m.createTypedLiteral(uimaToken.getEnd(), XSDnonNegativeInteger));
-
+
// Link sentence <-> word
nifWord.addProperty(pSentence, nifSentence);
nifSentence.addProperty(pWord, nifWord);
-
+
// Link word sequence
if (previousNifWord != null) {
previousNifWord.addProperty(pNextWord, nifWord);
nifWord.addProperty(pPreviousWord, previousNifWord);
}
previousNifWord = nifWord;
-
+
// Convert stem
if (uimaToken.getStemValue() != null) {
nifWord.addProperty(pStem, uimaToken.getStemValue());
}
-
+
// Convert lemma
if (uimaToken.getLemmaValue() != null) {
nifWord.addProperty(pLemma, uimaToken.getLemmaValue());
}
-
+
// Convert posTag (this is discouraged, the better alternative should be oliaLink)
if (uimaToken.getPosValue() != null) {
nifWord.addProperty(pPosTag, uimaToken.getPosValue());
}
}
}
-
+
// Convert named entities
//
// Actually, the named entity in NIF is different from the one in DKPro Core. NIF uses
@@ -188,36 +186,36 @@ public static void convert(JCas aJCas, OntModel aTarget)
// uses, we'd need a named entity linker, not just a recognizer.
//
// We create NEs using the NIF 2.1 class "EntityOccurence".
- //
+ //
// So here, we check if the DKPro Core NE value/identifier looks like a URI and if yes, then
// we store it into the NIF taIdentRef property - otherwise we ignore it because NIF does
// not have the concept of a NE category.
for (NamedEntity uimaNamedEntity : select(aJCas, NamedEntity.class)) {
String neClass = uimaNamedEntity.getValue();
String neIdentifier = uimaNamedEntity.getIdentifier();
-
+
boolean neClassIsUri = neClass != null && IRIs.check(neClass);
boolean neIdentifierIsUri = neIdentifier != null && IRIs.check(neIdentifier);
-
+
if (!neClassIsUri && !neIdentifierIsUri) {
continue;
}
-
+
String neUri = String.format("%s#offset_%d_%d", docuri, uimaNamedEntity.getBegin(),
uimaNamedEntity.getEnd());
Individual nifNamedEntity = m.createIndividual(neUri, tEntityOccurrence);
nifNamedEntity.addRDFType(tOffsetBasedString);
nifNamedEntity.addProperty(pReferenceContext, context);
nifNamedEntity.addLiteral(pAnchorOf, uimaNamedEntity.getCoveredText());
- nifNamedEntity.addLiteral(pBeginIndex,
+ nifNamedEntity.addLiteral(pBeginIndex,
m.createTypedLiteral(uimaNamedEntity.getBegin(), XSDnonNegativeInteger));
nifNamedEntity.addLiteral(pEndIndex,
m.createTypedLiteral(uimaNamedEntity.getEnd(), XSDnonNegativeInteger));
-
+
if (neClassIsUri) {
nifNamedEntity.addProperty(pTaClassRef, m.createResource(neClass));
}
-
+
if (neIdentifierIsUri) {
nifNamedEntity.addProperty(pTaIdentRef, m.createResource(neIdentifier));
}
diff --git a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/ITS.java b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/ITS.java
index 693dbdbe1fa..1c9243fb2f3 100644
--- a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/ITS.java
+++ b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/ITS.java
@@ -25,10 +25,10 @@
public class ITS
{
public static final String PREFIX_ITS = "itsrdf";
-
+
public static final String NS_ITS = "http://www.w3.org/2005/11/its/rdf#";
public static final String PROP_TA_IDENT_REF = NS_ITS + "taIdentRef";
-
+
public static final String PROP_TA_CLASS_REF = NS_ITS + "taClassRef";
}
diff --git a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/NIF.java b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/NIF.java
index f9c760bd8f7..b48446a48c3 100644
--- a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/NIF.java
+++ b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/NIF.java
@@ -30,7 +30,7 @@
public class NIF
{
public static final String PREFIX_NIF = "nif";
-
+
public static final String NS_NIF = "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#";
/**
@@ -41,7 +41,7 @@ public class NIF
* first character of a text).
*/
public static final String PROP_BEGIN_INDEX = NS_NIF + "beginIndex";
-
+
/**
* The end index of a character range as defined in
* RFC 5147 Section 2.2.1 and
@@ -50,7 +50,7 @@ public class NIF
* first character of a text).
*/
public static final String PROP_END_INDEX = NS_NIF + "endIndex";
-
+
/**
* Links a URI of a string to its reference context of type nif:Context. The reference context
* determines the calculation of begin and end index
@@ -58,7 +58,7 @@ public class NIF
* Each String that is not an instance of nif:Context MUST have exactly one reference context.
*/
public static final String PROP_REFERENCE_CONTEXT = NS_NIF + "referenceContext";
-
+
/**
* The reference text as rdf:Literal for this nif:Context resource.
*
@@ -71,33 +71,33 @@ public class NIF
* character position and indices.
*/
public static final String PROP_IS_STRING = NS_NIF + "isString";
-
+
/**
* The string, which the URI is representing as an RDF Literal. Some use cases require this
* property, as it is necessary for certain sparql queries.
*/
public static final String PROP_ANCHOR_OF = NS_NIF + "anchorOf";
-
+
/**
* This property links sentences to their words.
*/
public static final String PROP_WORD = NS_NIF + "word";
-
+
/**
* See nif:nextSentence
*/
public static final String PROP_NEXT_WORD = NS_NIF + "nextWord";
-
+
/**
* see nif:nextSentence
*/
public static final String PROP_PREVIOUS_WORD = NS_NIF + "previousWord";
-
+
/**
* This property links words and other structures to their sentence.
*/
public static final String PROP_SENTENCE = NS_NIF + "sentence";
-
+
/**
* This property (and nif:previousSentence, nif:nextWord, nif:previousWord and their transitive
* extension) can be used to make resources of nif:Sentence and nif:Word traversable, it can not
@@ -107,22 +107,22 @@ public class NIF
* skos:broader and skos:broaderTransitive.
*/
public static final String PROP_NEXT_SENTENCE = NS_NIF + "nextSentence";
-
+
/**
* see nif:nextSentence
*/
public static final String PROP_PREVIOUS_SENTENCE = NS_NIF + "previousSentence";
-
+
/**
* The lemma(s) of the nif:String.
*/
public static final String PROP_LEMMA = NS_NIF + "lemma";
-
+
/**
* The stem(s) of the nif:String.
*/
public static final String PROP_STEM = NS_NIF + "stem";
-
+
/**
* To include the pos tag as it comes out of the NLP tool as RDF Literal. This property is
* discouraged to use alone, please use oliaLink and oliaCategory. We included it, because some
@@ -133,7 +133,7 @@ public class NIF
*/
@Deprecated
public static final String PROP_POS_TAG = NS_NIF + "posTag";
-
+
/**
* The confidence of an annotation as decimal between 0 and 1.
*/
@@ -150,7 +150,7 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String PROP_TA_MS_CLASS_REF = NS_NIF + "taMsClassRef";
-
+
/**
* A title within a text.
*
@@ -159,7 +159,7 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String TYPE_TITLE = NS_NIF + "Title";
-
+
/**
* A paragraph.
*
@@ -168,7 +168,7 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String TYPE_PARAGRAPH = NS_NIF + "Paragraph";
-
+
/**
* The Word class represents strings that are tokens or words. A string is a Word, if it is a
* word. We don't nitpic about whether it is a a pronoun, a name, a punctuation mark or an
@@ -210,14 +210,16 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String TYPE_WORD = NS_NIF + "Word";
-
+
/**
* A sentence.
*
- * @see NIF 2.0 Core Ontology
+ * @see NIF
+ * 2.0 Core Ontology
*/
public static final String TYPE_SENTENCE = NS_NIF + "Sentence";
-
+
/**
* The string that serves as a context for its substrings. The Unicode String given in the
* nif:isString property must be used to calculate the begin and endIndex for all nif:Strings
@@ -229,7 +231,7 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String TYPE_CONTEXT = NS_NIF + "Context";
-
+
/**
* Individuals of this class are a string, i.e. Unicode characters, who have been given a URI
* and are used in the subject of an RDF statement.
@@ -246,7 +248,7 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String TYPE_STRING = NS_NIF + "String";
-
+
/**
* A nif:Phrase can be a nif:String, that is a chunk of several words or a word itself (e.g. a
* NounPhrase as a Named Entity). The term is underspecified and can be compatible with many
@@ -258,7 +260,7 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String TYPE_PHRASE = NS_NIF + "Phrase";
-
+
/**
* cf. Linked-Data Aware URI Schemes for Referencing Text Fragments by Sebastian Hellmann, Jens
* Lehmann und Sören Auer in EKAW 2012 http://jens-lehmann.org/files/2012/ekaw_nif.pdf
@@ -270,15 +272,14 @@ public class NIF
* 2.0 Core Ontology
*/
public static final String TYPE_OFFSET_BASED_STRING = NS_NIF + "OffsetBasedString";
-
+
/**
* Text span annotation denoting that a word or phrase has been detected as occurrence of a
* named entity. (Use this without further annotation property assertions if you just want to
* express the detection of the occurrence when neither the mentioned entity nor its category
* was identified.)
*
- * @see NIF
+ * @see NIF
* 2.1 Core Ontology
*/
public static final String TYPE_ENTITY_OCCURRENCE = NS_NIF + "EntityOccurrence";
diff --git a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/Nif2DKPro.java b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/Nif2DKPro.java
index cd20ed34e41..6bec99760ef 100644
--- a/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/Nif2DKPro.java
+++ b/inception/inception-io-nif/src/main/java/org/dkpro/core/io/nif/internal/Nif2DKPro.java
@@ -51,7 +51,7 @@ public void setPosMappingProvider(MappingProvider aPosMappingProvider)
{
posMappingProvider = aPosMappingProvider;
}
-
+
public void convert(Statement aContext, JCas aJCas)
{
Model m = aContext.getModel();
@@ -60,7 +60,7 @@ public void convert(Statement aContext, JCas aJCas)
final Resource tWord = m.createResource(NIF.TYPE_WORD);
final Resource tTitle = m.createResource(NIF.TYPE_TITLE);
final Resource tParagraph = m.createResource(NIF.TYPE_PARAGRAPH);
-
+
final Property pReferenceContext = m.createProperty(NIF.PROP_REFERENCE_CONTEXT);
final Property pIsString = m.createProperty(NIF.PROP_IS_STRING);
final Property pBeginIndex = m.createProperty(NIF.PROP_BEGIN_INDEX);
@@ -73,44 +73,39 @@ public void convert(Statement aContext, JCas aJCas)
final Property pTaClassRef = m.createProperty(ITS.PROP_TA_CLASS_REF);
// Convert context node -> document text
- String text = m
- .getProperty(aContext.getSubject(), pIsString)
- .getString();
+ String text = m.getProperty(aContext.getSubject(), pIsString).getString();
aJCas.setDocumentText(text);
// Convert headings/titles
- Iterator headingIterator = m
- .listResourcesWithProperty(RDF.type, tTitle)
- .filterKeep(res -> res.getProperty(
- pReferenceContext).getResource().equals(aContext.getSubject()));
+ Iterator headingIterator = m.listResourcesWithProperty(RDF.type, tTitle)
+ .filterKeep(res -> res.getProperty(pReferenceContext).getResource()
+ .equals(aContext.getSubject()));
for (Resource nifTitle : new IteratorIterable(headingIterator)) {
int begin = nifTitle.getProperty(pBeginIndex).getInt();
int end = nifTitle.getProperty(pEndIndex).getInt();
Heading uimaHeading = new Heading(aJCas, begin, end);
uimaHeading.addToIndexes();
-
+
assert assertSanity(nifTitle, uimaHeading);
}
// Convert paragraphs
- Iterator paragraphIterator = m
- .listResourcesWithProperty(RDF.type, tParagraph)
- .filterKeep(res -> res.getProperty(
- pReferenceContext).getResource().equals(aContext.getSubject()));
+ Iterator paragraphIterator = m.listResourcesWithProperty(RDF.type, tParagraph)
+ .filterKeep(res -> res.getProperty(pReferenceContext).getResource()
+ .equals(aContext.getSubject()));
for (Resource nifParagraph : new IteratorIterable(paragraphIterator)) {
int begin = nifParagraph.getProperty(pBeginIndex).getInt();
int end = nifParagraph.getProperty(pEndIndex).getInt();
Paragraph uimaParagraph = new Paragraph(aJCas, begin, end);
uimaParagraph.addToIndexes();
-
+
assert assertSanity(nifParagraph, uimaParagraph);
}
// Convert sentences
List nifSentences = m
- .listResourcesWithProperty(RDF.type, tSentence)
- .filterKeep(res -> res.getProperty(
- pReferenceContext).getResource().equals(aContext.getSubject()))
+ .listResourcesWithProperty(RDF.type, tSentence).filterKeep(res -> res
+ .getProperty(pReferenceContext).getResource().equals(aContext.getSubject()))
.toList();
nifSentences.sort((a, b) -> a.getProperty(pBeginIndex).getInt()
- b.getProperty(pBeginIndex).getInt());
@@ -119,15 +114,14 @@ public void convert(Statement aContext, JCas aJCas)
int end = nifSentence.getProperty(pEndIndex).getInt();
Sentence uimaSentence = new Sentence(aJCas, begin, end);
uimaSentence.addToIndexes();
-
+
assert assertSanity(nifSentence, uimaSentence);
}
-
+
// Convert tokens
- Iterator tokenIterator = m
- .listResourcesWithProperty(RDF.type, tWord)
- .filterKeep(res -> res.getProperty(
- pReferenceContext).getResource().equals(aContext.getSubject()));
+ Iterator tokenIterator = m.listResourcesWithProperty(RDF.type, tWord)
+ .filterKeep(res -> res.getProperty(pReferenceContext).getResource()
+ .equals(aContext.getSubject()));
for (Resource nifWord : new IteratorIterable(tokenIterator)) {
int begin = nifWord.getProperty(pBeginIndex).getInt();
int end = nifWord.getProperty(pEndIndex).getInt();
@@ -135,7 +129,7 @@ public void convert(Statement aContext, JCas aJCas)
uimaToken.addToIndexes();
assert assertSanity(nifWord, uimaToken);
-
+
// Convert lemma
if (nifWord.hasProperty(pLemma)) {
Lemma uimaLemma = new Lemma(aJCas, uimaToken.getBegin(), uimaToken.getEnd());
@@ -143,7 +137,7 @@ public void convert(Statement aContext, JCas aJCas)
uimaLemma.addToIndexes();
uimaToken.setLemma(uimaLemma);
}
-
+
// Convert stem
if (nifWord.hasProperty(pLemma)) {
Stem uimaStem = new Stem(aJCas, uimaToken.getBegin(), uimaToken.getEnd());
@@ -151,7 +145,7 @@ public void convert(Statement aContext, JCas aJCas)
uimaStem.addToIndexes();
uimaToken.setStem(uimaStem);
}
-
+
// Convert posTag (this is discouraged, the better alternative should be oliaLink)
if (nifWord.hasProperty(pPosTag)) {
String tag = nifWord.getProperty(pStem).getString();
@@ -164,18 +158,18 @@ public void convert(Statement aContext, JCas aJCas)
uimaToken.setPos(uimaPos);
}
}
-
+
// Convert named entities
//
// NIF uses taIdentRef to link to a unique instance of an entity and taClassRef to identify
// the category of the entity. Named entity recognizers in DKPro Core just categorizes the
// entity, e.g. as a person, location, or whatnot. For what NIF uses, we'd need a named
// entity linker, not just a recognizer. Furthermore, the DKPro Core named entity
- // recognizers are not mapped to a common tag set (unlike e.g. POS which is mapped to
+ // recognizers are not mapped to a common tag set (unlike e.g. POS which is mapped to
// the universal POS tags).
- //
+ //
// So, what we do here is treating the URI of the taClassRef in NIF simply as the
- // named entity category and store it.
+ // named entity category and store it.
//
// Here we use duck-typing, i.e. it has a taClassRef property then it is likely a named
// entity. NIF 2.1 [1] appears to introduce a representation of named entities using the
@@ -185,19 +179,16 @@ public void convert(Statement aContext, JCas aJCas)
// [1] http://nif.readthedocs.io/en/2.1-rc/prov-and-conf.html
// [2] https://datahub.io/dataset/kore-50-nif-ner-corpus
Set nifNamedEntitiesTaIdentRef = m
- .listResourcesWithProperty(pTaIdentRef)
- .filterKeep(res -> res.getProperty(
- pReferenceContext).getResource().equals(aContext.getSubject()))
+ .listResourcesWithProperty(pTaIdentRef).filterKeep(res -> res
+ .getProperty(pReferenceContext).getResource().equals(aContext.getSubject()))
.toSet();
Set nifNamedEntitiesTaClassRef = m
- .listResourcesWithProperty(pTaClassRef)
- .filterKeep(res -> res.getProperty(
- pReferenceContext).getResource().equals(aContext.getSubject()))
+ .listResourcesWithProperty(pTaClassRef).filterKeep(res -> res
+ .getProperty(pReferenceContext).getResource().equals(aContext.getSubject()))
.toSet();
Set nifNamedEntitiesTaMsClassRef = m
- .listResourcesWithProperty(pTaMsClassRef)
- .filterKeep(res -> res.getProperty(
- pReferenceContext).getResource().equals(aContext.getSubject()))
+ .listResourcesWithProperty(pTaMsClassRef).filterKeep(res -> res
+ .getProperty(pReferenceContext).getResource().equals(aContext.getSubject()))
.toSet();
Set nifNamedEntities = new HashSet();
nifNamedEntities.addAll(nifNamedEntitiesTaIdentRef);
@@ -207,7 +198,7 @@ public void convert(Statement aContext, JCas aJCas)
int begin = nifNamedEntity.getProperty(pBeginIndex).getInt();
int end = nifNamedEntity.getProperty(pEndIndex).getInt();
NamedEntity uimaNamedEntity = new NamedEntity(aJCas, begin, end);
-
+
// If there is a most-specific class, then we use that
if (nifNamedEntity.hasProperty(pTaMsClassRef)) {
uimaNamedEntity
@@ -218,24 +209,24 @@ else if (nifNamedEntity.hasProperty(pTaClassRef)) {
uimaNamedEntity
.setValue(nifNamedEntity.getProperty(pTaClassRef).getResource().getURI());
}
-
- // If the entity is linked, then we keep the identifier
+
+ // If the entity is linked, then we keep the identifier
if (nifNamedEntity.hasProperty(pTaIdentRef)) {
uimaNamedEntity.setIdentifier(
nifNamedEntity.getProperty(pTaIdentRef).getResource().getURI());
}
uimaNamedEntity.addToIndexes();
-
+
assert assertSanity(nifNamedEntity, uimaNamedEntity);
}
}
-
+
private static boolean assertSanity(Resource aNif, Annotation aUima)
{
final Property pAnchorOf = aNif.getModel().createProperty(NIF.PROP_ANCHOR_OF);
-
+
int docLength = aUima.getCAS().getDocumentText().length();
-
+
if (aNif.hasProperty(pAnchorOf)) {
String nifText = aNif.getProperty(pAnchorOf).getString();
String uimaText = aUima.getCoveredText();
@@ -243,7 +234,7 @@ private static boolean assertSanity(Resource aNif, Annotation aUima)
}
assert aUima.getBegin() >= 0 && aUima.getBegin() <= docLength;
assert aUima.getEnd() >= 0 && aUima.getEnd() <= docLength;
-
+
return true;
}
}
diff --git a/inception/inception-io-perseus/pom.xml b/inception/inception-io-perseus/pom.xml
index 9379f8af88b..f663a802c20 100644
--- a/inception/inception-io-perseus/pom.xml
+++ b/inception/inception-io-perseus/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-perseusINCEpTION - IO - Perseus
@@ -29,6 +29,10 @@
de.tudarmstadt.ukp.inception.appinception-api-formats
+
+ de.tudarmstadt.ukp.inception.app
+ inception-model
+ org.springframework
diff --git a/inception/inception-io-perseus/src/main/java/de/tudarmstadt/ukp/inception/io/perseus/PerseusFormatSupport.java b/inception/inception-io-perseus/src/main/java/de/tudarmstadt/ukp/inception/io/perseus/PerseusFormatSupport.java
index ba381bf14e5..5c244799674 100644
--- a/inception/inception-io-perseus/src/main/java/de/tudarmstadt/ukp/inception/io/perseus/PerseusFormatSupport.java
+++ b/inception/inception-io-perseus/src/main/java/de/tudarmstadt/ukp/inception/io/perseus/PerseusFormatSupport.java
@@ -25,6 +25,7 @@
import org.dkpro.core.io.perseus.PerseusReader;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.inception.io.perseus.config.PerseusFormatAutoConfiguration;
/**
@@ -64,7 +65,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(PerseusReader.class, aTSD);
diff --git a/inception/inception-io-tcf/pom.xml b/inception/inception-io-tcf/pom.xml
index cac3fd8d392..522beecf9d9 100644
--- a/inception/inception-io-tcf/pom.xml
+++ b/inception/inception-io-tcf/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-tcfINCEpTION - IO - TCF
diff --git a/inception/inception-io-tcf/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tcf/TcfFormatSupport.java b/inception/inception-io-tcf/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tcf/TcfFormatSupport.java
index c1c7bab665b..b5aa0996416 100644
--- a/inception/inception-io-tcf/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tcf/TcfFormatSupport.java
+++ b/inception/inception-io-tcf/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tcf/TcfFormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(TcfReader.class, aTSD);
diff --git a/inception/inception-io-tei/pom.xml b/inception/inception-io-tei/pom.xml
index 1e30ca7423e..1446a96234a 100644
--- a/inception/inception-io-tei/pom.xml
+++ b/inception/inception-io-tei/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-teiINCEpTION - IO - TEI
diff --git a/inception/inception-io-tei/src/main/java/de/tudarmstadt/ukp/inception/io/tei/TeiFormatSupport.java b/inception/inception-io-tei/src/main/java/de/tudarmstadt/ukp/inception/io/tei/TeiFormatSupport.java
index 8d7cd6dba30..d65d152af20 100644
--- a/inception/inception-io-tei/src/main/java/de/tudarmstadt/ukp/inception/io/tei/TeiFormatSupport.java
+++ b/inception/inception-io-tei/src/main/java/de/tudarmstadt/ukp/inception/io/tei/TeiFormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(TeiReader.class, aTSD);
diff --git a/inception/inception-io-text/pom.xml b/inception/inception-io-text/pom.xml
index f5a56b3e69e..5fb4ba0f859 100644
--- a/inception/inception-io-text/pom.xml
+++ b/inception/inception-io-text/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-textINCEpTION - IO - Text
diff --git a/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/LineOrientedTextFormatSupport.java b/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/LineOrientedTextFormatSupport.java
index 48b0b0c01a2..caeee878f9e 100644
--- a/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/LineOrientedTextFormatSupport.java
+++ b/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/LineOrientedTextFormatSupport.java
@@ -24,6 +24,7 @@
import org.apache.uima.resource.metadata.TypeSystemDescription;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.text.config.TextFormatsAutoConfiguration;
/**
@@ -57,7 +58,8 @@ public boolean isReadable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(LineOrientedTextReader.class, aTSD);
diff --git a/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/PretokenizedTextFormatSupport.java b/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/PretokenizedTextFormatSupport.java
index efbf0f85d61..32023271fb9 100644
--- a/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/PretokenizedTextFormatSupport.java
+++ b/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/PretokenizedTextFormatSupport.java
@@ -24,6 +24,7 @@
import org.apache.uima.resource.metadata.TypeSystemDescription;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.text.config.TextFormatsAutoConfiguration;
/**
@@ -57,7 +58,8 @@ public boolean isReadable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(PretokenizedLineOrientedTextReader.class, aTSD);
diff --git a/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/TextFormatSupport.java b/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/TextFormatSupport.java
index 94b888e461f..a7662be8eeb 100644
--- a/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/TextFormatSupport.java
+++ b/inception/inception-io-text/src/main/java/de/tudarmstadt/ukp/clarin/webanno/text/TextFormatSupport.java
@@ -69,7 +69,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(TextReader.class, aTSD);
diff --git a/inception/inception-io-webanno-tsv/pom.xml b/inception/inception-io-webanno-tsv/pom.xml
index 8df715154dc..67385021e73 100644
--- a/inception/inception-io-webanno-tsv/pom.xml
+++ b/inception/inception-io-webanno-tsv/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-webanno-tsvINCEpTION - IO - TSV
@@ -104,21 +104,6 @@
-
- org.apache.logging.log4j
- log4j-core
- test
-
-
- org.apache.logging.log4j
- log4j-slf4j-impl
- test
-
-
- org.slf4j
- log4j-over-slf4j
- test
- org.dkpro.coredkpro-core-io-xmi-asl
@@ -126,24 +111,6 @@
-
-
-
- org.apache.maven.plugins
- maven-dependency-plugin
-
-
-
- org.apache.logging.log4j:log4j-slf4j-impl
- org.slf4j:log4j-over-slf4j
- org.apache.logging.log4j:log4j-core
-
-
-
-
-
diff --git a/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv1FormatSupport.java b/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv1FormatSupport.java
index 4ed7d2d4021..482867cfdc2 100644
--- a/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv1FormatSupport.java
+++ b/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv1FormatSupport.java
@@ -24,6 +24,7 @@
import org.apache.uima.resource.metadata.TypeSystemDescription;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.tsv.config.WebAnnoFormatsAutoConfiguration;
/**
@@ -63,7 +64,8 @@ public boolean isProneToInconsistencies()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(WebannoTsv1Reader.class, aTSD);
diff --git a/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv2FormatSupport.java b/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv2FormatSupport.java
index aecebdea2b9..7704f578578 100644
--- a/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv2FormatSupport.java
+++ b/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv2FormatSupport.java
@@ -24,6 +24,7 @@
import org.apache.uima.resource.metadata.TypeSystemDescription;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.tsv.config.WebAnnoFormatsAutoConfiguration;
/**
@@ -63,7 +64,8 @@ public boolean isProneToInconsistencies()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(WebannoTsv2Reader.class, aTSD);
diff --git a/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv3FormatSupport.java b/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv3FormatSupport.java
index 466b472bae9..fa5e9e5c6e4 100644
--- a/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv3FormatSupport.java
+++ b/inception/inception-io-webanno-tsv/src/main/java/de/tudarmstadt/ukp/clarin/webanno/tsv/WebAnnoTsv3FormatSupport.java
@@ -73,7 +73,8 @@ public boolean isProneToInconsistencies()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(WebannoTsv3XReader.class, aTSD);
diff --git a/inception/inception-io-xmi/pom.xml b/inception/inception-io-xmi/pom.xml
index fe49ee672fc..d1b418bed7f 100644
--- a/inception/inception-io-xmi/pom.xml
+++ b/inception/inception-io-xmi/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-xmiINCEpTION - IO - XMI
diff --git a/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/BinaryCasFormatSupport.java b/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/BinaryCasFormatSupport.java
index 08bda37b1a4..afa9721e7d0 100644
--- a/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/BinaryCasFormatSupport.java
+++ b/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/BinaryCasFormatSupport.java
@@ -75,7 +75,8 @@ public boolean isProneToInconsistencies()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(BinaryCasReader.class, aTSD);
diff --git a/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiFormatSupport.java b/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiFormatSupport.java
index 3534342b120..f00ad21b1d4 100644
--- a/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiFormatSupport.java
+++ b/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiFormatSupport.java
@@ -75,7 +75,8 @@ public boolean isProneToInconsistencies()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(XmiReader.class, XmiReader.PARAM_LENIENT, true);
diff --git a/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiXml11FormatSupport.java b/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiXml11FormatSupport.java
index 83dbca32301..7164e1eb790 100644
--- a/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiXml11FormatSupport.java
+++ b/inception/inception-io-xmi/src/main/java/de/tudarmstadt/ukp/clarin/webanno/xmi/XmiXml11FormatSupport.java
@@ -75,7 +75,8 @@ public boolean isProneToInconsistencies()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(XmiReader.class, XmiReader.PARAM_LENIENT, true);
diff --git a/inception/inception-io-xml/pom.xml b/inception/inception-io-xml/pom.xml
index 6f69a15663f..655b7e1f5d2 100644
--- a/inception/inception-io-xml/pom.xml
+++ b/inception/inception-io-xml/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-io-xmlINCEpTION - IO - XML
diff --git a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/XmlFormatSupport.java b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/XmlFormatSupport.java
index 7a011884155..fdc28cbd66c 100644
--- a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/XmlFormatSupport.java
+++ b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/XmlFormatSupport.java
@@ -62,7 +62,8 @@ public boolean isWritable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(XmlDocumentReader.class, aTSD);
diff --git a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/Cas2SaxEvents.java b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/Cas2SaxEvents.java
index 1901328eed5..20f1dc92834 100644
--- a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/Cas2SaxEvents.java
+++ b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/Cas2SaxEvents.java
@@ -35,19 +35,21 @@
import org.xml.sax.SAXException;
import org.xml.sax.helpers.AttributesImpl;
+import de.tudarmstadt.ukp.clarin.webanno.support.xml.ContentHandlerAdapter;
+
public class Cas2SaxEvents
{
private static final String XMLNS = "xmlns";
private static final String XMLNS_PREFIX = "xmlns:";
- protected final ContentHandler handler;
+ protected final ContentHandlerAdapter handler;
private final LinkedHashMap namespaceMappings = new LinkedHashMap<>();
private boolean namespaces = false;
public Cas2SaxEvents(ContentHandler aHandler)
{
- handler = aHandler;
+ handler = new ContentHandlerAdapter(aHandler);
}
public void setNamespaces(boolean aNamespaces)
@@ -97,6 +99,19 @@ public void process(XmlElement aElement) throws SAXException
handler.startElement(uri, localName, qName, attributes);
+ processChildren(aElement);
+
+ handler.endElement(uri, localName, qName);
+
+ if (namespaces) {
+ for (String xmlns : localMappings.keySet()) {
+ handler.endPrefixMapping(xmlns);
+ }
+ }
+ }
+
+ public void processChildren(XmlElement aElement) throws SAXException
+ {
if (aElement.getChildren() != null) {
for (XmlNode child : aElement.getChildren()) {
if (child instanceof XmlElement) {
@@ -107,15 +122,6 @@ else if (child instanceof XmlTextNode) {
}
}
}
-
- handler.endElement(uri, localName, qName);
-
- if (namespaces) {
- for (Entry xmlns : localMappings.entrySet()) {
- handler.endPrefixMapping(xmlns.getKey());
- localMappings.remove(xmlns.getKey());
- }
- }
}
public Map prefixMappings(XmlElement aElement)
diff --git a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/CasXmlHandler.java b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/CasXmlHandler.java
index 932063ea473..cf7e73a7a49 100644
--- a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/CasXmlHandler.java
+++ b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/CasXmlHandler.java
@@ -78,7 +78,9 @@ public void startDocument() throws SAXException
docNode = new XmlDocument(jcas);
docNode.setBegin(text.length());
- listeners.forEach(l -> l.startDocument(docNode));
+ for (var l : listeners) {
+ l.startDocument(docNode);
+ }
}
@Override
@@ -87,7 +89,9 @@ public void endDocument() throws SAXException
docNode.setEnd(text.length());
docNode.addToIndexes();
- listeners.forEach(l -> l.endDocument(docNode));
+ for (var l : listeners) {
+ l.endDocument(docNode);
+ }
jcas.setDocumentText(text.toString());
};
@@ -107,7 +111,7 @@ public void startElement(String aUri, String aLocalName, String aQName, Attribut
element.setLocalName(trimToNull(aLocalName));
element.setQName(trimToNull(aQName));
- if (aAttributes.getLength() > 0) {
+ if (aAttributes != null && aAttributes.getLength() > 0) {
var attributes = new FSArray(jcas, aAttributes.getLength());
for (int i = 0; i < aAttributes.getLength(); i++) {
XmlAttribute attribute = new XmlAttribute(jcas);
@@ -134,7 +138,9 @@ public void startElement(String aUri, String aLocalName, String aQName, Attribut
stack.push(new StackFrame(element, capture));
- listeners.forEach(l -> l.startElement(element));
+ for (var l : listeners) {
+ l.startElement(element);
+ }
}
@Override
@@ -154,7 +160,9 @@ public void endElement(String aUri, String aLocalName, String aQName) throws SAX
element.setChildren(children);
}
- listeners.forEach(l -> l.endElement(element));
+ for (var l : listeners) {
+ l.endElement(element);
+ }
element.addToIndexes();
}
@@ -234,22 +242,22 @@ public boolean isCapturingText()
public static interface ElementListener
{
- default void startDocument(XmlDocument aDocument)
+ default void startDocument(XmlDocument aDocument) throws SAXException
{
// Do nothing
}
- default void endDocument(XmlDocument aDocument)
+ default void endDocument(XmlDocument aDocument) throws SAXException
{
// Do nothing
}
- default void startElement(XmlElement aElement)
+ default void startElement(XmlElement aElement) throws SAXException
{
// Do nothing
}
- default void endElement(XmlElement aElement)
+ default void endElement(XmlElement aElement) throws SAXException
{
// Do nothing
}
diff --git a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtils.java b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtils.java
index 443a4af3ede..b2809d3e3d8 100644
--- a/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtils.java
+++ b/inception/inception-io-xml/src/main/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtils.java
@@ -18,16 +18,38 @@
package de.tudarmstadt.ukp.inception.io.xml.dkprocore;
import static java.util.Arrays.asList;
+import static javax.xml.transform.OutputKeys.INDENT;
+import static javax.xml.transform.OutputKeys.METHOD;
+import static javax.xml.transform.OutputKeys.OMIT_XML_DECLARATION;
import static org.apache.commons.lang3.ArrayUtils.indexOf;
import static org.apache.commons.lang3.ArrayUtils.subarray;
import static org.apache.uima.fit.util.FSCollectionFactory.createFSArray;
+import java.io.IOException;
+import java.io.StringReader;
+import java.io.StringWriter;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Objects;
import java.util.Optional;
+import java.util.function.Consumer;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.sax.SAXTransformerFactory;
+import javax.xml.transform.sax.TransformerHandler;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.uima.jcas.JCas;
import org.dkpro.core.api.xml.type.XmlAttribute;
import org.dkpro.core.api.xml.type.XmlElement;
import org.dkpro.core.api.xml.type.XmlNode;
+import org.dkpro.core.api.xml.type.XmlTextNode;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import de.tudarmstadt.ukp.inception.support.xml.XmlParserUtils;
public class XmlNodeUtils
{
@@ -36,7 +58,54 @@ public static boolean hasAttributeWithValue(XmlElement e, String aAttribute, Str
return getAttributeValue(e, aAttribute).map(v -> aValue.equals(v)).orElse(false);
}
- public static Optional getAttributeValue(XmlElement aElement, String aString)
+ static String serializeCasToXmlString(JCas aJCas) throws IOException
+ {
+ try (var out = new StringWriter()) {
+ SAXTransformerFactory tf = XmlParserUtils.newTransformerFactory();
+ TransformerHandler th = tf.newTransformerHandler();
+ th.getTransformer().setOutputProperty(OMIT_XML_DECLARATION, "yes");
+ th.getTransformer().setOutputProperty(METHOD, "xml");
+ th.getTransformer().setOutputProperty(INDENT, "no");
+ th.setResult(new StreamResult(out));
+
+ Cas2SaxEvents serializer = new Cas2SaxEvents(th);
+ serializer.process(aJCas);
+
+ return out.toString();
+ }
+ catch (SAXException | TransformerConfigurationException e) {
+ throw new IOException(e);
+ }
+ }
+
+ static void parseXmlStringToCas(JCas aJCas, String aXml) throws IOException
+ {
+ try (var reader = new StringReader(aXml)) {
+ parseXmlToCas(aJCas, new InputSource(reader));
+ }
+ }
+
+ static void parseXmlToCas(JCas aJCas, InputSource aSource) throws IOException
+ {
+ CasXmlHandler handler = new CasXmlHandler(aJCas);
+
+ try {
+ var parser = XmlParserUtils.newSaxParser();
+ parser.parse(aSource, handler);
+ }
+ catch (ParserConfigurationException | SAXException e) {
+ throw new IOException(e);
+ }
+ }
+
+ public static boolean hasAttributeValue(XmlElement aElement, String aAttribute, String aValue)
+ {
+ return getAttributeValue(aElement, aAttribute) //
+ .map(value -> Objects.equals(value, aValue)) //
+ .orElse(false);
+ }
+
+ public static Optional getAttributeValue(XmlElement aElement, String aAttribute)
{
var attributes = aElement.getAttributes();
@@ -45,11 +114,92 @@ public static Optional getAttributeValue(XmlElement aElement, String aSt
}
return attributes.select(XmlAttribute.class) //
- .filter(a -> aString.equals(a.getQName())) //
+ .filter(a -> aAttribute.equals(a.getQName())) //
.findFirst() //
.map(XmlAttribute::getValue);
}
+ public static String getMandatoryAttributeValue(XmlElement aElement, String aAttribute)
+ {
+ var attributes = aElement.getAttributes();
+
+ if (attributes == null) {
+ throw new IllegalArgumentException("Element has no attribute [" + aAttribute + "]");
+ }
+
+ return attributes.select(XmlAttribute.class) //
+ .filter(a -> aAttribute.equals(a.getQName())) //
+ .findFirst() //
+ .map(XmlAttribute::getValue) //
+ .orElseThrow(() -> new IllegalArgumentException(
+ "Element has no attribute [" + aAttribute + "]"));
+ }
+
+ public static String textContent(XmlElement aElement)
+ {
+ var buf = new StringBuilder();
+ dfs(aElement, n -> {
+ if (n instanceof XmlTextNode) {
+ var tn = (XmlTextNode) n;
+ if (tn.getCaptured()) {
+ buf.append(tn.getCoveredText());
+ }
+ else {
+ buf.append(tn.getText());
+ }
+ }
+ });
+ return buf.toString();
+ }
+
+ public static List dfs(XmlNode aNode)
+ {
+ var nodes = new ArrayList();
+ dfs(aNode, nodes::add);
+ return nodes;
+ }
+
+ private static void dfs(XmlNode aNode, Consumer aVisitor)
+ {
+ if (aNode instanceof XmlElement) {
+ var children = ((XmlElement) aNode).getChildren();
+ if (children != null) {
+ children.forEach($ -> dfs($, aVisitor));
+ }
+ }
+ aVisitor.accept(aNode);
+ }
+
+ /**
+ * Removes the given element and all descendants except captures text nodes. Captured text nodes
+ * must be preserved, otherwise it may break rendering or serialization because the text of the
+ * captured text nodes is considered part of the document text.
+ *
+ * @param aElement
+ * the element to remove.
+ */
+ public static void removeWithDescendantsFromTree(XmlElement aElement)
+ {
+ ArrayList newSiblings = new ArrayList<>();
+ var parent = aElement.getParent();
+ var siblings = parent.getChildren().toArray(new XmlNode[parent.getChildren().size()]);
+ var i = indexOf(siblings, aElement);
+ asList(subarray(siblings, 0, i)).forEach(newSiblings::add);
+ for (var node : dfs(aElement)) {
+ if (node instanceof XmlElement) {
+ removeElement((XmlElement) node);
+ }
+ if (node instanceof XmlTextNode && ((XmlTextNode) node).getCaptured()) {
+ newSiblings.add(node);
+ }
+ else {
+ node.removeFromIndexes();
+ }
+ }
+ asList(subarray(siblings, i + 1, siblings.length)).forEach(newSiblings::add);
+ parent.setChildren(createFSArray(aElement.getJCas(), newSiblings));
+ }
+
public static void removeFromTree(XmlElement... aElement)
{
for (var e : aElement) {
@@ -58,13 +208,74 @@ public static void removeFromTree(XmlElement... aElement)
var siblings = parent.getChildren().toArray(new XmlNode[parent.getChildren().size()]);
var i = indexOf(siblings, e);
asList(subarray(siblings, 0, i)).forEach(newSiblings::add);
- e.getChildren().forEach(child -> {
- child.setParent(parent);
- newSiblings.add(child);
- });
+ var children = e.getChildren();
+ if (children != null) {
+ children.forEach(child -> hoistNode(newSiblings, parent, child));
+ }
asList(subarray(siblings, i + 1, siblings.length)).forEach(newSiblings::add);
parent.setChildren(createFSArray(e.getJCas(), newSiblings));
- e.removeFromIndexes();
+ removeElement(e);
+ }
+ }
+
+ private static void removeElement(XmlElement e)
+ {
+ var attributes = e.getAttributes();
+ if (attributes != null) {
+ for (var attribute : attributes) {
+ attribute.removeFromIndexes();
+ }
+ attributes.removeFromIndexes();
+ }
+ e.removeFromIndexes();
+ }
+
+ private static void hoistNode(ArrayList newSiblings, XmlElement parent, XmlNode child)
+ {
+ child.setParent(parent);
+ newSiblings.add(child);
+ }
+
+ public static List selectElements(XmlElement aElement, List aPath)
+ {
+ if (aPath.size() == 0 || !aElement.getQName().equals(aPath.get(0))) {
+ return Collections.emptyList();
+ }
+
+ if (aPath.size() == 1) {
+ if (!aElement.getQName().equals(aPath.get(0))) {
+ return Collections.emptyList();
+ }
+
+ return asList(aElement);
+ }
+
+ var result = new ArrayList();
+ for (XmlElement child : aElement.getChildren().select(XmlElement.class)) {
+ result.addAll(selectElements(child, aPath.subList(1, aPath.size())));
+ }
+ return result;
+ }
+
+ public static Optional firstChild(XmlElement aElement, String aQName)
+ {
+ if (aElement.getChildren() == null) {
+ return Optional.empty();
}
+
+ return aElement.getChildren().select(XmlElement.class)
+ .filter(e -> aQName.equals(e.getQName())).findFirst();
}
+
+ public static List rootPath(XmlElement aElement)
+ {
+ var path = new ArrayList();
+ var e = aElement;
+ while (e != null) {
+ path.add(0, e.getQName());
+ e = e.getParent();
+ }
+ return path;
+ }
+
}
diff --git a/inception/inception-io-xml/src/test/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtilsTest.java b/inception/inception-io-xml/src/test/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtilsTest.java
index 98230e23333..785a345d4e7 100644
--- a/inception/inception-io-xml/src/test/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtilsTest.java
+++ b/inception/inception-io-xml/src/test/java/de/tudarmstadt/ukp/inception/io/xml/dkprocore/XmlNodeUtilsTest.java
@@ -17,6 +17,10 @@
*/
package de.tudarmstadt.ukp.inception.io.xml.dkprocore;
+import static de.tudarmstadt.ukp.inception.io.xml.dkprocore.XmlNodeUtils.parseXmlStringToCas;
+import static de.tudarmstadt.ukp.inception.io.xml.dkprocore.XmlNodeUtils.removeWithDescendantsFromTree;
+import static de.tudarmstadt.ukp.inception.io.xml.dkprocore.XmlNodeUtils.selectElements;
+import static de.tudarmstadt.ukp.inception.io.xml.dkprocore.XmlNodeUtils.serializeCasToXmlString;
import static java.util.Arrays.asList;
import static org.apache.uima.fit.util.FSCollectionFactory.createFSArray;
import static org.assertj.core.api.Assertions.assertThat;
@@ -68,4 +72,49 @@ void testRemoveFromTree() throws Exception
.extracting(Annotation::getCoveredText) //
.containsExactly("This", "is", "a", "test");
}
+
+ @Test
+ void testRemoveWithDescendantsFromTree() throws Exception
+ {
+ var jcas = JCasFactory.createJCas();
+ parseXmlStringToCas(jcas, "This is a test.");
+
+ var el2 = jcas.select(XmlElement.class) //
+ .filter(e -> e.getQName().equals("e1")) //
+ .findFirst().get();
+
+ removeWithDescendantsFromTree(el2);
+
+ assertThat(serializeCasToXmlString(jcas)).isEqualTo("This is a test.");
+ }
+
+ @Test
+ void testRemoveWithDescendantsFromTree2() throws Exception
+ {
+ var jcas = JCasFactory.createJCas();
+ parseXmlStringToCas(jcas, "This is a test.");
+
+ var el2 = jcas.select(XmlElement.class) //
+ .filter(e -> e.getQName().equals("e2")) //
+ .findFirst().get();
+
+ removeWithDescendantsFromTree(el2);
+
+ assertThat(serializeCasToXmlString(jcas))
+ .isEqualTo("This is a test.");
+ }
+
+ @Test
+ void testSelectElements() throws Exception
+ {
+ var jcas = JCasFactory.createJCas();
+ parseXmlStringToCas(jcas, "This is a test.");
+
+ var root = jcas.select(XmlDocument.class).get().getRoot();
+ var result = selectElements(root, asList("root", "e1"));
+
+ assertThat(result) //
+ .extracting(XmlElement::getQName) //
+ .containsExactly("e1");
+ }
}
diff --git a/inception/inception-js-api/pom.xml b/inception/inception-js-api/pom.xml
index 9e6f5c331db..2f919272f11 100644
--- a/inception/inception-js-api/pom.xml
+++ b/inception/inception-js-api/pom.xml
@@ -20,7 +20,7 @@
inception-appde.tudarmstadt.ukp.inception.app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOT4.0.0inception-js-api
diff --git a/inception/inception-js-api/src/main/ts/src/diam/DiamAjax.ts b/inception/inception-js-api/src/main/ts/src/diam/DiamAjax.ts
index 1036a0f286e..a005ed454e6 100644
--- a/inception/inception-js-api/src/main/ts/src/diam/DiamAjax.ts
+++ b/inception/inception-js-api/src/main/ts/src/diam/DiamAjax.ts
@@ -51,6 +51,10 @@ export interface DiamAjax {
loadLazyDetails(id: VID, type: string, database: string, key: string): Promise;
+ loadPreferences (key: string): Promise;
+
+ savePreferences (key: string, data: Record): Promise;
+
triggerExtensionAction(id: VID): void;
openContextMenu(id: VID, evt: MouseEvent): void;
diff --git a/inception/inception-js-api/src/main/ts/src/editor/AnnotationEditorProperties.ts b/inception/inception-js-api/src/main/ts/src/editor/AnnotationEditorProperties.ts
index 0ad22c886dd..0f20f02a005 100644
--- a/inception/inception-js-api/src/main/ts/src/editor/AnnotationEditorProperties.ts
+++ b/inception/inception-js-api/src/main/ts/src/editor/AnnotationEditorProperties.ts
@@ -2,13 +2,13 @@
* Licensed to the Technische Universität Darmstadt under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
- * regarding copyright ownership. The Technische Universität Darmstadt
+ * regarding copyright ownership. The Technische Universität Darmstadt
* licenses this file to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License.
- *
+ *
* http://www.apache.org/licenses/LICENSE-2.0
- *
+ *
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -17,9 +17,10 @@
*/
export interface AnnotationEditorProperties {
- editorFactory: string;
- scriptSources: ReadonlyArray;
- stylesheetSources: ReadonlyArray;
- diamAjaxCallbackUrl: string;
- diamWsUrl: string;
-}
\ No newline at end of file
+ editorFactory: string
+ scriptSources: ReadonlyArray
+ stylesheetSources: ReadonlyArray
+ diamAjaxCallbackUrl: string
+ diamWsUrl: string
+ loadingIndicatorDisabled: boolean
+}
diff --git a/inception/inception-js-api/src/main/ts/src/util/ViewportTracker.ts b/inception/inception-js-api/src/main/ts/src/util/ViewportTracker.ts
index cca098b3b9b..0893e79ceda 100644
--- a/inception/inception-js-api/src/main/ts/src/util/ViewportTracker.ts
+++ b/inception/inception-js-api/src/main/ts/src/util/ViewportTracker.ts
@@ -60,7 +60,11 @@ export class ViewportTracker {
if (!style.display) {
return false
}
- return !style.display.startsWith('inline')
+
+ return style.display === 'block' || style.display === 'flex' || style.display === 'grid' ||
+ style.display.includes('table')
+
+ // return !style.display.startsWith('inline') && !style.display.includes('math')
}
private initializeElementTracking (element: Element): void {
@@ -74,6 +78,10 @@ export class ViewportTracker {
.filter(e => this.shouldTrack(e))
console.debug(`Found ${trackingCandidates.length} tracking candidates`)
+ // const displayStyles = new Set()
+ // trackingCandidates.map(e => getComputedStyle(e).display).forEach(e => displayStyles.add(e))
+ // console.debug('Display styles found: ', displayStyles)
+
if (trackingCandidates.length > 0) {
trackingCandidates = trackingCandidates.map(e => {
if (!this.sectionSelector || e.matches(this.sectionSelector)) {
@@ -100,7 +108,7 @@ export class ViewportTracker {
leafTrackingCandidates.forEach(e => this.observer.observe(e))
const endTime = new Date().getTime()
- console.log(`Tracking visibility of ${leafTrackingCandidates.size} elements in ${Math.abs(endTime - startTime)}ms`)
+ console.debug(`Tracking visibility of ${leafTrackingCandidates.size} elements in ${Math.abs(endTime - startTime)}ms`)
}
private handleIntersectRange (entries: IntersectionObserverEntry[], observer: IntersectionObserver): void {
@@ -109,15 +117,16 @@ export class ViewportTracker {
entries.forEach(entry => {
if (entry.isIntersecting) {
+ const sizeBefore = this._visibleElements.size
this._visibleElements.add(entry.target)
- visibleElementsAdded++
+ if (sizeBefore < this._visibleElements.size) visibleElementsAdded++
} else {
this._visibleElements.delete(entry.target)
}
})
if (visibleElementsAdded || !this.initialized) {
- console.log(`Visible elements changed: ${visibleElementsAdded} added, ${this._visibleElements.size} visible elements in total`)
+ console.debug(`Visible elements changed: ${visibleElementsAdded} added, ${this._visibleElements.size} visible elements in total`)
// the first time the callback is called, we want to make sure that the annotations are
// loaded at least once
this.initialized = true
@@ -143,7 +152,7 @@ export class ViewportTracker {
})
const endTime = new Date().getTime()
- console.log(`Visible: ${begin}-${end} (${this._visibleElements.size} visible elements, ${Math.abs(endTime - startTime)}ms)`)
+ console.debug(`Visible: ${begin}-${end} (${this._visibleElements.size} visible elements, ${Math.abs(endTime - startTime)}ms)`)
return [begin, end]
}
}
diff --git a/inception/inception-js-api/src/main/ts_template/package-lock.json b/inception/inception-js-api/src/main/ts_template/package-lock.json
index 0758b7709d6..ee532f4ca23 100644
--- a/inception/inception-js-api/src/main/ts_template/package-lock.json
+++ b/inception/inception-js-api/src/main/ts_template/package-lock.json
@@ -20,7 +20,7 @@
"chai": "^4.3.6",
"esbuild": "~0.16.17",
"esbuild-runner-plugins": "^2.3.0-plugins.0",
- "esbuild-sass-plugin": "^2.5.0",
+ "esbuild-sass-plugin": "~2.5.0",
"eslint": "^8.31.0",
"eslint-config-standard": "^17.0.0",
"eslint-plugin-chai-friendly": "^0.7.2",
@@ -388,15 +388,39 @@
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}
},
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+ "resolved": "https://registry.npmjs.org/@eslint-community/eslint-utils/-/eslint-utils-4.4.0.tgz",
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+ "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.5.1.tgz",
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+ "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-2.0.3.tgz",
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"debug": "^4.3.2",
- "espree": "^9.4.0",
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"ignore": "^5.2.0",
"import-fresh": "^3.2.1",
@@ -411,6 +435,15 @@
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}
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+ "resolved": "https://registry.npmjs.org/@eslint/js/-/js-8.41.0.tgz",
+ "integrity": "sha512-LxcyMGxwmTh2lY9FwHPGWOHmYFCZvbrFCBZL4FzSSsxsRPuhrYUg/49/0KDfW8tnIEaEHtfmn6+NPN+1DqaNmA==",
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+ }
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"resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.11.8.tgz",
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+ "resolved": "https://registry.npmjs.org/@types/chai/-/chai-4.3.5.tgz",
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+ "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.12.tgz",
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"dev": true
},
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@@ -509,14 +542,14 @@
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+ "version": "20.2.5",
+ "resolved": "https://registry.npmjs.org/@types/node/-/node-20.2.5.tgz",
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},
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- "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.3.13.tgz",
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+ "version": "7.5.0",
+ "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.5.0.tgz",
+ "integrity": "sha512-G8hZ6XJiHnuhQKR7ZmysCeJWE08o8T0AXtk5darsCaTVsYZhhgUrq53jizaR2FvsoeCwJhlmwTjkXBY5Pn/ZHw==",
"dev": true
},
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@@ -528,19 +561,19 @@
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- "resolved": "https://registry.npmjs.org/@typescript-eslint/eslint-plugin/-/eslint-plugin-5.53.0.tgz",
- "integrity": "sha512-alFpFWNucPLdUOySmXCJpzr6HKC3bu7XooShWM+3w/EL6J2HIoB2PFxpLnq4JauWVk6DiVeNKzQlFEaE+X9sGw==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/eslint-plugin/-/eslint-plugin-5.59.8.tgz",
+ "integrity": "sha512-JDMOmhXteJ4WVKOiHXGCoB96ADWg9q7efPWHRViT/f09bA8XOMLAVHHju3l0MkZnG1izaWXYmgvQcUjTRcpShQ==",
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- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/type-utils": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/type-utils": "5.59.8",
+ "@typescript-eslint/utils": "5.59.8",
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"grapheme-splitter": "^1.0.4",
"ignore": "^5.2.0",
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- "regexpp": "^3.2.0",
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},
@@ -562,14 +595,14 @@
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- "integrity": "sha512-MKBw9i0DLYlmdOb3Oq/526+al20AJZpANdT6Ct9ffxcV8nKCHz63t/S0IhlTFNsBIHJv+GY5SFJ0XfqVeydQrQ==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-5.59.8.tgz",
+ "integrity": "sha512-AnR19RjJcpjoeGojmwZtCwBX/RidqDZtzcbG3xHrmz0aHHoOcbWnpDllenRDmDvsV0RQ6+tbb09/kyc+UT9Orw==",
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- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
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@@ -589,13 +622,13 @@
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+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-5.59.8.tgz",
+ "integrity": "sha512-/w08ndCYI8gxGf+9zKf1vtx/16y8MHrZs5/tnjHhMLNSixuNcJavSX4wAiPf4aS5x41Es9YPCn44MIe4cxIlig==",
"dev": true,
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0"
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8"
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@@ -606,13 +639,13 @@
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+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/type-utils/-/type-utils-5.59.8.tgz",
+ "integrity": "sha512-+5M518uEIHFBy3FnyqZUF3BMP+AXnYn4oyH8RF012+e7/msMY98FhGL5SrN29NQ9xDgvqCgYnsOiKp1VjZ/fpA==",
"dev": true,
"dependencies": {
- "@typescript-eslint/typescript-estree": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@typescript-eslint/typescript-estree": "5.59.8",
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"tsutils": "^3.21.0"
},
@@ -633,9 +666,9 @@
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+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-5.59.8.tgz",
+ "integrity": "sha512-+uWuOhBTj/L6awoWIg0BlWy0u9TyFpCHrAuQ5bNfxDaZ1Ppb3mx6tUigc74LHcbHpOHuOTOJrBoAnhdHdaea1w==",
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@@ -646,13 +679,13 @@
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- "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-5.53.0.tgz",
- "integrity": "sha512-eKmipH7QyScpHSkhbptBBYh9v8FxtngLquq292YTEQ1pxVs39yFBlLC1xeIZcPPz1RWGqb7YgERJRGkjw8ZV7w==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-5.59.8.tgz",
+ "integrity": "sha512-Jy/lPSDJGNow14vYu6IrW790p7HIf/SOV1Bb6lZ7NUkLc2iB2Z9elESmsaUtLw8kVqogSbtLH9tut5GCX1RLDg==",
"dev": true,
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8",
"debug": "^4.3.4",
"globby": "^11.1.0",
"is-glob": "^4.0.3",
@@ -673,18 +706,18 @@
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- "integrity": "sha512-VUOOtPv27UNWLxFwQK/8+7kvxVC+hPHNsJjzlJyotlaHjLSIgOCKj9I0DBUjwOOA64qjBwx5afAPjksqOxMO0g==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-5.59.8.tgz",
+ "integrity": "sha512-Tr65630KysnNn9f9G7ROF3w1b5/7f6QVCJ+WK9nhIocWmx9F+TmCAcglF26Vm7z8KCTwoKcNEBZrhlklla3CKg==",
"dev": true,
"dependencies": {
+ "@eslint-community/eslint-utils": "^4.2.0",
"@types/json-schema": "^7.0.9",
"@types/semver": "^7.3.12",
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/typescript-estree": "5.59.8",
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- "eslint-utils": "^3.0.0",
"semver": "^7.3.7"
},
"engines": {
@@ -699,12 +732,12 @@
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- "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.53.0.tgz",
- "integrity": "sha512-JqNLnX3leaHFZEN0gCh81sIvgrp/2GOACZNgO4+Tkf64u51kTpAyWFOY8XHx8XuXr3N2C9zgPPHtcpMg6z1g0w==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.59.8.tgz",
+ "integrity": "sha512-pJhi2ms0x0xgloT7xYabil3SGGlojNNKjK/q6dB3Ey0uJLMjK2UDGJvHieiyJVW/7C3KI+Z4Q3pEHkm4ejA+xQ==",
"dev": true,
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
"eslint-visitor-keys": "^3.3.0"
},
"engines": {
@@ -804,6 +837,19 @@
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"dev": true
},
+ "node_modules/array-buffer-byte-length": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/array-buffer-byte-length/-/array-buffer-byte-length-1.0.0.tgz",
+ "integrity": "sha512-LPuwb2P+NrQw3XhxGc36+XSvuBPopovXYTR9Ew++Du9Yb/bx5AzBfrIsBoj0EZUifjQU+sHL21sseZ3jerWO/A==",
+ "dev": true,
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "is-array-buffer": "^3.0.1"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"node_modules/array-includes": {
"version": "3.1.6",
"resolved": "https://registry.npmjs.org/array-includes/-/array-includes-3.1.6.tgz",
@@ -1245,18 +1291,18 @@
"dev": true
},
"node_modules/es-abstract": {
- "version": "1.21.1",
- "resolved": "https://registry.npmjs.org/es-abstract/-/es-abstract-1.21.1.tgz",
- "integrity": "sha512-QudMsPOz86xYz/1dG1OuGBKOELjCh99IIWHLzy5znUB6j8xG2yMA7bfTV86VSqKF+Y/H08vQPR+9jyXpuC6hfg==",
+ "version": "1.21.2",
+ "resolved": "https://registry.npmjs.org/es-abstract/-/es-abstract-1.21.2.tgz",
+ "integrity": "sha512-y/B5POM2iBnIxCiernH1G7rC9qQoM77lLIMQLuob0zhp8C56Po81+2Nj0WFKnd0pNReDTnkYryc+zhOzpEIROg==",
"dev": true,
"dependencies": {
+ "array-buffer-byte-length": "^1.0.0",
"available-typed-arrays": "^1.0.5",
"call-bind": "^1.0.2",
"es-set-tostringtag": "^2.0.1",
"es-to-primitive": "^1.2.1",
- "function-bind": "^1.1.1",
"function.prototype.name": "^1.1.5",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"get-symbol-description": "^1.0.0",
"globalthis": "^1.0.3",
"gopd": "^1.0.1",
@@ -1264,8 +1310,8 @@
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"has-proto": "^1.0.1",
"has-symbols": "^1.0.3",
- "internal-slot": "^1.0.4",
- "is-array-buffer": "^3.0.1",
+ "internal-slot": "^1.0.5",
+ "is-array-buffer": "^3.0.2",
"is-callable": "^1.2.7",
"is-negative-zero": "^2.0.2",
"is-regex": "^1.1.4",
@@ -1273,11 +1319,12 @@
"is-string": "^1.0.7",
"is-typed-array": "^1.1.10",
"is-weakref": "^1.0.2",
- "object-inspect": "^1.12.2",
+ "object-inspect": "^1.12.3",
"object-keys": "^1.1.1",
"object.assign": "^4.1.4",
"regexp.prototype.flags": "^1.4.3",
"safe-regex-test": "^1.0.0",
+ "string.prototype.trim": "^1.2.7",
"string.prototype.trimend": "^1.0.6",
"string.prototype.trimstart": "^1.0.6",
"typed-array-length": "^1.0.4",
@@ -1421,12 +1468,15 @@
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- "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.34.0.tgz",
- "integrity": "sha512-1Z8iFsucw+7kSqXNZVslXS8Ioa4u2KM7GPwuKtkTFAqZ/cHMcEaR+1+Br0wLlot49cNxIiZk5wp8EAbPcYZxTg==",
+ "version": "8.41.0",
+ "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.41.0.tgz",
+ "integrity": "sha512-WQDQpzGBOP5IrXPo4Hc0814r4/v2rrIsB0rhT7jtunIalgg6gYXWhRMOejVO8yH21T/FGaxjmFjBMNqcIlmH1Q==",
"dev": true,
"dependencies": {
- "@eslint/eslintrc": "^1.4.1",
+ "@eslint-community/eslint-utils": "^4.2.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@eslint/eslintrc": "^2.0.3",
+ "@eslint/js": "8.41.0",
"@humanwhocodes/config-array": "^0.11.8",
"@humanwhocodes/module-importer": "^1.0.1",
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@@ -1436,24 +1486,22 @@
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- "eslint-utils": "^3.0.0",
- "eslint-visitor-keys": "^3.3.0",
- "espree": "^9.4.0",
- "esquery": "^1.4.0",
+ "eslint-scope": "^7.2.0",
+ "eslint-visitor-keys": "^3.4.1",
+ "espree": "^9.5.2",
+ "esquery": "^1.4.2",
"esutils": "^2.0.2",
"fast-deep-equal": "^3.1.3",
"file-entry-cache": "^6.0.1",
"find-up": "^5.0.0",
"glob-parent": "^6.0.2",
"globals": "^13.19.0",
- "grapheme-splitter": "^1.0.4",
+ "graphemer": "^1.4.0",
"ignore": "^5.2.0",
"import-fresh": "^3.0.0",
"imurmurhash": "^0.1.4",
"is-glob": "^4.0.0",
"is-path-inside": "^3.0.3",
- "js-sdsl": "^4.1.4",
"js-yaml": "^4.1.0",
"json-stable-stringify-without-jsonify": "^1.0.1",
"levn": "^0.4.1",
@@ -1461,7 +1509,6 @@
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"natural-compare": "^1.4.0",
"optionator": "^0.9.1",
- "regexpp": "^3.2.0",
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"strip-json-comments": "^3.1.0",
"text-table": "^0.2.0"
@@ -1477,9 +1524,9 @@
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{
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}
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"eslint-plugin-import": "^2.25.2",
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+ "resolved": "https://registry.npmjs.org/eslint-module-utils/-/eslint-module-utils-2.8.0.tgz",
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@@ -1679,9 +1729,9 @@
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+ "version": "15.7.0",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.7.0.tgz",
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@@ -1756,18 +1806,21 @@
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+ "version": "3.4.1",
+ "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-3.4.1.tgz",
+ "integrity": "sha512-pZnmmLwYzf+kWaM/Qgrvpen51upAktaaiI01nsJD/Yr3lMOdNtq0cxkrrg16w64VtisN6okbs7Q8AfGqj4c9fA==",
"dev": true,
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
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- "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.1.1.tgz",
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+ "version": "7.2.0",
+ "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.2.0.tgz",
+ "integrity": "sha512-DYj5deGlHBfMt15J7rdtyKNq/Nqlv5KfU4iodrQ019XESsRnwXH9KAE0y3cwtUHDo2ob7CypAnCqefh6vioWRw==",
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@@ -1775,6 +1828,9 @@
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"node_modules/eslint/node_modules/estraverse": {
@@ -1787,14 +1843,14 @@
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+ "version": "9.5.2",
+ "resolved": "https://registry.npmjs.org/espree/-/espree-9.5.2.tgz",
+ "integrity": "sha512-7OASN1Wma5fum5SrNhFMAMJxOUAbhyfQ8dQ//PJaJbNw0URTPWqIghHWt1MmAANKhHZIYOHruW4Kw4ruUWOdGw==",
"dev": true,
"dependencies": {
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"acorn-jsx": "^5.3.2",
- "eslint-visitor-keys": "^3.3.0"
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@@ -1804,9 +1860,9 @@
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+ "resolved": "https://registry.npmjs.org/esquery/-/esquery-1.5.0.tgz",
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@@ -2081,13 +2137,14 @@
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+ "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.2.1.tgz",
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"dev": true,
"dependencies": {
"function-bind": "^1.1.1",
"has": "^1.0.3",
+ "has-proto": "^1.0.1",
"has-symbols": "^1.0.3"
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+ "version": "4.2.11",
+ "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.11.tgz",
+ "integrity": "sha512-RbJ5/jmFcNNCcDV5o9eTnBLJ/HszWV0P73bc+Ff4nS/rJj+YaS6IGyiOL0VoBYX+l1Wrl3k63h/KrH+nhJ0XvQ==",
"dev": true
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"dev": true
},
+ "node_modules/graphemer": {
+ "version": "1.4.0",
+ "resolved": "https://registry.npmjs.org/graphemer/-/graphemer-1.4.0.tgz",
+ "integrity": "sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==",
+ "dev": true
+ },
"node_modules/has": {
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"resolved": "https://registry.npmjs.org/has/-/has-1.0.3.tgz",
@@ -2316,9 +2379,9 @@
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- "resolved": "https://registry.npmjs.org/immutable/-/immutable-4.2.4.tgz",
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+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/immutable/-/immutable-4.3.0.tgz",
+ "integrity": "sha512-0AOCmOip+xgJwEVTQj1EfiDDOkPmuyllDuTuEX+DDXUgapLAsBIfkg3sxCYyCEA8mQqZrrxPUGjcOQ2JS3WLkg==",
"dev": true,
"peer": true
},
@@ -2378,13 +2441,13 @@
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- "resolved": "https://registry.npmjs.org/is-array-buffer/-/is-array-buffer-3.0.1.tgz",
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+ "version": "3.0.2",
+ "resolved": "https://registry.npmjs.org/is-array-buffer/-/is-array-buffer-3.0.2.tgz",
+ "integrity": "sha512-y+FyyR/w8vfIRq4eQcM1EYgSTnmHXPqaF+IgzgraytCFq5Xh8lllDVmAZolPJiZttZLeFSINPYMaEJ7/vWUa1w==",
"dev": true,
"dependencies": {
"call-bind": "^1.0.2",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"is-typed-array": "^1.1.10"
},
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@@ -2450,9 +2513,9 @@
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- "resolved": "https://registry.npmjs.org/is-core-module/-/is-core-module-2.11.0.tgz",
- "integrity": "sha512-RRjxlvLDkD1YJwDbroBHMb+cukurkDWNyHx7D3oNB5x9rb5ogcksMC5wHCadcXoo67gVr/+3GFySh3134zi6rw==",
+ "version": "2.12.1",
+ "resolved": "https://registry.npmjs.org/is-core-module/-/is-core-module-2.12.1.tgz",
+ "integrity": "sha512-Q4ZuBAe2FUsKtyQJoQHlvP8OvBERxO3jEmy1I7hcRXcJBGGHFh/aJBswbXuS9sgrDH2QUO8ilkwNPHvHMd8clg==",
"dev": true,
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@@ -2679,16 +2742,6 @@
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"dev": true
},
- "node_modules/js-sdsl": {
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- "resolved": "https://registry.npmjs.org/js-sdsl/-/js-sdsl-4.3.0.tgz",
- "integrity": "sha512-mifzlm2+5nZ+lEcLJMoBK0/IH/bDg8XnJfd/Wq6IP+xoCjLZsTOnV2QpxlVbX9bMnkl5PdEjNtBJ9Cj1NjifhQ==",
- "dev": true,
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/js-sdsl"
- }
- },
"node_modules/js-yaml": {
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"resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz",
@@ -3293,9 +3346,9 @@
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- "resolved": "https://registry.npmjs.org/rambda/-/rambda-7.4.0.tgz",
- "integrity": "sha512-A9hihu7dUTLOUCM+I8E61V4kRXnN4DwYeK0DwCBydC1MqNI1PidyAtbtpsJlBBzK4icSctEcCQ1bGcLpBuETUQ==",
+ "version": "7.5.0",
+ "resolved": "https://registry.npmjs.org/rambda/-/rambda-7.5.0.tgz",
+ "integrity": "sha512-y/M9weqWAH4iopRd7EHDEQQvpFPHj1AA3oHozE9tfITHUtTR7Z9PSlIRRG2l1GuW7sefC1cXFfIcF+cgnShdBA==",
"dev": true
},
"node_modules/randombytes": {
@@ -3320,14 +3373,14 @@
}
},
"node_modules/regexp.prototype.flags": {
- "version": "1.4.3",
- "resolved": "https://registry.npmjs.org/regexp.prototype.flags/-/regexp.prototype.flags-1.4.3.tgz",
- "integrity": "sha512-fjggEOO3slI6Wvgjwflkc4NFRCTZAu5CnNfBd5qOMYhWdn67nJBBu34/TkD++eeFmd8C9r9jfXJ27+nSiRkSUA==",
+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/regexp.prototype.flags/-/regexp.prototype.flags-1.5.0.tgz",
+ "integrity": "sha512-0SutC3pNudRKgquxGoRGIz946MZVHqbNfPjBdxeOhBrdgDKlRoXmYLQN9xRbrR09ZXWeGAdPuif7egofn6v5LA==",
"dev": true,
"dependencies": {
"call-bind": "^1.0.2",
- "define-properties": "^1.1.3",
- "functions-have-names": "^1.2.2"
+ "define-properties": "^1.2.0",
+ "functions-have-names": "^1.2.3"
},
"engines": {
"node": ">= 0.4"
@@ -3358,12 +3411,12 @@
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"node_modules/resolve": {
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- "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.1.tgz",
- "integrity": "sha512-nBpuuYuY5jFsli/JIs1oldw6fOQCBioohqWZg/2hiaOybXOft4lonv85uDOKXdf8rhyK159cxU5cDcK/NKk8zw==",
+ "version": "1.22.2",
+ "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.2.tgz",
+ "integrity": "sha512-Sb+mjNHOULsBv818T40qSPeRiuWLyaGMa5ewydRLFimneixmVy2zdivRl+AF6jaYPC8ERxGDmFSiqui6SfPd+g==",
"dev": true,
"dependencies": {
- "is-core-module": "^2.9.0",
+ "is-core-module": "^2.11.0",
"path-parse": "^1.0.7",
"supports-preserve-symlinks-flag": "^1.0.0"
},
@@ -3466,9 +3519,9 @@
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"node_modules/sass": {
- "version": "1.58.3",
- "resolved": "https://registry.npmjs.org/sass/-/sass-1.58.3.tgz",
- "integrity": "sha512-Q7RaEtYf6BflYrQ+buPudKR26/lH+10EmO9bBqbmPh/KeLqv8bjpTNqxe71ocONqXq+jYiCbpPUmQMS+JJPk4A==",
+ "version": "1.62.1",
+ "resolved": "https://registry.npmjs.org/sass/-/sass-1.62.1.tgz",
+ "integrity": "sha512-NHpxIzN29MXvWiuswfc1W3I0N8SXBd8UR26WntmDlRYf0bSADnwnOjsyMZ3lMezSlArD33Vs3YFhp7dWvL770A==",
"dev": true,
"peer": true,
"dependencies": {
@@ -3480,13 +3533,13 @@
"sass": "sass.js"
},
"engines": {
- "node": ">=12.0.0"
+ "node": ">=14.0.0"
}
},
"node_modules/semver": {
- "version": "7.3.8",
- "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz",
- "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==",
+ "version": "7.5.1",
+ "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.1.tgz",
+ "integrity": "sha512-Wvss5ivl8TMRZXXESstBA4uR5iXgEN/VC5/sOcuXdVLzcdkz4HWetIoRfG5gb5X+ij/G9rw9YoGn3QoQ8OCSpw==",
"dev": true,
"dependencies": {
"lru-cache": "^6.0.0"
@@ -3594,6 +3647,23 @@
"node": ">=8"
}
},
+ "node_modules/string.prototype.trim": {
+ "version": "1.2.7",
+ "resolved": "https://registry.npmjs.org/string.prototype.trim/-/string.prototype.trim-1.2.7.tgz",
+ "integrity": "sha512-p6TmeT1T3411M8Cgg9wBTMRtY2q9+PNy9EV1i2lIXUN/btt763oIfxwN3RR8VU6wHX8j/1CFy0L+YuThm6bgOg==",
+ "dev": true,
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "define-properties": "^1.1.4",
+ "es-abstract": "^1.20.4"
+ },
+ "engines": {
+ "node": ">= 0.4"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"node_modules/string.prototype.trimend": {
"version": "1.0.6",
"resolved": "https://registry.npmjs.org/string.prototype.trimend/-/string.prototype.trimend-1.0.6.tgz",
@@ -3787,13 +3857,13 @@
}
},
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- "version": "3.14.1",
- "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-3.14.1.tgz",
- "integrity": "sha512-fxDhWnFSLt3VuTwtvJt5fpwxBHg5AdKWMsgcPOOIilyjymcYVZoCQF8fvFRezCNfblEXmi+PcM1eYHeOAgXCOQ==",
+ "version": "3.14.2",
+ "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-3.14.2.tgz",
+ "integrity": "sha512-o/9iXgCYc5L/JxCHPe3Hvh8Q/2xm5Z+p18PESBU6Ff33695QnCHBEjcytY2q19ua7Mbl/DavtBOLq+oG0RCL+g==",
"dev": true,
"dependencies": {
"@types/json5": "^0.0.29",
- "json5": "^1.0.1",
+ "json5": "^1.0.2",
"minimist": "^1.2.6",
"strip-bom": "^3.0.0"
}
@@ -4039,9 +4109,9 @@
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},
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- "version": "17.7.1",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.1.tgz",
- "integrity": "sha512-cwiTb08Xuv5fqF4AovYacTFNxk62th7LKJ6BL9IGUpTJrWoU7/7WdQGTP2SjKf1dUNBGzDd28p/Yfs/GI6JrLw==",
+ "version": "17.7.2",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz",
+ "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==",
"dev": true,
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diff --git a/inception/inception-js-api/src/main/ts_template/package.json b/inception/inception-js-api/src/main/ts_template/package.json
index 2ad4dea8f98..61be672bf58 100644
--- a/inception/inception-js-api/src/main/ts_template/package.json
+++ b/inception/inception-js-api/src/main/ts_template/package.json
@@ -10,7 +10,7 @@
},
"scripts": {
"build": "node build.mjs",
- "test": "mocha -r esbuild-runner-plugins/register './test/**/*.test.ts' --extension ts --reporter mocha-junit-reporter --reporter-options mochaFile='../../../target/surefire-reports/mocha-test-report.xml'",
+ "test": "mocha -r esbuild-runner-plugins/register \"./test/**/*.test.ts\" --extension ts --reporter mocha-junit-reporter --reporter-options mochaFile=\"../../../target/surefire-reports/mocha-test-report.xml\"",
"test-dev": "ts-mocha test/**/*.ts"
},
"dependencies": {
diff --git a/inception/inception-kb-fact-linking/pom.xml b/inception/inception-kb-fact-linking/pom.xml
index 4c4931b7eb9..4414087a873 100644
--- a/inception/inception-kb-fact-linking/pom.xml
+++ b/inception/inception-kb-fact-linking/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-kb-fact-linkingINCEpTION - Knowledge Base - Fact Linking
@@ -119,6 +119,10 @@
com.googlecode.wicket-jquery-uiwicket-kendo-ui
+
+ org.danekja
+ jdk-serializable-functional
+ org.slf4j
diff --git a/inception/inception-kb/pom.xml b/inception/inception-kb/pom.xml
index 1e75fce1ba4..b1187844165 100644
--- a/inception/inception-kb/pom.xml
+++ b/inception/inception-kb/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-kbINCEpTION - Knowledge Base - Core
diff --git a/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/KnowledgeBaseServiceRemoteTest.java b/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/KnowledgeBaseServiceRemoteTest.java
index 0cfb52bd181..2bd597ec8a2 100644
--- a/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/KnowledgeBaseServiceRemoteTest.java
+++ b/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/KnowledgeBaseServiceRemoteTest.java
@@ -321,26 +321,27 @@ public static List data() throws Exception
"http://dbpedia.org/ontology/Organisation", rootConcepts, parentChildConcepts));
}
- {
- KnowledgeBaseProfile profile = PROFILES.get("yago");
- KnowledgeBase kb_yago = new KnowledgeBase();
- kb_yago.setName(profile.getName());
- kb_yago.setType(profile.getType());
- kb_yago.setReification(profile.getReification());
- kb_yago.setFullTextSearchIri(profile.getAccess().getFullTextSearchIri());
- kb_yago.applyMapping(profile.getMapping());
- kb_yago.applyRootConcepts(profile);
- kb_yago.setDefaultLanguage(profile.getDefaultLanguage());
- kb_yago.setMaxResults(maxResults);
- rootConcepts = new HashSet();
- rootConcepts.add("http://schema.org/Thing");
- parentChildConcepts = new HashMap();
- parentChildConcepts.put("http://schema.org/Thing",
- "http://yago-knowledge.org/resource/wikicat_Alleged_UFO-related_entities");
- kbList.add(new TestConfiguration(profile.getAccess().getAccessUrl(), kb_yago,
- "http://yago-knowledge.org/resource/Elvis_Presley", rootConcepts,
- parentChildConcepts));
- }
+ // YAGO seems to have problem atm 29-04-2023
+ // {
+ // KnowledgeBaseProfile profile = PROFILES.get("yago");
+ // KnowledgeBase kb_yago = new KnowledgeBase();
+ // kb_yago.setName(profile.getName());
+ // kb_yago.setType(profile.getType());
+ // kb_yago.setReification(profile.getReification());
+ // kb_yago.setFullTextSearchIri(profile.getAccess().getFullTextSearchIri());
+ // kb_yago.applyMapping(profile.getMapping());
+ // kb_yago.applyRootConcepts(profile);
+ // kb_yago.setDefaultLanguage(profile.getDefaultLanguage());
+ // kb_yago.setMaxResults(maxResults);
+ // rootConcepts = new HashSet();
+ // rootConcepts.add("http://schema.org/Thing");
+ // parentChildConcepts = new HashMap();
+ // parentChildConcepts.put("http://schema.org/Thing",
+ // "http://yago-knowledge.org/resource/wikicat_Alleged_UFO-related_entities");
+ // kbList.add(new TestConfiguration(profile.getAccess().getAccessUrl(), kb_yago,
+ // "http://yago-knowledge.org/resource/Elvis_Presley", rootConcepts,
+ // parentChildConcepts));
+ // }
{
KnowledgeBaseProfile profile = PROFILES.get("zbw-stw-economics");
diff --git a/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderGenericTest.java b/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderGenericTest.java
index 0f183a2a100..42664f3a96d 100644
--- a/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderGenericTest.java
+++ b/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderGenericTest.java
@@ -50,7 +50,8 @@
@Tag("slow")
public class SPARQLQueryBuilderGenericTest
{
- private static final List SKIPPED_PROFILES = asList("babel_net");
+ // YAGO seems to have problem atm 29-04-2023
+ private static final List SKIPPED_PROFILES = asList("babel_net", "yago");
public static List data() throws Exception
{
diff --git a/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderTest.java b/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderTest.java
index 6ae41390ef0..bf11e01a981 100644
--- a/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderTest.java
+++ b/inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/querybuilder/SPARQLQueryBuilderTest.java
@@ -60,6 +60,7 @@
import org.eclipse.rdf4j.rio.Rio;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Tag;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInfo;
@@ -1684,6 +1685,7 @@ public void thatChildrenOfExplicitRootCanBeRetrieved_DBPedia()
"http://www.w3.org/2002/07/owl#Thing", 0);
}
+ @Disabled("YAGO seems to have problem atm 29-04-2023")
@Tag("slow")
@Test
public void thatChildrenOfExplicitRootCanBeRetrieved_YAGO()
diff --git a/inception/inception-layer-docmetadata/pom.xml b/inception/inception-layer-docmetadata/pom.xml
index 6a144227064..c8ea8adc090 100644
--- a/inception/inception-layer-docmetadata/pom.xml
+++ b/inception/inception-layer-docmetadata/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-layer-docmetadataINCEpTION - Document Metadata Support
@@ -126,5 +126,9 @@
org.wicketstuffwicketstuff-annotationeventdispatcher
+
+ org.danekja
+ jdk-serializable-functional
+
\ No newline at end of file
diff --git a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/event/DocumentMetadataEvent.java b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/event/DocumentMetadataEvent.java
index a74db0895a5..47ba502b511 100644
--- a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/event/DocumentMetadataEvent.java
+++ b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/event/DocumentMetadataEvent.java
@@ -60,7 +60,7 @@ public String toString()
builder.append("docID=");
builder.append(getDocument().getId());
builder.append(", user=");
- builder.append(getUser());
+ builder.append(getDocumentOwner());
}
builder.append("]");
return builder.toString();
diff --git a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerAdapter.java b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerAdapter.java
index 3ee8327d568..ef86472bc2f 100644
--- a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerAdapter.java
+++ b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerAdapter.java
@@ -106,7 +106,7 @@ public AnnotationBaseFS add(SourceDocument aDocument, String aUsername, CAS aCas
AnnotationBaseFS newAnnotation = aCas.createFS(type);
aCas.addFsToIndexes(newAnnotation);
- publishEvent(new DocumentMetadataCreatedEvent(this, aDocument, aUsername, getLayer(),
+ publishEvent(() -> new DocumentMetadataCreatedEvent(this, aDocument, aUsername, getLayer(),
newAnnotation));
return newAnnotation;
@@ -118,7 +118,8 @@ public void delete(SourceDocument aDocument, String aUsername, CAS aCas, VID aVi
AnnotationBaseFS fs = (AnnotationBaseFS) ICasUtil.selectFsByAddr(aCas, aVid.getId());
aCas.removeFsFromIndexes(fs);
- publishEvent(new DocumentMetadataDeletedEvent(this, aDocument, aUsername, getLayer(), fs));
+ publishEvent(
+ () -> new DocumentMetadataDeletedEvent(this, aDocument, aUsername, getLayer(), fs));
}
public AnnotationBaseFS restore(SourceDocument aDocument, String aUsername, CAS aCas, VID aVid)
@@ -127,7 +128,8 @@ public AnnotationBaseFS restore(SourceDocument aDocument, String aUsername, CAS
aCas.addFsToIndexes(fs);
- publishEvent(new DocumentMetadataCreatedEvent(this, aDocument, aUsername, getLayer(), fs));
+ publishEvent(
+ () -> new DocumentMetadataCreatedEvent(this, aDocument, aUsername, getLayer(), fs));
return fs;
}
diff --git a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerSingletonCreatingWatcher.java b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerSingletonCreatingWatcher.java
index 8949cf6a40e..5acf06ab5ac 100644
--- a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerSingletonCreatingWatcher.java
+++ b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/layer/DocumentMetadataLayerSingletonCreatingWatcher.java
@@ -80,7 +80,7 @@ public void onBeforeDocumentOpenedEvent(BeforeDocumentOpenedEvent aEvent)
DocumentMetadataLayerAdapter adapter = (DocumentMetadataLayerAdapter) annotationService
.getAdapter(layer);
if (cas.select(adapter.getAnnotationType(cas)).isEmpty()) {
- adapter.add(aEvent.getDocument(), aEvent.getUser(), cas);
+ adapter.add(aEvent.getDocument(), aEvent.getSessionOwner(), cas);
}
}
}
diff --git a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/log/DocumentMetadataEventAdapter.java b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/log/DocumentMetadataEventAdapter.java
index 1af91bf4545..bc84ca0591d 100644
--- a/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/log/DocumentMetadataEventAdapter.java
+++ b/inception/inception-layer-docmetadata/src/main/java/de/tudarmstadt/ukp/inception/ui/core/docanno/log/DocumentMetadataEventAdapter.java
@@ -51,7 +51,7 @@ public long getProject(DocumentMetadataEvent aEvent)
@Override
public String getAnnotator(DocumentMetadataEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getDocumentOwner();
}
@Override
diff --git a/inception/inception-log/pom.xml b/inception/inception-log/pom.xml
index 03bf555dc26..a9f6fd91f33 100644
--- a/inception/inception-log/pom.xml
+++ b/inception/inception-log/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-logINCEpTION - Log
diff --git a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/BulkAnnotationEventAdapter.java b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/BulkAnnotationEventAdapter.java
index fad538a6710..b736a8da4f5 100644
--- a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/BulkAnnotationEventAdapter.java
+++ b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/BulkAnnotationEventAdapter.java
@@ -48,6 +48,6 @@ public long getProject(BulkAnnotationEvent aEvent)
@Override
public String getAnnotator(BulkAnnotationEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getDocumentOwner();
}
}
diff --git a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainLinkEventAdapter.java b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainLinkEventAdapter.java
index 19e29a115bb..2cbacd67356 100644
--- a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainLinkEventAdapter.java
+++ b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainLinkEventAdapter.java
@@ -51,7 +51,7 @@ public long getProject(ChainLinkEvent aEvent)
@Override
public String getAnnotator(ChainLinkEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getDocumentOwner();
}
@Override
diff --git a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainSpanEventAdapter.java b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainSpanEventAdapter.java
index a15a556632a..bd413794fcb 100644
--- a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainSpanEventAdapter.java
+++ b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/ChainSpanEventAdapter.java
@@ -50,7 +50,7 @@ public long getProject(ChainSpanEvent aEvent)
@Override
public String getAnnotator(ChainSpanEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getDocumentOwner();
}
@Override
diff --git a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/DocumentOpenedEventAdapter.java b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/DocumentOpenedEventAdapter.java
index f950a07b802..5abd0ff940a 100644
--- a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/DocumentOpenedEventAdapter.java
+++ b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/DocumentOpenedEventAdapter.java
@@ -47,12 +47,12 @@ public long getProject(DocumentOpenedEvent aEvent)
@Override
public String getUser(DocumentOpenedEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getSessionOwner();
}
@Override
public String getAnnotator(DocumentOpenedEvent aEvent)
{
- return aEvent.getAnnotator();
+ return aEvent.getDocumentOwner();
}
}
diff --git a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/FeatureValueUpdatedEventAdapter.java b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/FeatureValueUpdatedEventAdapter.java
index b13de3dd8b0..55b476d3234 100644
--- a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/FeatureValueUpdatedEventAdapter.java
+++ b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/FeatureValueUpdatedEventAdapter.java
@@ -50,7 +50,7 @@ public long getProject(FeatureValueUpdatedEvent aEvent)
@Override
public String getAnnotator(FeatureValueUpdatedEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getDocumentOwner();
}
@Override
diff --git a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/RelationEventAdapter.java b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/RelationEventAdapter.java
index e4a9d49ffae..cac396a12b7 100644
--- a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/RelationEventAdapter.java
+++ b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/RelationEventAdapter.java
@@ -54,7 +54,7 @@ public long getDocument(RelationEvent aEvent)
@Override
public String getAnnotator(RelationEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getDocumentOwner();
}
@Override
diff --git a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/SpanEventAdapter.java b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/SpanEventAdapter.java
index f26fe376952..5d5267304aa 100644
--- a/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/SpanEventAdapter.java
+++ b/inception/inception-log/src/main/java/de/tudarmstadt/ukp/inception/log/adapter/SpanEventAdapter.java
@@ -50,7 +50,7 @@ public long getProject(SpanEvent aEvent)
@Override
public String getAnnotator(SpanEvent aEvent)
{
- return aEvent.getUser();
+ return aEvent.getDocumentOwner();
}
@Override
diff --git a/inception/inception-model-export/pom.xml b/inception/inception-model-export/pom.xml
index c1945dec717..7e2a67a021f 100644
--- a/inception/inception-model-export/pom.xml
+++ b/inception/inception-model-export/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-model-exportINCEpTION - Core - Export Model
diff --git a/inception/inception-model-export/src/main/java/de/tudarmstadt/ukp/clarin/webanno/export/model/ExportedAnnotationFeature.java b/inception/inception-model-export/src/main/java/de/tudarmstadt/ukp/clarin/webanno/export/model/ExportedAnnotationFeature.java
index 78a08127cb5..c36c6d66eb9 100644
--- a/inception/inception-model-export/src/main/java/de/tudarmstadt/ukp/clarin/webanno/export/model/ExportedAnnotationFeature.java
+++ b/inception/inception-model-export/src/main/java/de/tudarmstadt/ukp/clarin/webanno/export/model/ExportedAnnotationFeature.java
@@ -87,6 +87,9 @@ public class ExportedAnnotationFeature
@JsonProperty("curatable")
private boolean curatable = true;
+ @JsonProperty("rank")
+ private int rank = 0;
+
public String getName()
{
return name;
@@ -277,6 +280,16 @@ public void setCuratable(boolean aCuratable)
curatable = aCuratable;
}
+ public int getRank()
+ {
+ return rank;
+ }
+
+ public void setRank(int aRank)
+ {
+ rank = aRank;
+ }
+
@Override
public int hashCode()
{
diff --git a/inception/inception-model/pom.xml b/inception/inception-model/pom.xml
index 36f67582080..519d7095d02 100644
--- a/inception/inception-model/pom.xml
+++ b/inception/inception-model/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-modelINCEpTION - Core - Model
diff --git a/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationDocument.java b/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationDocument.java
index 653793cd0f7..5423287544d 100644
--- a/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationDocument.java
+++ b/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationDocument.java
@@ -41,7 +41,6 @@
/**
* A persistence object for meta-data of annotation documents. The content of annotation document is
* stored in a file system.
- *
*/
@Entity
@Table(name = "annotation_document", uniqueConstraints = {
@@ -123,7 +122,7 @@ public AnnotationDocument()
public AnnotationDocument(String aUser, SourceDocument aDocument)
{
- user = aUser;
+ setUser(aUser);
document = aDocument;
name = aDocument.getName();
project = aDocument.getProject();
diff --git a/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationFeature.java b/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationFeature.java
index 08c954c14da..50fbab9d11f 100644
--- a/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationFeature.java
+++ b/inception/inception-model/src/main/java/de/tudarmstadt/ukp/clarin/webanno/model/AnnotationFeature.java
@@ -133,6 +133,9 @@ public class AnnotationFeature
private boolean curatable = true;
+ @Column(nullable = false)
+ private int rank;
+
public AnnotationFeature()
{
// Nothing to do
@@ -202,6 +205,7 @@ private AnnotationFeature(Builder builder)
this.linkTypeTargetFeatureName = builder.linkTypeTargetFeatureName;
this.traits = builder.traits;
this.curatable = builder.curatable;
+ this.rank = builder.rank;
}
public Long getId()
@@ -560,6 +564,16 @@ public void setCuratable(boolean aCuratable)
curatable = aCuratable;
}
+ public int getRank()
+ {
+ return rank;
+ }
+
+ public void setRank(int aRank)
+ {
+ rank = aRank;
+ }
+
@Override
public String toString()
{
@@ -655,6 +669,7 @@ public static final class Builder
private String linkTypeTargetFeatureName;
private String traits;
private boolean curatable = true;
+ private int rank = 0;
private Builder()
{
@@ -808,6 +823,12 @@ public Builder withCuratable(boolean curatable)
return this;
}
+ public Builder withRank(int aRank)
+ {
+ this.rank = aRank;
+ return this;
+ }
+
public AnnotationFeature build()
{
return new AnnotationFeature(this);
diff --git a/inception/inception-model/src/main/resources/de/tudarmstadt/ukp/clarin/webanno/model/db-changelog.xml b/inception/inception-model/src/main/resources/de/tudarmstadt/ukp/clarin/webanno/model/db-changelog.xml
index 3b32535a45a..a53d923c4b1 100644
--- a/inception/inception-model/src/main/resources/de/tudarmstadt/ukp/clarin/webanno/model/db-changelog.xml
+++ b/inception/inception-model/src/main/resources/de/tudarmstadt/ukp/clarin/webanno/model/db-changelog.xml
@@ -1425,4 +1425,17 @@
ALTER TABLE project ALTER "disableExport" TYPE BOOLEAN USING ("disableExport"::int::bool)
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/inception/inception-pdf-editor/pom.xml b/inception/inception-pdf-editor/pom.xml
index b4aaa4023e8..f8647eb2e1f 100644
--- a/inception/inception-pdf-editor/pom.xml
+++ b/inception/inception-pdf-editor/pom.xml
@@ -20,13 +20,10 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTINCEpTION - Editor - PDF (pdfbox ${pdfbox.version})inception-pdf-editor
-
- 2.0.26
- de.tudarmstadt.ukp.inception.app
@@ -94,12 +91,10 @@
org.apache.pdfboxpdfbox
- ${pdfbox.version}org.apache.pdfboxfontbox
- ${pdfbox.version}
diff --git a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditor.java b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditor.java
index d936310a83f..cd19019d1c7 100644
--- a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditor.java
+++ b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditor.java
@@ -47,7 +47,6 @@
import de.tudarmstadt.ukp.clarin.webanno.api.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorExtensionRegistry;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
import de.tudarmstadt.ukp.inception.editor.view.DocumentViewFactory;
@@ -94,9 +93,10 @@ public class PdfAnnotationEditor
private @SpringBean ServletContext servletContext;
public PdfAnnotationEditor(String aId, IModel aModel,
- AnnotationActionHandler aActionHandler, CasProvider aCasProvider)
+ AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
+ String aEditorFactoryId)
{
- super(aId, aModel, aActionHandler, aCasProvider);
+ super(aId, aModel, aActionHandler, aCasProvider, aEditorFactoryId);
try {
documentModel = new DocumentModel(getCasProvider().get().getDocumentText());
@@ -117,9 +117,7 @@ protected Component makeView()
return new WrongFileFormatPanel(VIS, format);
}
- AnnotationDocument annDoc = documentService.getAnnotationDocument(state.getDocument(),
- state.getUser());
- view = (PdfDocumentIFrameView) viewFactory.createView(VIS, Model.of(annDoc),
+ view = (PdfDocumentIFrameView) viewFactory.createView(VIS, Model.of(state.getDocument()),
viewFactory.getId());
return view;
}
@@ -136,6 +134,7 @@ protected AnnotationEditorProperties getProperties()
referenceToUrl(servletContext, PdfAnnotationEditorCssResourceReference.get())));
props.setScriptSources(asList(referenceToUrl(servletContext,
PdfAnnotationEditorJavascriptResourceReference.get())));
+ props.setLoadingIndicatorDisabled(true);
return props;
}
diff --git a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditorFactory.java b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditorFactory.java
index c51bff8365b..29211ca8565 100644
--- a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditorFactory.java
+++ b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditorFactory.java
@@ -66,7 +66,7 @@ public int accepts(Project aProject, String aFormat)
public AnnotationEditorBase create(String aId, IModel aModel,
AnnotationActionHandler aActionHandler, CasProvider aCasProvider)
{
- return new PdfAnnotationEditor(aId, aModel, aActionHandler, aCasProvider);
+ return new PdfAnnotationEditor(aId, aModel, aActionHandler, aCasProvider, getBeanName());
}
@Override
diff --git a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfFormatSupport.java b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfFormatSupport.java
index e2bd6825ead..647c867ea75 100644
--- a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfFormatSupport.java
+++ b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfFormatSupport.java
@@ -25,6 +25,7 @@
import org.dkpro.core.io.pdf.PdfReader;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.inception.pdfeditor.config.PdfAnnotationEditorSupportAutoConfiguration;
/**
@@ -62,7 +63,8 @@ public boolean isReadable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(PdfReader.class, aTSD);
diff --git a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameView.java b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameView.java
index f404f26ffcc..c904cd1256f 100644
--- a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameView.java
+++ b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameView.java
@@ -46,7 +46,6 @@
import org.xml.sax.SAXException;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.inception.pdfeditor.PdfAnnotationEditor;
import de.tudarmstadt.ukp.inception.pdfeditor.pdfanno.model.PdfExtractFile;
@@ -72,8 +71,7 @@ public class PdfDocumentIFrameView
private PdfExtractFile pdfExtractFile;
- public PdfDocumentIFrameView(String aId, IModel aDoc,
- String aEditorFactoryId)
+ public PdfDocumentIFrameView(String aId, IModel aDoc, String aEditorFactoryId)
{
super(aId, aDoc);
@@ -87,7 +85,7 @@ public PdfDocumentIFrameView(String aId, IModel aDoc,
@Override
public void onRequest()
{
- SourceDocument doc = aDoc.getObject().getDocument();
+ SourceDocument doc = aDoc.getObject();
File pdfFile = documentService.getSourceDocumentFile(doc);
@@ -120,7 +118,7 @@ public void respond(AjaxRequestTarget aTarget)
{
initialize(aTarget);
String pdftext = pdfExtractFile.getPdftxt();
- SourceDocument doc = aDoc.getObject().getDocument();
+ SourceDocument doc = aDoc.getObject();
StringResourceStream resource = new StringResourceStream(pdftext, "text/plain");
@@ -177,14 +175,14 @@ public PdfExtractFile getPdfExtractFile()
}
@SuppressWarnings("unchecked")
- public IModel getModel()
+ public IModel getModel()
{
- return (IModel) getDefaultModel();
+ return (IModel) getDefaultModel();
}
private void initialize(AjaxRequestTarget aTarget)
{
- File pdfFile = documentService.getSourceDocumentFile(getModel().getObject().getDocument());
+ File pdfFile = documentService.getSourceDocumentFile(getModel().getObject());
try {
String pdfText = PDFExtractor.processFileToString(pdfFile);
diff --git a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameViewFactory.java b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameViewFactory.java
index 06ce5169ba2..9a35c34cdd0 100644
--- a/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameViewFactory.java
+++ b/inception/inception-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/pdfanno/PdfDocumentIFrameViewFactory.java
@@ -20,7 +20,7 @@
import org.apache.wicket.Component;
import org.apache.wicket.model.IModel;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
+import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.inception.editor.view.DocumentViewFactory;
import de.tudarmstadt.ukp.inception.pdfeditor.config.PdfAnnotationEditorSupportAutoConfiguration;
@@ -45,14 +45,13 @@ public String getId()
}
@Override
- public boolean accepts(AnnotationDocument aContext)
+ public boolean accepts(SourceDocument aContext)
{
return false;
}
@Override
- public Component createView(String aId, IModel aDoc,
- String aEditorFactoryId)
+ public Component createView(String aId, IModel aDoc, String aEditorFactoryId)
{
return new PdfDocumentIFrameView(aId, aDoc, aEditorFactoryId);
}
diff --git a/inception/inception-pdf-editor/src/main/ts_template/package-lock.json b/inception/inception-pdf-editor/src/main/ts_template/package-lock.json
index d66bee25f2f..6e78338ea6c 100644
--- a/inception/inception-pdf-editor/src/main/ts_template/package-lock.json
+++ b/inception/inception-pdf-editor/src/main/ts_template/package-lock.json
@@ -51,7 +51,7 @@
"cross-env": "^7.0.3",
"esbuild": "~0.16.17",
"esbuild-runner-plugins": "^2.3.0-plugins.0",
- "esbuild-sass-plugin": "^2.5.0",
+ "esbuild-sass-plugin": "~2.5.0",
"eslint": "^8.31.0",
"eslint-config-standard": "^17.0.0",
"eslint-plugin-import": "^2.26.0",
@@ -82,7 +82,7 @@
"chai": "^4.3.6",
"esbuild": "~0.16.17",
"esbuild-runner-plugins": "^2.3.0-plugins.0",
- "esbuild-sass-plugin": "^2.5.0",
+ "esbuild-sass-plugin": "~2.5.0",
"eslint": "^8.31.0",
"eslint-config-standard": "^17.0.0",
"eslint-plugin-chai-friendly": "^0.7.2",
@@ -113,14 +113,36 @@
"node": ">=12"
}
},
+ "../../../../inception-js-api/src/main/ts/node_modules/@eslint-community/eslint-utils": {
+ "version": "4.4.0",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "eslint-visitor-keys": "^3.3.0"
+ },
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "peerDependencies": {
+ "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
+ }
+ },
+ "../../../../inception-js-api/src/main/ts/node_modules/@eslint-community/regexpp": {
+ "version": "4.5.1",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": "^12.0.0 || ^14.0.0 || >=16.0.0"
+ }
+ },
"../../../../inception-js-api/src/main/ts/node_modules/@eslint/eslintrc": {
- "version": "1.4.1",
+ "version": "2.0.3",
"dev": true,
"license": "MIT",
"dependencies": {
"ajv": "^6.12.4",
"debug": "^4.3.2",
- "espree": "^9.4.0",
+ "espree": "^9.5.2",
"globals": "^13.19.0",
"ignore": "^5.2.0",
"import-fresh": "^3.2.1",
@@ -135,6 +157,14 @@
"url": "https://opencollective.com/eslint"
}
},
+ "../../../../inception-js-api/src/main/ts/node_modules/@eslint/js": {
+ "version": "8.41.0",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ }
+ },
"../../../../inception-js-api/src/main/ts/node_modules/@humanwhocodes/config-array": {
"version": "0.11.8",
"dev": true,
@@ -202,12 +232,12 @@
"license": "Apache-2.0"
},
"../../../../inception-js-api/src/main/ts/node_modules/@types/chai": {
- "version": "4.3.4",
+ "version": "4.3.5",
"dev": true,
"license": "MIT"
},
"../../../../inception-js-api/src/main/ts/node_modules/@types/json-schema": {
- "version": "7.0.11",
+ "version": "7.0.12",
"dev": true,
"license": "MIT"
},
@@ -222,11 +252,11 @@
"license": "MIT"
},
"../../../../inception-js-api/src/main/ts/node_modules/@types/node": {
- "version": "18.14.0",
+ "version": "20.2.5",
"license": "MIT"
},
"../../../../inception-js-api/src/main/ts/node_modules/@types/semver": {
- "version": "7.3.13",
+ "version": "7.5.0",
"dev": true,
"license": "MIT"
},
@@ -238,18 +268,18 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/eslint-plugin": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/type-utils": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/type-utils": "5.59.8",
+ "@typescript-eslint/utils": "5.59.8",
"debug": "^4.3.4",
"grapheme-splitter": "^1.0.4",
"ignore": "^5.2.0",
"natural-compare-lite": "^1.4.0",
- "regexpp": "^3.2.0",
"semver": "^7.3.7",
"tsutils": "^3.21.0"
},
@@ -271,13 +301,13 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/parser": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/typescript-estree": "5.59.8",
"debug": "^4.3.4"
},
"engines": {
@@ -297,12 +327,12 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/scope-manager": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0"
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8"
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
@@ -313,12 +343,12 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/type-utils": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/typescript-estree": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@typescript-eslint/typescript-estree": "5.59.8",
+ "@typescript-eslint/utils": "5.59.8",
"debug": "^4.3.4",
"tsutils": "^3.21.0"
},
@@ -339,7 +369,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/types": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"engines": {
@@ -351,12 +381,12 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/typescript-estree": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8",
"debug": "^4.3.4",
"globby": "^11.1.0",
"is-glob": "^4.0.3",
@@ -377,17 +407,17 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/utils": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
+ "@eslint-community/eslint-utils": "^4.2.0",
"@types/json-schema": "^7.0.9",
"@types/semver": "^7.3.12",
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/typescript-estree": "5.59.8",
"eslint-scope": "^5.1.1",
- "eslint-utils": "^3.0.0",
"semver": "^7.3.7"
},
"engines": {
@@ -402,11 +432,11 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/@typescript-eslint/visitor-keys": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
"eslint-visitor-keys": "^3.3.0"
},
"engines": {
@@ -498,6 +528,18 @@
"dev": true,
"license": "Python-2.0"
},
+ "../../../../inception-js-api/src/main/ts/node_modules/array-buffer-byte-length": {
+ "version": "1.0.0",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "is-array-buffer": "^3.0.1"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"../../../../inception-js-api/src/main/ts/node_modules/array-includes": {
"version": "3.1.6",
"dev": true,
@@ -901,17 +943,17 @@
"license": "MIT"
},
"../../../../inception-js-api/src/main/ts/node_modules/es-abstract": {
- "version": "1.21.1",
+ "version": "1.21.2",
"dev": true,
"license": "MIT",
"dependencies": {
+ "array-buffer-byte-length": "^1.0.0",
"available-typed-arrays": "^1.0.5",
"call-bind": "^1.0.2",
"es-set-tostringtag": "^2.0.1",
"es-to-primitive": "^1.2.1",
- "function-bind": "^1.1.1",
"function.prototype.name": "^1.1.5",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"get-symbol-description": "^1.0.0",
"globalthis": "^1.0.3",
"gopd": "^1.0.1",
@@ -919,8 +961,8 @@
"has-property-descriptors": "^1.0.0",
"has-proto": "^1.0.1",
"has-symbols": "^1.0.3",
- "internal-slot": "^1.0.4",
- "is-array-buffer": "^3.0.1",
+ "internal-slot": "^1.0.5",
+ "is-array-buffer": "^3.0.2",
"is-callable": "^1.2.7",
"is-negative-zero": "^2.0.2",
"is-regex": "^1.1.4",
@@ -928,11 +970,12 @@
"is-string": "^1.0.7",
"is-typed-array": "^1.1.10",
"is-weakref": "^1.0.2",
- "object-inspect": "^1.12.2",
+ "object-inspect": "^1.12.3",
"object-keys": "^1.1.1",
"object.assign": "^4.1.4",
"regexp.prototype.flags": "^1.4.3",
"safe-regex-test": "^1.0.0",
+ "string.prototype.trim": "^1.2.7",
"string.prototype.trimend": "^1.0.6",
"string.prototype.trimstart": "^1.0.6",
"typed-array-length": "^1.0.4",
@@ -1068,11 +1111,14 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/eslint": {
- "version": "8.34.0",
+ "version": "8.41.0",
"dev": true,
"license": "MIT",
"dependencies": {
- "@eslint/eslintrc": "^1.4.1",
+ "@eslint-community/eslint-utils": "^4.2.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@eslint/eslintrc": "^2.0.3",
+ "@eslint/js": "8.41.0",
"@humanwhocodes/config-array": "^0.11.8",
"@humanwhocodes/module-importer": "^1.0.1",
"@nodelib/fs.walk": "^1.2.8",
@@ -1082,24 +1128,22 @@
"debug": "^4.3.2",
"doctrine": "^3.0.0",
"escape-string-regexp": "^4.0.0",
- "eslint-scope": "^7.1.1",
- "eslint-utils": "^3.0.0",
- "eslint-visitor-keys": "^3.3.0",
- "espree": "^9.4.0",
- "esquery": "^1.4.0",
+ "eslint-scope": "^7.2.0",
+ "eslint-visitor-keys": "^3.4.1",
+ "espree": "^9.5.2",
+ "esquery": "^1.4.2",
"esutils": "^2.0.2",
"fast-deep-equal": "^3.1.3",
"file-entry-cache": "^6.0.1",
"find-up": "^5.0.0",
"glob-parent": "^6.0.2",
"globals": "^13.19.0",
- "grapheme-splitter": "^1.0.4",
+ "graphemer": "^1.4.0",
"ignore": "^5.2.0",
"import-fresh": "^3.0.0",
"imurmurhash": "^0.1.4",
"is-glob": "^4.0.0",
"is-path-inside": "^3.0.3",
- "js-sdsl": "^4.1.4",
"js-yaml": "^4.1.0",
"json-stable-stringify-without-jsonify": "^1.0.1",
"levn": "^0.4.1",
@@ -1107,7 +1151,6 @@
"minimatch": "^3.1.2",
"natural-compare": "^1.4.0",
"optionator": "^0.9.1",
- "regexpp": "^3.2.0",
"strip-ansi": "^6.0.1",
"strip-json-comments": "^3.1.0",
"text-table": "^0.2.0"
@@ -1123,7 +1166,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/eslint-config-standard": {
- "version": "17.0.0",
+ "version": "17.1.0",
"dev": true,
"funding": [
{
@@ -1140,10 +1183,13 @@
}
],
"license": "MIT",
+ "engines": {
+ "node": ">=12.0.0"
+ },
"peerDependencies": {
"eslint": "^8.0.1",
"eslint-plugin-import": "^2.25.2",
- "eslint-plugin-n": "^15.0.0",
+ "eslint-plugin-n": "^15.0.0 || ^16.0.0 ",
"eslint-plugin-promise": "^6.0.0"
}
},
@@ -1166,7 +1212,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/eslint-module-utils": {
- "version": "2.7.4",
+ "version": "2.8.0",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -1311,7 +1357,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/eslint-plugin-n": {
- "version": "15.6.1",
+ "version": "15.7.0",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -1383,15 +1429,18 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/eslint-visitor-keys": {
- "version": "3.3.0",
+ "version": "3.4.1",
"dev": true,
"license": "Apache-2.0",
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"../../../../inception-js-api/src/main/ts/node_modules/eslint/node_modules/eslint-scope": {
- "version": "7.1.1",
+ "version": "7.2.0",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
@@ -1400,6 +1449,9 @@
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"../../../../inception-js-api/src/main/ts/node_modules/eslint/node_modules/estraverse": {
@@ -1411,13 +1463,13 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/espree": {
- "version": "9.4.1",
+ "version": "9.5.2",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
"acorn": "^8.8.0",
"acorn-jsx": "^5.3.2",
- "eslint-visitor-keys": "^3.3.0"
+ "eslint-visitor-keys": "^3.4.1"
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
@@ -1427,7 +1479,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/esquery": {
- "version": "1.4.2",
+ "version": "1.5.0",
"dev": true,
"license": "BSD-3-Clause",
"dependencies": {
@@ -1676,12 +1728,13 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/get-intrinsic": {
- "version": "1.2.0",
+ "version": "1.2.1",
"dev": true,
"license": "MIT",
"dependencies": {
"function-bind": "^1.1.1",
"has": "^1.0.3",
+ "has-proto": "^1.0.1",
"has-symbols": "^1.0.3"
},
"funding": {
@@ -1792,7 +1845,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/graceful-fs": {
- "version": "4.2.10",
+ "version": "4.2.11",
"dev": true,
"license": "ISC"
},
@@ -1801,6 +1854,11 @@
"dev": true,
"license": "MIT"
},
+ "../../../../inception-js-api/src/main/ts/node_modules/graphemer": {
+ "version": "1.4.0",
+ "dev": true,
+ "license": "MIT"
+ },
"../../../../inception-js-api/src/main/ts/node_modules/has": {
"version": "1.0.3",
"dev": true,
@@ -1892,7 +1950,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/immutable": {
- "version": "4.2.4",
+ "version": "4.3.0",
"dev": true,
"license": "MIT",
"peer": true
@@ -1948,12 +2006,12 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/is-array-buffer": {
- "version": "3.0.1",
+ "version": "3.0.2",
"dev": true,
"license": "MIT",
"dependencies": {
"call-bind": "^1.0.2",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"is-typed-array": "^1.1.10"
},
"funding": {
@@ -2014,7 +2072,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/is-core-module": {
- "version": "2.11.0",
+ "version": "2.12.1",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -2224,15 +2282,6 @@
"dev": true,
"license": "ISC"
},
- "../../../../inception-js-api/src/main/ts/node_modules/js-sdsl": {
- "version": "4.3.0",
- "dev": true,
- "license": "MIT",
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/js-sdsl"
- }
- },
"../../../../inception-js-api/src/main/ts/node_modules/js-yaml": {
"version": "4.1.0",
"dev": true,
@@ -2785,7 +2834,7 @@
"license": "MIT"
},
"../../../../inception-js-api/src/main/ts/node_modules/rambda": {
- "version": "7.4.0",
+ "version": "7.5.0",
"dev": true,
"license": "MIT"
},
@@ -2809,13 +2858,13 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/regexp.prototype.flags": {
- "version": "1.4.3",
+ "version": "1.5.0",
"dev": true,
"license": "MIT",
"dependencies": {
"call-bind": "^1.0.2",
- "define-properties": "^1.1.3",
- "functions-have-names": "^1.2.2"
+ "define-properties": "^1.2.0",
+ "functions-have-names": "^1.2.3"
},
"engines": {
"node": ">= 0.4"
@@ -2844,11 +2893,11 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/resolve": {
- "version": "1.22.1",
+ "version": "1.22.2",
"dev": true,
"license": "MIT",
"dependencies": {
- "is-core-module": "^2.9.0",
+ "is-core-module": "^2.11.0",
"path-parse": "^1.0.7",
"supports-preserve-symlinks-flag": "^1.0.0"
},
@@ -2945,7 +2994,7 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/sass": {
- "version": "1.58.3",
+ "version": "1.62.1",
"dev": true,
"license": "MIT",
"peer": true,
@@ -2958,11 +3007,11 @@
"sass": "sass.js"
},
"engines": {
- "node": ">=12.0.0"
+ "node": ">=14.0.0"
}
},
"../../../../inception-js-api/src/main/ts/node_modules/semver": {
- "version": "7.3.8",
+ "version": "7.5.1",
"dev": true,
"license": "ISC",
"dependencies": {
@@ -3062,6 +3111,22 @@
"node": ">=8"
}
},
+ "../../../../inception-js-api/src/main/ts/node_modules/string.prototype.trim": {
+ "version": "1.2.7",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "define-properties": "^1.1.4",
+ "es-abstract": "^1.20.4"
+ },
+ "engines": {
+ "node": ">= 0.4"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"../../../../inception-js-api/src/main/ts/node_modules/string.prototype.trimend": {
"version": "1.0.6",
"dev": true,
@@ -3240,12 +3305,12 @@
}
},
"../../../../inception-js-api/src/main/ts/node_modules/tsconfig-paths": {
- "version": "3.14.1",
+ "version": "3.14.2",
"dev": true,
"license": "MIT",
"dependencies": {
"@types/json5": "^0.0.29",
- "json5": "^1.0.1",
+ "json5": "^1.0.2",
"minimist": "^1.2.6",
"strip-bom": "^3.0.0"
}
@@ -3468,7 +3533,7 @@
"license": "ISC"
},
"../../../../inception-js-api/src/main/ts/node_modules/yargs": {
- "version": "17.7.1",
+ "version": "17.7.2",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -3548,14 +3613,36 @@
"node": ">=12"
}
},
+ "node_modules/@eslint-community/eslint-utils": {
+ "version": "4.4.0",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "eslint-visitor-keys": "^3.3.0"
+ },
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "peerDependencies": {
+ "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
+ }
+ },
+ "node_modules/@eslint-community/regexpp": {
+ "version": "4.5.1",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": "^12.0.0 || ^14.0.0 || >=16.0.0"
+ }
+ },
"node_modules/@eslint/eslintrc": {
- "version": "1.4.1",
+ "version": "2.0.3",
"dev": true,
"license": "MIT",
"dependencies": {
"ajv": "^6.12.4",
"debug": "^4.3.2",
- "espree": "^9.4.0",
+ "espree": "^9.5.2",
"globals": "^13.19.0",
"ignore": "^5.2.0",
"import-fresh": "^3.2.1",
@@ -3570,6 +3657,14 @@
"url": "https://opencollective.com/eslint"
}
},
+ "node_modules/@eslint/js": {
+ "version": "8.41.0",
+ "dev": true,
+ "license": "MIT",
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ }
+ },
"node_modules/@humanwhocodes/config-array": {
"version": "0.11.8",
"dev": true,
@@ -3642,7 +3737,7 @@
"license": "MIT"
},
"node_modules/@types/json-schema": {
- "version": "7.0.11",
+ "version": "7.0.12",
"dev": true,
"license": "MIT"
},
@@ -3652,7 +3747,7 @@
"license": "MIT"
},
"node_modules/@types/semver": {
- "version": "7.3.13",
+ "version": "7.5.0",
"dev": true,
"license": "MIT"
},
@@ -3662,18 +3757,18 @@
"license": "MIT"
},
"node_modules/@typescript-eslint/eslint-plugin": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/type-utils": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/type-utils": "5.59.8",
+ "@typescript-eslint/utils": "5.59.8",
"debug": "^4.3.4",
"grapheme-splitter": "^1.0.4",
"ignore": "^5.2.0",
"natural-compare-lite": "^1.4.0",
- "regexpp": "^3.2.0",
"semver": "^7.3.7",
"tsutils": "^3.21.0"
},
@@ -3695,13 +3790,13 @@
}
},
"node_modules/@typescript-eslint/parser": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/typescript-estree": "5.59.8",
"debug": "^4.3.4"
},
"engines": {
@@ -3721,12 +3816,12 @@
}
},
"node_modules/@typescript-eslint/scope-manager": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0"
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8"
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
@@ -3737,12 +3832,12 @@
}
},
"node_modules/@typescript-eslint/type-utils": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/typescript-estree": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@typescript-eslint/typescript-estree": "5.59.8",
+ "@typescript-eslint/utils": "5.59.8",
"debug": "^4.3.4",
"tsutils": "^3.21.0"
},
@@ -3763,7 +3858,7 @@
}
},
"node_modules/@typescript-eslint/types": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"engines": {
@@ -3775,12 +3870,12 @@
}
},
"node_modules/@typescript-eslint/typescript-estree": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8",
"debug": "^4.3.4",
"globby": "^11.1.0",
"is-glob": "^4.0.3",
@@ -3801,17 +3896,17 @@
}
},
"node_modules/@typescript-eslint/utils": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
+ "@eslint-community/eslint-utils": "^4.2.0",
"@types/json-schema": "^7.0.9",
"@types/semver": "^7.3.12",
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/typescript-estree": "5.59.8",
"eslint-scope": "^5.1.1",
- "eslint-utils": "^3.0.0",
"semver": "^7.3.7"
},
"engines": {
@@ -3826,11 +3921,11 @@
}
},
"node_modules/@typescript-eslint/visitor-keys": {
- "version": "5.53.0",
+ "version": "5.59.8",
"dev": true,
"license": "MIT",
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
"eslint-visitor-keys": "^3.3.0"
},
"engines": {
@@ -3902,6 +3997,18 @@
"dev": true,
"license": "Python-2.0"
},
+ "node_modules/array-buffer-byte-length": {
+ "version": "1.0.0",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "is-array-buffer": "^3.0.1"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"node_modules/array-includes": {
"version": "3.1.6",
"dev": true,
@@ -4156,17 +4263,17 @@
"license": "MIT"
},
"node_modules/es-abstract": {
- "version": "1.21.1",
+ "version": "1.21.2",
"dev": true,
"license": "MIT",
"dependencies": {
+ "array-buffer-byte-length": "^1.0.0",
"available-typed-arrays": "^1.0.5",
"call-bind": "^1.0.2",
"es-set-tostringtag": "^2.0.1",
"es-to-primitive": "^1.2.1",
- "function-bind": "^1.1.1",
"function.prototype.name": "^1.1.5",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"get-symbol-description": "^1.0.0",
"globalthis": "^1.0.3",
"gopd": "^1.0.1",
@@ -4174,8 +4281,8 @@
"has-property-descriptors": "^1.0.0",
"has-proto": "^1.0.1",
"has-symbols": "^1.0.3",
- "internal-slot": "^1.0.4",
- "is-array-buffer": "^3.0.1",
+ "internal-slot": "^1.0.5",
+ "is-array-buffer": "^3.0.2",
"is-callable": "^1.2.7",
"is-negative-zero": "^2.0.2",
"is-regex": "^1.1.4",
@@ -4183,11 +4290,12 @@
"is-string": "^1.0.7",
"is-typed-array": "^1.1.10",
"is-weakref": "^1.0.2",
- "object-inspect": "^1.12.2",
+ "object-inspect": "^1.12.3",
"object-keys": "^1.1.1",
"object.assign": "^4.1.4",
"regexp.prototype.flags": "^1.4.3",
"safe-regex-test": "^1.0.0",
+ "string.prototype.trim": "^1.2.7",
"string.prototype.trimend": "^1.0.6",
"string.prototype.trimstart": "^1.0.6",
"typed-array-length": "^1.0.4",
@@ -4294,11 +4402,14 @@
}
},
"node_modules/eslint": {
- "version": "8.34.0",
+ "version": "8.41.0",
"dev": true,
"license": "MIT",
"dependencies": {
- "@eslint/eslintrc": "^1.4.1",
+ "@eslint-community/eslint-utils": "^4.2.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@eslint/eslintrc": "^2.0.3",
+ "@eslint/js": "8.41.0",
"@humanwhocodes/config-array": "^0.11.8",
"@humanwhocodes/module-importer": "^1.0.1",
"@nodelib/fs.walk": "^1.2.8",
@@ -4308,24 +4419,22 @@
"debug": "^4.3.2",
"doctrine": "^3.0.0",
"escape-string-regexp": "^4.0.0",
- "eslint-scope": "^7.1.1",
- "eslint-utils": "^3.0.0",
- "eslint-visitor-keys": "^3.3.0",
- "espree": "^9.4.0",
- "esquery": "^1.4.0",
+ "eslint-scope": "^7.2.0",
+ "eslint-visitor-keys": "^3.4.1",
+ "espree": "^9.5.2",
+ "esquery": "^1.4.2",
"esutils": "^2.0.2",
"fast-deep-equal": "^3.1.3",
"file-entry-cache": "^6.0.1",
"find-up": "^5.0.0",
"glob-parent": "^6.0.2",
"globals": "^13.19.0",
- "grapheme-splitter": "^1.0.4",
+ "graphemer": "^1.4.0",
"ignore": "^5.2.0",
"import-fresh": "^3.0.0",
"imurmurhash": "^0.1.4",
"is-glob": "^4.0.0",
"is-path-inside": "^3.0.3",
- "js-sdsl": "^4.1.4",
"js-yaml": "^4.1.0",
"json-stable-stringify-without-jsonify": "^1.0.1",
"levn": "^0.4.1",
@@ -4333,7 +4442,6 @@
"minimatch": "^3.1.2",
"natural-compare": "^1.4.0",
"optionator": "^0.9.1",
- "regexpp": "^3.2.0",
"strip-ansi": "^6.0.1",
"strip-json-comments": "^3.1.0",
"text-table": "^0.2.0"
@@ -4349,7 +4457,7 @@
}
},
"node_modules/eslint-config-standard": {
- "version": "17.0.0",
+ "version": "17.1.0",
"dev": true,
"funding": [
{
@@ -4366,10 +4474,13 @@
}
],
"license": "MIT",
+ "engines": {
+ "node": ">=12.0.0"
+ },
"peerDependencies": {
"eslint": "^8.0.1",
"eslint-plugin-import": "^2.25.2",
- "eslint-plugin-n": "^15.0.0",
+ "eslint-plugin-n": "^15.0.0 || ^16.0.0 ",
"eslint-plugin-promise": "^6.0.0"
}
},
@@ -4392,7 +4503,7 @@
}
},
"node_modules/eslint-module-utils": {
- "version": "2.7.4",
+ "version": "2.8.0",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -4511,7 +4622,7 @@
}
},
"node_modules/eslint-plugin-n": {
- "version": "15.6.1",
+ "version": "15.7.0",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -4583,15 +4694,18 @@
}
},
"node_modules/eslint-visitor-keys": {
- "version": "3.3.0",
+ "version": "3.4.1",
"dev": true,
"license": "Apache-2.0",
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"node_modules/eslint/node_modules/eslint-scope": {
- "version": "7.1.1",
+ "version": "7.2.0",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
@@ -4600,6 +4714,9 @@
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"node_modules/eslint/node_modules/estraverse": {
@@ -4611,13 +4728,13 @@
}
},
"node_modules/espree": {
- "version": "9.4.1",
+ "version": "9.5.2",
"dev": true,
"license": "BSD-2-Clause",
"dependencies": {
"acorn": "^8.8.0",
"acorn-jsx": "^5.3.2",
- "eslint-visitor-keys": "^3.3.0"
+ "eslint-visitor-keys": "^3.4.1"
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
@@ -4627,7 +4744,7 @@
}
},
"node_modules/esquery": {
- "version": "1.4.2",
+ "version": "1.5.0",
"dev": true,
"license": "BSD-3-Clause",
"dependencies": {
@@ -4855,12 +4972,13 @@
}
},
"node_modules/get-intrinsic": {
- "version": "1.2.0",
+ "version": "1.2.1",
"dev": true,
"license": "MIT",
"dependencies": {
"function-bind": "^1.1.1",
"has": "^1.0.3",
+ "has-proto": "^1.0.1",
"has-symbols": "^1.0.3"
},
"funding": {
@@ -4971,7 +5089,7 @@
}
},
"node_modules/graceful-fs": {
- "version": "4.2.10",
+ "version": "4.2.11",
"dev": true,
"license": "ISC"
},
@@ -4980,6 +5098,11 @@
"dev": true,
"license": "MIT"
},
+ "node_modules/graphemer": {
+ "version": "1.4.0",
+ "dev": true,
+ "license": "MIT"
+ },
"node_modules/has": {
"version": "1.0.3",
"dev": true,
@@ -5113,12 +5236,12 @@
}
},
"node_modules/is-array-buffer": {
- "version": "3.0.1",
+ "version": "3.0.2",
"dev": true,
"license": "MIT",
"dependencies": {
"call-bind": "^1.0.2",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"is-typed-array": "^1.1.10"
},
"funding": {
@@ -5163,7 +5286,7 @@
}
},
"node_modules/is-core-module": {
- "version": "2.11.0",
+ "version": "2.12.1",
"dev": true,
"license": "MIT",
"dependencies": {
@@ -5343,15 +5466,6 @@
"dev": true,
"license": "ISC"
},
- "node_modules/js-sdsl": {
- "version": "4.3.0",
- "dev": true,
- "license": "MIT",
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/js-sdsl"
- }
- },
"node_modules/js-yaml": {
"version": "4.1.0",
"dev": true,
@@ -5703,13 +5817,13 @@
"license": "MIT"
},
"node_modules/regexp.prototype.flags": {
- "version": "1.4.3",
+ "version": "1.5.0",
"dev": true,
"license": "MIT",
"dependencies": {
"call-bind": "^1.0.2",
- "define-properties": "^1.1.3",
- "functions-have-names": "^1.2.2"
+ "define-properties": "^1.2.0",
+ "functions-have-names": "^1.2.3"
},
"engines": {
"node": ">= 0.4"
@@ -5738,11 +5852,11 @@
}
},
"node_modules/resolve": {
- "version": "1.22.1",
+ "version": "1.22.2",
"dev": true,
"license": "MIT",
"dependencies": {
- "is-core-module": "^2.9.0",
+ "is-core-module": "^2.11.0",
"path-parse": "^1.0.7",
"supports-preserve-symlinks-flag": "^1.0.0"
},
@@ -5820,7 +5934,7 @@
}
},
"node_modules/semver": {
- "version": "7.3.8",
+ "version": "7.5.1",
"dev": true,
"license": "ISC",
"dependencies": {
@@ -5886,6 +6000,22 @@
"node": ">=8"
}
},
+ "node_modules/string.prototype.trim": {
+ "version": "1.2.7",
+ "dev": true,
+ "license": "MIT",
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "define-properties": "^1.1.4",
+ "es-abstract": "^1.20.4"
+ },
+ "engines": {
+ "node": ">= 0.4"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"node_modules/string.prototype.trimend": {
"version": "1.0.6",
"dev": true,
@@ -5986,12 +6116,12 @@
"license": "MIT"
},
"node_modules/tsconfig-paths": {
- "version": "3.14.1",
+ "version": "3.14.2",
"dev": true,
"license": "MIT",
"dependencies": {
"@types/json5": "^0.0.29",
- "json5": "^1.0.1",
+ "json5": "^1.0.2",
"minimist": "^1.2.6",
"strip-bom": "^3.0.0"
}
@@ -6194,7 +6324,7 @@
"license": "ISC"
},
"node_modules/yargs": {
- "version": "17.7.1",
+ "version": "17.7.2",
"dev": true,
"license": "MIT",
"dependencies": {
diff --git a/inception/inception-pdf-editor2/pom.xml b/inception/inception-pdf-editor2/pom.xml
index c4fe4a7bf35..e6d6fddc9af 100644
--- a/inception/inception-pdf-editor2/pom.xml
+++ b/inception/inception-pdf-editor2/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTINCEpTION - Editor - PDF (pdfbox ${pdfbox.version}; pdfjs ${pdfjs.version})inception-pdf-editor2
@@ -106,12 +106,10 @@
org.apache.pdfboxpdfbox
- ${pdfbox.version}org.apache.pdfboxfontbox
- ${pdfbox.version}
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditor.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditor.java
index 4cd62a580f1..696cd4a2937 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditor.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditor.java
@@ -27,7 +27,6 @@
import de.tudarmstadt.ukp.clarin.webanno.api.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
import de.tudarmstadt.ukp.inception.editor.AnnotationEditorExtensionRegistry;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
import de.tudarmstadt.ukp.inception.editor.view.DocumentViewFactory;
@@ -59,9 +58,10 @@ public class PdfAnnotationEditor
private @SpringBean ServletContext servletContext;
public PdfAnnotationEditor(String aId, IModel aModel,
- AnnotationActionHandler aActionHandler, CasProvider aCasProvider)
+ AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
+ String aEditorFactoryId)
{
- super(aId, aModel, aActionHandler, aCasProvider);
+ super(aId, aModel, aActionHandler, aCasProvider, aEditorFactoryId);
}
@Override
@@ -73,9 +73,7 @@ protected Component makeView()
return new WrongFileFormatPanel(VIS, format);
}
- AnnotationDocument annDoc = documentService.getAnnotationDocument(state.getDocument(),
- state.getUser());
- view = (PdfDocumentIFrameView) viewFactory.createView(VIS, Model.of(annDoc),
+ view = (PdfDocumentIFrameView) viewFactory.createView(VIS, Model.of(state.getDocument()),
viewFactory.getId());
return view;
}
@@ -92,6 +90,7 @@ protected AnnotationEditorProperties getProperties()
referenceToUrl(servletContext, PdfAnnotationEditorCssResourceReference.get())));
props.setScriptSources(asList(referenceToUrl(servletContext,
PdfAnnotationEditorJavascriptResourceReference.get())));
+ props.setLoadingIndicatorDisabled(true);
return props;
}
}
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditorFactory.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditorFactory.java
index 2cb7d04333d..77c96b4500d 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditorFactory.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/PdfAnnotationEditorFactory.java
@@ -64,7 +64,7 @@ public int accepts(Project aProject, String aFormat)
public AnnotationEditorBase create(String aId, IModel aModel,
AnnotationActionHandler aActionHandler, CasProvider aCasProvider)
{
- return new PdfAnnotationEditor(aId, aModel, aActionHandler, aCasProvider);
+ return new PdfAnnotationEditor(aId, aModel, aActionHandler, aCasProvider, getBeanName());
}
@Override
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/format/PdfFormatSupport.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/format/PdfFormatSupport.java
index 3cc565653cb..b590d681ea7 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/format/PdfFormatSupport.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/format/PdfFormatSupport.java
@@ -24,6 +24,7 @@
import org.apache.uima.resource.metadata.TypeSystemDescription;
import de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.inception.pdfeditor2.config.PdfAnnotationEditor2SupportAutoConfiguration;
/**
@@ -58,7 +59,8 @@ public boolean isReadable()
}
@Override
- public CollectionReaderDescription getReaderDescription(TypeSystemDescription aTSD)
+ public CollectionReaderDescription getReaderDescription(Project aProject,
+ TypeSystemDescription aTSD)
throws ResourceInitializationException
{
return createReaderDescription(VisualPdfReader.class, aTSD);
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/pdfbox/GlyphPositionUtils.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/pdfbox/GlyphPositionUtils.java
index 9f0c6b62183..acaa73764ae 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/pdfbox/GlyphPositionUtils.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/pdfbox/GlyphPositionUtils.java
@@ -156,7 +156,7 @@ public static Shape calculateFontBounds(TextPosition text, AffineTransform flipA
}
// source:
- // https://github.com/apache/pdfbox/blob/10d1e91af4eb9a06af7e95460533bf3ebc1b1280/pdfbox/src/main/java/org/apache/pdfbox/text/PDFTextStripper.java#L1911
+ // https://github.com/apache/pdfbox/blob/2.0.28/pdfbox/src/main/java/org/apache/pdfbox/text/PDFTextStripper.java#L1911
// The support for extracting the glyph order was added for INCEpTION
/**
* Normalize certain Unicode characters. For example, convert the single "fi" ligature to "f"
@@ -195,8 +195,17 @@ public static String normalizeWord(String word, List glyphOrder)
}
else {
// Trim because some decompositions have an extra space, such as U+FC5E
- builder.append(Normalizer
- .normalize(word.substring(q, q + 1), Normalizer.Form.NFKC).trim());
+ String normalized = Normalizer
+ .normalize(word.substring(q, q + 1), Normalizer.Form.NFKC).trim();
+
+ // Hebrew in Alphabetic Presentation Forms from FB1D to FB4F and
+ // Arabic Presentation Forms-A from FB50 to FDFF and
+ // Arabic Presentation Forms-B from FE70 to FEFF
+ if (0xFB1D <= c && normalized.length() > 1) {
+ // Reverse the order of decomposed Hebrew and Arabic letters
+ normalized = new StringBuilder(normalized).reverse().toString();
+ }
+ builder.append(normalized);
}
p = q + 1;
}
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameView.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameView.java
index 41e83d78768..d64b8e7f6b2 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameView.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameView.java
@@ -45,7 +45,6 @@
import org.slf4j.LoggerFactory;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil;
import de.tudarmstadt.ukp.inception.pdfeditor2.PdfAnnotationEditor;
@@ -67,8 +66,7 @@ public class PdfDocumentIFrameView
private AbstractAjaxBehavior pdfProvider;
private AbstractAjaxBehavior vModelProvider;
- public PdfDocumentIFrameView(String aId, IModel aDoc,
- String aEditorFactoryId)
+ public PdfDocumentIFrameView(String aId, IModel aDoc, String aEditorFactoryId)
{
super(aId, aDoc);
@@ -79,7 +77,7 @@ public PdfDocumentIFrameView(String aId, IModel aDoc,
@Override
public void onRequest()
{
- SourceDocument doc = aDoc.getObject().getDocument();
+ SourceDocument doc = aDoc.getObject();
File pdfFile = documentService.getSourceDocumentFile(doc);
@@ -115,10 +113,10 @@ public void respond(AjaxRequestTarget aTarget)
});
}
- private void sendVModel(IModel aDoc, AjaxRequestTarget aTarget)
+ private void sendVModel(IModel aDoc, AjaxRequestTarget aTarget)
{
try {
- CAS cas = documentService.readAnnotationCas(aDoc.getObject());
+ CAS cas = documentService.createOrReadInitialCas(aDoc.getObject());
VModel vModel;
var pdfPages = cas.select(PdfPage.class).asList();
@@ -141,8 +139,8 @@ private void sendVModel(IModel aDoc, AjaxRequestTarget aTarg
getRequestCycle().scheduleRequestHandlerAfterCurrent(handler);
}
catch (IOException e) {
- handleError("Unable to create visual model for ["
- + aDoc.getObject().getDocument().getName() + "]", e, aTarget);
+ handleError("Unable to create visual model for [" + aDoc.getObject().getName() + "]", e,
+ aTarget);
}
}
@@ -150,7 +148,7 @@ private VModel visualModelFromPdfSource() throws IOException
{
LOG.info("Loading visual model from source");
VModel vModel;
- File file = documentService.getSourceDocumentFile(getModel().getObject().getDocument());
+ File file = documentService.getSourceDocumentFile(getModel().getObject());
try (PDDocument doc = PDDocument.load(file)) {
var extractor = new VisualPDFTextStripper();
extractor.writeText(doc, new StringWriter());
@@ -176,9 +174,10 @@ protected void onComponentTag(ComponentTag aTag)
super.onComponentTag(aTag);
}
- public IModel getModel()
+ @SuppressWarnings("unchecked")
+ public IModel getModel()
{
- return (IModel) getDefaultModel();
+ return (IModel) getDefaultModel();
}
private void handleError(String aMessage, Throwable aCause, AjaxRequestTarget aTarget)
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameViewFactory.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameViewFactory.java
index 60685f5ceed..b4e9a0e7647 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameViewFactory.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/PdfDocumentIFrameViewFactory.java
@@ -20,7 +20,7 @@
import org.apache.wicket.Component;
import org.apache.wicket.model.IModel;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
+import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.inception.editor.view.DocumentViewFactory;
import de.tudarmstadt.ukp.inception.pdfeditor2.config.PdfAnnotationEditor2SupportAutoConfiguration;
@@ -42,14 +42,13 @@ public String getId()
}
@Override
- public boolean accepts(AnnotationDocument aContext)
+ public boolean accepts(SourceDocument aContext)
{
return false;
}
@Override
- public Component createView(String aId, IModel aDoc,
- String aEditorFactoryId)
+ public Component createView(String aId, IModel aDoc, String aEditorFactoryId)
{
return new PdfDocumentIFrameView(aId, aDoc, aEditorFactoryId);
}
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/pdfjs/PdfJsViewerPage.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/pdfjs/PdfJsViewerPage.java
index 7d2a6e884be..77561ff3c1d 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/pdfjs/PdfJsViewerPage.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/view/pdfjs/PdfJsViewerPage.java
@@ -67,6 +67,12 @@ public void renderHead(IHeaderResponse aResponse)
// the sidebar automatically opens and causes a re-scaling which leads to a wrong
// scroll position!
" PDFViewerApplicationOptions.set('sidebarViewOnLoad', 0);", //
+ // Disable the PDF.js search and instead delegate to the browser search
+ " delete PDFViewerApplication.supportsIntegratedFind;", //
+ " PDFViewerApplication.supportsIntegratedFind = true;", //
+ // Disable the PDF.js printing
+ " delete PDFViewerApplication.supportsPrinting;", //
+ " PDFViewerApplication.supportsPrinting = false;", //
"});");
aResponse.render(JavaScriptHeaderItem.forScript(script, "initialization"));
}
diff --git a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/visual/VisualPDFTextStripper.java b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/visual/VisualPDFTextStripper.java
index a8b84f786af..1c4d1c8a9f3 100644
--- a/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/visual/VisualPDFTextStripper.java
+++ b/inception/inception-pdf-editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/visual/VisualPDFTextStripper.java
@@ -170,21 +170,24 @@ protected void writeString(String aText, List aTextPositions) thro
int unicodeLength;
assert (unicodeLength = aTextPositions.stream() //
- .map(TextPosition::getUnicode)//
+ .map(TextPosition::getVisuallyOrderedUnicode)//
.map(g -> normalizeWord(g, null))//
.mapToInt(String::length).sum()) == aText.length() : "Line length ["
+ aText.length() + "] should match glyph unicode length [" + unicodeLength
+ "] - [" + aText + "] <-> [" + aTextPositions.stream() //
- .map(TextPosition::getUnicode) //
+ .map(TextPosition::getVisuallyOrderedUnicode) //
.map(g -> normalizeWord(g, null)) //
.collect(joining())
+ "]";
- var originalWord = aTextPositions.stream().map(TextPosition::getUnicode).collect(joining());
+ var originalWord = aTextPositions.stream() //
+ .map(TextPosition::getVisuallyOrderedUnicode) //
+ .collect(joining());
var glyphOrder = new ArrayList();
var text = normalizeWord(originalWord, glyphOrder);
- assert text.equals(aText) : "Text from PDFbox should match text from TextPositions";
+ assert text.equals(aText) : "Text from PDFbox [" + aText
+ + "]Â should match text from TextPositions [" + text + "]";
if (glyphOrder.isEmpty()) {
var cs = new ProtoVChunk(getBuffer().length(), aText, 0, false);
@@ -200,7 +203,7 @@ protected void writeString(String aText, List aTextPositions) thro
// Account for glyphs that were mapped to more than one character by normalization
// e.g. expanded ligatures
- String normalizedUnicode = normalizeWord(pos.getUnicode(), null);
+ String normalizedUnicode = normalizeWord(pos.getVisuallyOrderedUnicode(), null);
normalizedUnicode = reconcileGlyphWithText(aText, false, normalizedUnicode, cs.end);
@@ -250,7 +253,7 @@ protected void writeString(String aText, List aTextPositions) thro
// Account for glyphs that were mapped to more than one character by normalization
// e.g. expanded ligatures
- String normalizedUnicode = normalizeWord(pos.getUnicode(), null);
+ String normalizedUnicode = normalizeWord(pos.getVisuallyOrderedUnicode(), null);
var begin = cs.rtl ? gPos - (normalizedUnicode.length() - 1) : gPos;
normalizedUnicode = reconcileGlyphWithText(aText, rtl, normalizedUnicode, begin);
@@ -396,7 +399,7 @@ boolean isEmpty()
private void assertAlignedTextPositions(String aText, List aTextPositions)
{
int cumulativePositionLength = aTextPositions.stream()
- .mapToInt(t -> normalizeWord(t.getUnicode(), null).length()) //
+ .mapToInt(t -> normalizeWord(t.getVisuallyOrderedUnicode(), null).length()) //
.sum();
if (aText.length() != cumulativePositionLength) {
@@ -405,7 +408,7 @@ private void assertAlignedTextPositions(String aText, List aTextPo
System.out.println(" Text [" + aText + "]");
StringBuilder sb = new StringBuilder();
for (TextPosition p : aTextPositions) {
- sb.append(p.getUnicode());
+ sb.append(p.getVisuallyOrderedUnicode());
}
String posText = sb.toString();
System.out.println(" Pos [" + posText + "]");
diff --git a/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.css b/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.css
index cd6c0a42461..275db5c3eb2 100644
--- a/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.css
+++ b/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.css
@@ -2218,7 +2218,7 @@ a.secondaryToolbarButton[href="#"] {
user-select: none;
}
#thumbnailView {
- width: calc(100% - 60px);
+ width: calc(100% - 1px);
padding: 10px 30px 0;
}
diff --git a/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.html b/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.html
index a7de4f32cb0..ed9be822b5a 100644
--- a/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.html
+++ b/inception/inception-pdf-editor2/src/main/ts/pdfjs-web/viewer.html
@@ -241,7 +241,7 @@
-
-
+
+
diff --git a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/sidebar/RecommenderInfoPanel.java b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/sidebar/RecommenderInfoPanel.java
index b508d230fc4..f471f1df7f2 100644
--- a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/sidebar/RecommenderInfoPanel.java
+++ b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/sidebar/RecommenderInfoPanel.java
@@ -19,7 +19,6 @@
import static de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil.getDocumentTitle;
import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.visibleWhen;
-import static de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion.FLAG_TRANSIENT_ACCEPTED;
import static java.util.stream.Collectors.groupingBy;
import static org.apache.commons.lang3.StringUtils.repeat;
@@ -49,18 +48,18 @@
import de.agilecoders.wicket.extensions.markup.html.bootstrap.icon.FontAwesome5IconType;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
import de.tudarmstadt.ukp.clarin.webanno.security.model.User;
import de.tudarmstadt.ukp.clarin.webanno.support.bootstrap.BootstrapModalDialog;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaAjaxLink;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.AjaxDownloadLink;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.TempFileResource;
+import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanAdapter;
import de.tudarmstadt.ukp.inception.annotation.storage.CasMetadataUtils;
import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
import de.tudarmstadt.ukp.inception.recommendation.api.evaluation.EvaluationResult;
import de.tudarmstadt.ukp.inception.recommendation.api.model.EvaluatedRecommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordChangeLocation;
import de.tudarmstadt.ukp.inception.recommendation.api.model.Predictions;
import de.tudarmstadt.ukp.inception.recommendation.api.model.Preferences;
import de.tudarmstadt.ukp.inception.recommendation.api.model.Progress;
@@ -94,14 +93,14 @@ public RecommenderInfoPanel(String aId, IModel aModel)
setOutputMarkupId(true);
- User user = aModel.getObject().getUser();
+ var sessionOwner = userService.getCurrentUser();
detailsDialog = new BootstrapModalDialog("detailsDialog").trapFocus().closeOnEscape()
.closeOnClick();
add(detailsDialog);
add(new Label("progress", LoadableDetachableModel.of(() -> {
- Progress p = recommendationService.getProgressTowardsNextEvaluation(user,
+ Progress p = recommendationService.getProgressTowardsNextEvaluation(sessionOwner,
aModel.getObject().getProject());
return repeat(" ", p.getDone())
+ repeat(" ", p.getTodo());
@@ -119,7 +118,7 @@ protected void populateItem(ListItem item)
{
Recommender recommender = item.getModelObject();
Optional evaluatedRecommender = recommendationService
- .getEvaluatedRecommender(user, recommender);
+ .getEvaluatedRecommender(sessionOwner, recommender);
item.add(new Label("name", recommender.getName()));
WebMarkupContainer state = new WebMarkupContainer("state");
@@ -168,24 +167,27 @@ protected void populateItem(ListItem item)
resultsContainer.add(new Label("testSampleCount",
evalResult.map(EvaluationResult::getTestSetSize).orElse(0)));
- resultsContainer.add(new LambdaAjaxLink("acceptBest",
+ item.add(resultsContainer);
+
+ item.add(new LambdaAjaxLink("acceptBest",
_tgt -> actionAcceptBest(_tgt, recommender))
.setVisible(evaluatedRecommender.map(EvaluatedRecommender::isActive)
.orElse(false)));
- resultsContainer.add(new LambdaAjaxLink("showDetails",
- _tgt -> actionShowDetails(_tgt, recommender)));
+ item.add(new LambdaAjaxLink("showDetails",
+ _tgt -> actionShowDetails(_tgt, recommender))
+ .setVisible(evalResult.map(r -> !r.isEvaluationSkipped())
+ .orElse(evalResult.isPresent())));
AjaxDownloadLink exportModel = new AjaxDownloadLink("exportModel",
LoadableDetachableModel.of(() -> exportModelName(recommender)),
- LoadableDetachableModel.of(() -> exportModel(user, recommender)));
+ LoadableDetachableModel
+ .of(() -> exportModel(sessionOwner.getUsername(), recommender)));
exportModel.add(visibleWhen(
() -> recommendationService.getRecommenderFactory(recommender).isPresent()
&& recommendationService.getRecommenderFactory(recommender).get()
.isModelExportSupported()));
- resultsContainer.add(exportModel);
-
- item.add(resultsContainer);
+ item.add(exportModel);
item.add(new Label("noEvaluationMessage",
evaluatedRecommender.map(EvaluatedRecommender::getReasonForState)
@@ -208,7 +210,7 @@ private String exportModelName(Recommender aRecommender)
.map(e -> e.getExportModelName(aRecommender)).orElse(null);
}
- private IResourceStream exportModel(User aUser, Recommender aRecommender)
+ private IResourceStream exportModel(String aSessionOwner, Recommender aRecommender)
{
Optional> maybeEngine = recommendationService
.getRecommenderFactory(aRecommender);
@@ -220,7 +222,7 @@ private IResourceStream exportModel(User aUser, Recommender aRecommender)
RecommendationEngine engine = maybeEngine.get().build(aRecommender);
- Optional context = recommendationService.getContext(aUser,
+ Optional context = recommendationService.getContext(aSessionOwner,
aRecommender);
if (context.isEmpty()) {
@@ -237,15 +239,14 @@ public AnnotatorState getModelObject()
}
@OnEvent
- public void onRenderAnnotations(PredictionsSwitchedEvent aEvent)
+ public void onPredictionsSwitched(PredictionsSwitchedEvent aEvent)
{
aEvent.getRequestTarget().add(this);
}
private void actionShowDetails(AjaxRequestTarget aTarget, Recommender aRecommender)
{
- RecommenderStatusDetailPanel panel = new RecommenderStatusDetailPanel(
- ModalDialog.CONTENT_ID,
+ var panel = new RecommenderStatusDetailPanel(ModalDialog.CONTENT_ID,
LoadableDetachableModel.of(() -> recommendationService
.getEvaluatedRecommender(userService.getCurrentUser(), aRecommender).get())
.map(EvaluatedRecommender::getEvaluationResult));
@@ -255,21 +256,22 @@ private void actionShowDetails(AjaxRequestTarget aTarget, Recommender aRecommend
private void actionAcceptBest(AjaxRequestTarget aTarget, Recommender aRecommender)
throws AnnotationException, IOException
{
- User user = userService.getCurrentUser();
+ User sessionOwner = userService.getCurrentUser();
AnnotatorState state = getModelObject();
AnnotationPageBase page = findParent(AnnotationPageBase.class);
CAS cas = page.getEditorCas();
- Predictions predictions = recommendationService.getPredictions(user, state.getProject());
+ Predictions predictions = recommendationService.getPredictions(sessionOwner,
+ state.getProject());
if (predictions == null) {
error("Recommenders did not yet provide any suggestions.");
aTarget.addChildren(getPage(), IFeedback.class);
return;
}
- Preferences pref = recommendationService.getPreferences(user, state.getProject());
+ Preferences pref = recommendationService.getPreferences(sessionOwner, state.getProject());
// TODO #176 use the document Id once it it available in the CAS
String sourceDocumentName = CasMetadataUtils.getSourceDocumentName(cas)
@@ -295,21 +297,17 @@ private void actionAcceptBest(AjaxRequestTarget aTarget, Recommender aRecommende
continue;
}
- SpanSuggestion suggestion = suggestions.get(0);
+ var suggestion = suggestions.get(0);
try {
// Upsert an annotation based on the suggestion
- AnnotationLayer layer = annotationService.getLayer(suggestion.getLayerId());
- AnnotationFeature feature = annotationService.getFeature(suggestion.getFeature(),
- layer);
+ var layer = annotationService.getLayer(suggestion.getLayerId());
+ var feature = annotationService.getFeature(suggestion.getFeature(), layer);
+ var adapter = (SpanAdapter) annotationService.getAdapter(layer);
// int address =
- recommendationService.upsertSpanFeature(annotationService, state.getDocument(),
- state.getUser().getUsername(), cas, layer, feature, suggestion.getLabel(),
- suggestion.getBegin(), suggestion.getEnd());
-
- // Hide the suggestion. This is faster than having to recalculate the visibility
- // status for the entire document or even for the part visible on screen.
- suggestion.hide(FLAG_TRANSIENT_ACCEPTED);
+ recommendationService.acceptSuggestion(sessionOwner.getUsername(),
+ state.getDocument(), state.getUser().getUsername(), cas, adapter, feature,
+ suggestion, LearningRecordChangeLocation.REC_SIDEBAR);
// // Log the action to the learning record
// learningRecordService.logRecord(document, aState.getUser().getUsername(),
diff --git a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/NonTrainableRecommenderActivationTask.java b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/NonTrainableRecommenderActivationTask.java
index b94d98106c5..3fdd328d5c1 100644
--- a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/NonTrainableRecommenderActivationTask.java
+++ b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/NonTrainableRecommenderActivationTask.java
@@ -150,8 +150,9 @@ private Optional considerRecommender(User user, Recommende
private EvaluatedRecommender activateNonTrainableRecommender(User user, Recommender recommender,
RecommendationEngine aEngine)
{
- RecommenderContext ctx = aEngine.newContext(recommendationService
- .getContext(user, recommender).orElse(RecommenderContext.EMPTY_CONTEXT));
+ RecommenderContext ctx = aEngine
+ .newContext(recommendationService.getContext(user.getUsername(), recommender)
+ .orElse(RecommenderContext.emptyContext()));
ctx.setUser(user);
ctx.close();
recommendationService.putContext(user, recommender, ctx);
@@ -166,9 +167,11 @@ private EvaluatedRecommender activateNonTrainableRecommender(User user, Recommen
private EvaluatedRecommender skipTrainableRecommender(User user, Recommender recommender)
{
String recommenderName = recommender.getName();
- log.info("[{}][{}]: Recommender requires training " + "- skipping recommender",
+ log.debug(
+ "[{}][{}]: Recommender requires training - deferring activation to selection task",
user.getUsername(), recommenderName);
- info("Recommender [%s] requires training - skipping recommender", recommenderName);
+ info("Recommender [%s] requires training - deferring activation to selection task",
+ recommenderName);
return EvaluatedRecommender.makeInactiveWithoutEvaluation(recommender, "Requires training");
}
@@ -204,13 +207,14 @@ private Optional freshenRecommender(User aUser, Recommender r)
recommender = recommendationService.getRecommender(r.getId());
}
catch (NoResultException e) {
- log.info("[{}][{}]: Recommender no longer available... skipping", aUser.getUsername(),
+ log.info("[{}][{}]: Recommender no longer available - skipping", aUser.getUsername(),
r.getName());
return Optional.empty();
}
if (!recommender.isEnabled()) {
- log.debug("[{}][{}]: Disabled - skipping", aUser.getUsername(), recommender.getName());
+ log.debug("[{}][{}]: Recommender is disabled - skipping", aUser.getUsername(),
+ recommender.getName());
return Optional.empty();
}
diff --git a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java
index ce1f99b5944..c9641dcd31d 100644
--- a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java
+++ b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java
@@ -31,16 +31,13 @@
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.security.model.User;
+import de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst;
import de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage;
import de.tudarmstadt.ukp.inception.annotation.storage.CasStorageSession;
import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
import de.tudarmstadt.ukp.inception.recommendation.api.model.Predictions;
import de.tudarmstadt.ukp.inception.recommendation.event.RecommenderTaskNotificationEvent;
-/**
- * This consumer predicts new annotations for a given annotation layer, if a classification tool for
- * this layer was selected previously.
- */
public class PredictionTask
extends RecommendationTask_ImplBase
{
@@ -53,71 +50,111 @@ public class PredictionTask
private final SourceDocument currentDocument;
private final int predictionBegin;
private final int predictionEnd;
-
- public PredictionTask(User aUser, String aTrigger, SourceDocument aCurrentDocument)
+ private final String dataOwner;
+
+ /**
+ * Create a new training task.
+ *
+ * @param aSessionOwner
+ * the user owning the training session.
+ * @param aTrigger
+ * the trigger that caused the selection to be scheduled.
+ * @param aCurrentDocument
+ * the document currently open in the editor.
+ * @param aDataOwner
+ * the user owning the annotations currently shown in the editor (this can differ
+ * from the user owning the session e.g. if a manager views another users annotations
+ * or a curator is performing curation to the {@link WebAnnoConst#CURATION_USER})
+ */
+ public PredictionTask(User aSessionOwner, String aTrigger, SourceDocument aCurrentDocument,
+ String aDataOwner)
{
- this(aUser, aTrigger, aCurrentDocument, -1, -1);
+ this(aSessionOwner, aTrigger, aCurrentDocument, -1, -1, aDataOwner);
}
- public PredictionTask(User aUser, String aTrigger, SourceDocument aCurrentDocument, int aBegin,
- int aEnd)
+ public PredictionTask(User aSessionOwner, String aTrigger, SourceDocument aCurrentDocument,
+ int aBegin, int aEnd, String aDataOwner)
{
- super(aUser, aCurrentDocument.getProject(), aTrigger);
+ super(aSessionOwner, aCurrentDocument.getProject(), aTrigger);
currentDocument = aCurrentDocument;
predictionBegin = aBegin;
predictionEnd = aEnd;
+ dataOwner = aDataOwner;
}
@Override
public void execute()
{
- try (CasStorageSession session = CasStorageSession.openNested()) {
- long startTime = System.currentTimeMillis();
- User user = getUser().orElseThrow();
- String username = user.getUsername();
- Project project = getProject();
- Predictions predictions;
-
- List docs = documentService.listSourceDocuments(project);
-
- // Limit prediction to a single document and inherit the rest?
- if (recommendationService.isPredictForAllDocuments(username, project)) {
- log.debug(
- "[{}][{}]: Starting prediction for project [{}] on [{}] docs triggered by [{}]",
- getId(), username, project, docs.size(), getTrigger());
-
- predictions = recommendationService.computePredictions(user, project, docs);
- }
- else {
- List inherit = docs.stream() //
- .filter(d -> !d.equals(currentDocument)) //
- .collect(toList());
-
- log.debug(
- "[{}][{}]: Starting prediction for project [{}] on one doc "
- + "(inheriting [{}]) triggered by [{}]",
- getId(), username, project, inherit.size(), getTrigger());
-
- predictions = recommendationService.computePredictions(user, project,
- currentDocument, inherit, predictionBegin, predictionEnd);
- }
+ try (var session = CasStorageSession.openNested()) {
+ var project = getProject();
+ var sessionOwner = getUser().orElseThrow();
+ var sessionOwnerName = sessionOwner.getUsername();
+ var startTime = System.currentTimeMillis();
+ var predictions = generatePredictions(sessionOwner);
predictions.inheritLog(getLogMessages());
+ logPredictionComplete(predictions, startTime, sessionOwnerName);
- log.debug("[{}][{}]: Prediction complete ({} ms)", getId(), username,
- currentTimeMillis() - startTime);
-
- recommendationService.putIncomingPredictions(user, project, predictions);
+ recommendationService.putIncomingPredictions(sessionOwner, project, predictions);
- appEventPublisher.publishEvent(
- RecommenderTaskNotificationEvent.builder(this, project, user.getUsername()) //
- .withMessage(LogMessage.info(this, "New preditions available")) //
- .build());
+ appEventPublisher.publishEvent(RecommenderTaskNotificationEvent
+ .builder(this, project, sessionOwner.getUsername()) //
+ .withMessage(LogMessage.info(this, "New predictions available")) //
+ .build());
// We reset this in case the state was not properly cleared, e.g. the AL session
// was started but then the browser closed. Places where it is set include
// - ActiveLearningSideBar::moveToNextRecommendation
- recommendationService.setPredictForAllDocuments(username, project, false);
+ recommendationService.setPredictForAllDocuments(sessionOwnerName, project, false);
+ }
+ }
+
+ private Predictions generatePredictions(User sessionOwner)
+ {
+ var project = getProject();
+ var sessionOwnerName = sessionOwner.getUsername();
+ var docs = documentService.listSourceDocuments(project);
+
+ // Do we need to predict ALL documents (e.g. in active learning mode)
+ if (recommendationService.isPredictForAllDocuments(sessionOwnerName, project)) {
+ logPredictionStartedForAllDocuments(sessionOwnerName, project, docs);
+ return recommendationService.computePredictions(sessionOwner, project, docs, dataOwner);
}
+
+ // Limit prediction to a single document and inherit the rest
+ var inherit = docs.stream() //
+ .filter(d -> !d.equals(currentDocument)) //
+ .collect(toList());
+
+ logPredictionStartedForOneDocument(sessionOwnerName, project, inherit);
+
+ return recommendationService.computePredictions(sessionOwner, project, currentDocument,
+ dataOwner, inherit, predictionBegin, predictionEnd);
+ }
+
+ private void logPredictionComplete(Predictions aPredictions, long startTime, String username)
+ {
+ var duration = currentTimeMillis() - startTime;
+ log.debug("[{}][{}]: Prediction complete ({} ms)", getId(), username, duration);
+ aPredictions.log(LogMessage.info(this, "Prediction complete (%d ms).", duration));
+ }
+
+ private void logPredictionStartedForOneDocument(String username, Project project,
+ List inherit)
+ {
+ log.debug(
+ "[{}][{}]: Starting prediction for project [{}] on one document "
+ + "(inheriting [{}]) triggered by [{}]",
+ getId(), username, project, inherit.size(), getTrigger());
+ info("Starting prediction triggered by [%s]...", getTrigger());
+ }
+
+ private void logPredictionStartedForAllDocuments(String username, Project project,
+ List docs)
+ {
+ log.debug(
+ "[{}][{}]: Starting prediction for project [{}] on [{}] documents triggered by [{}]",
+ getId(), username, project, docs.size(), getTrigger());
+ info("Starting prediction triggered by [%s]...", getTrigger());
}
}
diff --git a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/SelectionTask.java b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/SelectionTask.java
index 4c5a4faa235..c042b884318 100644
--- a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/SelectionTask.java
+++ b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/SelectionTask.java
@@ -40,6 +40,7 @@
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.security.model.User;
+import de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst;
import de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage;
import de.tudarmstadt.ukp.inception.annotation.storage.CasStorageSession;
import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
@@ -73,31 +74,56 @@ public class SelectionTask
private @Autowired SchedulingService schedulingService;
private final SourceDocument currentDocument;
-
+ private final String dataOwner;
+
+ /**
+ * Create a new selection task.
+ *
+ * @param aUser
+ * the user owning the selection session.
+ * @param aProject
+ * the project to perform the selection on.
+ * @param aTrigger
+ * the trigger that caused the selection to be scheduled.
+ * @param aCurrentDocument
+ * the document currently open in the editor.
+ * @param aDataOwner
+ * the user owning the annotations currently shown in the editor (this can differ
+ * from the user owning the session e.g. if a manager views another users annotations
+ * or a curator is performing curation to the {@link WebAnnoConst#CURATION_USER})
+ */
public SelectionTask(User aUser, Project aProject, String aTrigger,
- SourceDocument aCurrentDocument)
+ SourceDocument aCurrentDocument, String aDataOwner)
{
super(aUser, aProject, aTrigger);
+
+ if (getUser().isEmpty()) {
+ throw new IllegalArgumentException("SelectionTask requires a user");
+ }
+
currentDocument = aCurrentDocument;
+ dataOwner = aDataOwner;
}
@Override
public void execute()
{
try (CasStorageSession session = CasStorageSession.open()) {
+ var sessionOwner = getUser().orElseThrow();
+ String sessionOwnerName = sessionOwner.getUsername();
+ var startTime = System.currentTimeMillis();
Project project = getProject();
- User user = getUser().orElseThrow();
- String userName = user.getUsername();
+ logSelectionStarted(sessionOwner);
// Read the CASes only when they are accessed the first time. This allows us to skip
// reading the CASes in case that no layer / recommender is available or if no
// recommender requires evaluation.
- LazyInitializer> casses = new LazyInitializer>()
+ var casLoader = new LazyInitializer>()
{
@Override
protected List initialize()
{
- return readCasses(project, userName);
+ return readCasses(project, dataOwner);
}
};
@@ -107,76 +133,133 @@ protected List initialize()
continue;
}
- List recommenders = recommendationService.listRecommenders(layer);
+ var recommenders = recommendationService.listRecommenders(layer);
if (recommenders == null || recommenders.isEmpty()) {
- log.trace("[{}][{}]: No recommenders, skipping selection.", userName,
- layer.getUiName());
+ logNoRecommenders(sessionOwnerName, layer);
continue;
}
seenRecommender = true;
- List evaluatedRecommenders = new ArrayList<>();
+ var evaluatedRecommenders = new ArrayList();
for (Recommender r : recommenders) {
// Make sure we have the latest recommender config from the DB - the one from
// the active recommenders list may be outdated
- Optional optRecommender = freshenRecommender(user, r);
+ Optional optRecommender = freshenRecommender(sessionOwner, r);
if (optRecommender.isEmpty()) {
+ logRecommenderGone(sessionOwner, r);
continue;
}
Recommender recommender = optRecommender.get();
- String recommenderName = recommender.getName();
-
try {
long start = System.currentTimeMillis();
- evaluate(user, recommender, casses).ifPresent(evaluatedRecommender -> {
- var result = evaluatedRecommender.getEvaluationResult();
-
- evaluatedRecommenders.add(evaluatedRecommender);
- appEventPublisher.publishEvent(new RecommenderEvaluationResultEvent(
- this, recommender, user.getUsername(), result,
- currentTimeMillis() - start, evaluatedRecommender.isActive()));
- });
+ evaluate(sessionOwner, recommender, casLoader)
+ .ifPresent(evaluatedRecommender -> {
+ var result = evaluatedRecommender.getEvaluationResult();
+
+ evaluatedRecommenders.add(evaluatedRecommender);
+ appEventPublisher
+ .publishEvent(new RecommenderEvaluationResultEvent(this,
+ recommender, sessionOwner.getUsername(), result,
+ currentTimeMillis() - start,
+ evaluatedRecommender.isActive()));
+ });
}
// Catching Throwable is intentional here as we want to continue the execution
// even if a particular recommender fails.
catch (Throwable e) {
- log.error("[{}][{}]: Failed", user.getUsername(), recommenderName, e);
- appEventPublisher.publishEvent(RecommenderTaskNotificationEvent
- .builder(this, project, user.getUsername()) //
- .withMessage(LogMessage.error(this, e.getMessage())) //
- .build());
+ logEvaluationFailed(project, sessionOwner, recommender.getName(), e);
}
}
- recommendationService.setEvaluatedRecommenders(user, layer, evaluatedRecommenders);
+ recommendationService.setEvaluatedRecommenders(sessionOwner, layer,
+ evaluatedRecommenders);
- appEventPublisher.publishEvent(RecommenderTaskNotificationEvent
- .builder(this, getProject(), user.getUsername()) //
- .withMessage(LogMessage.info(this, "Evaluation complete")) //
- .build());
+ logEvaluationSuccessful(sessionOwner);
}
if (!seenRecommender) {
- log.trace("[{}]: No recommenders configured, skipping training.", userName);
+ logNoRecommendersSeen(sessionOwnerName);
return;
}
- if (!recommendationService.hasActiveRecommenders(user.getUsername(), project)) {
- log.debug("[{}]: No recommenders active, skipping training.", userName);
+ if (!recommendationService.hasActiveRecommenders(sessionOwner.getUsername(), project)) {
+ logNoRecommendersActive(sessionOwnerName);
return;
}
- TrainingTask trainingTask = new TrainingTask(user, getProject(),
- "SelectionTask after activating recommenders", currentDocument);
- trainingTask.inheritLog(this);
- schedulingService.enqueue(trainingTask);
+ logSelectionComplete(startTime, sessionOwnerName);
+
+ scheduleTrainingTask(sessionOwner);
}
}
+ private void logSelectionComplete(long startTime, String username)
+ {
+ var duration = currentTimeMillis() - startTime;
+ log.debug("[{}][{}]: Selection complete ({} ms)", getId(), username, duration);
+ info("Selection complete (%d ms).", duration);
+ }
+
+ private void logRecommenderGone(User user, Recommender aRecommender)
+ {
+ log.debug("[{}][{}][{}]: Recommender no longer available... skipping", getId(),
+ user.getUsername(), aRecommender.getName());
+ }
+
+ private void logSelectionStarted(User sessionOwner)
+ {
+ log.info("[{}]: Starting selection triggered by [{}]", sessionOwner.getUsername(),
+ getTrigger());
+ info("Starting selection triggered by [%s]", getTrigger());
+ }
+
+ private void scheduleTrainingTask(User sessionOwner)
+ {
+ TrainingTask trainingTask = new TrainingTask(sessionOwner, getProject(),
+ "SelectionTask after activating recommenders", currentDocument, dataOwner);
+ trainingTask.inheritLog(this);
+ schedulingService.enqueue(trainingTask);
+ }
+
+ private void logNoRecommendersActive(String sessionOwnerName)
+ {
+ log.debug("[{}]: No recommenders active, skipping training.", sessionOwnerName);
+ }
+
+ private void logNoRecommendersSeen(String sessionOwnerName)
+ {
+ log.trace("[{}]: No recommenders configured, skipping training.", sessionOwnerName);
+ }
+
+ private void logEvaluationSuccessful(User sessionOwner)
+ {
+ log.info("[{}]: Evaluation complete", sessionOwner.getUsername());
+ appEventPublisher.publishEvent(RecommenderTaskNotificationEvent
+ .builder(this, getProject(), sessionOwner.getUsername()) //
+ .withMessage(LogMessage.info(this, "Evaluation complete")) //
+ .build());
+ }
+
+ private void logEvaluationFailed(Project project, User sessionOwner, String recommenderName,
+ Throwable e)
+ {
+ log.error("[{}][{}]: Evaluation failed", sessionOwner.getUsername(), recommenderName, e);
+ appEventPublisher.publishEvent(
+ RecommenderTaskNotificationEvent.builder(this, project, sessionOwner.getUsername()) //
+ .withMessage(LogMessage.error(this, e.getMessage())) //
+ .build());
+ }
+
+ private void logNoRecommenders(String sessionOwnerName, AnnotationLayer layer)
+ {
+ log.trace("[{}][{}]: No recommenders, skipping selection.", sessionOwnerName,
+ layer.getUiName());
+ }
+
private Optional evaluate(User user, Recommender recommender,
LazyInitializer> aCasses)
throws RecommendationException, ConcurrentException
diff --git a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/TrainingTask.java b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/TrainingTask.java
index 6d98074ea4a..51f9547c267 100644
--- a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/TrainingTask.java
+++ b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/TrainingTask.java
@@ -21,15 +21,16 @@
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasAccessMode.SHARED_READ_ONLY_ACCESS;
import static de.tudarmstadt.ukp.inception.recommendation.api.recommender.TrainingCapability.TRAINING_NOT_SUPPORTED;
import static de.tudarmstadt.ukp.inception.recommendation.api.recommender.TrainingCapability.TRAINING_REQUIRED;
+import static java.lang.System.currentTimeMillis;
import static java.util.stream.Collectors.toList;
import static org.apache.commons.lang3.exception.ExceptionUtils.getRootCauseMessage;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
-import java.util.Optional;
+import java.util.Objects;
+import org.apache.commons.lang3.concurrent.ConcurrentException;
import org.apache.commons.lang3.concurrent.LazyInitializer;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.Type;
@@ -40,29 +41,23 @@
import org.springframework.context.ApplicationEventPublisher;
import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentState;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.security.model.User;
+import de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst;
import de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage;
import de.tudarmstadt.ukp.inception.annotation.storage.CasStorageSession;
import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
import de.tudarmstadt.ukp.inception.recommendation.api.model.EvaluatedRecommender;
import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
-import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngine;
-import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngineFactory;
import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommenderContext;
-import de.tudarmstadt.ukp.inception.recommendation.api.recommender.TrainingCapability;
import de.tudarmstadt.ukp.inception.recommendation.event.RecommenderTaskNotificationEvent;
import de.tudarmstadt.ukp.inception.scheduling.SchedulingService;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import jakarta.persistence.NoResultException;
-/**
- * This consumer trains a new classifier model, if a classification tool was selected before.
- */
public class TrainingTask
extends RecommendationTask_ImplBase
{
@@ -70,251 +65,223 @@ public class TrainingTask
private @Autowired AnnotationSchemaService annoService;
private @Autowired DocumentService documentService;
- private @Autowired RecommendationService recommendationService;
+ private @Autowired RecommendationService recommenderService;
private @Autowired SchedulingService schedulingService;
private @Autowired ApplicationEventPublisher appEventPublisher;
private final SourceDocument currentDocument;
-
+ private final String dataOwner;
+
+ /**
+ * Create a new training task.
+ *
+ * @param aUser
+ * the user owning the training session.
+ * @param aProject
+ * the project to perform the selection on.
+ * @param aTrigger
+ * the trigger that caused the selection to be scheduled.
+ * @param aCurrentDocument
+ * the document currently open in the editor.
+ * @param aDataOwner
+ * the user owning the annotations currently shown in the editor (this can differ
+ * from the user owning the session e.g. if a manager views another users annotations
+ * or a curator is performing curation to the {@link WebAnnoConst#CURATION_USER})
+ */
public TrainingTask(User aUser, Project aProject, String aTrigger,
- SourceDocument aCurrentDocument)
+ SourceDocument aCurrentDocument, String aDataOwner)
{
super(aUser, aProject, aTrigger);
+
+ if (getUser().isEmpty()) {
+ throw new IllegalArgumentException("TrainingTask requires a user");
+ }
+
currentDocument = aCurrentDocument;
+ dataOwner = aDataOwner;
}
@Override
public void execute()
{
try (CasStorageSession session = CasStorageSession.open()) {
- Project project = getProject();
- User user = getUser().orElseThrow();
+ executeTraining();
+ }
+ }
- log.debug("[{}][{}]: Starting training for project {} triggered by [{}]...", getId(),
- user.getUsername(), project, getTrigger());
- info("Starting training triggered by [%s]...", getTrigger());
+ private void executeTraining()
+ {
+ long overallStartTime = currentTimeMillis();
+ User sessionOwner = getUser().orElseThrow();
+
+ logTrainingOverallStart(sessionOwner);
- // Read the CASes only when they are accessed the first time. This allows us to skip
- // reading the CASes in case that no layer / recommender is available or if no
- // recommender requires evaluation.
- LazyInitializer> casses = new LazyInitializer>()
+ // Read the CASes only when they are accessed the first time. This allows us to skip
+ // reading the CASes in case that no layer / recommender is available or if no
+ // recommender requires evaluation.
+ var casLoader = new LazyInitializer>()
+ {
+ @Override
+ protected List initialize()
{
- @Override
- protected List initialize()
- {
- return readCasses(project, user);
- }
- };
+ return readCasses(getProject(), dataOwner);
+ }
+ };
+
+ boolean seenSuccessfulTraining = false;
+ boolean seenNonTrainingRecommender = false;
- boolean seenSuccessfulTraining = false;
- boolean seenNonTrainingRecommender = false;
+ for (var layer : annoService.listAnnotationLayer(getProject())) {
+ if (!layer.isEnabled()) {
+ continue;
+ }
- for (AnnotationLayer layer : annoService.listAnnotationLayer(project)) {
- if (!layer.isEnabled()) {
+ var evaluatedRecommenders = recommenderService.getActiveRecommenders(sessionOwner,
+ layer);
+
+ if (evaluatedRecommenders.isEmpty()) {
+ logNoActiveRecommenders(sessionOwner, layer);
+ continue;
+ }
+
+ for (var evaluatedRecommender : evaluatedRecommenders) {
+ // Make sure we have the latest recommender config from the DB - the one from
+ // the active recommenders list may be outdated
+ Recommender recommender;
+ try {
+ recommender = recommenderService
+ .getRecommender(evaluatedRecommender.getRecommender().getId());
+ }
+ catch (NoResultException e) {
+ logRecommenderGone(sessionOwner, evaluatedRecommender);
continue;
}
- List recommenders = recommendationService
- .getActiveRecommenders(user, layer);
-
- if (recommenders.isEmpty()) {
- log.trace("[{}][{}][{}]: No active recommenders, skipping training.", getId(),
- user.getUsername(), layer.getUiName());
- info("No active recommenders for layer [%s], skipping training.",
- layer.getUiName());
+ if (!recommender.isEnabled()) {
+ logRecommenderDisabled(sessionOwner, evaluatedRecommender);
continue;
}
- for (EvaluatedRecommender r : recommenders) {
- // Make sure we have the latest recommender config from the DB - the one from
- // the active recommenders list may be outdated
- Recommender recommender;
- try {
- recommender = recommendationService
- .getRecommender(r.getRecommender().getId());
+ long startTime = currentTimeMillis();
+
+ try {
+ var maybeFactory = recommenderService.getRecommenderFactory(recommender);
+ if (maybeFactory.isEmpty()) {
+ logUnsupportedRecommenderType(sessionOwner, evaluatedRecommender);
+ continue;
}
- catch (NoResultException e) {
- log.debug("[{}][{}][{}]: Recommender no longer available... skipping",
- getId(), user.getUsername(), r.getRecommender().getName());
+
+ var factory = maybeFactory.get();
+ if (!factory.accepts(recommender.getLayer(), recommender.getFeature())) {
+ logInvalidRecommenderConfiguration(sessionOwner, evaluatedRecommender,
+ recommender);
continue;
}
- if (!recommender.isEnabled()) {
- log.debug("[{}][{}][{}]: Disabled - skipping", user.getUsername(), getId(),
- r.getRecommender().getName());
+ var engine = factory.build(recommender);
+ var ctx = engine.newContext(
+ recommenderService.getContext(sessionOwner.getUsername(), recommender)
+ .orElse(RecommenderContext.emptyContext()));
+ ctx.setUser(sessionOwner);
+
+ // If engine does not support training, mark engine ready and skip to
+ // prediction
+ if (engine.getTrainingCapability() == TRAINING_NOT_SUPPORTED) {
+ seenNonTrainingRecommender = true;
+ logTrainingNotSupported(sessionOwner, recommender);
+ commitContext(sessionOwner, recommender, ctx);
continue;
}
- long startTime = System.currentTimeMillis();
-
- try {
- Optional> maybeFactory = recommendationService
- .getRecommenderFactory(recommender);
-
- if (maybeFactory.isEmpty()) {
- log.warn("[{}][{}]: No factory found - skipping recommender",
- user.getUsername(), r.getRecommender().getName());
- continue;
- }
-
- RecommendationEngineFactory factory = maybeFactory.get();
-
- if (!factory.accepts(recommender.getLayer(), recommender.getFeature())) {
- log.debug(
- "[{}][{}][{}]: Recommender configured with invalid layer or "
- + "feature - skipping recommender",
- getId(), user.getUsername(), r.getRecommender().getName());
- error("Recommender [%s] configured with invalid layer or feature - skipping recommender.",
- r.getRecommender().getName());
- appEventPublisher.publishEvent(RecommenderTaskNotificationEvent
- .builder(this, getProject(), user.getUsername()) //
- .withMessage(LogMessage.error(this,
- "Recommender [%s] configured with invalid layer or "
- + "feature - skipping training recommender.",
- recommender.getName()))
- .build());
- continue;
- }
-
- RecommendationEngine recommendationEngine = factory.build(recommender);
-
- RecommenderContext ctx = recommendationEngine
- .newContext(recommendationService.getContext(user, recommender)
- .orElse(RecommenderContext.EMPTY_CONTEXT));
- ctx.setUser(user);
-
- TrainingCapability capability = recommendationEngine
- .getTrainingCapability();
-
- // If engine does not support training, mark engine ready and skip to
- // prediction
- if (capability == TRAINING_NOT_SUPPORTED) {
- seenNonTrainingRecommender = true;
- log.debug("[{}][{}][{}]: Engine does not support training", getId(),
- user.getUsername(), recommender.getName());
- ctx.close();
- recommendationService.putContext(user, recommender, ctx);
- continue;
- }
-
- List cassesForTraining = casses.get().stream() //
- .filter(e -> !recommender.getStatesIgnoredForTraining()
- .contains(e.state))
- .filter(e -> containsTargetTypeAndFeature(recommender, e.cas))
- .map(e -> e.cas).collect(toList());
-
- // If no data for training is available, but the engine requires training,
- // do not mark as ready
- if (cassesForTraining.isEmpty() && capability == TRAINING_REQUIRED) {
- log.debug(
- "[{}][{}][{}]: There are no annotations available to train on",
- getId(), user.getUsername(), recommender.getName());
- warn("There are no [%s] annotations available to train on.",
- layer.getUiName());
- // This can happen if there were already predictions based on existing
- // annotations, but all annotations have been removed/deleted. To ensure
- // that the prediction run removes the stale predictions, we need to
- // call it a success here.
- seenSuccessfulTraining = true;
- continue;
- }
-
- log.debug("[{}][{}][{}]: Training model on [{}] out of [{}] documents ...",
- getId(), user.getUsername(), recommender.getName(),
- cassesForTraining.size(), casses.get().size());
- info("Training model for [%s] on [%d] out of [%d] documents ...",
- layer.getUiName(), cassesForTraining.size(), casses.get().size());
-
- recommendationEngine.train(ctx, cassesForTraining);
- inheritLog(ctx.getMessages());
-
- long duration = System.currentTimeMillis() - startTime;
-
- if (!recommendationEngine.isReadyForPrediction(ctx)) {
- int docNum = casses.get().size();
- int trainDocNum = cassesForTraining.size();
- log.debug(
- "[{}][{}][{}]: Training on [{}] out of [{}] documents not successful ({} ms)",
- getId(), user.getUsername(), recommender.getName(), trainDocNum,
- docNum, duration);
- info("Training not successful (%d ms).", duration);
- // The recommender may decide for legitimate reasons not to train and
- // then this event is annoying
- // appEventPublisher.publishEvent(new RecommenderTaskEvent(this,
- // user.getUsername(),
- // format("Training on %d out of %d documents not successful (%d ms)",
- // trainDocNum, docNum, duration),
- // recommender));
- continue;
- }
-
- log.debug(
- "[{}][{}][{}]: Training successful on [{}] out of [{}] documents ({} ms)",
- getId(), user.getUsername(), recommender.getName(),
- cassesForTraining.size(), casses.get().size(), duration);
- info("Training successful on [%d] out of [%d] documents (%d ms)",
- cassesForTraining.size(), casses.get().size(), duration);
+ var trainingCasses = casLoader.get().stream() //
+ .filter(e -> !recommender.getStatesIgnoredForTraining()
+ .contains(e.state)) //
+ .map(e -> e.getCas()) //
+ .filter(Objects::nonNull)
+ .filter(cas -> containsTargetTypeAndFeature(recommender, cas)) //
+ .collect(toList());
+
+ // If no data for training is available, but the engine requires training,
+ // do not mark as ready
+ if (trainingCasses.isEmpty()
+ && engine.getTrainingCapability() == TRAINING_REQUIRED) {
+ logNoDataAvailableForTraining(sessionOwner, layer, recommender);
+ // This can happen if there were already predictions based on existing
+ // annotations, but all annotations have been removed/deleted. To ensure
+ // that the prediction run removes the stale predictions, we need to
+ // call it a success here.
seenSuccessfulTraining = true;
-
- ctx.close();
- recommendationService.putContext(user, recommender, ctx);
+ continue;
}
- // Catching Throwable is intentional here as we want to continue the execution
- // even if a particular recommender fails.
- catch (Throwable e) {
- long duration = System.currentTimeMillis() - startTime;
- log.error("[{}][{}][{}]: Training failed ({} ms)", getId(),
- user.getUsername(), recommender.getName(),
- (System.currentTimeMillis() - startTime), e);
- error("Training failed (%d ms): %s", duration, getRootCauseMessage(e));
- appEventPublisher
- .publishEvent(RecommenderTaskNotificationEvent
- .builder(this, getProject(), user.getUsername()) //
- .withMessage(LogMessage.error(this,
- "Training failed (%d ms) with %s", duration,
- e.getMessage()))
- .build());
+
+ logTrainingRecommenderStart(sessionOwner, casLoader, layer, recommender,
+ trainingCasses);
+
+ engine.train(ctx, trainingCasses);
+ inheritLog(ctx.getMessages());
+
+ long duration = currentTimeMillis() - startTime;
+
+ if (!engine.isReadyForPrediction(ctx)) {
+ logTrainingFailure(sessionOwner, recommender, duration, casLoader.get(),
+ trainingCasses);
+ continue;
}
- }
- }
- if (!seenSuccessfulTraining && !seenNonTrainingRecommender) {
- log.debug(
- "[{}][{}]: No recommenders trained successfully and no non-training "
- + "recommenders, skipping prediction.",
- getId(), user.getUsername());
- return;
+ logTrainingSuccessful(sessionOwner, casLoader, recommender, trainingCasses,
+ duration);
+ seenSuccessfulTraining = true;
+
+ commitContext(sessionOwner, recommender, ctx);
+ }
+ // Catching Throwable is intentional here as we want to continue the execution
+ // even if a particular recommender fails.
+ catch (Throwable e) {
+ handleError(sessionOwner, recommender, startTime, e);
+ }
}
+ }
- PredictionTask predictionTask = new PredictionTask(user,
- String.format("TrainingTask %s complete", getId()), currentDocument);
- predictionTask.inheritLog(this);
- schedulingService.enqueue(predictionTask);
+ if (!seenSuccessfulTraining && !seenNonTrainingRecommender) {
+ logNothingWasTrained(sessionOwner);
+ return;
}
+
+ logTrainingOverallEnd(overallStartTime, sessionOwner);
+
+ schedulePredictionTask(sessionOwner);
}
- private List readCasses(Project aProject, User aUser)
+ private void schedulePredictionTask(User user)
{
- List casses = new ArrayList<>();
- Map allDocuments = documentService
- .listAllDocuments(aProject, aUser);
- for (Map.Entry entry : allDocuments.entrySet()) {
- try {
- SourceDocument sourceDocument = entry.getKey();
- AnnotationDocument annotationDocument = entry.getValue();
- AnnotationDocumentState state = annotationDocument != null
- ? annotationDocument.getState()
- : AnnotationDocumentState.NEW;
+ var predictionTask = new PredictionTask(user,
+ String.format("TrainingTask %s complete", getId()), currentDocument, dataOwner);
+ predictionTask.inheritLog(this);
+ schedulingService.enqueue(predictionTask);
+ }
- // During training, we should not have to modify the CASes... right? Fingers
- // crossed.
- CAS cas = documentService.readAnnotationCas(sourceDocument, aUser.getUsername(),
- AUTO_CAS_UPGRADE, SHARED_READ_ONLY_ACCESS);
- casses.add(new TrainingDocument(cas, state));
- }
- catch (IOException e) {
- log.error("Cannot read annotation CAS.", e);
- }
+ private void logTrainingOverallEnd(long overallStartTime, User user)
+ {
+ info("Training complete (%d ms).", currentTimeMillis() - overallStartTime);
+ }
+
+ private void commitContext(User user, Recommender recommender, RecommenderContext ctx)
+ {
+ ctx.close();
+ recommenderService.putContext(user, recommender, ctx);
+ }
+
+ private List readCasses(Project aProject, String aUser)
+ {
+ var casses = new ArrayList();
+ var allDocuments = documentService.listAllDocuments(aProject, aUser);
+ for (var entry : allDocuments.entrySet()) {
+ var sourceDocument = entry.getKey();
+ var annotationDocument = entry.getValue();
+ var state = annotationDocument != null ? annotationDocument.getState()
+ : AnnotationDocumentState.NEW;
+
+ casses.add(new TrainingDocument(sourceDocument, aUser, state));
}
return casses;
}
@@ -340,15 +307,167 @@ private boolean containsTargetTypeAndFeature(Recommender aRecommender, CAS aCas)
return CasUtil.iterator(aCas, type).hasNext();
}
- private static class TrainingDocument
+ private void logUnsupportedRecommenderType(User user, EvaluatedRecommender evaluatedRecommender)
{
- private final CAS cas;
+ log.warn("[{}][{}]: No factory found - skipping recommender", user.getUsername(),
+ evaluatedRecommender.getRecommender().getName());
+ }
+
+ private void logTrainingNotSupported(User user, Recommender recommender)
+ {
+ log.debug("[{}][{}][{}]: Engine does not support training", getId(), user.getUsername(),
+ recommender.getName());
+ }
+
+ private void logRecommenderDisabled(User user, EvaluatedRecommender evaluatedRecommender)
+ {
+ log.debug("[{}][{}][{}]: Disabled - skipping", user.getUsername(), getId(),
+ evaluatedRecommender.getRecommender().getName());
+ }
+
+ private void logRecommenderGone(User user, EvaluatedRecommender evaluatedRecommender)
+ {
+ log.debug("[{}][{}][{}]: Recommender no longer available... skipping", getId(),
+ user.getUsername(), evaluatedRecommender.getRecommender().getName());
+ }
+
+ private void logNothingWasTrained(User user)
+ {
+ log.debug("[{}][{}]: No recommenders trained successfully and no non-training "
+ + "recommenders, skipping prediction.", getId(), user.getUsername());
+ }
+
+ private void logNoActiveRecommenders(User user, AnnotationLayer layer)
+ {
+ log.trace("[{}][{}][{}]: No active recommenders, skipping training.", getId(),
+ user.getUsername(), layer.getUiName());
+ info("No active recommenders for layer [%s], skipping training.", layer.getUiName());
+ }
+
+ private void logInvalidRecommenderConfiguration(User user, EvaluatedRecommender r,
+ Recommender recommender)
+ {
+ log.debug(
+ "[{}][{}][{}]: Recommender configured with invalid layer or "
+ + "feature - skipping recommender",
+ getId(), user.getUsername(), r.getRecommender().getName());
+ error("Recommender [%s] configured with invalid layer or feature - skipping recommender.",
+ r.getRecommender().getName());
+ appEventPublisher.publishEvent(
+ RecommenderTaskNotificationEvent.builder(this, getProject(), user.getUsername()) //
+ .withMessage(LogMessage.error(this,
+ "Recommender [%s] configured with invalid layer or "
+ + "feature - skipping training recommender.",
+ recommender.getName()))
+ .build());
+ }
+
+ private void logNoDataAvailableForTraining(User user, AnnotationLayer layer,
+ Recommender recommender)
+ {
+ log.debug("[{}][{}][{}]: There are no annotations available to train on", getId(),
+ user.getUsername(), recommender.getName());
+ warn("There are no [%s] annotations available to train on.", layer.getUiName());
+ }
+
+ private void logTrainingFailure(User user, Recommender recommender, long duration,
+ List aAllCasses, List aTrainCasses)
+ {
+ int docNum = aAllCasses.size();
+ int trainDocNum = aTrainCasses.size();
+
+ log.debug("[{}][{}][{}]: Training on [{}] out of [{}] documents not successful ({} ms)",
+ getId(), user.getUsername(), recommender.getName(), trainDocNum, docNum, duration);
+ info("Training not successful (%d ms).", duration);
+ // The recommender may decide for legitimate reasons not to train and
+ // then this event is annoying
+ // appEventPublisher.publishEvent(new RecommenderTaskEvent(this,
+ // user.getUsername(),
+ // format("Training on %d out of %d documents not successful (%d ms)",
+ // trainDocNum, docNum, duration),
+ // recommender));
+ }
+
+ private void logTrainingSuccessful(User user, LazyInitializer> casses,
+ Recommender recommender, List cassesForTraining, long duration)
+ throws ConcurrentException
+ {
+ log.debug("[{}][{}][{}]: Training successful on [{}] out of [{}] documents ({} ms)",
+ getId(), user.getUsername(), recommender.getName(), cassesForTraining.size(),
+ casses.get().size(), duration);
+ info("Training successful on [%d] out of [%d] documents (%d ms)", cassesForTraining.size(),
+ casses.get().size(), duration);
+ }
+
+ private void logTrainingOverallStart(User user)
+ {
+ log.debug("[{}][{}]: Starting training for project {} triggered by [{}]...", getId(),
+ user.getUsername(), getProject(), getTrigger());
+ info("Starting training triggered by [%s]...", getTrigger());
+ }
+
+ private void logTrainingRecommenderStart(User user,
+ LazyInitializer> casses, AnnotationLayer layer,
+ Recommender recommender, List cassesForTraining)
+ throws ConcurrentException
+ {
+ log.debug("[{}][{}][{}]: Training model on [{}] out of [{}] documents ...", getId(),
+ user.getUsername(), recommender.getName(), cassesForTraining.size(),
+ casses.get().size());
+ info("Training model for [%s] on [%d] out of [%d] documents ...", layer.getUiName(),
+ cassesForTraining.size(), casses.get().size());
+ }
+
+ private void handleError(User user, Recommender recommender, long startTime, Throwable e)
+ {
+ long duration = currentTimeMillis() - startTime;
+ log.error("[{}][{}][{}]: Training failed ({} ms)", getId(), user.getUsername(),
+ recommender.getName(), (currentTimeMillis() - startTime), e);
+
+ error("Training failed (%d ms): %s", duration, getRootCauseMessage(e));
+
+ appEventPublisher.publishEvent(
+ RecommenderTaskNotificationEvent.builder(this, getProject(), user.getUsername()) //
+ .withMessage(LogMessage.error(this, "Training failed (%d ms) with %s",
+ duration, e.getMessage()))
+ .build());
+ }
+
+ private class TrainingDocument
+ {
+ private final SourceDocument document;
+ private final String user;
private final AnnotationDocumentState state;
- private TrainingDocument(CAS aCas, AnnotationDocumentState aState)
+ private boolean attemptedLoading = false;
+ private CAS _cas;
+
+ private TrainingDocument(SourceDocument aDocument, String aAnnotator,
+ AnnotationDocumentState aState)
{
- cas = aCas;
+ document = aDocument;
+ user = aAnnotator;
state = aState;
}
+
+ public CAS getCas()
+ {
+ if (attemptedLoading) {
+ return _cas;
+ }
+
+ attemptedLoading = true;
+ try {
+ // During training, we should not have to modify the CASes... right? Fingers
+ // crossed.
+ _cas = documentService.readAnnotationCas(document, user, AUTO_CAS_UPGRADE,
+ SHARED_READ_ONLY_ACCESS);
+ }
+ catch (IOException e) {
+ log.error("Unable to load CAS to train recommender", e);
+ }
+
+ return _cas;
+ }
}
}
diff --git a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/util/OverlapIterator.java b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/util/OverlapIterator.java
index 9b1cc57d471..c0e7810ddf6 100644
--- a/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/util/OverlapIterator.java
+++ b/inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/util/OverlapIterator.java
@@ -101,7 +101,7 @@ public Offset getB()
return curb;
}
- public void ignoraA()
+ public void ignoreA()
{
ignorea[na] = true;
}
diff --git a/inception/inception-recommendation/src/main/resources/META-INF/asciidoc/user-guide/projects_recommendation.adoc b/inception/inception-recommendation/src/main/resources/META-INF/asciidoc/user-guide/projects_recommendation.adoc
index 1f0af654e16..74fee984fc3 100644
--- a/inception/inception-recommendation/src/main/resources/META-INF/asciidoc/user-guide/projects_recommendation.adoc
+++ b/inception/inception-recommendation/src/main/resources/META-INF/asciidoc/user-guide/projects_recommendation.adoc
@@ -29,6 +29,21 @@ meet the configured threshold, the recommender will not be used.
Recommenders can be configured in the *Project Settings* under the *Recommenders* tab. To create a new
recommender, click *Create*. Then, the layer, feature and the classifier type has to be selected.
+== Overall recommender settings
+
+The option **wait for suggestions from non-trainable recommenders when opening document** can be
+enabled overall. It is accessible from the settings dropdown on the recommender list panel.
+When this option is enabled, the system will wait for responses from all non-trainable recommenders
+in the project when a user is opening a document before actually displaying the document to the
+user. If this option is not checked, then recommendations may only appear after the user has
+performed some action such as creating an annotation.
+
+NOTE: Enable this option only if all of your non-trainable recommenders have a fast response time,
+ as otherwise your users may complain about a long delay when opening documents.
+
+
+== Per-recommender settings
+
By default, the name of new recommenders are auto-generated based on the choice of layer, feature and tool. However, you can deactivate this behavior by unchecking the *auto-generate* option next to the name field.
Recommenders can be enabled and disabled. This behaviour is configured by the *Enabled* checkbox.
diff --git a/inception/inception-recommendation/src/main/ts_template/package-lock.json b/inception/inception-recommendation/src/main/ts_template/package-lock.json
index f30880fba42..11d7cd0dd36 100644
--- a/inception/inception-recommendation/src/main/ts_template/package-lock.json
+++ b/inception/inception-recommendation/src/main/ts_template/package-lock.json
@@ -21,7 +21,7 @@
"chai": "^4.3.6",
"esbuild": "~0.16.17",
"esbuild-runner-plugins": "^2.3.0-plugins.0",
- "esbuild-sass-plugin": "^2.5.0",
+ "esbuild-sass-plugin": "~2.5.0",
"esbuild-svelte": "^0.7.3",
"eslint": "^8.31.0",
"eslint-config-standard": "^17.0.0",
@@ -45,9 +45,9 @@
}
},
"node_modules/@babel/code-frame": {
- "version": "7.18.6",
- "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz",
- "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==",
+ "version": "7.21.4",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.21.4.tgz",
+ "integrity": "sha512-LYvhNKfwWSPpocw8GI7gpK2nq3HSDuEPC/uSYaALSJu9xjsalaaYFOq0Pwt5KmVqwEbZlDu81aLXwBOmD/Fv9g==",
"dev": true,
"dependencies": {
"@babel/highlight": "^7.18.6"
@@ -151,9 +151,9 @@
}
},
"node_modules/@babel/runtime": {
- "version": "7.21.0",
- "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.21.0.tgz",
- "integrity": "sha512-xwII0//EObnq89Ji5AKYQaRYiW/nZ3llSv29d49IuxPhKbtJoLP+9QUUZ4nVragQVtaVGeZrpB+ZtG/Pdy/POw==",
+ "version": "7.22.3",
+ "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.22.3.tgz",
+ "integrity": "sha512-XsDuspWKLUsxwCp6r7EhsExHtYfbe5oAGQ19kqngTdCPUoPQzOPdUbD/pB9PJiwb2ptYKQDjSJT3R6dC+EPqfQ==",
"dev": true,
"dependencies": {
"regenerator-runtime": "^0.13.11"
@@ -514,15 +514,39 @@
"node": ">=12"
}
},
+ "node_modules/@eslint-community/eslint-utils": {
+ "version": "4.4.0",
+ "resolved": "https://registry.npmjs.org/@eslint-community/eslint-utils/-/eslint-utils-4.4.0.tgz",
+ "integrity": "sha512-1/sA4dwrzBAyeUoQ6oxahHKmrZvsnLCg4RfxW3ZFGGmQkSNQPFNLV9CUEFQP1x9EYXHTo5p6xdhZM1Ne9p/AfA==",
+ "dev": true,
+ "dependencies": {
+ "eslint-visitor-keys": "^3.3.0"
+ },
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "peerDependencies": {
+ "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
+ }
+ },
+ "node_modules/@eslint-community/regexpp": {
+ "version": "4.5.1",
+ "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.5.1.tgz",
+ "integrity": "sha512-Z5ba73P98O1KUYCCJTUeVpja9RcGoMdncZ6T49FCUl2lN38JtCJ+3WgIDBv0AuY4WChU5PmtJmOCTlN6FZTFKQ==",
+ "dev": true,
+ "engines": {
+ "node": "^12.0.0 || ^14.0.0 || >=16.0.0"
+ }
+ },
"node_modules/@eslint/eslintrc": {
- "version": "1.4.1",
- "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-1.4.1.tgz",
- "integrity": "sha512-XXrH9Uarn0stsyldqDYq8r++mROmWRI1xKMXa640Bb//SY1+ECYX6VzT6Lcx5frD0V30XieqJ0oX9I2Xj5aoMA==",
+ "version": "2.0.3",
+ "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-2.0.3.tgz",
+ "integrity": "sha512-+5gy6OQfk+xx3q0d6jGZZC3f3KzAkXc/IanVxd1is/VIIziRqqt3ongQz0FiTUXqTk0c7aDB3OaFuKnuSoJicQ==",
"dev": true,
"dependencies": {
"ajv": "^6.12.4",
"debug": "^4.3.2",
- "espree": "^9.4.0",
+ "espree": "^9.5.2",
"globals": "^13.19.0",
"ignore": "^5.2.0",
"import-fresh": "^3.2.1",
@@ -537,6 +561,15 @@
"url": "https://opencollective.com/eslint"
}
},
+ "node_modules/@eslint/js": {
+ "version": "8.41.0",
+ "resolved": "https://registry.npmjs.org/@eslint/js/-/js-8.41.0.tgz",
+ "integrity": "sha512-LxcyMGxwmTh2lY9FwHPGWOHmYFCZvbrFCBZL4FzSSsxsRPuhrYUg/49/0KDfW8tnIEaEHtfmn6+NPN+1DqaNmA==",
+ "dev": true,
+ "engines": {
+ "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ }
+ },
"node_modules/@humanwhocodes/config-array": {
"version": "0.11.8",
"resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.11.8.tgz",
@@ -571,9 +604,9 @@
"dev": true
},
"node_modules/@jridgewell/sourcemap-codec": {
- "version": "1.4.14",
- "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.14.tgz",
- "integrity": "sha512-XPSJHWmi394fuUuzDnGz1wiKqWfo1yXecHQMRf2l6hztTO+nPru658AyDngaBe7isIxEkRsPR3FZh+s7iVa4Uw==",
+ "version": "1.4.15",
+ "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.15.tgz",
+ "integrity": "sha512-eF2rxCRulEKXHTRiDrDy6erMYWqNw4LPdQ8UQA4huuxaQsVeRPFl2oM8oDGxMFhJUWZf9McpLtJasDDZb/Bpeg==",
"dev": true
},
"node_modules/@nodelib/fs.scandir": {
@@ -666,9 +699,9 @@
"dev": true
},
"node_modules/@types/chai": {
- "version": "4.3.4",
- "resolved": "https://registry.npmjs.org/@types/chai/-/chai-4.3.4.tgz",
- "integrity": "sha512-KnRanxnpfpjUTqTCXslZSEdLfXExwgNxYPdiO2WGUj8+HDjFi8R3k5RVKPeSCzLjCcshCAtVO2QBbVuAV4kTnw==",
+ "version": "4.3.5",
+ "resolved": "https://registry.npmjs.org/@types/chai/-/chai-4.3.5.tgz",
+ "integrity": "sha512-mEo1sAde+UCE6b2hxn332f1g1E8WfYRu6p5SvTKr2ZKC1f7gFJXk4h5PyGP9Dt6gCaG8y8XhwnXWC6Iy2cmBng==",
"dev": true
},
"node_modules/@types/events": {
@@ -678,9 +711,9 @@
"dev": true
},
"node_modules/@types/json-schema": {
- "version": "7.0.11",
- "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.11.tgz",
- "integrity": "sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ==",
+ "version": "7.0.12",
+ "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.12.tgz",
+ "integrity": "sha512-Hr5Jfhc9eYOQNPYO5WLDq/n4jqijdHNlDXjuAQkkt+mWdQR+XJToOHrsD4cPaMXpn6KO7y2+wM8AZEs8VpBLVA==",
"dev": true
},
"node_modules/@types/json5": {
@@ -695,47 +728,32 @@
"integrity": "sha512-Z61JK7DKDtdKTWwLeElSEBcWGRLY8g95ic5FoQqI9CMx0ns/Ghep3B4DfcEimiKMvtamNVULVNKEsiwV3aQmXw==",
"dev": true
},
- "node_modules/@types/node": {
- "version": "18.14.0",
- "resolved": "https://registry.npmjs.org/@types/node/-/node-18.14.0.tgz",
- "integrity": "sha512-5EWrvLmglK+imbCJY0+INViFWUHg1AHel1sq4ZVSfdcNqGy9Edv3UB9IIzzg+xPaUcAgZYcfVs2fBcwDeZzU0A==",
- "dev": true
- },
"node_modules/@types/pug": {
"version": "2.0.6",
"resolved": "https://registry.npmjs.org/@types/pug/-/pug-2.0.6.tgz",
"integrity": "sha512-SnHmG9wN1UVmagJOnyo/qkk0Z7gejYxOYYmaAwr5u2yFYfsupN3sg10kyzN8Hep/2zbHxCnsumxOoRIRMBwKCg==",
"dev": true
},
- "node_modules/@types/sass": {
- "version": "1.43.1",
- "resolved": "https://registry.npmjs.org/@types/sass/-/sass-1.43.1.tgz",
- "integrity": "sha512-BPdoIt1lfJ6B7rw35ncdwBZrAssjcwzI5LByIrYs+tpXlj/CAkuVdRsgZDdP4lq5EjyWzwxZCqAoFyHKFwp32g==",
- "dev": true,
- "dependencies": {
- "@types/node": "*"
- }
- },
"node_modules/@types/semver": {
- "version": "7.3.13",
- "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.3.13.tgz",
- "integrity": "sha512-21cFJr9z3g5dW8B0CVI9g2O9beqaThGQ6ZFBqHfwhzLDKUxaqTIy3vnfah/UPkfOiF2pLq+tGz+W8RyCskuslw==",
+ "version": "7.5.0",
+ "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.5.0.tgz",
+ "integrity": "sha512-G8hZ6XJiHnuhQKR7ZmysCeJWE08o8T0AXtk5darsCaTVsYZhhgUrq53jizaR2FvsoeCwJhlmwTjkXBY5Pn/ZHw==",
"dev": true
},
"node_modules/@typescript-eslint/eslint-plugin": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/eslint-plugin/-/eslint-plugin-5.53.0.tgz",
- "integrity": "sha512-alFpFWNucPLdUOySmXCJpzr6HKC3bu7XooShWM+3w/EL6J2HIoB2PFxpLnq4JauWVk6DiVeNKzQlFEaE+X9sGw==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/eslint-plugin/-/eslint-plugin-5.59.8.tgz",
+ "integrity": "sha512-JDMOmhXteJ4WVKOiHXGCoB96ADWg9q7efPWHRViT/f09bA8XOMLAVHHju3l0MkZnG1izaWXYmgvQcUjTRcpShQ==",
"dev": true,
"dependencies": {
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/type-utils": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/type-utils": "5.59.8",
+ "@typescript-eslint/utils": "5.59.8",
"debug": "^4.3.4",
"grapheme-splitter": "^1.0.4",
"ignore": "^5.2.0",
"natural-compare-lite": "^1.4.0",
- "regexpp": "^3.2.0",
"semver": "^7.3.7",
"tsutils": "^3.21.0"
},
@@ -757,14 +775,14 @@
}
},
"node_modules/@typescript-eslint/parser": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-5.53.0.tgz",
- "integrity": "sha512-MKBw9i0DLYlmdOb3Oq/526+al20AJZpANdT6Ct9ffxcV8nKCHz63t/S0IhlTFNsBIHJv+GY5SFJ0XfqVeydQrQ==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/parser/-/parser-5.59.8.tgz",
+ "integrity": "sha512-AnR19RjJcpjoeGojmwZtCwBX/RidqDZtzcbG3xHrmz0aHHoOcbWnpDllenRDmDvsV0RQ6+tbb09/kyc+UT9Orw==",
"dev": true,
"dependencies": {
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/typescript-estree": "5.59.8",
"debug": "^4.3.4"
},
"engines": {
@@ -784,13 +802,13 @@
}
},
"node_modules/@typescript-eslint/scope-manager": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-5.53.0.tgz",
- "integrity": "sha512-Opy3dqNsp/9kBBeCPhkCNR7fmdSQqA+47r21hr9a14Bx0xnkElEQmhoHga+VoaoQ6uDHjDKmQPIYcUcKJifS7w==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-5.59.8.tgz",
+ "integrity": "sha512-/w08ndCYI8gxGf+9zKf1vtx/16y8MHrZs5/tnjHhMLNSixuNcJavSX4wAiPf4aS5x41Es9YPCn44MIe4cxIlig==",
"dev": true,
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0"
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8"
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
@@ -801,13 +819,13 @@
}
},
"node_modules/@typescript-eslint/type-utils": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/type-utils/-/type-utils-5.53.0.tgz",
- "integrity": "sha512-HO2hh0fmtqNLzTAme/KnND5uFNwbsdYhCZghK2SoxGp3Ifn2emv+hi0PBUjzzSh0dstUIFqOj3bp0AwQlK4OWw==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/type-utils/-/type-utils-5.59.8.tgz",
+ "integrity": "sha512-+5M518uEIHFBy3FnyqZUF3BMP+AXnYn4oyH8RF012+e7/msMY98FhGL5SrN29NQ9xDgvqCgYnsOiKp1VjZ/fpA==",
"dev": true,
"dependencies": {
- "@typescript-eslint/typescript-estree": "5.53.0",
- "@typescript-eslint/utils": "5.53.0",
+ "@typescript-eslint/typescript-estree": "5.59.8",
+ "@typescript-eslint/utils": "5.59.8",
"debug": "^4.3.4",
"tsutils": "^3.21.0"
},
@@ -828,9 +846,9 @@
}
},
"node_modules/@typescript-eslint/types": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-5.53.0.tgz",
- "integrity": "sha512-5kcDL9ZUIP756K6+QOAfPkigJmCPHcLN7Zjdz76lQWWDdzfOhZDTj1irs6gPBKiXx5/6O3L0+AvupAut3z7D2A==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-5.59.8.tgz",
+ "integrity": "sha512-+uWuOhBTj/L6awoWIg0BlWy0u9TyFpCHrAuQ5bNfxDaZ1Ppb3mx6tUigc74LHcbHpOHuOTOJrBoAnhdHdaea1w==",
"dev": true,
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
@@ -841,13 +859,13 @@
}
},
"node_modules/@typescript-eslint/typescript-estree": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-5.53.0.tgz",
- "integrity": "sha512-eKmipH7QyScpHSkhbptBBYh9v8FxtngLquq292YTEQ1pxVs39yFBlLC1xeIZcPPz1RWGqb7YgERJRGkjw8ZV7w==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-5.59.8.tgz",
+ "integrity": "sha512-Jy/lPSDJGNow14vYu6IrW790p7HIf/SOV1Bb6lZ7NUkLc2iB2Z9elESmsaUtLw8kVqogSbtLH9tut5GCX1RLDg==",
"dev": true,
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/visitor-keys": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/visitor-keys": "5.59.8",
"debug": "^4.3.4",
"globby": "^11.1.0",
"is-glob": "^4.0.3",
@@ -868,18 +886,18 @@
}
},
"node_modules/@typescript-eslint/utils": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-5.53.0.tgz",
- "integrity": "sha512-VUOOtPv27UNWLxFwQK/8+7kvxVC+hPHNsJjzlJyotlaHjLSIgOCKj9I0DBUjwOOA64qjBwx5afAPjksqOxMO0g==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-5.59.8.tgz",
+ "integrity": "sha512-Tr65630KysnNn9f9G7ROF3w1b5/7f6QVCJ+WK9nhIocWmx9F+TmCAcglF26Vm7z8KCTwoKcNEBZrhlklla3CKg==",
"dev": true,
"dependencies": {
+ "@eslint-community/eslint-utils": "^4.2.0",
"@types/json-schema": "^7.0.9",
"@types/semver": "^7.3.12",
- "@typescript-eslint/scope-manager": "5.53.0",
- "@typescript-eslint/types": "5.53.0",
- "@typescript-eslint/typescript-estree": "5.53.0",
+ "@typescript-eslint/scope-manager": "5.59.8",
+ "@typescript-eslint/types": "5.59.8",
+ "@typescript-eslint/typescript-estree": "5.59.8",
"eslint-scope": "^5.1.1",
- "eslint-utils": "^3.0.0",
"semver": "^7.3.7"
},
"engines": {
@@ -894,12 +912,12 @@
}
},
"node_modules/@typescript-eslint/visitor-keys": {
- "version": "5.53.0",
- "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.53.0.tgz",
- "integrity": "sha512-JqNLnX3leaHFZEN0gCh81sIvgrp/2GOACZNgO4+Tkf64u51kTpAyWFOY8XHx8XuXr3N2C9zgPPHtcpMg6z1g0w==",
+ "version": "5.59.8",
+ "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.59.8.tgz",
+ "integrity": "sha512-pJhi2ms0x0xgloT7xYabil3SGGlojNNKjK/q6dB3Ey0uJLMjK2UDGJvHieiyJVW/7C3KI+Z4Q3pEHkm4ejA+xQ==",
"dev": true,
"dependencies": {
- "@typescript-eslint/types": "5.53.0",
+ "@typescript-eslint/types": "5.59.8",
"eslint-visitor-keys": "^3.3.0"
},
"engines": {
@@ -1045,6 +1063,19 @@
"deep-equal": "^2.0.5"
}
},
+ "node_modules/array-buffer-byte-length": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/array-buffer-byte-length/-/array-buffer-byte-length-1.0.0.tgz",
+ "integrity": "sha512-LPuwb2P+NrQw3XhxGc36+XSvuBPopovXYTR9Ew++Du9Yb/bx5AzBfrIsBoj0EZUifjQU+sHL21sseZ3jerWO/A==",
+ "dev": true,
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "is-array-buffer": "^3.0.1"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"node_modules/array-includes": {
"version": "3.1.6",
"resolved": "https://registry.npmjs.org/array-includes/-/array-includes-3.1.6.tgz",
@@ -1487,16 +1518,17 @@
}
},
"node_modules/deep-equal": {
- "version": "2.2.0",
- "resolved": "https://registry.npmjs.org/deep-equal/-/deep-equal-2.2.0.tgz",
- "integrity": "sha512-RdpzE0Hv4lhowpIUKKMJfeH6C1pXdtT1/it80ubgWqwI3qpuxUBpC1S4hnHg+zjnuOoDkzUtUCEEkG+XG5l3Mw==",
+ "version": "2.2.1",
+ "resolved": "https://registry.npmjs.org/deep-equal/-/deep-equal-2.2.1.tgz",
+ "integrity": "sha512-lKdkdV6EOGoVn65XaOsPdH4rMxTZOnmFyuIkMjM1i5HHCbfjC97dawgTAy0deYNfuqUqW+Q5VrVaQYtUpSd6yQ==",
"dev": true,
"dependencies": {
+ "array-buffer-byte-length": "^1.0.0",
"call-bind": "^1.0.2",
- "es-get-iterator": "^1.1.2",
- "get-intrinsic": "^1.1.3",
+ "es-get-iterator": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"is-arguments": "^1.1.1",
- "is-array-buffer": "^3.0.1",
+ "is-array-buffer": "^3.0.2",
"is-date-object": "^1.0.5",
"is-regex": "^1.1.4",
"is-shared-array-buffer": "^1.0.2",
@@ -1504,7 +1536,7 @@
"object-is": "^1.1.5",
"object-keys": "^1.1.1",
"object.assign": "^4.1.4",
- "regexp.prototype.flags": "^1.4.3",
+ "regexp.prototype.flags": "^1.5.0",
"side-channel": "^1.0.4",
"which-boxed-primitive": "^1.0.2",
"which-collection": "^1.0.1",
@@ -1612,9 +1644,9 @@
"dev": true
},
"node_modules/entities": {
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- "resolved": "https://registry.npmjs.org/entities/-/entities-4.4.0.tgz",
- "integrity": "sha512-oYp7156SP8LkeGD0GF85ad1X9Ai79WtRsZ2gxJqtBuzH+98YUV6jkHEKlZkMbcrjJjIVJNIDP/3WL9wQkoPbWA==",
+ "version": "4.5.0",
+ "resolved": "https://registry.npmjs.org/entities/-/entities-4.5.0.tgz",
+ "integrity": "sha512-V0hjH4dGPh9Ao5p0MoRY6BVqtwCjhz6vI5LT8AJ55H+4g9/4vbHx1I54fS0XuclLhDHArPQCiMjDxjaL8fPxhw==",
"dev": true,
"engines": {
"node": ">=0.12"
@@ -1624,18 +1656,18 @@
}
},
"node_modules/es-abstract": {
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- "resolved": "https://registry.npmjs.org/es-abstract/-/es-abstract-1.21.1.tgz",
- "integrity": "sha512-QudMsPOz86xYz/1dG1OuGBKOELjCh99IIWHLzy5znUB6j8xG2yMA7bfTV86VSqKF+Y/H08vQPR+9jyXpuC6hfg==",
+ "version": "1.21.2",
+ "resolved": "https://registry.npmjs.org/es-abstract/-/es-abstract-1.21.2.tgz",
+ "integrity": "sha512-y/B5POM2iBnIxCiernH1G7rC9qQoM77lLIMQLuob0zhp8C56Po81+2Nj0WFKnd0pNReDTnkYryc+zhOzpEIROg==",
"dev": true,
"dependencies": {
+ "array-buffer-byte-length": "^1.0.0",
"available-typed-arrays": "^1.0.5",
"call-bind": "^1.0.2",
"es-set-tostringtag": "^2.0.1",
"es-to-primitive": "^1.2.1",
- "function-bind": "^1.1.1",
"function.prototype.name": "^1.1.5",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"get-symbol-description": "^1.0.0",
"globalthis": "^1.0.3",
"gopd": "^1.0.1",
@@ -1643,8 +1675,8 @@
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"has-proto": "^1.0.1",
"has-symbols": "^1.0.3",
- "internal-slot": "^1.0.4",
- "is-array-buffer": "^3.0.1",
+ "internal-slot": "^1.0.5",
+ "is-array-buffer": "^3.0.2",
"is-callable": "^1.2.7",
"is-negative-zero": "^2.0.2",
"is-regex": "^1.1.4",
@@ -1652,11 +1684,12 @@
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"is-typed-array": "^1.1.10",
"is-weakref": "^1.0.2",
- "object-inspect": "^1.12.2",
+ "object-inspect": "^1.12.3",
"object-keys": "^1.1.1",
"object.assign": "^4.1.4",
"regexp.prototype.flags": "^1.4.3",
"safe-regex-test": "^1.0.0",
+ "string.prototype.trim": "^1.2.7",
"string.prototype.trimend": "^1.0.6",
"string.prototype.trimstart": "^1.0.6",
"typed-array-length": "^1.0.4",
@@ -1921,12 +1954,15 @@
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- "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.34.0.tgz",
- "integrity": "sha512-1Z8iFsucw+7kSqXNZVslXS8Ioa4u2KM7GPwuKtkTFAqZ/cHMcEaR+1+Br0wLlot49cNxIiZk5wp8EAbPcYZxTg==",
+ "version": "8.41.0",
+ "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.41.0.tgz",
+ "integrity": "sha512-WQDQpzGBOP5IrXPo4Hc0814r4/v2rrIsB0rhT7jtunIalgg6gYXWhRMOejVO8yH21T/FGaxjmFjBMNqcIlmH1Q==",
"dev": true,
"dependencies": {
- "@eslint/eslintrc": "^1.4.1",
+ "@eslint-community/eslint-utils": "^4.2.0",
+ "@eslint-community/regexpp": "^4.4.0",
+ "@eslint/eslintrc": "^2.0.3",
+ "@eslint/js": "8.41.0",
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@@ -1936,24 +1972,22 @@
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- "eslint-utils": "^3.0.0",
- "eslint-visitor-keys": "^3.3.0",
- "espree": "^9.4.0",
- "esquery": "^1.4.0",
+ "eslint-scope": "^7.2.0",
+ "eslint-visitor-keys": "^3.4.1",
+ "espree": "^9.5.2",
+ "esquery": "^1.4.2",
"esutils": "^2.0.2",
"fast-deep-equal": "^3.1.3",
"file-entry-cache": "^6.0.1",
"find-up": "^5.0.0",
"glob-parent": "^6.0.2",
"globals": "^13.19.0",
- "grapheme-splitter": "^1.0.4",
+ "graphemer": "^1.4.0",
"ignore": "^5.2.0",
"import-fresh": "^3.0.0",
"imurmurhash": "^0.1.4",
"is-glob": "^4.0.0",
"is-path-inside": "^3.0.3",
- "js-sdsl": "^4.1.4",
"js-yaml": "^4.1.0",
"json-stable-stringify-without-jsonify": "^1.0.1",
"levn": "^0.4.1",
@@ -1961,7 +1995,6 @@
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"strip-json-comments": "^3.1.0",
"text-table": "^0.2.0"
@@ -1977,9 +2010,9 @@
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- "resolved": "https://registry.npmjs.org/eslint-config-standard/-/eslint-config-standard-17.0.0.tgz",
- "integrity": "sha512-/2ks1GKyqSOkH7JFvXJicu0iMpoojkwB+f5Du/1SC0PtBL+s8v30k9njRZ21pm2drKYm2342jFnGWzttxPmZVg==",
+ "version": "17.1.0",
+ "resolved": "https://registry.npmjs.org/eslint-config-standard/-/eslint-config-standard-17.1.0.tgz",
+ "integrity": "sha512-IwHwmaBNtDK4zDHQukFDW5u/aTb8+meQWZvNFWkiGmbWjD6bqyuSSBxxXKkCftCUzc1zwCH2m/baCNDLGmuO5Q==",
"dev": true,
"funding": [
{
@@ -1995,10 +2028,13 @@
"url": "https://feross.org/support"
}
],
+ "engines": {
+ "node": ">=12.0.0"
+ },
"peerDependencies": {
"eslint": "^8.0.1",
"eslint-plugin-import": "^2.25.2",
- "eslint-plugin-n": "^15.0.0",
+ "eslint-plugin-n": "^15.0.0 || ^16.0.0 ",
"eslint-plugin-promise": "^6.0.0"
}
},
@@ -2023,9 +2059,9 @@
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- "resolved": "https://registry.npmjs.org/eslint-module-utils/-/eslint-module-utils-2.7.4.tgz",
- "integrity": "sha512-j4GT+rqzCoRKHwURX7pddtIPGySnX9Si/cgMI5ztrcqOPtk5dDEeZ34CQVPphnqkJytlc97Vuk05Um2mJ3gEQA==",
+ "version": "2.8.0",
+ "resolved": "https://registry.npmjs.org/eslint-module-utils/-/eslint-module-utils-2.8.0.tgz",
+ "integrity": "sha512-aWajIYfsqCKRDgUfjEXNN/JlrzauMuSEy5sbd7WXbtW3EH6A6MpwEh42c7qD+MqQo9QMJ6fWLAeIJynx0g6OAw==",
"dev": true,
"dependencies": {
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@@ -2179,9 +2215,9 @@
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- "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.6.1.tgz",
- "integrity": "sha512-R9xw9OtCRxxaxaszTQmQAlPgM+RdGjaL1akWuY/Fv9fRAi8Wj4CUKc6iYVG8QNRjRuo8/BqVYIpfqberJUEacA==",
+ "version": "15.7.0",
+ "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.7.0.tgz",
+ "integrity": "sha512-jDex9s7D/Qial8AGVIHq4W7NswpUD5DPDL2RH8Lzd9EloWUuvUkHfv4FRLMipH5q2UtyurorBkPeNi1wVWNh3Q==",
"dev": true,
"dependencies": {
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@@ -2266,18 +2302,21 @@
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- "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-3.3.0.tgz",
- "integrity": "sha512-mQ+suqKJVyeuwGYHAdjMFqjCyfl8+Ldnxuyp3ldiMBFKkvytrXUZWaiPCEav8qDHKty44bD+qV1IP4T+w+xXRA==",
+ "version": "3.4.1",
+ "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-3.4.1.tgz",
+ "integrity": "sha512-pZnmmLwYzf+kWaM/Qgrvpen51upAktaaiI01nsJD/Yr3lMOdNtq0cxkrrg16w64VtisN6okbs7Q8AfGqj4c9fA==",
"dev": true,
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"node_modules/eslint/node_modules/eslint-scope": {
- "version": "7.1.1",
- "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.1.1.tgz",
- "integrity": "sha512-QKQM/UXpIiHcLqJ5AOyIW7XZmzjkzQXYE54n1++wb0u9V/abW3l9uQnxX8Z5Xd18xyKIMTUAyQ0k1e8pz6LUrw==",
+ "version": "7.2.0",
+ "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.2.0.tgz",
+ "integrity": "sha512-DYj5deGlHBfMt15J7rdtyKNq/Nqlv5KfU4iodrQ019XESsRnwXH9KAE0y3cwtUHDo2ob7CypAnCqefh6vioWRw==",
"dev": true,
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@@ -2285,6 +2324,9 @@
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+ },
+ "funding": {
+ "url": "https://opencollective.com/eslint"
}
},
"node_modules/eslint/node_modules/estraverse": {
@@ -2297,14 +2339,14 @@
}
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- "resolved": "https://registry.npmjs.org/espree/-/espree-9.4.1.tgz",
- "integrity": "sha512-XwctdmTO6SIvCzd9810yyNzIrOrqNYV9Koizx4C/mRhf9uq0o4yHoCEU/670pOxOL/MSraektvSAji79kX90Vg==",
+ "version": "9.5.2",
+ "resolved": "https://registry.npmjs.org/espree/-/espree-9.5.2.tgz",
+ "integrity": "sha512-7OASN1Wma5fum5SrNhFMAMJxOUAbhyfQ8dQ//PJaJbNw0URTPWqIghHWt1MmAANKhHZIYOHruW4Kw4ruUWOdGw==",
"dev": true,
"dependencies": {
"acorn": "^8.8.0",
"acorn-jsx": "^5.3.2",
- "eslint-visitor-keys": "^3.3.0"
+ "eslint-visitor-keys": "^3.4.1"
},
"engines": {
"node": "^12.22.0 || ^14.17.0 || >=16.0.0"
@@ -2327,9 +2369,9 @@
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- "resolved": "https://registry.npmjs.org/esquery/-/esquery-1.4.2.tgz",
- "integrity": "sha512-JVSoLdTlTDkmjFmab7H/9SL9qGSyjElT3myyKp7krqjVFQCDLmj1QFaCLRFBszBKI0XVZaiiXvuPIX3ZwHe1Ng==",
+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/esquery/-/esquery-1.5.0.tgz",
+ "integrity": "sha512-YQLXUplAwJgCydQ78IMJywZCceoqk1oH01OERdSAJc/7U2AylwjhSCLDEtqwg811idIS/9fIU5GjG73IgjKMVg==",
"dev": true,
"dependencies": {
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@@ -2618,13 +2660,14 @@
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- "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.2.0.tgz",
- "integrity": "sha512-L049y6nFOuom5wGyRc3/gdTLO94dySVKRACj1RmJZBQXlbTMhtNIgkWkUHq+jYmZvKf14EW1EoJnnjbmoHij0Q==",
+ "version": "1.2.1",
+ "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.2.1.tgz",
+ "integrity": "sha512-2DcsyfABl+gVHEfCOaTrWgyt+tb6MSEGmKq+kI5HwLbIYgjgmMcV8KQ41uaKz1xxUcn9tJtgFbQUEVcEbd0FYw==",
"dev": true,
"dependencies": {
"function-bind": "^1.1.1",
"has": "^1.0.3",
+ "has-proto": "^1.0.1",
"has-symbols": "^1.0.3"
},
"funding": {
@@ -2742,9 +2785,9 @@
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- "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.10.tgz",
- "integrity": "sha512-9ByhssR2fPVsNZj478qUUbKfmL0+t5BDVyjShtyZZLiK7ZDAArFFfopyOTj0M05wE2tJPisA4iTnnXl2YoPvOA==",
+ "version": "4.2.11",
+ "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.11.tgz",
+ "integrity": "sha512-RbJ5/jmFcNNCcDV5o9eTnBLJ/HszWV0P73bc+Ff4nS/rJj+YaS6IGyiOL0VoBYX+l1Wrl3k63h/KrH+nhJ0XvQ==",
"dev": true
},
"node_modules/grapheme-splitter": {
@@ -2753,6 +2796,12 @@
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"dev": true
},
+ "node_modules/graphemer": {
+ "version": "1.4.0",
+ "resolved": "https://registry.npmjs.org/graphemer/-/graphemer-1.4.0.tgz",
+ "integrity": "sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==",
+ "dev": true
+ },
"node_modules/has": {
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"resolved": "https://registry.npmjs.org/has/-/has-1.0.3.tgz",
@@ -2904,9 +2953,9 @@
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- "resolved": "https://registry.npmjs.org/immutable/-/immutable-4.2.4.tgz",
- "integrity": "sha512-WDxL3Hheb1JkRN3sQkyujNlL/xRjAo3rJtaU5xeufUauG66JdMr32bLj4gF+vWl84DIA3Zxw7tiAjneYzRRw+w==",
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/immutable/-/immutable-4.3.0.tgz",
+ "integrity": "sha512-0AOCmOip+xgJwEVTQj1EfiDDOkPmuyllDuTuEX+DDXUgapLAsBIfkg3sxCYyCEA8mQqZrrxPUGjcOQ2JS3WLkg==",
"dev": true
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"node_modules/import-fresh": {
@@ -2981,13 +3030,13 @@
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- "resolved": "https://registry.npmjs.org/is-array-buffer/-/is-array-buffer-3.0.1.tgz",
- "integrity": "sha512-ASfLknmY8Xa2XtB4wmbz13Wu202baeA18cJBCeCy0wXUHZF0IPyVEXqKEcd+t2fNSLLL1vC6k7lxZEojNbISXQ==",
+ "version": "3.0.2",
+ "resolved": "https://registry.npmjs.org/is-array-buffer/-/is-array-buffer-3.0.2.tgz",
+ "integrity": "sha512-y+FyyR/w8vfIRq4eQcM1EYgSTnmHXPqaF+IgzgraytCFq5Xh8lllDVmAZolPJiZttZLeFSINPYMaEJ7/vWUa1w==",
"dev": true,
"dependencies": {
"call-bind": "^1.0.2",
- "get-intrinsic": "^1.1.3",
+ "get-intrinsic": "^1.2.0",
"is-typed-array": "^1.1.10"
},
"funding": {
@@ -3053,9 +3102,9 @@
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- "resolved": "https://registry.npmjs.org/is-core-module/-/is-core-module-2.11.0.tgz",
- "integrity": "sha512-RRjxlvLDkD1YJwDbroBHMb+cukurkDWNyHx7D3oNB5x9rb5ogcksMC5wHCadcXoo67gVr/+3GFySh3134zi6rw==",
+ "version": "2.12.1",
+ "resolved": "https://registry.npmjs.org/is-core-module/-/is-core-module-2.12.1.tgz",
+ "integrity": "sha512-Q4ZuBAe2FUsKtyQJoQHlvP8OvBERxO3jEmy1I7hcRXcJBGGHFh/aJBswbXuS9sgrDH2QUO8ilkwNPHvHMd8clg==",
"dev": true,
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@@ -3334,16 +3383,6 @@
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"dev": true
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- "resolved": "https://registry.npmjs.org/js-sdsl/-/js-sdsl-4.3.0.tgz",
- "integrity": "sha512-mifzlm2+5nZ+lEcLJMoBK0/IH/bDg8XnJfd/Wq6IP+xoCjLZsTOnV2QpxlVbX9bMnkl5PdEjNtBJ9Cj1NjifhQ==",
- "dev": true,
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/js-sdsl"
- }
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"node_modules/js-tokens": {
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"resolved": "https://registry.npmjs.org/js-tokens/-/js-tokens-4.0.0.tgz",
@@ -3524,9 +3563,9 @@
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- "resolved": "https://registry.npmjs.org/lz-string/-/lz-string-1.4.4.tgz",
- "integrity": "sha512-0ckx7ZHRPqb0oUm8zNr+90mtf9DQB60H1wMCjBtfi62Kl3a7JbHob6gA2bC+xRvZoOL+1hzUK8jeuEIQE8svEQ==",
+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/lz-string/-/lz-string-1.5.0.tgz",
+ "integrity": "sha512-h5bgJWpxJNswbU7qCrV0tIKQCaS3blPDrqKWx+QxzuzL1zGUzij9XCWLrSLsJPu5t+eWA/ycetzYAO5IOMcWAQ==",
"dev": true,
"bin": {
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@@ -3831,9 +3870,9 @@
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- "resolved": "https://registry.npmjs.org/nwsapi/-/nwsapi-2.2.2.tgz",
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+ "version": "2.2.5",
+ "resolved": "https://registry.npmjs.org/nwsapi/-/nwsapi-2.2.5.tgz",
+ "integrity": "sha512-6xpotnECFy/og7tKSBVmUNft7J3jyXAka4XvG6AUhFWRz+Q/Ljus7znJAA3bxColfQLdS+XsjoodtJfCgeTEFQ==",
"dev": true
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"node_modules/object-inspect": {
@@ -4125,9 +4164,9 @@
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- "resolved": "https://registry.npmjs.org/rambda/-/rambda-7.4.0.tgz",
- "integrity": "sha512-A9hihu7dUTLOUCM+I8E61V4kRXnN4DwYeK0DwCBydC1MqNI1PidyAtbtpsJlBBzK4icSctEcCQ1bGcLpBuETUQ==",
+ "version": "7.5.0",
+ "resolved": "https://registry.npmjs.org/rambda/-/rambda-7.5.0.tgz",
+ "integrity": "sha512-y/M9weqWAH4iopRd7EHDEQQvpFPHj1AA3oHozE9tfITHUtTR7Z9PSlIRRG2l1GuW7sefC1cXFfIcF+cgnShdBA==",
"dev": true
},
"node_modules/randombytes": {
@@ -4164,14 +4203,14 @@
"dev": true
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+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/regexp.prototype.flags/-/regexp.prototype.flags-1.5.0.tgz",
+ "integrity": "sha512-0SutC3pNudRKgquxGoRGIz946MZVHqbNfPjBdxeOhBrdgDKlRoXmYLQN9xRbrR09ZXWeGAdPuif7egofn6v5LA==",
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"dependencies": {
"call-bind": "^1.0.2",
- "define-properties": "^1.1.3",
- "functions-have-names": "^1.2.2"
+ "define-properties": "^1.2.0",
+ "functions-have-names": "^1.2.3"
},
"engines": {
"node": ">= 0.4"
@@ -4208,12 +4247,12 @@
"dev": true
},
"node_modules/resolve": {
- "version": "1.22.1",
- "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.1.tgz",
- "integrity": "sha512-nBpuuYuY5jFsli/JIs1oldw6fOQCBioohqWZg/2hiaOybXOft4lonv85uDOKXdf8rhyK159cxU5cDcK/NKk8zw==",
+ "version": "1.22.2",
+ "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.2.tgz",
+ "integrity": "sha512-Sb+mjNHOULsBv818T40qSPeRiuWLyaGMa5ewydRLFimneixmVy2zdivRl+AF6jaYPC8ERxGDmFSiqui6SfPd+g==",
"dev": true,
"dependencies": {
- "is-core-module": "^2.9.0",
+ "is-core-module": "^2.11.0",
"path-parse": "^1.0.7",
"supports-preserve-symlinks-flag": "^1.0.0"
},
@@ -4358,9 +4397,9 @@
}
},
"node_modules/sass": {
- "version": "1.58.3",
- "resolved": "https://registry.npmjs.org/sass/-/sass-1.58.3.tgz",
- "integrity": "sha512-Q7RaEtYf6BflYrQ+buPudKR26/lH+10EmO9bBqbmPh/KeLqv8bjpTNqxe71ocONqXq+jYiCbpPUmQMS+JJPk4A==",
+ "version": "1.62.1",
+ "resolved": "https://registry.npmjs.org/sass/-/sass-1.62.1.tgz",
+ "integrity": "sha512-NHpxIzN29MXvWiuswfc1W3I0N8SXBd8UR26WntmDlRYf0bSADnwnOjsyMZ3lMezSlArD33Vs3YFhp7dWvL770A==",
"dev": true,
"dependencies": {
"chokidar": ">=3.0.0 <4.0.0",
@@ -4371,7 +4410,7 @@
"sass": "sass.js"
},
"engines": {
- "node": ">=12.0.0"
+ "node": ">=14.0.0"
}
},
"node_modules/saxes": {
@@ -4387,9 +4426,9 @@
}
},
"node_modules/semver": {
- "version": "7.3.8",
- "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz",
- "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==",
+ "version": "7.5.1",
+ "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.1.tgz",
+ "integrity": "sha512-Wvss5ivl8TMRZXXESstBA4uR5iXgEN/VC5/sOcuXdVLzcdkz4HWetIoRfG5gb5X+ij/G9rw9YoGn3QoQ8OCSpw==",
"dev": true,
"dependencies": {
"lru-cache": "^6.0.0"
@@ -4523,6 +4562,23 @@
"node": ">=8"
}
},
+ "node_modules/string.prototype.trim": {
+ "version": "1.2.7",
+ "resolved": "https://registry.npmjs.org/string.prototype.trim/-/string.prototype.trim-1.2.7.tgz",
+ "integrity": "sha512-p6TmeT1T3411M8Cgg9wBTMRtY2q9+PNy9EV1i2lIXUN/btt763oIfxwN3RR8VU6wHX8j/1CFy0L+YuThm6bgOg==",
+ "dev": true,
+ "dependencies": {
+ "call-bind": "^1.0.2",
+ "define-properties": "^1.1.4",
+ "es-abstract": "^1.20.4"
+ },
+ "engines": {
+ "node": ">= 0.4"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/ljharb"
+ }
+ },
"node_modules/string.prototype.trimend": {
"version": "1.0.6",
"resolved": "https://registry.npmjs.org/string.prototype.trimend/-/string.prototype.trimend-1.0.6.tgz",
@@ -4621,23 +4677,22 @@
}
},
"node_modules/svelte": {
- "version": "3.55.1",
- "resolved": "https://registry.npmjs.org/svelte/-/svelte-3.55.1.tgz",
- "integrity": "sha512-S+87/P0Ve67HxKkEV23iCdAh/SX1xiSfjF1HOglno/YTbSTW7RniICMCofWGdJJbdjw3S+0PfFb1JtGfTXE0oQ==",
+ "version": "3.59.1",
+ "resolved": "https://registry.npmjs.org/svelte/-/svelte-3.59.1.tgz",
+ "integrity": "sha512-pKj8fEBmqf6mq3/NfrB9SLtcJcUvjYSWyePlfCqN9gujLB25RitWK8PvFzlwim6hD/We35KbPlRteuA6rnPGcQ==",
"dev": true,
"engines": {
"node": ">= 8"
}
},
"node_modules/svelte-preprocess": {
- "version": "5.0.1",
- "resolved": "https://registry.npmjs.org/svelte-preprocess/-/svelte-preprocess-5.0.1.tgz",
- "integrity": "sha512-0HXyhCoc9rsW4zGOgtInylC6qj259E1hpFnJMJWTf+aIfeqh4O/QHT31KT2hvPEqQfdjmqBR/kO2JDkkciBLrQ==",
+ "version": "5.0.4",
+ "resolved": "https://registry.npmjs.org/svelte-preprocess/-/svelte-preprocess-5.0.4.tgz",
+ "integrity": "sha512-ABia2QegosxOGsVlsSBJvoWeXy1wUKSfF7SWJdTjLAbx/Y3SrVevvvbFNQqrSJw89+lNSsM58SipmZJ5SRi5iw==",
"dev": true,
"hasInstallScript": true,
"dependencies": {
"@types/pug": "^2.0.6",
- "@types/sass": "^1.43.1",
"detect-indent": "^6.1.0",
"magic-string": "^0.27.0",
"sorcery": "^0.11.0",
@@ -4656,8 +4711,8 @@
"sass": "^1.26.8",
"stylus": "^0.55.0",
"sugarss": "^2.0.0 || ^3.0.0 || ^4.0.0",
- "svelte": "^3.23.0",
- "typescript": "^3.9.5 || ^4.0.0"
+ "svelte": "^3.23.0 || ^4.0.0-next.0 || ^4.0.0",
+ "typescript": ">=3.9.5 || ^4.0.0 || ^5.0.0"
},
"peerDependenciesMeta": {
"@babel/core": {
@@ -4788,13 +4843,13 @@
}
},
"node_modules/tsconfig-paths": {
- "version": "3.14.1",
- "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-3.14.1.tgz",
- "integrity": "sha512-fxDhWnFSLt3VuTwtvJt5fpwxBHg5AdKWMsgcPOOIilyjymcYVZoCQF8fvFRezCNfblEXmi+PcM1eYHeOAgXCOQ==",
+ "version": "3.14.2",
+ "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-3.14.2.tgz",
+ "integrity": "sha512-o/9iXgCYc5L/JxCHPe3Hvh8Q/2xm5Z+p18PESBU6Ff33695QnCHBEjcytY2q19ua7Mbl/DavtBOLq+oG0RCL+g==",
"dev": true,
"dependencies": {
"@types/json5": "^0.0.29",
- "json5": "^1.0.1",
+ "json5": "^1.0.2",
"minimist": "^1.2.6",
"strip-bom": "^3.0.0"
}
@@ -5098,9 +5153,9 @@
"dev": true
},
"node_modules/ws": {
- "version": "8.12.1",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.12.1.tgz",
- "integrity": "sha512-1qo+M9Ba+xNhPB+YTWUlK6M17brTut5EXbcBaMRN5pH5dFrXz7lzz1ChFSUq3bOUl8yEvSenhHmYUNJxFzdJew==",
+ "version": "8.13.0",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.13.0.tgz",
+ "integrity": "sha512-x9vcZYTrFPC7aSIbj7sRCYo7L/Xb8Iy+pW0ng0wt2vCJv7M9HOMy0UoN3rr+IFC7hb7vXoqS+P9ktyLLLhO+LA==",
"dev": true,
"engines": {
"node": ">=10.0.0"
@@ -5155,9 +5210,9 @@
"dev": true
},
"node_modules/yargs": {
- "version": "17.7.1",
- "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.1.tgz",
- "integrity": "sha512-cwiTb08Xuv5fqF4AovYacTFNxk62th7LKJ6BL9IGUpTJrWoU7/7WdQGTP2SjKf1dUNBGzDd28p/Yfs/GI6JrLw==",
+ "version": "17.7.2",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz",
+ "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==",
"dev": true,
"dependencies": {
"cliui": "^8.0.1",
diff --git a/inception/inception-recommendation/src/main/ts_template/package.json b/inception/inception-recommendation/src/main/ts_template/package.json
index c525ea76081..9274f003d30 100644
--- a/inception/inception-recommendation/src/main/ts_template/package.json
+++ b/inception/inception-recommendation/src/main/ts_template/package.json
@@ -6,7 +6,7 @@
"homepage": "https://github.com/inception-project/inception#readme",
"scripts": {
"build": "node build.mjs",
- "test": "mocha -r esbuild-runner-plugins/register -r jsdom-global/register './test/**/*.test.ts' --extension ts --reporter mocha-junit-reporter --reporter-options mochaFile='../../../target/surefire-reports/mocha-test-report.xml'"
+ "test": "mocha -r esbuild-runner-plugins/register -r jsdom-global/register \"./test/**/*.test.ts\" --extension ts --reporter mocha-junit-reporter --reporter-options mochaFile=\"../../../target/surefire-reports/mocha-test-report.xml\""
},
"repository": {
"type": "git",
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/LearningRecordExporterTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/LearningRecordExporterTest.java
new file mode 100644
index 00000000000..bd35a24617d
--- /dev/null
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/LearningRecordExporterTest.java
@@ -0,0 +1,157 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.recommendation.exporter;
+
+import static java.util.Arrays.asList;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.doNothing;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import java.io.File;
+import java.util.List;
+import java.util.zip.ZipFile;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import de.tudarmstadt.ukp.clarin.webanno.api.DocumentService;
+import de.tudarmstadt.ukp.clarin.webanno.api.export.FullProjectExportRequest;
+import de.tudarmstadt.ukp.clarin.webanno.api.export.ProjectExportTaskMonitor;
+import de.tudarmstadt.ukp.clarin.webanno.api.export.ProjectImportRequest;
+import de.tudarmstadt.ukp.clarin.webanno.export.model.ExportedProject;
+import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
+import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
+import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecord;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordChangeLocation;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionType;
+import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
+
+@ExtendWith(MockitoExtension.class)
+public class LearningRecordExporterTest
+{
+ private @Mock AnnotationSchemaService annotationService;
+ private @Mock DocumentService documentService;
+ private @Mock LearningRecordService learningRecordService;
+
+ private Project project;
+ private SourceDocument document;
+ private AnnotationLayer layer;
+ private AnnotationFeature feature;
+
+ private LearningRecordExporter sut;
+
+ @BeforeEach
+ public void setUp()
+ {
+ project = Project.builder() //
+ .withId(1l) //
+ .withName("Test Project") //
+ .build();
+
+ document = SourceDocument.builder() //
+ .withId(1l) //
+ .withProject(project) //
+ .withName("Document") //
+ .build();
+
+ layer = AnnotationLayer.builder() //
+ .withId(1l) //
+ .withProject(project) //
+ .withName("Layer") //
+ .build();
+
+ feature = AnnotationFeature.builder() //
+ .withId(1l) //
+ .withProject(project) //
+ .withName("feature1") //
+ .build();
+
+ when(annotationService.findLayer(project, layer.getName())).thenReturn(layer);
+ when(annotationService.getFeature(eq(feature.getName()), eq(layer))).thenReturn(feature);
+ when(documentService.getSourceDocument(project, document.getName())).thenReturn(document);
+
+ sut = new LearningRecordExporter(annotationService, documentService, learningRecordService);
+ }
+
+ @Test
+ public void thatExportingWorks()
+ {
+ when(learningRecordService.listLearningRecords(project)).thenReturn(records());
+
+ // Export the project and import it again
+ var captor = runExportImportAndFetchRecommenders();
+
+ // Check that after re-importing the exported data is identical to the original
+ assertThat(captor.getAllValues()) //
+ .usingRecursiveFieldByFieldElementComparatorIgnoringFields("id", "actionDate")
+ .containsExactlyInAnyOrderElementsOf(records());
+ }
+
+ private ArgumentCaptor runExportImportAndFetchRecommenders()
+ {
+ // Export the project
+ FullProjectExportRequest exportRequest = new FullProjectExportRequest(project, null, false);
+ ProjectExportTaskMonitor monitor = new ProjectExportTaskMonitor(project, null, "test");
+ ExportedProject exportedProject = new ExportedProject();
+ File file = mock(File.class);
+
+ sut.exportData(exportRequest, monitor, exportedProject, file);
+
+ // Import the project again
+ var captor = ArgumentCaptor.forClass(LearningRecord.class);
+ doNothing().when(learningRecordService).createLearningRecord(captor.capture());
+
+ ProjectImportRequest importRequest = new ProjectImportRequest(true);
+ ZipFile zipFile = mock(ZipFile.class);
+ sut.importData(importRequest, project, exportedProject, zipFile);
+
+ return captor;
+ }
+
+ private List records()
+ {
+ LearningRecord r1 = LearningRecord.builder() //
+ .withAnnotation("label") //
+ .withAnnotationFeature(feature) //
+ .withChangeLocation(LearningRecordChangeLocation.MAIN_EDITOR) //
+ .withId(1l) //
+ .withLayer(layer) //
+ .withOffsetBegin(10) //
+ .withOffsetEnd(20) //
+ .withOffsetBegin2(-1) //
+ .withOffsetEnd2(-1) //
+ .withSourceDocument(document) //
+ .withSuggestionType(SuggestionType.SPAN) //
+ .withTokenText("0123456789") //
+ .withUser("user1") //
+ .withUserAction(LearningRecordType.ACCEPTED) //
+ .build();
+
+ return asList(r1);
+ }
+}
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/OverlapIteratorTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/OverlapIteratorTest.java
index 5c737d96d32..0100cf54e1f 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/OverlapIteratorTest.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/OverlapIteratorTest.java
@@ -310,7 +310,7 @@ private List overlapping(final List a, final List b,
if (overlaps) {
result.add(it.getA());
- it.ignoraA();
+ it.ignoreA();
}
it.step();
}
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/RecommenderExporterTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/RecommenderExporterTest.java
index 3723bd2bfd7..41f0dab6890 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/RecommenderExporterTest.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/exporter/RecommenderExporterTest.java
@@ -31,7 +31,6 @@
import static org.mockito.Mockito.when;
import java.io.File;
-import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.zip.ZipFile;
@@ -173,7 +172,7 @@ private List recommenders()
recommender1.setThreshold(.1);
recommender1.setSkipEvaluation(true);
recommender1.setMaxRecommendations(3);
- recommender1.setStatesIgnoredForTraining(asSet(NEW, IN_PROGRESS, FINISHED));
+ recommender1.setStatesIgnoredForTraining(Set.of(NEW, IN_PROGRESS, FINISHED));
Recommender recommender2 = buildRecommender("2");
recommender2.setAlwaysSelected(false);
@@ -181,7 +180,7 @@ private List recommenders()
recommender2.setThreshold(.2);
recommender2.setSkipEvaluation(false);
recommender2.setMaxRecommendations(4);
- recommender2.setStatesIgnoredForTraining(asSet(NEW, IN_PROGRESS));
+ recommender2.setStatesIgnoredForTraining(Set.of(NEW, IN_PROGRESS));
Recommender recommender3 = buildRecommender("3");
recommender3.setAlwaysSelected(true);
@@ -189,7 +188,7 @@ private List recommenders()
recommender3.setThreshold(.3);
recommender3.setSkipEvaluation(false);
recommender3.setMaxRecommendations(5);
- recommender3.setStatesIgnoredForTraining(asSet(AnnotationDocumentState.values()));
+ recommender3.setStatesIgnoredForTraining(Set.of(AnnotationDocumentState.values()));
Recommender recommender4 = buildRecommender("4");
recommender4.setAlwaysSelected(false);
@@ -197,7 +196,7 @@ private List recommenders()
recommender4.setThreshold(.4);
recommender4.setSkipEvaluation(true);
recommender4.setMaxRecommendations(6);
- recommender4.setStatesIgnoredForTraining(asSet());
+ recommender4.setStatesIgnoredForTraining(Set.of());
return asList(recommender1, recommender2, recommender3, recommender4);
}
@@ -222,9 +221,4 @@ private Recommender buildRecommender(String id)
recommender.setProject(project);
return recommender;
}
-
- private static Set asSet(T... a)
- {
- return new HashSet<>(asList(a));
- }
}
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventWebsocketControllerImplTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventWebsocketControllerImplTest.java
index 47b21ce7119..d17431bf2b5 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventWebsocketControllerImplTest.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventWebsocketControllerImplTest.java
@@ -71,7 +71,6 @@
import de.tudarmstadt.ukp.clarin.webanno.security.ExtensiblePermissionEvaluator;
import de.tudarmstadt.ukp.clarin.webanno.security.InceptionDaoAuthenticationProvider;
import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
-import de.tudarmstadt.ukp.clarin.webanno.security.config.InceptionSecurityAutoConfiguration;
import de.tudarmstadt.ukp.clarin.webanno.security.config.SecurityAutoConfiguration;
import de.tudarmstadt.ukp.clarin.webanno.security.model.User;
import de.tudarmstadt.ukp.clarin.webanno.support.ApplicationContextProvider;
@@ -99,11 +98,10 @@
exclude = { //
LiquibaseAutoConfiguration.class })
@ImportAutoConfiguration({ //
- InceptionSecurityAutoConfiguration.class, //
- CasDoctorAutoConfiguration.class, //
- DocumentServiceAutoConfiguration.class, //
CasStorageServiceAutoConfiguration.class, //
+ DocumentServiceAutoConfiguration.class, //
DocumentImportExportServiceAutoConfiguration.class, //
+ CasDoctorAutoConfiguration.class, //
SecurityAutoConfiguration.class, //
WebsocketSecurityConfig.class, //
WebsocketAutoConfiguration.class, //
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/Fixtures.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/Fixtures.java
index 9b606d89520..fa84dfe8ab4 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/Fixtures.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/Fixtures.java
@@ -17,6 +17,7 @@
*/
package de.tudarmstadt.ukp.inception.recommendation.service;
+import static de.tudarmstadt.ukp.inception.recommendation.api.model.AutoAcceptMode.NEVER;
import static java.util.stream.Collectors.toList;
import java.util.ArrayList;
@@ -66,7 +67,7 @@ static SuggestionDocumentGroup makeSpanSuggestionGroup(SourceDoc
for (int[] val : vals) {
suggestions.add(new SpanSuggestion(val[0], RECOMMENDER_ID, RECOMMENDER_NAME,
aFeat.getLayer().getId(), aFeat.getName(), doc.getName(), val[1], val[2],
- COVERED_TEXT, null, UI_LABEL, CONFIDENCE, CONFIDENCE_EXPLANATION));
+ COVERED_TEXT, null, UI_LABEL, CONFIDENCE, CONFIDENCE_EXPLANATION, NEVER));
}
return new SuggestionDocumentGroup<>(suggestions);
@@ -79,7 +80,7 @@ static SuggestionDocumentGroup makeRelationSuggestionGroup(
for (int[] val : vals) {
suggestions.add(new RelationSuggestion(val[0], RECOMMENDER_ID, RECOMMENDER_NAME,
aFeat.getLayer().getId(), aFeat.getName(), doc.getName(), val[1], val[2],
- val[3], val[4], null, UI_LABEL, CONFIDENCE, CONFIDENCE_EXPLANATION));
+ val[3], val[4], null, UI_LABEL, CONFIDENCE, CONFIDENCE_EXPLANATION, NEVER));
}
return new SuggestionDocumentGroup<>(suggestions);
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/LearningRecordServiceImplIntegrationTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/LearningRecordServiceImplIntegrationTest.java
deleted file mode 100644
index f159cd2a7bf..00000000000
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/LearningRecordServiceImplIntegrationTest.java
+++ /dev/null
@@ -1,217 +0,0 @@
-/*
- * Licensed to the Technische Universität Darmstadt under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The Technische Universität Darmstadt
- * licenses this file to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.tudarmstadt.ukp.inception.recommendation.service;
-
-import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordChangeLocation.DETAIL_EDITOR;
-import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordChangeLocation.MAIN_EDITOR;
-import static org.assertj.core.api.Assertions.assertThat;
-
-import java.util.List;
-
-import org.apache.uima.cas.CAS;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.liquibase.LiquibaseAutoConfiguration;
-import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
-import org.springframework.boot.test.autoconfigure.orm.jpa.TestEntityManager;
-import org.springframework.transaction.annotation.Transactional;
-
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
-import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
-import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecord;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.RelationSuggestion;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.SpanSuggestion;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionType;
-
-@Transactional
-@DataJpaTest(excludeAutoConfiguration = LiquibaseAutoConfiguration.class)
-public class LearningRecordServiceImplIntegrationTest
-{
- private static final String USER_NAME = "testUser";
- private static final String FEATURE_NAME = "testFeature";
-
- private @Autowired TestEntityManager testEntityManager;
-
- private LearningRecordService sut;
-
- @BeforeEach
- public void setUp() throws Exception
- {
- sut = new LearningRecordServiceImpl(testEntityManager.getEntityManager());
- }
-
- @AfterEach
- public void tearDown()
- {
- testEntityManager.clear();
- }
-
- @Test
- public void thatApplicationContextStarts()
- {
- }
-
- @Test
- public void thatSpanSuggestionsCanBeRecorded()
- {
- SourceDocument sourceDoc = createSourceDocument("doc");
- AnnotationLayer layer = createAnnotationLayer("layer");
- AnnotationFeature feature = createAnnotationFeature(layer, FEATURE_NAME);
-
- SpanSuggestion suggestion = new SpanSuggestion(42, 1337, "testRecommender", layer.getId(),
- feature.getName(), sourceDoc.getName(), 7, 14, "aCoveredText", "testLabel",
- "testUiLabel", 0.42, "Test confidence");
-
- sut.logSpanRecord(sourceDoc, USER_NAME, suggestion, layer, feature,
- LearningRecordType.ACCEPTED, MAIN_EDITOR);
-
- List records = sut.listRecords(USER_NAME, layer);
- assertThat(records).hasSize(1);
-
- LearningRecord record = records.get(0);
- assertThat(record).hasFieldOrProperty("id") //
- .hasFieldOrPropertyWithValue("sourceDocument", sourceDoc) //
- .hasFieldOrPropertyWithValue("user", USER_NAME) //
- .hasFieldOrPropertyWithValue("layer", layer) //
- .hasFieldOrPropertyWithValue("annotationFeature", feature) //
- .hasFieldOrPropertyWithValue("offsetBegin", 7) //
- .hasFieldOrPropertyWithValue("offsetEnd", 14) //
- .hasFieldOrPropertyWithValue("offsetBegin2", -1) //
- .hasFieldOrPropertyWithValue("offsetEnd2", -1) //
- .hasFieldOrPropertyWithValue("tokenText", "aCoveredText") //
- .hasFieldOrPropertyWithValue("annotation", "testLabel") //
- .hasFieldOrPropertyWithValue("changeLocation", MAIN_EDITOR) //
- .hasFieldOrPropertyWithValue("userAction", LearningRecordType.ACCEPTED) //
- .hasFieldOrPropertyWithValue("suggestionType", SuggestionType.SPAN);
- }
-
- @Test
- public void thatRelationSuggestionsCanBeRecorded()
- {
- SourceDocument sourceDoc = createSourceDocument("doc");
- AnnotationLayer layer = createAnnotationLayer("layer");
- AnnotationFeature feature = createAnnotationFeature(layer, FEATURE_NAME);
-
- RelationSuggestion suggestion = new RelationSuggestion(42, 1337, "testRecommender",
- layer.getId(), feature.getName(), sourceDoc.getName(), 7, 14, 21, 28, "testLabel",
- "testUiLabel", 0.42, "Test confidence");
-
- sut.logRelationRecord(sourceDoc, USER_NAME, suggestion, layer, feature,
- LearningRecordType.REJECTED, DETAIL_EDITOR);
-
- List records = sut.listRecords(USER_NAME, layer);
- assertThat(records).hasSize(1);
-
- LearningRecord record = records.get(0);
- assertThat(record).hasFieldOrProperty("id") //
- .hasFieldOrPropertyWithValue("sourceDocument", sourceDoc) //
- .hasFieldOrPropertyWithValue("user", USER_NAME) //
- .hasFieldOrPropertyWithValue("layer", layer) //
- .hasFieldOrPropertyWithValue("annotationFeature", feature) //
- .hasFieldOrPropertyWithValue("offsetBegin", 7) //
- .hasFieldOrPropertyWithValue("offsetEnd", 14) //
- .hasFieldOrPropertyWithValue("offsetBegin2", 21) //
- .hasFieldOrPropertyWithValue("offsetEnd2", 28) //
- .hasFieldOrPropertyWithValue("tokenText", "") //
- .hasFieldOrPropertyWithValue("annotation", "testLabel") //
- .hasFieldOrPropertyWithValue("changeLocation", DETAIL_EDITOR) //
- .hasFieldOrPropertyWithValue("userAction", LearningRecordType.REJECTED) //
- .hasFieldOrPropertyWithValue("suggestionType", SuggestionType.RELATION);
- }
-
- @Test
- void thatListingRecordsForRendering()
- {
- SourceDocument sourceDoc1 = createSourceDocument("doc1");
- SourceDocument sourceDoc2 = createSourceDocument("doc2");
- AnnotationLayer layer1 = createAnnotationLayer("layer1");
- AnnotationLayer layer2 = createAnnotationLayer("layer2");
- AnnotationFeature feature1 = createAnnotationFeature(layer1, "feat1");
- AnnotationFeature feature2 = createAnnotationFeature(layer2, "feat1");
-
- sut.logSpanRecord(sourceDoc1, USER_NAME,
- new SpanSuggestion(42, 1337, "testRecommender", layer1.getId(), feature1.getName(),
- sourceDoc1.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
- 0.42, "Test confidence"),
- layer1, feature1, LearningRecordType.ACCEPTED, MAIN_EDITOR);
-
- sut.logSpanRecord(sourceDoc1, USER_NAME,
- new SpanSuggestion(42, 1337, "testRecommender2", layer2.getId(), feature2.getName(),
- sourceDoc1.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
- 0.42, "Test confidence"),
- layer2, feature2, LearningRecordType.ACCEPTED, MAIN_EDITOR);
-
- sut.logSpanRecord(sourceDoc2, USER_NAME,
- new SpanSuggestion(42, 1337, "testRecommender", layer1.getId(), feature1.getName(),
- sourceDoc2.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
- 0.42, "Test confidence"),
- layer1, feature1, LearningRecordType.ACCEPTED, MAIN_EDITOR);
-
- sut.logSpanRecord(sourceDoc2, USER_NAME,
- new SpanSuggestion(42, 1337, "testRecommender2", layer2.getId(), feature2.getName(),
- sourceDoc2.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
- 0.42, "Test confidence"),
- layer2, feature2, LearningRecordType.ACCEPTED, MAIN_EDITOR);
-
- assertThat(sut.listRecords(sourceDoc1, USER_NAME, feature1)).hasSize(1);
- assertThat(sut.listRecords(sourceDoc1, USER_NAME, feature2)).hasSize(1);
- assertThat(sut.listRecords(sourceDoc2, USER_NAME, feature1)).hasSize(1);
- assertThat(sut.listRecords(sourceDoc2, USER_NAME, feature2)).hasSize(1);
- assertThat(sut.listRecords(sourceDoc1, "otherUser", feature1)).hasSize(0);
- assertThat(sut.listRecords(sourceDoc1, "otherUser", feature2)).hasSize(0);
- }
-
- // Helper
-
- private SourceDocument createSourceDocument(String aName)
- {
- SourceDocument doc = new SourceDocument();
- doc.setName(aName);
- return testEntityManager.persist(doc);
- }
-
- private AnnotationLayer createAnnotationLayer(String aType)
- {
- AnnotationLayer layer = new AnnotationLayer();
- layer.setEnabled(true);
- layer.setName(aType);
- layer.setReadonly(false);
- layer.setType(aType);
- layer.setUiName(aType);
- layer.setAnchoringMode(false, false);
-
- return testEntityManager.persist(layer);
- }
-
- private AnnotationFeature createAnnotationFeature(AnnotationLayer aLayer, String aName)
- {
- AnnotationFeature feature = new AnnotationFeature();
- feature.setLayer(aLayer);
- feature.setName(aName);
- feature.setUiName(aName);
- feature.setType(CAS.TYPE_NAME_STRING);
-
- return testEntityManager.persist(feature);
- }
-}
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplIntegrationTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplIntegrationTest.java
index ed65df4f22f..632e1d48faf 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplIntegrationTest.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplIntegrationTest.java
@@ -17,15 +17,23 @@
*/
package de.tudarmstadt.ukp.inception.recommendation.service;
+import static de.tudarmstadt.ukp.clarin.webanno.model.OverlapMode.ANY_OVERLAP;
+import static de.tudarmstadt.ukp.clarin.webanno.model.OverlapMode.NO_OVERLAP;
+import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_AUTO_ACCEPT_MODE_SUFFIX;
import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_IS_PREDICTION;
import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_SCORE_EXPLANATION_SUFFIX;
import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_SCORE_SUFFIX;
+import static de.tudarmstadt.ukp.inception.recommendation.api.model.AutoAcceptMode.NEVER;
+import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordChangeLocation.DETAIL_EDITOR;
+import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordChangeLocation.MAIN_EDITOR;
+import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType.ACCEPTED;
import static de.tudarmstadt.ukp.inception.recommendation.service.RecommendationServiceImpl.getOffsetsAnchoredOnTokens;
import static java.util.Arrays.asList;
import static org.apache.uima.fit.factory.JCasFactory.createJCas;
import static org.apache.uima.fit.factory.JCasFactory.createText;
import static org.apache.uima.util.TypeSystemUtil.typeSystem2TypeSystemDescription;
import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.tuple;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.doCallRealMethod;
import static org.mockito.Mockito.mock;
@@ -59,15 +67,26 @@
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
+import de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst;
import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
+import de.tudarmstadt.ukp.inception.annotation.feature.string.StringFeatureSupport;
+import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanAdapter;
import de.tudarmstadt.ukp.inception.annotation.storage.CasStorageSession;
import de.tudarmstadt.ukp.inception.recommendation.api.RecommenderFactoryRegistry;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecord;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType;
import de.tudarmstadt.ukp.inception.recommendation.api.model.Offset;
import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.RelationSuggestion;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.SpanSuggestion;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionType;
import de.tudarmstadt.ukp.inception.recommendation.api.recommender.RecommendationEngineFactory;
+import de.tudarmstadt.ukp.inception.schema.layer.LayerSupportRegistry;
import de.tudarmstadt.ukp.inception.schema.service.AnnotationSchemaServiceImpl;
+import de.tudarmstadt.ukp.inception.schema.service.FeatureSupportRegistryImpl;
@ExtendWith(MockitoExtension.class)
@ContextConfiguration(classes = SpringConfig.class)
@@ -76,13 +95,18 @@
public class RecommendationServiceImplIntegrationTest
{
private static final String PROJECT_NAME = "Test project";
+ private static final String USER_NAME = "testUser";
+ private static final String FEATURE_NAME = "testFeature";
private @Autowired TestEntityManager testEntityManager;
- private RecommendationServiceImpl sut;
private @Mock RecommenderFactoryRegistry recommenderFactoryRegistry;
- private @Mock AnnotationSchemaServiceImpl annoService;
+ private @Mock AnnotationSchemaServiceImpl schemaService;
+ private @Mock LayerSupportRegistry layerSupportRegistry;
+
+ private RecommendationServiceImpl sut;
+ private FeatureSupportRegistryImpl featureSupportRegistry;
private Project project;
private AnnotationLayer layer;
private Recommender rec;
@@ -92,7 +116,10 @@ public class RecommendationServiceImplIntegrationTest
public void setUp() throws Exception
{
sut = new RecommendationServiceImpl(null, null, null, recommenderFactoryRegistry, null,
- annoService, null, null, testEntityManager.getEntityManager());
+ schemaService, null, testEntityManager.getEntityManager());
+
+ featureSupportRegistry = new FeatureSupportRegistryImpl(asList(new StringFeatureSupport()));
+ featureSupportRegistry.init();
project = createProject(PROJECT_NAME);
layer = createAnnotationLayer();
@@ -189,25 +216,33 @@ public void monkeyPatchTypeSystem_WithNer_CreatesScoreFeatures() throws Exceptio
JCas jCas = createText("I am text CAS", "de");
session.add("jCas", CasAccessMode.EXCLUSIVE_WRITE_ACCESS, jCas.getCas());
- when(annoService.getFullProjectTypeSystem(project))
+ when(schemaService.getFullProjectTypeSystem(project))
.thenReturn(typeSystem2TypeSystemDescription(jCas.getTypeSystem()));
- when(annoService.listAnnotationLayer(project)).thenReturn(asList(layer));
- doCallRealMethod().when(annoService).upgradeCas(any(CAS.class), any(CAS.class),
+ when(schemaService.listAnnotationFeature(project)).thenReturn(asList(feature));
+ doCallRealMethod().when(schemaService).upgradeCas(any(CAS.class), any(CAS.class),
any(TypeSystemDescription.class));
sut.cloneAndMonkeyPatchCAS(project, jCas.getCas(), jCas.getCas());
Type type = CasUtil.getType(jCas.getCas(), layer.getName());
- assertThat(type.getFeatures()).extracting(Feature::getShortName)
- .contains(feature.getName() + FEATURE_NAME_SCORE_SUFFIX)
- .contains(feature.getName() + FEATURE_NAME_SCORE_EXPLANATION_SUFFIX)
- .contains(FEATURE_NAME_IS_PREDICTION);
+ assertThat(type.getFeatures()) //
+ .extracting(Feature::getShortName) //
+ .containsExactlyInAnyOrder( //
+ "sofa", //
+ "begin", //
+ "end", //
+ "value", //
+ feature.getName() + FEATURE_NAME_SCORE_SUFFIX, //
+ feature.getName() + FEATURE_NAME_SCORE_EXPLANATION_SUFFIX, //
+ feature.getName() + FEATURE_NAME_AUTO_ACCEPT_MODE_SUFFIX, //
+ "identifier", //
+ FEATURE_NAME_IS_PREDICTION);
}
}
@Test
- void thatZeroWithAnnotationsAreCorretlyAnchoredOnTokens() throws Exception
+ void thatZeroWithAnnotationsAreCorrectlyAnchoredOnTokens() throws Exception
{
JCas jCas = createJCas();
TokenBuilder.create(Token.class, Sentence.class).buildTokens(jCas, " This is a test. ");
@@ -234,45 +269,264 @@ void thatZeroWithAnnotationsAreCorretlyAnchoredOnTokens() throws Exception
.isEqualTo(new Offset(9, 9));
}
+ @Test
+ void testUpsertSpanFeature() throws Exception
+ {
+ var docOwner = "dummy";
+ var doc = SourceDocument.builder() //
+ .withProject(project) //
+ .build();
+ var feature = AnnotationFeature.builder() //
+ .withName(NamedEntity._FeatName_value) //
+ .withType(CAS.TYPE_NAME_STRING) //
+ .build();
+ var layer = AnnotationLayer.builder() //
+ .forJCasClass(NamedEntity.class) //
+ .build();
+ var adapter = new SpanAdapter(layerSupportRegistry, featureSupportRegistry, null, layer,
+ () -> asList(), asList());
+
+ layer.setOverlapMode(NO_OVERLAP);
+ var cas = createJCas();
+ var targetFS = new NamedEntity(cas, 0, 10);
+ targetFS.addToIndexes();
+ assertThat(targetFS.getValue()).isNull();
+
+ var s1 = SpanSuggestion.builder().withLabel("V1").withPosition(new Offset(targetFS))
+ .build();
+ sut.acceptSuggestion(USER_NAME, doc, docOwner, cas.getCas(), adapter, feature, s1,
+ MAIN_EDITOR);
+
+ assertThat(targetFS.getValue()) //
+ .as("Label was merged into existing annotation replacing unset label") //
+ .isEqualTo("V1");
+
+ var s2 = SpanSuggestion.builder().withLabel("V2").withPosition(new Offset(targetFS))
+ .build();
+ sut.acceptSuggestion(USER_NAME, doc, docOwner, cas.getCas(), adapter, feature, s2,
+ MAIN_EDITOR);
+
+ assertThat(targetFS.getValue()) //
+ .as("Label was merged into existing annotation replacing previous label") //
+ .isEqualTo("V2");
+
+ var s3 = SpanSuggestion.builder().withLabel("V3").withPosition(new Offset(10, 20)).build();
+ sut.acceptSuggestion(USER_NAME, doc, docOwner, cas.getCas(), adapter, feature, s3,
+ MAIN_EDITOR);
+
+ assertThat(cas.select(NamedEntity.class).asList()) //
+ .as("Label was merged as new annotation") //
+ .extracting(NamedEntity::getBegin, NamedEntity::getEnd, NamedEntity::getValue)
+ .containsExactlyInAnyOrder( //
+ tuple(0, 10, "V2"), //
+ tuple(10, 20, "V3"));
+
+ layer.setOverlapMode(ANY_OVERLAP);
+ cas.reset();
+ targetFS = new NamedEntity(cas, 0, 10);
+ targetFS.addToIndexes();
+ assertThat(targetFS.getValue()).isNull();
+
+ var s4 = SpanSuggestion.builder().withLabel("V1").withPosition(new Offset(targetFS))
+ .build();
+ sut.acceptSuggestion(USER_NAME, doc, docOwner, cas.getCas(), adapter, feature, s4,
+ MAIN_EDITOR);
+
+ assertThat(targetFS.getValue()) //
+ .as("Label was merged into existing annotation replacing unset label") //
+ .isEqualTo("V1");
+
+ var s5 = SpanSuggestion.builder().withLabel("V2").withPosition(new Offset(targetFS))
+ .build();
+ sut.acceptSuggestion(USER_NAME, doc, docOwner, cas.getCas(), adapter, feature, s5,
+ MAIN_EDITOR);
+
+ assertThat(cas.select(NamedEntity.class).asList()) //
+ .as("Label was merged as new annotation") //
+ .extracting(NamedEntity::getBegin, NamedEntity::getEnd, NamedEntity::getValue)
+ .containsExactlyInAnyOrder( //
+ tuple(0, 10, "V1"), //
+ tuple(0, 10, "V2"));
+
+ var s6 = SpanSuggestion.builder().withLabel("V3").withPosition(new Offset(10, 20)).build();
+ sut.acceptSuggestion(USER_NAME, doc, docOwner, cas.getCas(), adapter, feature, s6,
+ MAIN_EDITOR);
+
+ assertThat(cas.select(NamedEntity.class).asList()) //
+ .as("Label was merged as new annotation") //
+ .extracting(NamedEntity::getBegin, NamedEntity::getEnd, NamedEntity::getValue)
+ .containsExactlyInAnyOrder( //
+ tuple(0, 10, "V1"), //
+ tuple(0, 10, "V2"), //
+ tuple(10, 20, "V3"));
+
+ new NamedEntity(cas, 0, 10).addToIndexes();
+ new NamedEntity(cas, 0, 10).addToIndexes();
+
+ var s7 = SpanSuggestion.builder().withLabel("V4").withPosition(new Offset(0, 10)).build();
+ sut.acceptSuggestion(USER_NAME, doc, docOwner, cas.getCas(), adapter, feature, s7,
+ MAIN_EDITOR);
+
+ assertThat(cas.select(NamedEntity.class).asList()) //
+ .as("Label was merged again into one of the entities without a label") //
+ .extracting(NamedEntity::getBegin, NamedEntity::getEnd, NamedEntity::getValue)
+ .containsExactlyInAnyOrder( //
+ tuple(0, 10, "V1"), //
+ tuple(0, 10, "V2"), //
+ tuple(0, 10, "V4"), //
+ tuple(0, 10, null), //
+ tuple(10, 20, "V3"));
+ }
+
+ @Test
+ public void thatSpanSuggestionsCanBeRecorded()
+ {
+ SourceDocument sourceDoc = createSourceDocument("doc");
+ AnnotationLayer layer = createAnnotationLayer("layer");
+ AnnotationFeature feature = createAnnotationFeature(layer, FEATURE_NAME);
+
+ var suggestion = SpanSuggestion.builder() //
+ .withId(42) //
+ .withRecommenderId(1337) //
+ .withRecommenderName("testRecommender") //
+ .withLayerId(layer.getId()) //
+ .withFeature(feature.getName()) //
+ .withDocumentName(sourceDoc.getName()) //
+ .withPosition(new Offset(7, 14)) //
+ .withCoveredText("aCoveredText") //
+ .withLabel("testLabel") //
+ .withUiLabel("testUiLabel") //
+ .withScore(0.42) //
+ .withScoreExplanation("Test confidence") //
+ .withAutoAcceptMode(NEVER) //
+ .build();
+
+ sut.logRecord(USER_NAME, sourceDoc, USER_NAME, suggestion, feature, ACCEPTED, MAIN_EDITOR);
+
+ var records = sut.listLearningRecords(USER_NAME, USER_NAME, layer);
+ assertThat(records).hasSize(1);
+
+ LearningRecord record = records.get(0);
+ assertThat(record).hasFieldOrProperty("id") //
+ .hasFieldOrPropertyWithValue("sourceDocument", sourceDoc) //
+ .hasFieldOrPropertyWithValue("user", USER_NAME) //
+ .hasFieldOrPropertyWithValue("layer", layer) //
+ .hasFieldOrPropertyWithValue("annotationFeature", feature) //
+ .hasFieldOrPropertyWithValue("offsetBegin", 7) //
+ .hasFieldOrPropertyWithValue("offsetEnd", 14) //
+ .hasFieldOrPropertyWithValue("offsetBegin2", -1) //
+ .hasFieldOrPropertyWithValue("offsetEnd2", -1) //
+ .hasFieldOrPropertyWithValue("tokenText", "aCoveredText") //
+ .hasFieldOrPropertyWithValue("annotation", "testLabel") //
+ .hasFieldOrPropertyWithValue("changeLocation", MAIN_EDITOR) //
+ .hasFieldOrPropertyWithValue("userAction", ACCEPTED) //
+ .hasFieldOrPropertyWithValue("suggestionType", SuggestionType.SPAN);
+ }
+
+ @Test
+ public void thatRelationSuggestionsCanBeRecorded()
+ {
+ SourceDocument sourceDoc = createSourceDocument("doc");
+ AnnotationLayer layer = createAnnotationLayer("layer");
+ AnnotationFeature feature = createAnnotationFeature(layer, FEATURE_NAME);
+
+ RelationSuggestion suggestion = new RelationSuggestion(42, 1337, "testRecommender",
+ layer.getId(), feature.getName(), sourceDoc.getName(), 7, 14, 21, 28, "testLabel",
+ "testUiLabel", 0.42, "Test confidence", NEVER);
+
+ sut.logRecord(USER_NAME, sourceDoc, USER_NAME, suggestion, feature,
+ LearningRecordType.REJECTED, DETAIL_EDITOR);
+
+ var records = sut.listLearningRecords(USER_NAME, USER_NAME, layer);
+ assertThat(records).hasSize(1);
+
+ LearningRecord record = records.get(0);
+ assertThat(record).hasFieldOrProperty("id") //
+ .hasFieldOrPropertyWithValue("sourceDocument", sourceDoc) //
+ .hasFieldOrPropertyWithValue("user", USER_NAME) //
+ .hasFieldOrPropertyWithValue("layer", layer) //
+ .hasFieldOrPropertyWithValue("annotationFeature", feature) //
+ .hasFieldOrPropertyWithValue("offsetBegin", 7) //
+ .hasFieldOrPropertyWithValue("offsetEnd", 14) //
+ .hasFieldOrPropertyWithValue("offsetBegin2", 21) //
+ .hasFieldOrPropertyWithValue("offsetEnd2", 28) //
+ .hasFieldOrPropertyWithValue("tokenText", "") //
+ .hasFieldOrPropertyWithValue("annotation", "testLabel") //
+ .hasFieldOrPropertyWithValue("changeLocation", DETAIL_EDITOR) //
+ .hasFieldOrPropertyWithValue("userAction", LearningRecordType.REJECTED) //
+ .hasFieldOrPropertyWithValue("suggestionType", SuggestionType.RELATION);
+ }
+
+ @Test
+ void thatListingRecordsForRendering()
+ {
+ var sourceDoc1 = createSourceDocument("doc1");
+ var sourceDoc2 = createSourceDocument("doc2");
+ var layer1 = createAnnotationLayer("layer1");
+ var layer2 = createAnnotationLayer("layer2");
+ var feature1 = createAnnotationFeature(layer1, "feat1");
+ var feature2 = createAnnotationFeature(layer2, "feat1");
+
+ sut.logRecord(USER_NAME, sourceDoc1, USER_NAME,
+ new SpanSuggestion(42, 1337, "testRecommender", layer1.getId(), feature1.getName(),
+ sourceDoc1.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
+ 0.42, "Test confidence", NEVER),
+ feature1, ACCEPTED, MAIN_EDITOR);
+
+ sut.logRecord(USER_NAME, sourceDoc1, USER_NAME,
+ new SpanSuggestion(42, 1337, "testRecommender2", layer2.getId(), feature2.getName(),
+ sourceDoc1.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
+ 0.42, "Test confidence", NEVER),
+ feature2, ACCEPTED, MAIN_EDITOR);
+
+ sut.logRecord(USER_NAME, sourceDoc2, USER_NAME,
+ new SpanSuggestion(42, 1337, "testRecommender", layer1.getId(), feature1.getName(),
+ sourceDoc2.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
+ 0.42, "Test confidence", NEVER),
+ feature1, ACCEPTED, MAIN_EDITOR);
+
+ sut.logRecord(USER_NAME, sourceDoc2, USER_NAME,
+ new SpanSuggestion(42, 1337, "testRecommender2", layer2.getId(), feature2.getName(),
+ sourceDoc2.getName(), 7, 14, "aCoveredText", "testLabel", "testUiLabel",
+ 0.42, "Test confidence", NEVER),
+ feature2, ACCEPTED, MAIN_EDITOR);
+
+ assertThat(sut.listLearningRecords(USER_NAME, sourceDoc1, USER_NAME, feature1)).hasSize(1);
+ assertThat(sut.listLearningRecords(USER_NAME, sourceDoc1, USER_NAME, feature2)).hasSize(1);
+ assertThat(sut.listLearningRecords(USER_NAME, sourceDoc2, USER_NAME, feature1)).hasSize(1);
+ assertThat(sut.listLearningRecords(USER_NAME, sourceDoc2, USER_NAME, feature2)).hasSize(1);
+ assertThat(sut.listLearningRecords(USER_NAME, sourceDoc1, "otherUser", feature1)).isEmpty();
+ assertThat(sut.listLearningRecords(USER_NAME, sourceDoc1, "otherUser", feature2)).isEmpty();
+ }
+
// Helper
- private Project createProject(String aName)
+ private SourceDocument createSourceDocument(String aName)
{
- Project l = new Project();
- l.setName(aName);
- return testEntityManager.persist(l);
+ var doc = new SourceDocument();
+ doc.setProject(project);
+ doc.setName(aName);
+ return testEntityManager.persist(doc);
}
- private AnnotationLayer createAnnotationLayer()
+ private AnnotationLayer createAnnotationLayer(String aType)
{
- AnnotationLayer l = new AnnotationLayer();
+ var l = new AnnotationLayer();
+ l.setProject(project);
l.setEnabled(true);
- l.setName(NamedEntity.class.getName());
+ l.setName(aType);
l.setReadonly(false);
- l.setType(NamedEntity.class.getName());
- l.setUiName("test ui name");
+ l.setType(WebAnnoConst.SPAN_TYPE);
+ l.setUiName(aType);
l.setAnchoringMode(false, false);
return testEntityManager.persist(l);
}
- private Recommender buildRecommender(Project aProject, AnnotationFeature aFeature)
- {
- Recommender recommender = new Recommender();
- recommender.setLayer(aFeature.getLayer());
- recommender.setFeature(aFeature);
- recommender.setProject(aProject);
- recommender.setAlwaysSelected(true);
- recommender.setSkipEvaluation(false);
- recommender.setMaxRecommendations(3);
- recommender.setTool("dummyRecommenderTool");
-
- return recommender;
- }
-
private AnnotationFeature createAnnotationFeature(AnnotationLayer aLayer, String aName)
{
- AnnotationFeature f = new AnnotationFeature();
+ var f = new AnnotationFeature();
+ f.setProject(project);
f.setLayer(aLayer);
f.setName(aName);
f.setUiName(aName);
@@ -280,4 +534,30 @@ private AnnotationFeature createAnnotationFeature(AnnotationLayer aLayer, String
return testEntityManager.persist(f);
}
+
+ private Project createProject(String aName)
+ {
+ var l = new Project();
+ l.setName(aName);
+ return testEntityManager.persist(l);
+ }
+
+ private AnnotationLayer createAnnotationLayer()
+ {
+ return createAnnotationLayer(NamedEntity._TypeName);
+ }
+
+ private Recommender buildRecommender(Project aProject, AnnotationFeature aFeature)
+ {
+ var r = new Recommender();
+ r.setLayer(aFeature.getLayer());
+ r.setFeature(aFeature);
+ r.setProject(aProject);
+ r.setAlwaysSelected(true);
+ r.setSkipEvaluation(false);
+ r.setMaxRecommendations(3);
+ r.setTool("dummyRecommenderTool");
+
+ return r;
+ }
}
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplTest.java
index c6218cd14c4..2aa41efbb4a 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplTest.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImplTest.java
@@ -22,9 +22,11 @@
import static de.tudarmstadt.ukp.clarin.webanno.model.AnchoringMode.SINGLE_TOKEN;
import static de.tudarmstadt.ukp.clarin.webanno.model.AnchoringMode.TOKENS;
import static de.tudarmstadt.ukp.clarin.webanno.support.uima.FeatureStructureBuilder.buildFS;
+import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_AUTO_ACCEPT_MODE_SUFFIX;
import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_IS_PREDICTION;
import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_SCORE_EXPLANATION_SUFFIX;
import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.FEATURE_NAME_SCORE_SUFFIX;
+import static de.tudarmstadt.ukp.inception.recommendation.api.model.AutoAcceptMode.NEVER;
import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType.REJECTED;
import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType.SKIPPED;
import static de.tudarmstadt.ukp.inception.recommendation.service.RecommendationServiceImpl.extractSuggestions;
@@ -280,6 +282,7 @@ void testExtractSuggestionsWithSpanSuggestions() throws Exception
predType.addFeature("value" + FEATURE_NAME_SCORE_SUFFIX, null, TYPE_NAME_DOUBLE);
predType.addFeature("value" + FEATURE_NAME_SCORE_EXPLANATION_SUFFIX, null,
TYPE_NAME_STRING);
+ predType.addFeature("value" + FEATURE_NAME_AUTO_ACCEPT_MODE_SUFFIX, null, TYPE_NAME_STRING);
predType.addFeature(FEATURE_NAME_IS_PREDICTION, null, TYPE_NAME_BOOLEAN);
var targetCas = createCas(mergeTypeSystems(asList(tsd, createTypeSystemDescription())));
@@ -350,7 +353,8 @@ private SpanSuggestion makeSuggestion(int aBegin, int aEnd, String aLabel, Sourc
aLabel, // aLabel
aLabel, // aUiLabel
0.0, // aScore
- "" // aScoreExplanation
+ "", // aScoreExplanation,
+ NEVER // autoAccept
);
}
}
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RelationSuggestionVisibilityCalculationTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RelationSuggestionVisibilityCalculationTest.java
index 364a9160d8f..2270f3baa95 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RelationSuggestionVisibilityCalculationTest.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/RelationSuggestionVisibilityCalculationTest.java
@@ -23,6 +23,8 @@
import static java.util.stream.Collectors.toList;
import static org.apache.uima.cas.CAS.TYPE_NAME_STRING;
import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.Mockito.doReturn;
+import static org.mockito.Mockito.spy;
import static org.mockito.Mockito.when;
import java.util.ArrayList;
@@ -43,32 +45,27 @@
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
import de.tudarmstadt.ukp.dkpro.core.api.syntax.type.dependency.Dependency;
-import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
import de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.RelationSuggestion;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionDocumentGroup;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import jakarta.persistence.EntityManager;
@ExtendWith(MockitoExtension.class)
public class RelationSuggestionVisibilityCalculationTest
{
- private @Mock LearningRecordService recordService;
+ private static final String TEST_USER = "Testuser";
+
private @Mock AnnotationSchemaService annoService;
private Project project;
private SourceDocument doc;
private AnnotationLayer layer;
private AnnotationFeature feature;
- private String user;
private RecommendationServiceImpl sut;
@BeforeEach
public void setUp() throws Exception
{
- user = "Testuser";
-
layer = new AnnotationLayer();
layer.setName(Dependency._TypeName);
layer.setId(42l);
@@ -86,19 +83,20 @@ public void setUp() throws Exception
.add(new AnnotationFeature(Dependency._FeatName_DependencyType, TYPE_NAME_STRING));
when(annoService.listSupportedFeatures(layer)).thenReturn(featureList);
- sut = new RecommendationServiceImpl(null, null, null, null, null, annoService, null,
- recordService, null, (EntityManager) null, null);
+ sut = spy(new RecommendationServiceImpl(null, null, null, null, null, annoService, null,
+ null, (EntityManager) null, null));
}
@Test
public void testCalculateVisibilityNoRecordsAllHidden() throws Exception
{
- when(recordService.listRecords(user, layer)).thenReturn(new ArrayList<>());
+ doReturn(new ArrayList<>()).when(sut).listLearningRecords(TEST_USER, TEST_USER, layer);
- CAS cas = getTestCas();
- SuggestionDocumentGroup suggestions = makeRelationSuggestionGroup(doc,
- feature, new int[][] { { 1, 0, 3, 13, 20 } });
- sut.calculateRelationSuggestionVisibility(cas, user, layer, suggestions, 0, 25);
+ var cas = getTestCas();
+ var suggestions = makeRelationSuggestionGroup(doc, feature,
+ new int[][] { { 1, 0, 3, 13, 20 } });
+ sut.calculateRelationSuggestionVisibility(TEST_USER, cas, TEST_USER, layer, suggestions, 0,
+ 25);
assertThat(getVisibleSuggestions(suggestions)) //
.as("No suggestions are visible as they overlap with annotations") //
@@ -114,12 +112,13 @@ public void testCalculateVisibilityNoRecordsAllHidden() throws Exception
@Test
public void thatVisibilityIsRestoredWhenOverlappingAnnotationIsRemoved() throws Exception
{
- when(recordService.listRecords(user, layer)).thenReturn(new ArrayList<>());
+ doReturn(new ArrayList<>()).when(sut).listLearningRecords(TEST_USER, TEST_USER, layer);
- CAS cas = getTestCas();
- SuggestionDocumentGroup suggestions = makeRelationSuggestionGroup(doc,
- feature, new int[][] { { 1, 0, 3, 13, 20 } });
- sut.calculateRelationSuggestionVisibility(cas, user, layer, suggestions, 0, 25);
+ var cas = getTestCas();
+ var suggestions = makeRelationSuggestionGroup(doc, feature,
+ new int[][] { { 1, 0, 3, 13, 20 } });
+ sut.calculateRelationSuggestionVisibility(TEST_USER, cas, TEST_USER, layer, suggestions, 0,
+ 25);
assertThat(getVisibleSuggestions(suggestions)) //
.as("No suggestions are visible as they overlap with annotations") //
@@ -130,7 +129,8 @@ public void thatVisibilityIsRestoredWhenOverlappingAnnotationIsRemoved() throws
cas.select(Dependency.class).forEach(Dependency::removeFromIndexes);
- sut.calculateRelationSuggestionVisibility(cas, user, layer, suggestions, 0, 25);
+ sut.calculateRelationSuggestionVisibility(TEST_USER, cas, TEST_USER, layer, suggestions, 0,
+ 25);
assertThat(getInvisibleSuggestions(suggestions)) //
.as("No suggestions are hidden as they no longer overlap with annotations") //
diff --git a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/SpanSuggestionVisibilityCalculationTest.java b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/SpanSuggestionVisibilityCalculationTest.java
index d4c66a18510..d8ed064b956 100644
--- a/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/SpanSuggestionVisibilityCalculationTest.java
+++ b/inception/inception-recommendation/src/test/java/de/tudarmstadt/ukp/inception/recommendation/service/SpanSuggestionVisibilityCalculationTest.java
@@ -20,9 +20,12 @@
import static de.tudarmstadt.ukp.inception.recommendation.service.Fixtures.getInvisibleSuggestions;
import static de.tudarmstadt.ukp.inception.recommendation.service.Fixtures.getVisibleSuggestions;
import static de.tudarmstadt.ukp.inception.recommendation.service.Fixtures.makeSpanSuggestionGroup;
+import static java.util.Arrays.asList;
import static java.util.stream.Collectors.toList;
import static org.apache.uima.cas.CAS.TYPE_NAME_STRING;
import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.Mockito.doReturn;
+import static org.mockito.Mockito.spy;
import static org.mockito.Mockito.when;
import java.util.ArrayList;
@@ -30,7 +33,6 @@
import org.apache.uima.cas.CAS;
import org.apache.uima.fit.factory.JCasFactory;
-import org.apache.uima.jcas.JCas;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@@ -39,13 +41,14 @@
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
+import de.tudarmstadt.ukp.clarin.webanno.model.OverlapMode;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity;
-import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
import de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion;
import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecord;
import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.Offset;
import de.tudarmstadt.ukp.inception.recommendation.api.model.SpanSuggestion;
import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionDocumentGroup;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
@@ -54,22 +57,20 @@
@ExtendWith(MockitoExtension.class)
public class SpanSuggestionVisibilityCalculationTest
{
- private @Mock LearningRecordService recordService;
+ private static final String TEST_USER = "Testuser";
+
private @Mock AnnotationSchemaService annoService;
private Project project;
private SourceDocument doc;
private AnnotationLayer layer;
private AnnotationFeature feature;
- private String user;
private RecommendationServiceImpl sut;
@BeforeEach
public void setUp() throws Exception
{
- user = "Testuser";
-
layer = new AnnotationLayer();
layer.setName(NamedEntity._TypeName);
layer.setId(42l);
@@ -86,22 +87,23 @@ public void setUp() throws Exception
featureList.add(new AnnotationFeature(NamedEntity._FeatName_value, TYPE_NAME_STRING));
when(annoService.listSupportedFeatures(layer)).thenReturn(featureList);
- sut = new RecommendationServiceImpl(null, null, null, null, null, annoService, null,
- recordService, (EntityManager) null);
+ sut = spy(new RecommendationServiceImpl(null, null, null, null, null, annoService, null,
+ (EntityManager) null));
}
@Test
public void testCalculateVisibilityNoRecordsAllHidden() throws Exception
{
- when(recordService.listRecords(user, layer)).thenReturn(new ArrayList<>());
+ doReturn(new ArrayList<>()).when(sut).listLearningRecords(TEST_USER, TEST_USER, layer);
- CAS cas = getTestCas();
- SuggestionDocumentGroup suggestions = makeSpanSuggestionGroup(doc, feature,
+ var cas = getTestCas();
+ var suggestions = makeSpanSuggestionGroup(doc, feature,
new int[][] { { 1, 0, 3 }, { 2, 13, 20 } });
- sut.calculateSpanSuggestionVisibility(doc, cas, user, layer, suggestions, 0, 25);
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas, TEST_USER, layer, suggestions, 0,
+ 25);
- List invisibleSuggestions = getInvisibleSuggestions(suggestions);
- List visibleSuggestions = getVisibleSuggestions(suggestions);
+ var invisibleSuggestions = getInvisibleSuggestions(suggestions);
+ var visibleSuggestions = getVisibleSuggestions(suggestions);
// check the invisible suggestions' states
assertThat(invisibleSuggestions).isNotEmpty();
@@ -119,15 +121,15 @@ public void testCalculateVisibilityNoRecordsAllHidden() throws Exception
@Test
public void testCalculateVisibilityNoRecordsNotHidden() throws Exception
{
- when(recordService.listRecords(user, layer)).thenReturn(new ArrayList<>());
+ doReturn(new ArrayList<>()).when(sut).listLearningRecords(TEST_USER, TEST_USER, layer);
- CAS cas = getTestCas();
- SuggestionDocumentGroup suggestions = makeSpanSuggestionGroup(doc, feature,
- new int[][] { { 1, 5, 10 } });
- sut.calculateSpanSuggestionVisibility(doc, cas, user, layer, suggestions, 0, 25);
+ var cas = getTestCas();
+ var suggestions = makeSpanSuggestionGroup(doc, feature, new int[][] { { 1, 5, 10 } });
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas, TEST_USER, layer, suggestions, 0,
+ 25);
- List invisibleSuggestions = getInvisibleSuggestions(suggestions);
- List visibleSuggestions = getVisibleSuggestions(suggestions);
+ var invisibleSuggestions = getInvisibleSuggestions(suggestions);
+ var visibleSuggestions = getVisibleSuggestions(suggestions);
// check the invisible suggestions' states
assertThat(visibleSuggestions).isNotEmpty();
@@ -146,15 +148,15 @@ public void testCalculateVisibilityRejected() throws Exception
rejectedRecord.setOffsetBegin(5);
rejectedRecord.setOffsetEnd(10);
records.add(rejectedRecord);
- when(recordService.listRecords(user, layer)).thenReturn(records);
+ doReturn(records).when(sut).listLearningRecords(TEST_USER, TEST_USER, layer);
- CAS cas = getTestCas();
- SuggestionDocumentGroup suggestions = makeSpanSuggestionGroup(doc, feature,
- new int[][] { { 1, 5, 10 } });
- sut.calculateSpanSuggestionVisibility(doc, cas, user, layer, suggestions, 0, 25);
+ var cas = getTestCas();
+ var suggestions = makeSpanSuggestionGroup(doc, feature, new int[][] { { 1, 5, 10 } });
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas, TEST_USER, layer, suggestions, 0,
+ 25);
- List invisibleSuggestions = getInvisibleSuggestions(suggestions);
- List visibleSuggestions = getVisibleSuggestions(suggestions);
+ var invisibleSuggestions = getInvisibleSuggestions(suggestions);
+ var visibleSuggestions = getVisibleSuggestions(suggestions);
// check the invisible suggestions' states
assertThat(visibleSuggestions).isEmpty();
@@ -168,12 +170,13 @@ public void testCalculateVisibilityRejected() throws Exception
@Test
public void thatVisibilityIsRestoredWhenOverlappingAnnotationIsRemoved() throws Exception
{
- when(recordService.listRecords(user, layer)).thenReturn(new ArrayList<>());
+ doReturn(new ArrayList<>()).when(sut).listLearningRecords(TEST_USER, TEST_USER, layer);
- CAS cas = getTestCas();
- SuggestionDocumentGroup suggestions = makeSpanSuggestionGroup(doc, feature,
+ var cas = getTestCas();
+ var suggestions = makeSpanSuggestionGroup(doc, feature,
new int[][] { { 1, 0, 3 }, { 2, 13, 20 } });
- sut.calculateSpanSuggestionVisibility(doc, cas, user, layer, suggestions, 0, 25);
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas, TEST_USER, layer, suggestions, 0,
+ 25);
assertThat(getVisibleSuggestions(suggestions)) //
.as("No suggestions are visible as they overlap with annotations") //
@@ -184,29 +187,95 @@ public void thatVisibilityIsRestoredWhenOverlappingAnnotationIsRemoved() throws
cas.select(NamedEntity.class).forEach(NamedEntity::removeFromIndexes);
- sut.calculateSpanSuggestionVisibility(doc, cas, user, layer, suggestions, 0, 25);
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas, TEST_USER, layer, suggestions, 0,
+ 25);
assertThat(getInvisibleSuggestions(suggestions)) //
.as("No suggestions are hidden as they no longer overlap with annotations") //
- .containsExactly();
+ .isEmpty();
assertThat(getVisibleSuggestions(suggestions)) //
.as("All suggestions are visible as they no longer overlap with annotations") //
.containsExactlyInAnyOrderElementsOf(
suggestions.stream().flatMap(g -> g.stream()).collect(toList()));
}
+ @Test
+ public void thatOverlappingSuggestionsAreNotHiddenWhenStackingIsEnabled() throws Exception
+ {
+ doReturn(new ArrayList<>()).when(sut).listLearningRecords(TEST_USER, TEST_USER, layer);
+
+ layer.setOverlapMode(OverlapMode.ANY_OVERLAP);
+
+ var cas = JCasFactory.createText("a b", "de");
+
+ var suggestion1 = SpanSuggestion.builder() //
+ .withId(1) //
+ .withDocumentName(doc.getName()) //
+ .withLayerId(layer.getId()) //
+ .withFeature(NamedEntity._FeatName_value) //
+ .withLabel("blah") //
+ .withPosition(new Offset(0, 1)) //
+ .build();
+ var suggestion2 = SpanSuggestion.builder() //
+ .withId(2) //
+ .withDocumentName(doc.getName()) //
+ .withLayerId(layer.getId()) //
+ .withFeature(NamedEntity._FeatName_value) //
+ .withLabel("blah") //
+ .withPosition(new Offset(1, 2)) //
+ .build();
+ var suggestions = new SuggestionDocumentGroup<>(asList(suggestion1, suggestion2));
+
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas.getCas(), TEST_USER, layer,
+ suggestions, 0, 2);
+
+ assertThat(getInvisibleSuggestions(suggestions)) //
+ .as("No suggestions are hidden as they do not overlap with annotations") //
+ .containsExactly();
+ assertThat(getVisibleSuggestions(suggestions)) //
+ .as("All suggestions are visible as they do not overlap with annotations") //
+ .containsExactlyInAnyOrderElementsOf(
+ suggestions.stream().flatMap(g -> g.stream()).collect(toList()));
+
+ var ne1 = new NamedEntity(cas, 0, 1);
+ ne1.addToIndexes();
+
+ assertThat(getInvisibleSuggestions(suggestions)) //
+ .as("First suggestion is still visible because as its label does not match the "
+ + "label of the annotation at the same position") //
+ .isEmpty();
+
+ ne1.setValue("blah");
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas.getCas(), TEST_USER, layer,
+ suggestions, 0, 2);
+
+ assertThat(getInvisibleSuggestions(suggestions)) //
+ .as("First suggestion is no longer visible because annotation with the same label exists") //
+ .containsExactly(suggestion1);
+
+ var ne2 = new NamedEntity(cas, 1, 2);
+ ne2.setValue("blah");
+ ne2.addToIndexes();
+ sut.calculateSpanSuggestionVisibility(TEST_USER, doc, cas.getCas(), TEST_USER, layer,
+ suggestions, 0, 2);
+
+ assertThat(getInvisibleSuggestions(suggestions)) //
+ .as("Second suggestion is noew also no longer visible because annotation with the same label exists") //
+ .containsExactly(suggestion1, suggestion2);
+ }
+
private CAS getTestCas() throws Exception
{
- String documentText = "Dies ist ein Testtext, ach ist der schoen, der schoenste von allen"
+ var documentText = "Dies ist ein Testtext, ach ist der schoen, der schoenste von allen"
+ " Testtexten.";
- JCas jcas = JCasFactory.createText(documentText, "de");
+ var jcas = JCasFactory.createText(documentText, "de");
- NamedEntity neLabel = new NamedEntity(jcas, 0, 3);
+ var neLabel = new NamedEntity(jcas, 0, 3);
neLabel.setValue("LOC");
neLabel.addToIndexes();
// the annotation's feature value is initialized as null
- NamedEntity neNoLabel = new NamedEntity(jcas, 13, 20);
+ var neNoLabel = new NamedEntity(jcas, 13, 20);
neNoLabel.addToIndexes();
return jcas.getCas();
diff --git a/inception/inception-remote/pom.xml b/inception/inception-remote/pom.xml
index a081c7e9288..dec9e26286f 100644
--- a/inception/inception-remote/pom.xml
+++ b/inception/inception-remote/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-remoteINCEpTION - Core - Remote API
diff --git a/inception/inception-review-editor/pom.xml b/inception/inception-review-editor/pom.xml
index 363dfa702b2..03f9ca78506 100644
--- a/inception/inception-review-editor/pom.xml
+++ b/inception/inception-review-editor/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTINCEpTION - Editor - Reviewinception-review-editor
@@ -89,6 +89,10 @@
org.wicketstuffwicketstuff-annotationeventdispatcher
+
+ org.danekja
+ jdk-serializable-functional
+ org.slf4j
diff --git a/inception/inception-scheduling/pom.xml b/inception/inception-scheduling/pom.xml
index cbd11b4965f..9dd7efd72f8 100644
--- a/inception/inception-scheduling/pom.xml
+++ b/inception/inception-scheduling/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-schedulingINCEpTION - Scheduling
diff --git a/inception/inception-scheduling/src/main/java/de/tudarmstadt/ukp/inception/scheduling/SchedulingService.java b/inception/inception-scheduling/src/main/java/de/tudarmstadt/ukp/inception/scheduling/SchedulingService.java
index fa2a2e73db4..9a6eb7243c5 100644
--- a/inception/inception-scheduling/src/main/java/de/tudarmstadt/ukp/inception/scheduling/SchedulingService.java
+++ b/inception/inception-scheduling/src/main/java/de/tudarmstadt/ukp/inception/scheduling/SchedulingService.java
@@ -77,5 +77,11 @@ public interface SchedulingService
*/
void stopAllTasksForProject(Project aProject);
+ /**
+ * Execute a task immediately and synchronously (blocking) in the current thread.
+ *
+ * @param aTask
+ * the task to be executed.
+ */
void executeSync(Task aTask);
}
diff --git a/inception/inception-schema/pom.xml b/inception/inception-schema/pom.xml
index 0d002d39119..d83748cc87b 100644
--- a/inception/inception-schema/pom.xml
+++ b/inception/inception-schema/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-schemaINCEpTION - Core - Annotation Schema
diff --git a/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/exporters/LayerExporter.java b/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/exporters/LayerExporter.java
index bb028f3c7ec..44e77043373 100644
--- a/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/exporters/LayerExporter.java
+++ b/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/exporters/LayerExporter.java
@@ -186,6 +186,7 @@ private ExportedAnnotationFeature exportFeatureDetails(AnnotationFeature feature
exFeature.setLinkTypeTargetFeatureName(feature.getLinkTypeTargetFeatureName());
exFeature.setTraits(feature.getTraits());
exFeature.setCuratable(feature.isCuratable());
+ exFeature.setRank(feature.getRank());
if (feature.getTagset() != null) {
TagSet tagSet = feature.getTagset();
@@ -332,6 +333,7 @@ else if (Token._TypeName.equals(aFeature.getLayer().getName())
aFeature.setLinkTypeTargetFeatureName(aExFeature.getLinkTypeTargetFeatureName());
aFeature.setTraits(aExFeature.getTraits());
aFeature.setCuratable(aExFeature.isCuratable());
+ aFeature.setRank(aExFeature.getRank());
if (aExFeature.getTagSet() != null) {
TagSet tagset = annotationService.getTagSet(aExFeature.getTagSet().getName(), aProject);
diff --git a/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/service/AnnotationSchemaServiceImpl.java b/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/service/AnnotationSchemaServiceImpl.java
index 64f53b9e3f7..14458aca179 100644
--- a/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/service/AnnotationSchemaServiceImpl.java
+++ b/inception/inception-schema/src/main/java/de/tudarmstadt/ukp/inception/schema/service/AnnotationSchemaServiceImpl.java
@@ -87,7 +87,9 @@
import de.tudarmstadt.ukp.clarin.webanno.api.event.TagUpdatedEvent;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocument;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
+import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature_;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
+import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer_;
import de.tudarmstadt.ukp.clarin.webanno.model.ImmutableTag;
import de.tudarmstadt.ukp.clarin.webanno.model.LinkMode;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
@@ -95,6 +97,7 @@
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.model.Tag;
import de.tudarmstadt.ukp.clarin.webanno.model.TagSet;
+import de.tudarmstadt.ukp.clarin.webanno.model.Tag_;
import de.tudarmstadt.ukp.clarin.webanno.support.uima.ICasUtil;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
@@ -240,16 +243,41 @@ public void updateTagRanks(TagSet aTagSet, List aTags)
}
int n = 0;
- for (Tag t : aTags) {
- if (!aTagSet.equals(t.getTagSet())) {
+ for (Tag tag : aTags) {
+ if (!aTagSet.equals(tag.getTagSet())) {
throw new IllegalArgumentException("All tags to be updated must belong to "
- + aTagSet + ", but [" + t + "] belongs to " + t.getTagSet());
+ + aTagSet + ", but [" + tag + "] belongs to " + tag.getTagSet());
}
- Tag dbTag = dbTags.get(t);
+ Tag dbTag = dbTags.get(tag);
if (dbTag != null) {
dbTag.setRank(n);
- t.setRank(n);
+ tag.setRank(n);
+ n++;
+ }
+ }
+ }
+
+ @Override
+ @Transactional
+ public void updateFeatureRanks(AnnotationLayer aLayer, List aFeatures)
+ {
+ var dbFeatures = new HashMap();
+ for (var t : listAnnotationFeature(aLayer)) {
+ dbFeatures.put(t, t);
+ }
+
+ int n = 0;
+ for (var feature : aFeatures) {
+ if (!aLayer.equals(feature.getLayer())) {
+ throw new IllegalArgumentException("All features to be updated must belong to "
+ + aLayer + ", but " + feature + " belongs to " + feature.getLayer());
+ }
+
+ var dbFeature = dbFeatures.get(feature);
+ if (dbFeature != null) {
+ dbFeature.setRank(n);
+ feature.setRank(n);
n++;
}
}
@@ -726,7 +754,7 @@ public List listAttachingFeatures(AnnotationLayer aLayer)
"FROM AnnotationFeature ", //
"WHERE type = :type AND", //
" project = :project", //
- "ORDER BY uiName");
+ "ORDER BY rank ASC, uiName ASC");
// This should not be cached because we do not have a proper foreign key relation to
// the type.
@@ -746,7 +774,7 @@ public List listAttachedLinkFeatures(AnnotationLayer aLayer)
"WHERE linkMode in (:modes) AND ", //
" project = :project AND ", //
" type in (:attachType) ", //
- "ORDER BY uiName");
+ "ORDER BY rank ASC, uiName ASC");
return entityManager.createQuery(query, AnnotationFeature.class)
.setParameter("modes", asList(LinkMode.SIMPLE, LinkMode.WITH_ROLE))
@@ -765,7 +793,7 @@ public List listAttachedSpanFeatures(AnnotationLayer aLayer)
"SELECT l.attachFeature", //
"FROM AnnotationLayer AS l", //
"WHERE l.attachType = :layer", //
- "ORDER BY l.attachFeature.uiName");
+ "ORDER BY l.attachFeature.rank ASC, l.attachFeature.uiName ASC");
return entityManager.createQuery(query, AnnotationFeature.class)
.setParameter("layer", aLayer).setHint(CACHEABLE, true) //
@@ -780,15 +808,16 @@ public List listAnnotationFeature(AnnotationLayer aLayer)
return new ArrayList<>();
}
- String query = String.join("\n", //
- "FROM AnnotationFeature", //
- "WHERE layer = :layer", //
- "ORDER BY uiName");
+ var cb = entityManager.getCriteriaBuilder();
+ var query = cb.createQuery(AnnotationFeature.class);
+ var root = query.from(AnnotationFeature.class);
- return entityManager.createQuery(query, AnnotationFeature.class)
- .setParameter("layer", aLayer) //
- .setHint(CACHEABLE, true) //
- .getResultList();
+ query //
+ .where(cb.equal(root.get(AnnotationFeature_.layer), aLayer))
+ .orderBy(cb.asc(root.get(AnnotationFeature_.rank)),
+ cb.asc(root.get(AnnotationFeature_.uiName)));
+
+ return entityManager.createQuery(query).setHint(CACHEABLE, true).getResultList();
}
@Override
@@ -799,26 +828,35 @@ public List listEnabledFeatures(AnnotationLayer aLayer)
return new ArrayList<>();
}
- String query = String.join("\n", //
- "FROM AnnotationFeature", //
- "WHERE layer = :layer", //
- "AND enabled = true", //
- "ORDER BY uiName"); //
+ var cb = entityManager.getCriteriaBuilder();
+ var query = cb.createQuery(AnnotationFeature.class);
+ var root = query.from(AnnotationFeature.class);
- return entityManager.createQuery(query, AnnotationFeature.class)
- .setParameter("layer", aLayer) //
- .setHint(CACHEABLE, true) //
- .getResultList();
+ query //
+ .where(cb.and( //
+ cb.equal(root.get(AnnotationFeature_.layer), aLayer),
+ cb.isTrue(root.get(AnnotationFeature_.enabled))))
+ .orderBy(cb.asc(root.get(AnnotationFeature_.rank)),
+ cb.asc(root.get(AnnotationFeature_.uiName)));
+
+ return entityManager.createQuery(query).setHint(CACHEABLE, true).getResultList();
}
@Override
@Transactional
public List listAnnotationFeature(Project aProject)
{
- return entityManager.createQuery(
- "FROM AnnotationFeature f WHERE project =:project ORDER BY f.layer.uiName, f.uiName",
- AnnotationFeature.class) //
- .setParameter("project", aProject) //
+ var cb = entityManager.getCriteriaBuilder();
+ var query = cb.createQuery(AnnotationFeature.class);
+ var root = query.from(AnnotationFeature.class);
+
+ query //
+ .where(cb.equal(root.get(AnnotationFeature_.project), aProject)) //
+ .orderBy(cb.asc(root.get(AnnotationFeature_.layer).get(AnnotationLayer_.uiName)),
+ cb.asc(root.get(AnnotationFeature_.rank)),
+ cb.asc(root.get(AnnotationFeature_.uiName)));
+
+ return entityManager.createQuery(query) //
.setHint(CACHEABLE, true) //
.getResultList();
}
@@ -831,11 +869,16 @@ public List listTags(TagSet aTagSet)
return emptyList();
}
- return entityManager
- .createQuery("FROM Tag WHERE tagSet = :tagSet ORDER BY rank ASC, name ASC",
- Tag.class)
- .setParameter("tagSet", aTagSet) //
- .getResultList();
+ var cb = entityManager.getCriteriaBuilder();
+ var query = cb.createQuery(Tag.class);
+ var root = query.from(Tag.class);
+
+ query //
+ .where(cb.equal(root.get(Tag_.tagSet), aTagSet)) //
+ .orderBy(cb.asc(root.get(Tag_.rank)), //
+ cb.asc(root.get(Tag_.name)));
+
+ return entityManager.createQuery(query).getResultList();
}
private List loadImmutableTags(TagSet aTagSet)
diff --git a/inception/inception-search-core/pom.xml b/inception/inception-search-core/pom.xml
index d89f0e498ea..b3f5ad50f2b 100644
--- a/inception/inception-search-core/pom.xml
+++ b/inception/inception-search-core/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-search-coreINCEpTION - Search - Core
diff --git a/inception/inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java b/inception/inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java
index cad9ce987ca..033ec57c129 100644
--- a/inception/inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java
+++ b/inception/inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java
@@ -284,6 +284,13 @@ public void beforeProjectRemove(BeforeProjectRemovedEvent aEvent) throws IOExcep
{
Project project = aEvent.getProject();
+ if (isBeingDeleted(project.getId())) {
+ log.trace(
+ "Ignoring repeated attempt to delete project which is already in progress of being deleted",
+ project);
+ return;
+ }
+
log.trace("Removing index for project {} because project is being removed", project);
try (PooledIndex pooledIndex = acquireIndex(project.getId())) {
@@ -314,6 +321,17 @@ public void afterProjectRemove(AfterProjectRemovedEvent aEvent) throws IOExcepti
private final Map indexes = new HashMap<>();
+ private boolean isBeingDeleted(long aProjectId)
+ {
+ synchronized (indexes) {
+ PooledIndex pooledIndex = indexes.get(aProjectId);
+ if (pooledIndex != null && pooledIndex.isTombstone()) {
+ return true;
+ }
+ return false;
+ }
+ }
+
private PooledIndex acquireIndex(long aProjectId)
{
synchronized (indexes) {
diff --git a/inception/inception-search-mtas/pom.xml b/inception/inception-search-mtas/pom.xml
index 27acf6a0655..10d62bc56b2 100644
--- a/inception/inception-search-mtas/pom.xml
+++ b/inception/inception-search-mtas/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-search-mtasINCEpTION - Search - MTAS
diff --git a/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasDocumentIndex.java b/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasDocumentIndex.java
index e4bf24e1d71..a9e96072b89 100644
--- a/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasDocumentIndex.java
+++ b/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasDocumentIndex.java
@@ -1071,11 +1071,12 @@ else if (annotationDocumentId != -1
.filter(t -> t.getPositionStart() >= matchStart
&& t.getPositionEnd() < matchEnd)
.mapToInt(MtasTokenString::getOffsetStart).min()
- .getAsInt());
+ .orElse(matchStart));
result.setOffsetEnd(tokens.stream()
.filter(t -> t.getPositionStart() >= matchStart
&& t.getPositionEnd() < matchEnd)
- .mapToInt(MtasTokenString::getOffsetEnd).max().getAsInt());
+ .mapToInt(MtasTokenString::getOffsetEnd).max()
+ .orElse(matchEnd));
result.setTokenStart(matchStart);
result.setTokenLength(matchEnd - matchStart);
result.setReadOnly(annotationDocument != null
diff --git a/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasUimaParser.java b/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasUimaParser.java
index 27c03ffb48a..e3bd3370e8d 100644
--- a/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasUimaParser.java
+++ b/inception/inception-search-mtas/src/main/java/de/tudarmstadt/ukp/inception/search/index/mtas/MtasUimaParser.java
@@ -431,8 +431,8 @@ private int indexFeatures(AnnotationFS aAnnotation, String aLayer, String aPrefi
MultiValuedMap fieldsAndValues = fis.get().indexFeatureValue(aLayer,
aAnnotation, aPrefix, feature);
for (Entry e : fieldsAndValues.entries()) {
- indexFeatureValue(e.getKey(), e.getValue(), mtasId++, aAnnotation.getBegin(),
- aAnnotation.getEnd(), aRange, aFSAddress);
+ indexFeatureValue(getIndexedName(e.getKey()), e.getValue(), mtasId++,
+ aAnnotation.getBegin(), aAnnotation.getEnd(), aRange, aFSAddress);
}
if (LOG.isTraceEnabled()) {
diff --git a/inception/inception-security/pom.xml b/inception/inception-security/pom.xml
index ca4af90dd9d..101920a173d 100644
--- a/inception/inception-security/pom.xml
+++ b/inception/inception-security/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-securityINCEpTION - Core - Security
@@ -67,6 +67,10 @@
org.apache.wicketwicket-auth-roles
+
+ org.danekja
+ jdk-serializable-functional
+
diff --git a/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/SpringAuthenticatedWebSession.java b/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/SpringAuthenticatedWebSession.java
index 744f3924eed..c42fd0dbfc0 100644
--- a/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/SpringAuthenticatedWebSession.java
+++ b/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/SpringAuthenticatedWebSession.java
@@ -43,7 +43,6 @@
import de.tudarmstadt.ukp.clarin.webanno.security.config.AuthenticationConfigurationHolder;
import de.tudarmstadt.ukp.clarin.webanno.support.logging.Logging;
import de.tudarmstadt.ukp.clarin.webanno.support.spring.ApplicationEventPublisherHolder;
-import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpSession;
/**
@@ -95,8 +94,7 @@ public boolean authenticate(String username, String password)
try {
Request request = RequestCycle.get().getRequest();
if (request instanceof ServletWebRequest) {
- HttpServletRequest containerRequest = ((ServletWebRequest) request)
- .getContainerRequest();
+ var containerRequest = ((ServletWebRequest) request).getContainerRequest();
// Kill current session and create a new one
containerRequest.getSession().invalidate();
@@ -109,6 +107,11 @@ public boolean authenticate(String username, String password)
springSecuritySignIn(authentication);
+ // If this is called, the authentication object has been created artificially and not
+ // via the authenticationManager, so we need to send the login even manually
+ applicationEventPublisherHolder.get()
+ .publishEvent(new AuthenticationSuccessEvent(authentication));
+
return true;
}
catch (AuthenticationException e) {
diff --git a/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDao.java b/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDao.java
index 19c81e6ef0d..16d4536dde9 100644
--- a/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDao.java
+++ b/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDao.java
@@ -107,6 +107,10 @@ public interface UserDao
*/
User get(String aUsername);
+ User getUserOrCurationUser(String aUsername);
+
+ User getCurationUser();
+
User getUserByRealmAndUiName(String aRealm, String aUiName);
/**
diff --git a/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDaoImpl.java b/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDaoImpl.java
index 66c49e52188..015dadb22b0 100644
--- a/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDaoImpl.java
+++ b/inception/inception-security/src/main/java/de/tudarmstadt/ukp/clarin/webanno/security/UserDaoImpl.java
@@ -253,15 +253,33 @@ public int deleteAllUsersFromRealm(String aRealm)
return usersInRealm.size();
}
- else {
- String query = String.join("\n", //
- "DELETE FROM " + User.class.getName(), //
- "WHERE realm = :realm");
- return entityManager.createQuery(query) //
- .setParameter("realm", aRealm) //
- .executeUpdate();
+ String query = String.join("\n", //
+ "DELETE FROM " + User.class.getName(), //
+ "WHERE realm = :realm");
+
+ return entityManager.createQuery(query) //
+ .setParameter("realm", aRealm) //
+ .executeUpdate();
+ }
+
+ @Override
+ public User getCurationUser()
+ {
+ return new User(CURATION_USER);
+ }
+
+ @Override
+ @Transactional
+ public User getUserOrCurationUser(String aUsername)
+ {
+ Validate.notBlank(aUsername, "User must be specified");
+
+ if (CURATION_USER.equals(aUsername)) {
+ return getCurationUser();
}
+
+ return get(aUsername);
}
@Override
diff --git a/inception/inception-sharing/pom.xml b/inception/inception-sharing/pom.xml
index 6d0a081fd1b..c1257ca8870 100644
--- a/inception/inception-sharing/pom.xml
+++ b/inception/inception-sharing/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-sharingINCEpTION - Sharing
@@ -142,6 +142,10 @@
com.googlecode.wicket-jquery-uiwicket-kendo-ui
+
+ org.danekja
+ jdk-serializable-functional
+
diff --git a/inception/inception-support-standalone/pom.xml b/inception/inception-support-standalone/pom.xml
index 7e2a2a567da..8fc31bd559f 100644
--- a/inception/inception-support-standalone/pom.xml
+++ b/inception/inception-support-standalone/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-support-standaloneINCEpTION - Core - Support for standalone mode
diff --git a/inception/inception-support-standalone/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/standalone/LoadingSplashScreen.java b/inception/inception-support-standalone/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/standalone/LoadingSplashScreen.java
index c8fc9836971..20b38dbaa26 100644
--- a/inception/inception-support-standalone/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/standalone/LoadingSplashScreen.java
+++ b/inception/inception-support-standalone/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/standalone/LoadingSplashScreen.java
@@ -67,17 +67,27 @@ public static Optional setupScreen(URL aSplashScreenImageUrl, URL
return Optional.empty();
}
- SplashWindow window = new SplashWindow(aSplashScreenImageUrl, aIconUrl, aApplicationName);
- window.setVisible(true);
+ try {
+ SplashWindow window = new SplashWindow(aSplashScreenImageUrl, aIconUrl,
+ aApplicationName);
+ window.setVisible(true);
- return Optional.of(window);
+ return Optional.of(window);
+ }
+ catch (UnsatisfiedLinkError e) {
+ return Optional.empty();
+ }
}
public static Optional setupScreen(String aApplicationName)
{
- URL splasHScreenImageUrl = LoadingSplashScreen.class.getResource("/splash.png");
+ URL splashScreenImageUrl = LoadingSplashScreen.class.getResource("/splash.png");
URL iconUrl = LoadingSplashScreen.class.getResource("/icon.png");
- return setupScreen(splasHScreenImageUrl, iconUrl, aApplicationName);
+ if (splashScreenImageUrl == null || iconUrl == null) {
+ LOG.error("Unable to locate splash screen and icon resources");
+ return Optional.empty();
+ }
+ return setupScreen(splashScreenImageUrl, iconUrl, aApplicationName);
}
public static class SplashWindow
diff --git a/inception/inception-support/pom.xml b/inception/inception-support/pom.xml
index 335cbdba4fa..7edcdf1b5a3 100644
--- a/inception/inception-support/pom.xml
+++ b/inception/inception-support/pom.xml
@@ -20,11 +20,16 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-supportINCEpTION - Support library
+
+ jakarta.annotation
+ jakarta.annotation-api
+
+
org.apache.uimauimaj-core
@@ -177,9 +182,12 @@
jakarta.servletjakarta.servlet-api
- provided
-
+
+ com.networknt
+ json-schema-validator
+
+
org.slf4j
@@ -213,18 +221,21 @@
src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicket/input/remove-input-behavior.js
-
- src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/sass/*.java
-
- src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicketstuff/UrlParametersReceivingBehavior.java
- src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/bootstrap/select/css/*
- src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/bootstrap/select/js/*
+
+ org.apache.maven.plugins
+ maven-dependency-plugin
+
+
+ jakarta.annotation:jakarta.annotation-api
+
+
+
-
\ No newline at end of file
+
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/JSONUtil.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/JSONUtil.java
index 43928060ff2..1aab6b84997 100644
--- a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/JSONUtil.java
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/JSONUtil.java
@@ -18,11 +18,14 @@
package de.tudarmstadt.ukp.clarin.webanno.support;
import static com.fasterxml.jackson.databind.DeserializationFeature.READ_UNKNOWN_ENUM_VALUES_USING_DEFAULT_VALUE;
+import static java.util.stream.Collectors.toList;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringWriter;
+import java.net.URL;
+import java.util.List;
import org.apache.commons.io.FileUtils;
@@ -35,6 +38,11 @@
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import com.networknt.schema.JsonSchema;
+import com.networknt.schema.JsonSchemaFactory;
+import com.networknt.schema.SpecVersion;
+
+import de.tudarmstadt.ukp.clarin.webanno.support.logging.LogMessage;
public class JSONUtil
{
@@ -107,6 +115,24 @@ public static T fromJsonString(Class aClass, String aJSON) throws IOExcep
}
}
+ public static T fromValidatedJsonString(Class aClass, String aJSON, JsonSchema aSchema)
+ throws IOException
+ {
+ if (aJSON == null) {
+ return null;
+ }
+
+ var mapper = getObjectMapper();
+ var jsonNode = mapper.readTree(aJSON);
+ var result = aSchema.validateAndCollect(jsonNode);
+ if (!result.getValidationMessages().isEmpty()) {
+ throw new IOException("JSON does not match JSON schema: "
+ + result.getValidationMessages().iterator().next().getMessage());
+ }
+
+ return mapper.treeToValue(jsonNode, aClass);
+ }
+
public static T fromJsonStream(Class aClass, InputStream aSrc) throws IOException
{
return getObjectMapper().readValue(aSrc, aClass);
@@ -140,6 +166,24 @@ public static String toInterpretableJsonString(JsonNode aTree) throws IOExceptio
return out.toString();
}
+ public static JsonSchema loadJsonSchema(InputStream aSource)
+ {
+ var factory = JsonSchemaFactory.getInstance(SpecVersion.VersionFlag.V202012);
+ return factory.getSchema(aSource);
+ }
+
+ public static List validateJsonString(URL aSchemaUrl, String aJsonString)
+ throws IOException
+ {
+ try (var schemaStream = aSchemaUrl.openStream()) {
+ var jsonNode = getObjectMapper().readTree(aJsonString);
+ var jsonSchema = loadJsonSchema(schemaStream);
+ return jsonSchema.validate(jsonNode).stream() //
+ .map(e -> LogMessage.error(JSONUtil.class, "%s", e.getMessage())) //
+ .collect(toList());
+ }
+ }
+
private static class JavaScriptCharacterEscapes
extends CharacterEscapes
{
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/PersistentEnumIntegerUserType.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/PersistentEnumIntegerUserType.java
new file mode 100644
index 00000000000..f710b8b91f4
--- /dev/null
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/PersistentEnumIntegerUserType.java
@@ -0,0 +1,124 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.clarin.webanno.support;
+
+import java.io.Serializable;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Types;
+
+import org.hibernate.HibernateException;
+import org.hibernate.engine.spi.SharedSessionContractImplementor;
+import org.hibernate.usertype.UserType;
+
+/**
+ * user-defined enum "types"
+ *
+ * @param
+ * the enum type
+ *
+ */
+public abstract class PersistentEnumIntegerUserType>
+ implements UserType, Serializable
+{
+ private static final long serialVersionUID = -3080625439869047088L;
+
+ @Override
+ public T assemble(Serializable cached, Object owner) throws HibernateException
+ {
+ return (T) cached;
+ }
+
+ @Override
+ public T deepCopy(T value) throws HibernateException
+ {
+ return value;
+ }
+
+ @Override
+ public Serializable disassemble(T value) throws HibernateException
+ {
+ return (Serializable) value;
+ }
+
+ @Override
+ public boolean equals(T x, T y) throws HibernateException
+ {
+ return x == y;
+ }
+
+ @Override
+ public int hashCode(T x) throws HibernateException
+ {
+ return x == null ? 0 : x.hashCode();
+ }
+
+ @Override
+ public boolean isMutable()
+ {
+ return false;
+ }
+
+ @Override
+ public T nullSafeGet(ResultSet rs, int aPosition, SharedSessionContractImplementor session,
+ Object owner)
+ throws HibernateException, SQLException
+ {
+ int dbValue = rs.getInt(aPosition);
+ if (rs.wasNull()) {
+ return null;
+ }
+
+ var constants = returnedClass().getEnumConstants();
+ if (dbValue >= 0 && dbValue < constants.length) {
+ return constants[dbValue];
+ }
+
+ throw new IllegalStateException(
+ "Unknown " + returnedClass().getSimpleName() + " value [" + dbValue + "]");
+ }
+
+ @Override
+ public void nullSafeSet(PreparedStatement st, T value, int index,
+ SharedSessionContractImplementor session)
+ throws HibernateException, SQLException
+ {
+ if (value == null) {
+ st.setNull(index, Types.INTEGER);
+ }
+ else {
+ st.setString(index, ((PersistentEnum) value).getId());
+ }
+ }
+
+ @Override
+ public T replace(T original, T target, Object owner) throws HibernateException
+ {
+ return original;
+ }
+
+ @Override
+ public abstract Class returnedClass();
+
+ @Override
+ public int getSqlType()
+ {
+ return Types.INTEGER;
+ }
+}
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.html b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.html
index d25962dabe7..9ce12fc69a3 100644
--- a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.html
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.html
@@ -28,15 +28,17 @@
-
+
+
+
-
-
-
+
+
+
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.java
index f528efc6ae2..9b4235bb91f 100644
--- a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.java
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/dialog/ChallengeResponseDialogContentPanel_ImplBase.java
@@ -45,6 +45,7 @@ public abstract class ChallengeResponseDialogContentPanel_ImplBase
private Label title;
private Label expectedResponse;
private TextField responseField;
+ private LambdaAjaxButton confirm;
private LambdaAjaxLink cancel;
private ResourceModel titleModel;
@@ -75,11 +76,21 @@ public ChallengeResponseDialogContentPanel_ImplBase(String aId, ResourceModel aT
cancel.setOutputMarkupId(true);
queue(new Label("feedback"));
- queue(new LambdaAjaxButton<>("confirm", this::onConfirmInternal));
+ queue(confirm = new LambdaAjaxButton<>("confirm", this::onConfirmInternal));
queue(new LambdaAjaxLink("closeDialog", this::onCancelInternal));
queue(title, expectedResponse, responseField, cancel, form);
}
+ public LambdaAjaxButton getConfirmButton()
+ {
+ return confirm;
+ }
+
+ public TextField getResponseField()
+ {
+ return responseField;
+ }
+
@Deprecated
public void onShow(AjaxRequestTarget aTarget)
{
@@ -168,7 +179,7 @@ public void setCancelAction(AjaxCallback aCancelAction)
cancelAction = aCancelAction;
}
- private class State
+ protected class State
implements Serializable
{
private static final long serialVersionUID = 4483229579553569947L;
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/AnnotationBuilder.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/AnnotationBuilder.java
index 61e6e82c176..a2d0cb924da 100644
--- a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/AnnotationBuilder.java
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/AnnotationBuilder.java
@@ -35,6 +35,13 @@ public AnnotationBuilder(CAS aCas, Type aType)
super(aCas, aType);
}
+ public AnnotationBuilder at(AnnotationFS aAnnotation)
+ {
+ withFeature(CAS.FEATURE_BASE_NAME_BEGIN, aAnnotation.getBegin());
+ withFeature(CAS.FEATURE_BASE_NAME_END, aAnnotation.getEnd());
+ return this;
+ }
+
public AnnotationBuilder at(int aBegin, int aEnd)
{
withFeature(CAS.FEATURE_BASE_NAME_BEGIN, aBegin);
@@ -51,6 +58,11 @@ public AnnotationBuilder on(String aPattern)
return this;
}
+ public static AnnotationBuilder buildAnnotation(CAS aCas, Type aType)
+ {
+ return new AnnotationBuilder(aCas, aType);
+ }
+
public static AnnotationBuilder buildAnnotation(CAS aCas,
Class aType)
{
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/FeatureStructureBuilder.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/FeatureStructureBuilder.java
index fbea7eabe51..6ca91c5d426 100644
--- a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/FeatureStructureBuilder.java
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/uima/FeatureStructureBuilder.java
@@ -25,6 +25,7 @@
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.reflect.MethodUtils;
import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.Feature;
import org.apache.uima.cas.FeatureStructure;
import org.apache.uima.cas.Type;
import org.apache.uima.fit.util.CasUtil;
@@ -49,6 +50,12 @@ public FeatureStructureBuilder withFeature(String aName, Object aValue)
return this;
}
+ public FeatureStructureBuilder withFeature(Feature aFeature, Object aValue)
+ {
+ features.put(aFeature.getShortName(), aValue);
+ return this;
+ }
+
public T buildWithoutAddingToIndexes()
{
T subject = cas.createFS(type);
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicket/resource/ContextSensitivePackageStringResourceLoader.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicket/resource/ContextSensitivePackageStringResourceLoader.java
new file mode 100644
index 00000000000..ebc89f83928
--- /dev/null
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicket/resource/ContextSensitivePackageStringResourceLoader.java
@@ -0,0 +1,46 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.clarin.webanno.support.wicket.resource;
+
+import java.lang.StackWalker.Option;
+import java.util.Locale;
+import java.util.Set;
+
+import org.apache.wicket.Localizer;
+import org.apache.wicket.resource.loader.PackageStringResourceLoader;
+
+public class ContextSensitivePackageStringResourceLoader
+ extends PackageStringResourceLoader
+{
+ private static final Set IGNORED_PREFIXES = Set.of(
+ ContextSensitivePackageStringResourceLoader.class.getPackageName() + ".",
+ Localizer.class.getPackageName() + ".");
+
+ @Override
+ public String loadStringResource(Class aClazz, String aKey, Locale aLocale, String aStyle,
+ String aVariation)
+ {
+ var context = StackWalker.getInstance(Option.RETAIN_CLASS_REFERENCE)
+ .walk(s -> s.dropWhile(
+ f -> IGNORED_PREFIXES.stream().anyMatch(f.getClassName()::startsWith))
+ .findFirst());
+
+ return context.map(v -> super.loadStringResource(v.getDeclaringClass(), aKey, aLocale,
+ aStyle, aVariation)).orElse(null);
+ }
+}
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicket/resource/Strings.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicket/resource/Strings.java
new file mode 100644
index 00000000000..e0eb494958c
--- /dev/null
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/wicket/resource/Strings.java
@@ -0,0 +1,32 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.clarin.webanno.support.wicket.resource;
+
+public class Strings
+{
+ public static String getString(String aKey)
+ {
+ return getString(aKey, null);
+ }
+
+ public static String getString(String aKey, String aDefaultValue)
+ {
+ return org.apache.wicket.Application.get().getResourceSettings().getLocalizer()
+ .getString(aKey, null, aDefaultValue);
+ }
+}
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/xml/ContentHandlerAdapter.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/xml/ContentHandlerAdapter.java
index 60425e24285..effbcd0bad0 100644
--- a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/xml/ContentHandlerAdapter.java
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/clarin/webanno/support/xml/ContentHandlerAdapter.java
@@ -37,6 +37,11 @@ public class ContentHandlerAdapter
protected final ContentHandler delegate;
+ public ContentHandlerAdapter()
+ {
+ delegate = null;
+ }
+
public ContentHandlerAdapter(ContentHandler aDelegate)
{
delegate = aDelegate;
@@ -45,30 +50,50 @@ public ContentHandlerAdapter(ContentHandler aDelegate)
@Override
public void setDocumentLocator(Locator aLocator)
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.setDocumentLocator(aLocator);
}
@Override
public void startDocument() throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.startDocument();
}
@Override
public void endDocument() throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.endDocument();
}
@Override
public void startPrefixMapping(String aPrefix, String aUri) throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.startPrefixMapping(aPrefix, aUri);
}
@Override
public void endPrefixMapping(String aPrefix) throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.endPrefixMapping(aPrefix);
}
@@ -117,6 +142,10 @@ public void startElement(String aLocalName, Map aAttributes) thr
public void startElement(String aUri, String aLocalName, String aQName, Attributes aAtts)
throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.startElement(aUri, aLocalName, aQName, aAtts);
}
@@ -133,6 +162,10 @@ public void endElement(QName aElement) throws SAXException
@Override
public void endElement(String aUri, String aLocalName, String aQName) throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.endElement(aUri, aLocalName, aQName);
}
@@ -144,24 +177,40 @@ public void characters(String aString) throws SAXException
@Override
public void characters(char[] aCh, int aStart, int aLength) throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.characters(aCh, aStart, aLength);
}
@Override
public void ignorableWhitespace(char[] aCh, int aStart, int aLength) throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.ignorableWhitespace(aCh, aStart, aLength);
}
@Override
public void processingInstruction(String aTarget, String aData) throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.processingInstruction(aTarget, aData);
}
@Override
public void skippedEntity(String aName) throws SAXException
{
+ if (delegate == null) {
+ return;
+ }
+
delegate.skippedEntity(aName);
}
}
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/xml/XmlParserUtils.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/xml/XmlParserUtils.java
index 54c6d73eac7..a79a600acf0 100644
--- a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/xml/XmlParserUtils.java
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/xml/XmlParserUtils.java
@@ -32,6 +32,9 @@
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.events.StartElement;
+import javax.xml.stream.events.XMLEvent;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.sax.SAXTransformerFactory;
@@ -148,4 +151,19 @@ public static SAXParser newSaxParser()
{
return newSaxParser(newSaxParserFactory());
}
+
+ public static XMLInputFactory newXmlInputFactory()
+ {
+ XMLInputFactory xmlInputFactory = XMLInputFactory.newFactory();
+ xmlInputFactory.setProperty(XMLInputFactory.SUPPORT_DTD, false);
+ xmlInputFactory.setProperty(XMLInputFactory.IS_SUPPORTING_EXTERNAL_ENTITIES, false);
+ xmlInputFactory.setProperty(XMLInputFactory.IS_VALIDATING, false);
+ return xmlInputFactory;
+ }
+
+ public static boolean isStartElement(XMLEvent aEvent, String aElement)
+ {
+ return aEvent.isStartElement()
+ && ((StartElement) aEvent).getName().getLocalPart().equals(aElement);
+ }
}
diff --git a/inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/xml/sanitizer/IllegalXmlCharacterSanitizingContentHandler.java b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/xml/sanitizer/IllegalXmlCharacterSanitizingContentHandler.java
new file mode 100644
index 00000000000..625335b2db5
--- /dev/null
+++ b/inception/inception-support/src/main/java/de/tudarmstadt/ukp/inception/support/xml/sanitizer/IllegalXmlCharacterSanitizingContentHandler.java
@@ -0,0 +1,124 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.support.xml.sanitizer;
+
+import org.xml.sax.Attributes;
+import org.xml.sax.ContentHandler;
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.AttributesImpl;
+
+import de.tudarmstadt.ukp.clarin.webanno.support.xml.ContentHandlerAdapter;
+
+/**
+ * Replaces characters which are illegal in XML 1.0 or XML 1.1 with a replacement character. The
+ * characters are replaced in text nodes as well as in attribute values.
+ */
+public class IllegalXmlCharacterSanitizingContentHandler
+ extends ContentHandlerAdapter
+{
+ private boolean xml11 = false;
+ private char replacementChar = ' ';
+
+ public IllegalXmlCharacterSanitizingContentHandler(ContentHandler aDelegate)
+ {
+ super(aDelegate);
+ }
+
+ public void setXml11(boolean aXml11)
+ {
+ xml11 = aXml11;
+ }
+
+ public void setReplacementChar(char aReplacementChar)
+ {
+ replacementChar = aReplacementChar;
+ }
+
+ @Override
+ public void startElement(String aUri, String aLocalName, String aQName, Attributes aAtts)
+ throws SAXException
+ {
+ var newAtts = new AttributesImpl();
+ for (int i = 0; i < aAtts.getLength(); i++) {
+ var uri = aAtts.getURI(i);
+ var localName = aAtts.getLocalName(i);
+ var qName = aAtts.getQName(i);
+ var type = aAtts.getType(i);
+ var value = sanitizeIllegalXmlCharacters(aAtts.getValue(i));
+ newAtts.addAttribute(uri, localName, qName, type, value);
+ }
+
+ super.startElement(aUri, aLocalName, aQName, newAtts);
+ }
+
+ @Override
+ public void characters(char[] aCh, int aStart, int aLength) throws SAXException
+ {
+ String s = sanitizeIllegalXmlCharacters(new String(aCh, aStart, aLength));
+ delegate.characters(s.toCharArray(), 0, s.length());
+ }
+
+ @Override
+ public void ignorableWhitespace(char[] aCh, int aStart, int aLength) throws SAXException
+ {
+ String s = sanitizeIllegalXmlCharacters(new String(aCh, aStart, aLength));
+ delegate.ignorableWhitespace(s.toCharArray(), 0, s.length());
+ }
+
+ private String sanitizeIllegalXmlCharacters(String aText)
+ {
+ char[] chars = aText.toCharArray();
+ for (int i = 0; i < chars.length; i++) {
+ char c = chars[i];
+ if ((c >= 0xD800) && (c <= 0xDBFF)) {
+ // The case for Unicode code points #x10000-#x10FFFF. Check if a high surrogate is
+ // followed by a low surrogate, which is the only allowable combination.
+ int iNext = i + 1;
+ if (iNext < chars.length) {
+ char cNext = chars[iNext];
+ if (!((cNext >= 0xDC00) && (cNext <= 0xDFFF))) {
+ chars[i] = replacementChar;
+ continue;
+ }
+ else {
+ i++;
+ continue;
+ }
+ }
+ }
+
+ if (!isValidXmlUtf16int(c)) {
+ // Replace invalid UTF-16 codepoints
+ chars[i] = replacementChar;
+ }
+ }
+
+ return new String(chars);
+ }
+
+ private boolean isValidXmlUtf16int(char c)
+ {
+ if (xml11) {
+ return (c >= 0x1 && c <= 0xD7FF) || (c >= 0xE000) && (c <= 0xFFFD);
+ }
+ else {
+ return ((c == 0x9) || (c == 0xA) || (c == 0xD) || ((c >= 0x20) && (c <= 0xD7FF))
+ || (c >= 0xE000 && c <= 0xFFFD));
+ }
+ }
+}
diff --git a/inception/inception-support/src/main/java/org/apache/uima/cas/impl/FixedBinaryCasSerDes.java b/inception/inception-support/src/main/java/org/apache/uima/cas/impl/FixedBinaryCasSerDes.java
deleted file mode 100644
index d39a5538538..00000000000
--- a/inception/inception-support/src/main/java/org/apache/uima/cas/impl/FixedBinaryCasSerDes.java
+++ /dev/null
@@ -1,478 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-package org.apache.uima.cas.impl;
-
-import java.lang.reflect.Field;
-import java.lang.reflect.Method;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.function.Consumer;
-
-import org.apache.commons.lang3.reflect.FieldUtils;
-import org.apache.commons.lang3.reflect.MethodUtils;
-import org.apache.uima.UimaSerializable;
-import org.apache.uima.cas.CAS;
-import org.apache.uima.cas.CASRuntimeException;
-import org.apache.uima.cas.impl.SlotKinds.SlotKind;
-import org.apache.uima.internal.util.Int2ObjHashMap;
-import org.apache.uima.internal.util.Misc;
-import org.apache.uima.jcas.cas.BooleanArray;
-import org.apache.uima.jcas.cas.ByteArray;
-import org.apache.uima.jcas.cas.DoubleArray;
-import org.apache.uima.jcas.cas.FSArray;
-import org.apache.uima.jcas.cas.FloatArray;
-import org.apache.uima.jcas.cas.IntegerArray;
-import org.apache.uima.jcas.cas.LongArray;
-import org.apache.uima.jcas.cas.ShortArray;
-import org.apache.uima.jcas.cas.Sofa;
-import org.apache.uima.jcas.cas.StringArray;
-import org.apache.uima.jcas.cas.TOP;
-import org.apache.uima.jcas.tcas.Annotation;
-
-/**
- * Workaround UIMA bug while UIMA 3.4.1 has not yet been released.
- *
- * @see "https://github.com/inception-project/inception/issues/3799"
- * @see "https://github.com/apache/uima-uimaj/issues/304"
- */
-public class FixedBinaryCasSerDes
- extends BinaryCasSerDes
-{
- private static final boolean SOFA_IN_NORMAL_ORDER = false;
- private static final int arrayLengthFeatOffset = 1;
- private static final int arrayContentOffset = 2;
-
- private static Field baseCasField = FieldUtils.getDeclaredField(BinaryCasSerDes.class,
- "baseCas", true);
- private static Field tsiField = FieldUtils.getDeclaredField(BinaryCasSerDes.class, "tsi", true);
- private static Method updateStringFeatureMethod = MethodUtils.getMatchingMethod(
- BinaryCasSerDes.class, "updateStringFeature", TOP.class, FeatureImpl.class,
- String.class, List.class);
- private static Method getSofaFromAnnotBaseMethod = MethodUtils.getMatchingMethod(
- BinaryCasSerDes.class, "getSofaFromAnnotBase", int.class, StringHeap.class,
- Int2ObjHashMap.class, CommonSerDesSequential.class);
- private static Method heapFeatMethod = MethodUtils.getMatchingMethod(BinaryCasSerDes.class,
- "heapFeat", int.class, FeatureImpl.class);
- private static Method makeSofaFromHeapMethod = MethodUtils.getMatchingMethod(
- BinaryCasSerDes.class, "makeSofaFromHeap", int.class, StringHeap.class,
- CommonSerDesSequential.class, boolean.class);
- private static Method setFeatOrDeferMethod = MethodUtils.getMatchingMethod(
- BinaryCasSerDes.class, "setFeatOrDefer", int.class, FeatureImpl.class, List.class,
- Consumer.class, Int2ObjHashMap.class);
-
- static {
- updateStringFeatureMethod.setAccessible(true);
- getSofaFromAnnotBaseMethod.setAccessible(true);
- heapFeatMethod.setAccessible(true);
- makeSofaFromHeapMethod.setAccessible(true);
- setFeatOrDeferMethod.setAccessible(true);
- }
-
- public static void inject(CAS aCas)
- {
- CASImpl casImpl = (CASImpl) aCas;
- CASImpl baseCas = casImpl.getBaseCAS();
- try {
- FieldUtils.writeDeclaredField(casImpl.svd, "bcsd", new FixedBinaryCasSerDes(baseCas),
- true);
- }
- catch (IllegalAccessException e) {
- throw new RuntimeException(e);
- }
- }
-
- public FixedBinaryCasSerDes(CASImpl aBaseCAS)
- {
- super(aBaseCAS);
- }
-
- @Override
- void reinit(int[] heapMetadata, int[] heapArray, String[] stringTable, int[] fsIndex,
- byte[] byteHeapArray, short[] shortHeapArray, long[] longHeapArray)
- {
- CASImpl baseCas = getBaseCas();
-
- CommonSerDesSequential csds = new CommonSerDesSequential(baseCas); // for non Delta case,
- // not
- // held on to
- // compare with compress form 4, which does cas.getCsds() or cas.newCsds() which saves it in
- // cas.svd
- csds.setup(null, 1);
- heap = new Heap();
- byteHeap = new ByteHeap();
- shortHeap = new ShortHeap();
- longHeap = new LongHeap();
- stringHeap = new StringHeap();
-
- createStringTableFromArray(stringTable);
-
- heap.reinit(heapMetadata, heapArray);
- if (byteHeapArray != null) {
- byteHeap.reinit(byteHeapArray);
- }
- if (shortHeapArray != null) {
- shortHeap.reinit(shortHeapArray);
- }
- if (longHeapArray != null) {
- longHeap.reinit(longHeapArray);
- }
-
- createFSsFromHeaps(false, 1, csds); // false means not delta
-
- reinitIndexedFSs(fsIndex, false, i -> csds.addr2fs.get(i));
- }
-
- private void createFSsFromHeaps(boolean isDelta, int startPos, CommonSerDesSequential csds)
- {
- CASImpl baseCas = getBaseCas();
-
- final int heapsz = heap.getCellsUsed();
- final Int2ObjHashMap addr2fs = csds.addr2fs;
- TypeSystemImpl tsi = baseCas.getTypeSystemImpl();
- setTsi(tsi);
- TOP fs;
- TypeImpl type;
- CASImpl initialView = baseCas.getInitialView(); // creates if needed
-
- List fixups4forwardFsRefs = new ArrayList<>();
- List fixups4UimaSerialization = new ArrayList<>();
-
- for (int heapIndex = startPos; heapIndex < heapsz; heapIndex += getFsSpaceReq(fs, type)) {
- int typecode = heap.heap[heapIndex];
- // if (isBeforeV3 && typecode > TypeSystemConstants.lastBuiltinV2TypeCode) {
- // typecode = typecode + TypeSystemConstants.numberOfNewBuiltInsSinceV2;
- // }
- type = tsi.getTypeForCode(heap.heap[heapIndex]);
- if (type == null) {
- throw new CASRuntimeException(CASRuntimeException.deserialized_type_not_found,
- heap.heap[heapIndex]);
- }
- if (type.isArray()) {
- final int len = heap.heap[heapIndex + arrayLengthFeatOffset];
-
- fs = baseCas.createArray(type, len);
- csds.addFS(fs, heapIndex);
-
- if (len > 0) {
- final int bhi = heap.heap[heapIndex + arrayContentOffset];
- final int hhi = heapIndex + arrayContentOffset;
-
- switch (type.getComponentSlotKind()) {
-
- case Slot_BooleanRef: {
- boolean[] ba = ((BooleanArray) fs)._getTheArray();
- for (int ai = 0; ai < len; ai++) {
- ba[ai] = byteHeap.heap[bhi + ai] == (byte) 1;
- }
- break;
- }
-
- case Slot_ByteRef:
- System.arraycopy(byteHeap.heap, bhi, ((ByteArray) fs)._getTheArray(), 0,
- len);
- break;
-
- case Slot_ShortRef:
- System.arraycopy(shortHeap.heap, bhi, ((ShortArray) fs)._getTheArray(), 0,
- len);
- break;
-
- case Slot_LongRef:
- System.arraycopy(longHeap.heap, bhi, ((LongArray) fs)._getTheArray(), 0,
- len);
- break;
-
- case Slot_DoubleRef: {
- double[] da = ((DoubleArray) fs)._getTheArray();
- for (int ai = 0; ai < len; ai++) {
- da[ai] = CASImpl.long2double(longHeap.heap[bhi + ai]);
- }
- break;
- }
-
- case Slot_Int:
- System.arraycopy(heap.heap, hhi, ((IntegerArray) fs)._getTheArray(), 0,
- len);
- break;
-
- case Slot_Float: {
- float[] fa = ((FloatArray) fs)._getTheArray();
- for (int ai = 0; ai < len; ai++) {
- fa[ai] = CASImpl.int2float(heap.heap[hhi + ai]);
- }
- break;
- }
-
- case Slot_StrRef: {
- String[] sa = ((StringArray) fs)._getTheArray();
- for (int ai = 0; ai < len; ai++) {
- sa[ai] = stringHeap.getStringForCode(heap.heap[hhi + ai]);
- }
- break;
- }
-
- case Slot_HeapRef: {
- TOP[] fsa = ((FSArray) fs)._getTheArray();
- for (int ai = 0; ai < len; ai++) {
- int a = heap.heap[hhi + ai];
- if (a == 0) {
- continue;
- }
- TOP item = addr2fs.get(a);
- if (item != null) {
- fsa[ai] = item;
- }
- else {
- final int aiSaved = ai;
- final int addrSaved = a;
- fixups4forwardFsRefs.add(() -> {
- fsa[aiSaved] = addr2fs.get(addrSaved);
- });
- }
- }
- break;
- }
-
- default:
- Misc.internalError();
-
- } // end of switch
- }
- }
- else { // end of arrays
- // start of normal non-array
- CASImpl view = null;
- boolean isSofa = false;
- boolean documentAnnotationPreviouslyIndexed = false;
- if (type.isAnnotationBaseType()) {
- Sofa sofa = _getSofaFromAnnotBase(heapIndex, stringHeap, addr2fs, csds); // creates
- // sofa
- // if
- // needed
- // and
- // exists
- // (forward
- // ref
- // case)
- view = (sofa == null) ? baseCas.getInitialView() : baseCas.getView(sofa);
- if (type == tsi.docType) {
- Annotation documentAnnotationPrevious = view
- .getDocumentAnnotationNoCreate();
- if (documentAnnotationPrevious == null) {
- // document annotation not present
- fs = view.createDocumentAnnotationNoRemoveNoIndex(0); // create but
- // don't index
- view.set_deserialized_doc_annot_not_indexed((Annotation) fs); // for use
- // by
- // other
- // code
- // that
- // sets
- // length,
- // if
- // this is
- // not
- // indexed
- // documentAnnotationPreviouslyIndex == false, preset above
- }
- else {
- fs = documentAnnotationPrevious;
- // remove from Corruptable indexes, because we'll be updating it.
- view.removeFromCorruptableIndexAnyView(fs, view.getAddbackSingle());
- documentAnnotationPreviouslyIndexed = true;
- }
- }
- else {
- fs = view.createFS(type);
- if (fs instanceof UimaSerializable) {
- final UimaSerializable ufs = (UimaSerializable) fs;
- fixups4UimaSerialization.add(() -> ufs._init_from_cas_data());
- }
- }
- }
- else if (type == tsi.sofaType) {
- fs = _makeSofaFromHeap(heapIndex, stringHeap, csds, SOFA_IN_NORMAL_ORDER); // creates
- // Sofa
- // if
- // not
- // already
- // created
- // due
- // to
- // annotationbase
- // code
- // above
- isSofa = true;
- }
- else {
- fs = initialView.createFS(type);
- if (fs instanceof UimaSerializable) {
- final UimaSerializable ufs = (UimaSerializable) fs;
- fixups4UimaSerialization.add(() -> ufs._init_from_cas_data());
- }
- }
- if (!isSofa) { // if it was a sofa, other code added or pended it
- csds.addFS(fs, heapIndex);
- }
-
- for (final FeatureImpl feat : type.getFeatureImpls()) {
- SlotKind slotKind = feat.getSlotKind();
- switch (slotKind) {
- case Slot_Boolean:
- case Slot_Byte:
- case Slot_Short:
- case Slot_Int:
- case Slot_Float:
- if (!isSofa || feat != tsi.sofaNum) {
- fs._setIntLikeValueNcNj(slotKind, feat, _heapFeat(heapIndex, feat));
- }
- break;
-
- case Slot_LongRef:
- fs._setLongValueNcNj(feat, longHeap.heap[_heapFeat(heapIndex, feat)]);
- break;
- case Slot_DoubleRef:
- fs._setDoubleValueNcNj(feat,
- CASImpl.long2double(longHeap.heap[_heapFeat(heapIndex, feat)]));
- break;
- case Slot_StrRef: {
- String s = stringHeap.getStringForCode(_heapFeat(heapIndex, feat));
- if (_updateStringFeature(fs, feat, s, fixups4forwardFsRefs)) {
- fs._setStringValueNcNj(feat, s);
- }
- break;
- }
-
- case Slot_HeapRef: {
- final TOP finalFs = fs;
- if (feat == tsi.annotBaseSofaFeat) {
- break; // already set
- }
- _setFeatOrDefer(heapIndex, feat, fixups4forwardFsRefs, item -> {
- if (feat == tsi.sofaArray) {
- ((Sofa) finalFs).setLocalSofaData(item);
- }
- else {
- finalFs._setFeatureValueNcNj(feat, item);
- }
- }, addr2fs);
- break;
- }
-
- default:
- Misc.internalError();
- } // end of switch
- } // end of for-loop-over-all-features
-
- if (type == tsi.docType && documentAnnotationPreviouslyIndexed) {
- view.addbackSingle(fs);
- }
- } // end of non-array, normal fs
- } // end of loop over all fs in main array
-
- for (Runnable r : fixups4forwardFsRefs) {
- r.run();
- }
-
- for (Runnable r : fixups4UimaSerialization) {
- r.run();
- }
- }
-
- private void _setFeatOrDefer(int aHeapIndex, FeatureImpl aFeat,
- List aFixups4forwardFsRefs, Consumer aSetter,
- Int2ObjHashMap aAddr2fs)
- {
- try {
- setFeatOrDeferMethod.invoke(this, aHeapIndex, aFeat, aFixups4forwardFsRefs, aSetter,
- aAddr2fs);
- }
- catch (Exception e) {
- throw new RuntimeException(e);
- }
- }
-
- private boolean _updateStringFeature(TOP aFs, FeatureImpl aFeat, String aS,
- List aFixups4forwardFsRefs)
- {
- try {
- return (boolean) updateStringFeatureMethod.invoke(this, aFs, aFeat, aS,
- aFixups4forwardFsRefs);
- }
- catch (Exception e) {
- throw new RuntimeException(e);
- }
- }
-
- private int _heapFeat(int aHeapIndex, FeatureImpl aFeat)
- {
- try {
- return (int) heapFeatMethod.invoke(this, aHeapIndex, aFeat);
- }
- catch (Exception e) {
- throw new RuntimeException(e);
- }
- }
-
- private TOP _makeSofaFromHeap(int aHeapIndex, StringHeap aStringHeap,
- CommonSerDesSequential aCsds, boolean aSofaInNormalOrder)
- {
- try {
- return (TOP) makeSofaFromHeapMethod.invoke(this, aHeapIndex, aStringHeap, aCsds,
- aSofaInNormalOrder);
- }
- catch (Exception e) {
- throw new RuntimeException(e);
- }
- }
-
- private Sofa _getSofaFromAnnotBase(int annotBaseAddr, StringHeap stringHeap2,
- Int2ObjHashMap addr2fs, CommonSerDesSequential csds)
- {
- try {
- return (Sofa) getSofaFromAnnotBaseMethod.invoke(this, annotBaseAddr, stringHeap2,
- addr2fs, csds);
- }
- catch (Exception e) {
- throw new RuntimeException(e);
- }
- }
-
- private void setTsi(TypeSystemImpl aTsi)
- {
- try {
- FieldUtils.writeField(tsiField, this, aTsi, true);
- }
- catch (IllegalAccessException e) {
- throw new RuntimeException(e);
- }
- }
-
- private CASImpl getBaseCas()
- {
- CASImpl baseCas;
- try {
- baseCas = (CASImpl) FieldUtils.readField(baseCasField, this, true);
- }
- catch (IllegalAccessException e) {
- throw new RuntimeException(e);
- }
- return baseCas;
- }
-}
diff --git a/inception/inception-support/src/main/resources/META-INF/DEPENDENCIES-EMBEDDED.spdx.json b/inception/inception-support/src/main/resources/META-INF/DEPENDENCIES-EMBEDDED.spdx.json
index eca7baa46d0..d2dbdfa0ead 100644
--- a/inception/inception-support/src/main/resources/META-INF/DEPENDENCIES-EMBEDDED.spdx.json
+++ b/inception/inception-support/src/main/resources/META-INF/DEPENDENCIES-EMBEDDED.spdx.json
@@ -12,17 +12,6 @@
"hasFiles": [
"de/tudarmstadt/ukp/clarin/webanno/support/wicket/AjaxDownloadBehavior.java"
]
- },
- {
- "name": "vue3-sfc-loader",
- "versionInfo": "0.2.21",
- "originator": "Franck Freiburger",
- "homepage": "https://github.com/FranckFreiburger/vue3-sfc-loader",
- "licenseDeclared": "MIT",
- "hasFiles": [
- "de/tudarmstadt/ukp/inception/support/vue/vue3-sfc-loader.min.js",
- "de/tudarmstadt/ukp/inception/support/vue/vue3-sfc-loader.min.js.map"
- ]
}
]
}
\ No newline at end of file
diff --git a/inception/inception-support/src/test/java/de/tudarmstadt/ukp/inception/support/xml/sanitizer/IllegalXmlCharacterSanitizingContentHandlerTest.java b/inception/inception-support/src/test/java/de/tudarmstadt/ukp/inception/support/xml/sanitizer/IllegalXmlCharacterSanitizingContentHandlerTest.java
new file mode 100644
index 00000000000..6a563b8abeb
--- /dev/null
+++ b/inception/inception-support/src/test/java/de/tudarmstadt/ukp/inception/support/xml/sanitizer/IllegalXmlCharacterSanitizingContentHandlerTest.java
@@ -0,0 +1,131 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The Technische Universität Darmstadt
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.support.xml.sanitizer;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import org.junit.jupiter.api.Test;
+import org.xml.sax.SAXException;
+
+import de.tudarmstadt.ukp.clarin.webanno.support.xml.ContentHandlerAdapter;
+
+//CHECKSTYLE:OFF
+class IllegalXmlCharacterSanitizingContentHandlerTest
+{
+ @Test
+ void testXml10() throws Exception
+ {
+ var stringCollector = new ContentToString();
+ var adapter = new IllegalXmlCharacterSanitizingContentHandler(stringCollector);
+ adapter.setXml11(false);
+ adapter.setReplacementChar('\uFFFD');
+
+ char[] input = { '\u0000', '\u0001', '\u0002', '\u0003', '\u0004', '\u0005', '\u0006',
+ '\u0007', '\u0008', '\u0009', '\n', '\u000b', '\u000c', '\r', '\u000e', '\u000f',
+ '\u0010', '\u0011', '\u0012', '\u0013', '\u0014', '\u0015', '\u0016', '\u0017',
+ '\u0018', '\u0019', '\u001a', '\u001b', '\u001c', '\u001d', '\u001e', '\u001f',
+ '\u0020', '\uD800' };
+ adapter.characters(input, 0, input.length);
+ assertThat(stringCollector.toString().toCharArray()).hasSameSizeAs(input);
+ assertThat(stringCollector.toString().toCharArray()).containsExactly('\uFFFD', '\uFFFD',
+ '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\u0009',
+ '\n', '\uFFFD', '\uFFFD', '\r', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD',
+ '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD',
+ '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\uFFFD', '\u0020', '\uFFFD');
+ }
+
+ @Test
+ void testXml11() throws Exception
+ {
+ var stringCollector = new ContentToString();
+ var adapter = new IllegalXmlCharacterSanitizingContentHandler(stringCollector);
+ adapter.setXml11(true);
+ adapter.setReplacementChar('\uFFFD');
+
+ char[] input = { '\u0000', '\u0001', '\u0002', '\u0003', '\u0004', '\u0005', '\u0006',
+ '\u0007', '\u0008', '\u0009', '\n', '\u000b', '\u000c', '\r', '\u000e', '\u000f',
+ '\u0010', '\u0011', '\u0012', '\u0013', '\u0014', '\u0015', '\u0016', '\u0017',
+ '\u0018', '\u0019', '\u001a', '\u001b', '\u001c', '\u001d', '\u001e', '\u001f',
+ '\u0020', '\uD800' };
+ adapter.characters(input, 0, input.length);
+ assertThat(stringCollector.toString().toCharArray()).hasSameSizeAs(input);
+ assertThat(stringCollector.toString().toCharArray()).containsExactly('\uFFFD', '\u0001',
+ '\u0002', '\u0003', '\u0004', '\u0005', '\u0006', '\u0007', '\u0008', '\u0009',
+ '\n', '\u000b', '\u000c', '\r', '\u000e', '\u000f', '\u0010', '\u0011', '\u0012',
+ '\u0013', '\u0014', '\u0015', '\u0016', '\u0017', '\u0018', '\u0019', '\u001a',
+ '\u001b', '\u001c', '\u001d', '\u001e', '\u001f', '\u0020', '\uFFFD');
+ }
+
+ @Test
+ void testWithSurrogate() throws Exception
+ {
+ var stringCollector = new ContentToString();
+ var adapter = new IllegalXmlCharacterSanitizingContentHandler(stringCollector);
+ adapter.setXml11(false);
+ adapter.setReplacementChar('\uFFFD');
+
+ var input = "🙋ðŸ½â€â™€ï¸";
+ adapter.characters(input);
+ assertThat(stringCollector.toString()).hasSameSizeAs(input);
+ assertThat(stringCollector.toString()).isEqualTo("🙋ðŸ½â€â™€ï¸");
+ }
+
+ @Test
+ void testWithBrokenSurrogate() throws Exception
+ {
+ var stringCollector = new ContentToString();
+ var adapter = new IllegalXmlCharacterSanitizingContentHandler(stringCollector);
+ adapter.setXml11(false);
+ adapter.setReplacementChar('\uFFFD');
+
+ char[] input = { '\ude4b', '\ud83d' };
+ adapter.characters(input, 0, input.length);
+ assertThat(stringCollector.toString()).hasSameSizeAs(input);
+ assertThat(stringCollector.toString().toCharArray()).containsExactly('\uFFFD', '\uFFFD');
+ }
+
+ private static class ContentToString
+ extends ContentHandlerAdapter
+ {
+ private final StringBuilder text = new StringBuilder();
+
+ @Override
+ public void startDocument() throws SAXException
+ {
+ text.setLength(0);
+ }
+
+ @Override
+ public void characters(char[] aCh, int aStart, int aLength) throws SAXException
+ {
+ text.append(aCh, aStart, aLength);
+ }
+
+ @Override
+ public void ignorableWhitespace(char[] aCh, int aStart, int aLength) throws SAXException
+ {
+ text.append(aCh, aStart, aLength);
+ }
+
+ @Override
+ public String toString()
+ {
+ return text.toString();
+ }
+ }
+}
diff --git a/inception/inception-telemetry/pom.xml b/inception/inception-telemetry/pom.xml
index 999292b4587..8d5c78576fb 100644
--- a/inception/inception-telemetry/pom.xml
+++ b/inception/inception-telemetry/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-telemetryINCEpTION - Telemetry
@@ -109,6 +109,10 @@
com.googlecode.wicket-jquery-uiwicket-jquery-ui-core
+
+ org.danekja
+ jdk-serializable-functional
+ org.slf4j
diff --git a/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImpl.java b/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImpl.java
index a5a3086847f..0b2578bdb30 100644
--- a/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImpl.java
+++ b/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImpl.java
@@ -83,6 +83,7 @@ public class MatomoTelemetrySupportImpl
implements MatomoTelemetrySupport, DisposableBean
{
public static final String MATOMO_TELEMETRY_SUPPORT_ID = "MatomoTelemetry";
+ public static final int CURRENT_SETTINGS_VERSION = 3;
public static final String ACTION_BOOT = "boot";
public static final String ACTION_HELLO = "hello";
@@ -159,7 +160,7 @@ public String getId()
@Override
public int getVersion()
{
- return 2;
+ return CURRENT_SETTINGS_VERSION;
}
@Override
@@ -171,7 +172,7 @@ public boolean hasValidSettings()
return false;
}
- boolean outdated = settings.get().getVersion() < getVersion();
+ boolean outdated = settings.get().getVersion() != getVersion();
if (outdated) {
return false;
}
diff --git a/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/ToggleBox.java b/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/ToggleBox.java
index 91df421c519..9f94f660896 100644
--- a/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/ToggleBox.java
+++ b/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/ToggleBox.java
@@ -19,6 +19,8 @@
import static java.util.Arrays.asList;
+import org.apache.wicket.markup.html.form.IChoiceRenderer;
+
import com.googlecode.wicket.jquery.core.JQueryBehavior;
import com.googlecode.wicket.jquery.core.Options;
import com.googlecode.wicket.kendo.ui.form.dropdown.DropDownList;
@@ -36,7 +38,31 @@ public ToggleBox(String aId)
setRequired(true);
setNullValid(false);
- setChoices(asList(true, false));
+ setChoices(asList(false, true));
+ setChoiceRenderer(new IChoiceRenderer()
+ {
+ private static final long serialVersionUID = -180513167658049798L;
+
+ @Override
+ public String getDisplayValue(Boolean aObject)
+ {
+ if (aObject == null) {
+ return null;
+ }
+
+ return aObject ? "enabled" : "disabled";
+ }
+
+ @Override
+ public String getIdValue(Boolean aObject, int aIndex)
+ {
+ if (aObject == null) {
+ return null;
+ }
+
+ return aObject ? "true" : "false";
+ }
+ });
setEscapeModelStrings(false); // SAFE - ONLY RENDERING A FEW HARD-CODED CHOICES WITH ICONS
}
@@ -46,9 +72,9 @@ public void onConfigure(JQueryBehavior aBehavior)
super.onConfigure(aBehavior);
var template = Options.asString(String.join("\n", //
- "# if (data.value == '0') { #", //
+ "# if (data.value == 'false') { #", //
" Disabled", //
- "# } else if (data.value == '1') { #", //
+ "# } else if (data.value == 'true') { #", //
" Enabled", //
"# } else { #", //
" Choose...", //
diff --git a/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/ui/TelemetryFooterPanel.html b/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/ui/TelemetryFooterPanel.html
index 9b60f7dd8bd..ec7b5c5702d 100644
--- a/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/ui/TelemetryFooterPanel.html
+++ b/inception/inception-telemetry/src/main/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/ui/TelemetryFooterPanel.html
@@ -19,7 +19,7 @@
-
+
diff --git a/inception/inception-telemetry/src/test/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImplTest.java b/inception/inception-telemetry/src/test/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImplTest.java
index ef76fc96da0..df8e3d8561a 100644
--- a/inception/inception-telemetry/src/test/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImplTest.java
+++ b/inception/inception-telemetry/src/test/java/de/tudarmstadt/ukp/clarin/webanno/telemetry/matomo/MatomoTelemetrySupportImplTest.java
@@ -18,6 +18,7 @@
package de.tudarmstadt.ukp.clarin.webanno.telemetry.matomo;
import static de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil.fromJsonString;
+import static de.tudarmstadt.ukp.clarin.webanno.telemetry.matomo.MatomoTelemetrySupportImpl.CURRENT_SETTINGS_VERSION;
import static java.lang.String.format;
import static java.net.URLDecoder.decode;
import static java.nio.charset.StandardCharsets.UTF_8;
@@ -60,6 +61,7 @@ public class MatomoTelemetrySupportImplTest
private MockWebServer matomoServer;
private MatomoTelemetryServicePropertiesImpl properties;
private UUID instanceId;
+ private TelemetrySettings telemetrySettings;
@BeforeEach
public void setup() throws Exception
@@ -78,8 +80,8 @@ public void setup() throws Exception
when(identityService.getInstanceIdentity())
.thenReturn(new InstanceIdentity(instanceId.toString()));
- TelemetrySettings telemetrySettings = new TelemetrySettings();
- telemetrySettings.setVersion(2);
+ telemetrySettings = new TelemetrySettings();
+ telemetrySettings.setVersion(CURRENT_SETTINGS_VERSION);
telemetrySettings.setTraits("{\"enabled\": true}");
TelemetryService telemetryService = mock(TelemetryService.class);
when(telemetryService.readSettings(any())).thenReturn(Optional.of(telemetrySettings));
@@ -108,6 +110,8 @@ public void teardown() throws Exception
@Test
public void thatAliveIsRecieved() throws Exception
{
+ assertThat(sut.isEnabled()).isTrue();
+
matomoServer.enqueue(new MockResponse().setResponseCode(200));
sut.sendAlive();
@@ -135,6 +139,8 @@ public void thatAliveIsRecieved() throws Exception
@Test
public void thatPingIsRecieved() throws Exception
{
+ assertThat(sut.isEnabled()).isTrue();
+
matomoServer.enqueue(new MockResponse().setResponseCode(200));
sut.sendPing();
@@ -158,4 +164,15 @@ public void thatPingIsRecieved() throws Exception
assertThat(map.get("4")).isEqualTo(asList("enabledUsers", "2"));
assertThat(map.get("5")).isEqualTo(asList("deploymentMode", "DESKTOP"));
}
+
+ @Test
+ public void thatVersionMismatchDisablesTelemetry() throws Exception
+ {
+ assertThat(telemetrySettings.getVersion()).isEqualTo(CURRENT_SETTINGS_VERSION);
+ assertThat(sut.isEnabled()).isTrue();
+
+ telemetrySettings.setVersion(CURRENT_SETTINGS_VERSION - 1);
+ assertThat(telemetrySettings.getVersion()).isNotEqualTo(CURRENT_SETTINGS_VERSION);
+ assertThat(sut.isEnabled()).isFalse();
+ }
}
diff --git a/inception/inception-testing/pom.xml b/inception/inception-testing/pom.xml
index 55938eb4187..2eeb3f912e9 100644
--- a/inception/inception-testing/pom.xml
+++ b/inception/inception-testing/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-testingINCEpTION - Test Support library
diff --git a/inception/inception-tutorial/pom.xml b/inception/inception-tutorial/pom.xml
index ed9b63b730d..e9ba2a1ff74 100644
--- a/inception/inception-tutorial/pom.xml
+++ b/inception/inception-tutorial/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-tutorialINCEpTION - UI - Tutorial
diff --git a/inception/inception-ui-agreement/pom.xml b/inception/inception-ui-agreement/pom.xml
index 999a058b430..f89967f2ee0 100644
--- a/inception/inception-ui-agreement/pom.xml
+++ b/inception/inception-ui-agreement/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-ui-agreementINCEpTION - UI - Agreement
@@ -128,5 +128,9 @@
de.agilecoders.wicketwicket-bootstrap-extensions
+
+ org.danekja
+ jdk-serializable-functional
+
\ No newline at end of file
diff --git a/inception/inception-ui-annotation/pom.xml b/inception/inception-ui-annotation/pom.xml
index dd7483e7a26..d690fa77572 100644
--- a/inception/inception-ui-annotation/pom.xml
+++ b/inception/inception-ui-annotation/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-ui-annotationINCEpTION - UI - Annotation
@@ -122,6 +122,10 @@
org.wicketstuffwicketstuff-input-events
+
+ org.wicketstuff
+ wicketstuff-urlfragment
+ org.wicketstuffwicketstuff-annotation
diff --git a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/AnnotationPage.java b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/AnnotationPage.java
index b6c410f2804..f01c9ee88a4 100755
--- a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/AnnotationPage.java
+++ b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/AnnotationPage.java
@@ -18,6 +18,7 @@
package de.tudarmstadt.ukp.clarin.webanno.ui.annotation;
import static de.tudarmstadt.ukp.clarin.webanno.api.CasUpgradeMode.FORCE_CAS_UPGRADE;
+import static de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationEditorState.KEY_EDITOR_STATE;
import static de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase.PAGE_PARAM_DOCUMENT;
import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentState.IGNORE;
import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateChangeFlag.EXPLICIT_ANNOTATOR_USER_ACTION;
@@ -31,6 +32,7 @@
import static de.tudarmstadt.ukp.inception.rendering.selection.FocusPosition.TOP;
import java.io.IOException;
+import java.lang.invoke.MethodHandles;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@@ -101,13 +103,12 @@
public class AnnotationPage
extends AnnotationPageBase
{
- private static final String MID_EDITOR = "editor";
-
- private static final String MID_NUMBER_OF_PAGES = "numberOfPages";
+ private static final long serialVersionUID = 1378872465851908515L;
- private static final Logger LOG = LoggerFactory.getLogger(AnnotationPage.class);
+ private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
- private static final long serialVersionUID = 1378872465851908515L;
+ private static final String MID_EDITOR = "editor";
+ private static final String MID_NUMBER_OF_PAGES = "numberOfPages";
private @SpringBean DocumentService documentService;
private @SpringBean ProjectService projectService;
@@ -230,7 +231,7 @@ public void onAnnotationEvent(AnnotationEvent aEvent)
if (!Objects.equals(state.getProject(), aEvent.getProject())
|| !Objects.equals(state.getDocument(), aEvent.getDocument())
- || !Objects.equals(state.getUser().getUsername(), aEvent.getUser())) {
+ || !Objects.equals(state.getUser().getUsername(), aEvent.getDocumentOwner())) {
return;
}
@@ -253,7 +254,7 @@ public void onFeatureValueUpdatedEvent(FeatureValueUpdatedEvent aEvent)
if (!Objects.equals(state.getProject(), aEvent.getProject())
|| !Objects.equals(state.getDocument(), aEvent.getDocument())
- || !Objects.equals(state.getUser().getUsername(), aEvent.getUser())) {
+ || !Objects.equals(state.getUser().getUsername(), aEvent.getDocumentOwner())) {
return;
}
@@ -272,7 +273,15 @@ public void onViewStateChanged(AnnotatorViewportChangedEvent aEvent)
return;
}
- aEvent.getRequestHandler().add(centerArea.get(MID_NUMBER_OF_PAGES));
+ try {
+ aEvent.getRequestHandler().add(centerArea.get(MID_NUMBER_OF_PAGES));
+ }
+ catch (IllegalStateException e) {
+ // Ignore IllegalStateException if rendering of page has already progress so far that
+ // no new components can be added. We hope the caller will know what they are doing
+ // when they invoke this method so late in the render cycle and trigger a page-reload
+ // themselves.
+ }
actionRefreshDocument(aEvent.getRequestHandler());
}
@@ -421,6 +430,7 @@ protected void actionLoadDocument(AjaxRequestTarget aTarget, int aFocus)
// create one.
AnnotationDocument annotationDocument = documentService
.createOrGetAnnotationDocument(state.getDocument(), state.getUser());
+ var stateBeforeOpening = annotationDocument.getState();
// Read the CAS
// Update the annotation document CAS
@@ -510,7 +520,7 @@ protected void actionLoadDocument(AjaxRequestTarget aTarget, int aFocus)
applicationEventPublisherHolder.get().publishEvent(
new DocumentOpenedEvent(this, editorCas, getModelObject().getDocument(),
- getModelObject().getUser().getUsername(),
+ stateBeforeOpening, getModelObject().getUser().getUsername(),
userRepository.getCurrentUser().getUsername()));
}
catch (Exception e) {
@@ -538,13 +548,7 @@ public void actionRefreshDocument(AjaxRequestTarget aTarget)
}
}
- // Update URL for current document
- try {
- updateUrlFragment(aTarget);
- }
- catch (Exception e) {
- LOG.warn("Unable to request URL fragment update anymore", e);
- }
+ updateUrlFragment(aTarget);
}
@Override
@@ -681,7 +685,7 @@ public List listAccessibleDocuments(Project aProject, User a
{
final List allDocuments = new ArrayList<>();
Map docs = documentService.listAllDocuments(aProject,
- aUser);
+ aUser.getUsername());
User user = userRepository.getCurrentUser();
for (Entry e : docs.entrySet()) {
diff --git a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/docnav/DocumentNavigator.java b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/docnav/DocumentNavigator.java
index d4f85a0b177..68b859ed17f 100644
--- a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/docnav/DocumentNavigator.java
+++ b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/docnav/DocumentNavigator.java
@@ -17,7 +17,6 @@
*/
package de.tudarmstadt.ukp.clarin.webanno.ui.annotation.actionbar.docnav;
-import static de.tudarmstadt.ukp.clarin.webanno.model.PermissionLevel.MANAGER;
import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.visibleWhen;
import static wicket.contrib.input.events.EventType.click;
import static wicket.contrib.input.events.key.KeyType.Page_down;
@@ -32,10 +31,11 @@
import de.tudarmstadt.ukp.clarin.webanno.api.ProjectService;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.actionbar.export.ExportDocumentDialog;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
+import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaAjaxLink;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.input.InputBehavior;
import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.actionbar.open.OpenDocumentDialog;
-import de.tudarmstadt.ukp.inception.rendering.editorstate.AnnotatorState;
+import de.tudarmstadt.ukp.inception.documents.DocumentAccess;
import wicket.contrib.input.events.key.KeyType;
public class DocumentNavigator
@@ -44,6 +44,8 @@ public class DocumentNavigator
private static final long serialVersionUID = 7061696472939390003L;
private @SpringBean ProjectService projectService;
+ private @SpringBean UserDao userService;
+ private @SpringBean DocumentAccess documentAccess;
private AnnotationPageBase page;
@@ -64,12 +66,14 @@ public DocumentNavigator(String aId, AnnotationPageBase aPage)
add(new LambdaAjaxLink("showOpenDocumentDialog", this::actionShowOpenDocumentDialog));
add(exportDialog = new ExportDocumentDialog("exportDialog", page.getModel()));
- add(new LambdaAjaxLink("showExportDialog", exportDialog::show).add(visibleWhen(() -> {
- AnnotatorState state = page.getModelObject();
- return state.getProject() != null
- && (projectService.hasRole(state.getUser(), state.getProject(), MANAGER)
- || !state.getProject().isDisableExport());
- })));
+ add(new LambdaAjaxLink("showExportDialog", exportDialog::show)
+ .add(visibleWhen(this::isExportable)));
+ }
+
+ private boolean isExportable()
+ {
+ return documentAccess.canExportAnnotationDocument(userService.getCurrentUser(),
+ page.getModelObject().getProject());
}
/**
diff --git a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/undo/actions/AnnotationAction_ImplBase.java b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/undo/actions/AnnotationAction_ImplBase.java
index e578e7044b9..f652b23d46d 100644
--- a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/undo/actions/AnnotationAction_ImplBase.java
+++ b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/actionbar/undo/actions/AnnotationAction_ImplBase.java
@@ -40,7 +40,7 @@ public AnnotationAction_ImplBase(long aRequestId, AnnotationEvent aEvent, VID aV
requestId = aRequestId;
vid = aVid;
document = aEvent.getDocument();
- user = aEvent.getUser();
+ user = aEvent.getDocumentOwner();
layer = aEvent.getLayer();
}
diff --git a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java
index 45128f672f6..baab961888e 100644
--- a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java
+++ b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java
@@ -78,7 +78,6 @@
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.exception.IllegalPlacementException;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil;
-import de.tudarmstadt.ukp.clarin.webanno.constraints.evaluator.Evaluator;
import de.tudarmstadt.ukp.clarin.webanno.constraints.evaluator.PossibleValue;
import de.tudarmstadt.ukp.clarin.webanno.constraints.evaluator.RulesIndicator;
import de.tudarmstadt.ukp.clarin.webanno.constraints.evaluator.ValuesGenerator;
@@ -1212,7 +1211,7 @@ private boolean isAnnotationEventRelevant(AnnotationEvent aEvent)
return false;
}
- if (!state.getUser().getUsername().equals(aEvent.getUser())) {
+ if (!state.getUser().getUsername().equals(aEvent.getDocumentOwner())) {
return false;
}
@@ -1291,10 +1290,10 @@ private void populateTagsBasedOnRules(CAS aCas, FeatureState aModel)
// Fetch possible values from the constraint rules
List possibleValues;
try {
- FeatureStructure featureStructure = selectFsByAddr(aCas,
+ var featureStructure = selectFsByAddr(aCas,
state.getSelection().getAnnotation().getId());
- Evaluator evaluator = new ValuesGenerator();
+ var evaluator = new ValuesGenerator();
// Only show indicator if this feature can be affected by Constraint rules!
aModel.indicator.setAffected(evaluator.isThisAffectedByConstraintRules(featureStructure,
restrictionFeaturePath, state.getConstraints()));
diff --git a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/AnnotationSidebar_ImplBase.java b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/AnnotationSidebar_ImplBase.java
index 0bbb30dfc56..779c05df8a1 100644
--- a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/AnnotationSidebar_ImplBase.java
+++ b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/AnnotationSidebar_ImplBase.java
@@ -36,9 +36,9 @@ public abstract class AnnotationSidebar_ImplBase
{
private static final long serialVersionUID = 8637373389151630602L;
- private AnnotationActionHandler actionHandler;
- private CasProvider casProvider;
- private AnnotationPage annotationPage;
+ private final AnnotationActionHandler actionHandler;
+ private final CasProvider casProvider;
+ private final AnnotationPage annotationPage;
private @SpringBean DocumentService documentService;
public AnnotationSidebar_ImplBase(final String aId, final IModel aModel,
@@ -46,9 +46,9 @@ public AnnotationSidebar_ImplBase(final String aId, final IModel
AnnotationPage aAnnotationPage)
{
super(aId, aModel);
+
actionHandler = aActionHandler;
casProvider = aCasProvider;
-
annotationPage = aAnnotationPage;
// Allow AJAX updates.
diff --git a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/SidebarTabbedPanel.java b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/SidebarTabbedPanel.java
index 9f5ed3d90bd..d5127590f9c 100644
--- a/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/SidebarTabbedPanel.java
+++ b/inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/sidebar/SidebarTabbedPanel.java
@@ -82,7 +82,7 @@ private void showHideAction(AjaxRequestTarget aTarget)
{
expanded = !expanded;
saveSidebarState();
- WicketUtil.refreshPage(aTarget, getPage());
+ aTarget.add(findParent(SidebarPanel.class));
}
public boolean isExpanded()
diff --git a/inception/inception-ui-core/pom.xml b/inception/inception-ui-core/pom.xml
index b79f8448534..9ebe01c495a 100644
--- a/inception/inception-ui-core/pom.xml
+++ b/inception/inception-ui-core/pom.xml
@@ -20,7 +20,7 @@
de.tudarmstadt.ukp.inception.appinception-app
- 27.0-SNAPSHOT
+ 29.0-SNAPSHOTinception-ui-coreINCEpTION - UI - Core
@@ -76,6 +76,10 @@
org.springframework.bootspring-boot
+
+ org.springframework.boot
+ spring-boot-autoconfigure
+
@@ -185,5 +189,9 @@
jakarta.persistencejakarta.persistence-api
+
+ org.danekja
+ jdk-serializable-functional
+
\ No newline at end of file
diff --git a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.java b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.java
index 3ea79bf1dfa..bf33ad0ca7b 100644
--- a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.java
+++ b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.java
@@ -42,6 +42,7 @@
import static org.apache.wicket.settings.ExceptionSettings.SHOW_INTERNAL_ERROR_PAGE;
import java.io.File;
+import java.lang.invoke.MethodHandles;
import java.time.Duration;
import java.util.ArrayList;
import java.util.List;
@@ -55,8 +56,6 @@
import org.apache.wicket.csp.CSPRenderable;
import org.apache.wicket.csp.FixedCSPValue;
import org.apache.wicket.devutils.stateless.StatelessChecker;
-import org.apache.wicket.markup.html.IPackageResourceGuard;
-import org.apache.wicket.markup.html.SecurePackageResourceGuard;
import org.apache.wicket.protocol.http.ResourceIsolationRequestCycleListener;
import org.apache.wicket.request.Response;
import org.apache.wicket.request.cycle.IRequestCycleListener;
@@ -85,6 +84,7 @@
import de.tudarmstadt.ukp.clarin.webanno.support.SettingsUtil;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.PatternMatchingCrossOriginEmbedderPolicyRequestCycleListener;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.kendo.KendoFixDisabledInputComponentStylingBehavior;
+import de.tudarmstadt.ukp.clarin.webanno.support.wicket.resource.ContextSensitivePackageStringResourceLoader;
import de.tudarmstadt.ukp.clarin.webanno.ui.config.FontAwesomeResourceBehavior;
import de.tudarmstadt.ukp.clarin.webanno.ui.config.JQueryJavascriptBehavior;
import de.tudarmstadt.ukp.clarin.webanno.ui.config.JQueryUIResourceBehavior;
@@ -106,7 +106,7 @@
public abstract class WicketApplicationBase
extends WicketBootSecuredWebApplication
{
- private final Logger log = LoggerFactory.getLogger(getClass());
+ private final static Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
private @Autowired CspProperties cspProperties;
@@ -197,6 +197,8 @@ private void installPatternMatchingCrossOriginEmbedderPolicyRequestCycleListener
protected void initOnce()
{
+ initContextSensitivePackageStringResourceLoader();
+
// Allow nested string resource resolving using "#(key)"
initNestedStringResourceLoader();
@@ -209,8 +211,6 @@ protected void initOnce()
initNonCachingInDevEnvironment();
- initAccessToVueComponents();
-
initErrorPage();
}
@@ -218,13 +218,15 @@ private void initNonCachingInDevEnvironment()
{
if (DEVELOPMENT.equals(getConfigurationType())) {
// Do not cache pages in development mode - allows us to make changes to the HMTL
- // without
- // having to reload the application
+ // without having to reload the application
getMarkupSettings().getMarkupFactory().getMarkupCache().clear();
getResourceSettings().setCachingStrategy(NoOpResourceCachingStrategy.INSTANCE);
// Same for resources
getResourceSettings().setDefaultCacheDuration(Duration.ZERO);
+
+ // Same for properties
+ getResourceSettings().getLocalizer().setEnableCache(false);
}
}
@@ -265,7 +267,7 @@ protected void initBootstrap()
File customBootstrap = new File(getApplicationHome(), "bootstrap.css");
if (customBootstrap.exists()) {
- log.info("Using custom bootstrap at [{}]", customBootstrap);
+ LOG.info("Using custom bootstrap at [{}]", customBootstrap);
settings.setCssResourceReference(new FileSystemResourceReference(
"inception-bootstrap.css", customBootstrap.toPath()));
}
@@ -281,7 +283,7 @@ protected void addCustomCssToAllPages()
File customCss = new File(getApplicationHome(), "theme.css");
if (customCss.exists()) {
- log.info("Using custom CSS at [{}]", customCss);
+ LOG.info("Using custom CSS at [{}]", customCss);
getComponentInstantiationListeners().add(component -> {
if (component instanceof ApplicationPageBase) {
component.add(new CustomThemeCssResourceBehavior());
@@ -352,6 +354,12 @@ protected void initJQueryResourceReference()
getJavaScriptLibrarySettings().setJQueryReference(JQueryResourceReference.getV3());
}
+ protected void initContextSensitivePackageStringResourceLoader()
+ {
+ getResourceSettings().getStringResourceLoaders()
+ .add(new ContextSensitivePackageStringResourceLoader());
+ }
+
protected void initNestedStringResourceLoader()
{
List loaders = new ArrayList<>(
@@ -410,23 +418,4 @@ private void initErrorPage()
mountPage("/whoops/test", ErrorTestPage.class);
}
}
-
- private void initAccessToVueComponents()
- {
- IPackageResourceGuard resourceGuard = getResourceSettings().getPackageResourceGuard();
- if (resourceGuard instanceof SecurePackageResourceGuard) {
- SecurePackageResourceGuard securePackageResourceGuard = (SecurePackageResourceGuard) resourceGuard;
- securePackageResourceGuard.addPattern("+*.vue");
- }
- }
-
- @Override
- public String getMimeType(String aFileName)
- {
- if (aFileName.endsWith(".vue")) {
- return "text/javascript";
- }
-
- return super.getMimeType(aFileName);
- }
}
diff --git a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.properties b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.properties
index 07e74ecd436..e1b5ea06539 100644
--- a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.properties
+++ b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/WicketApplicationBase.properties
@@ -37,6 +37,8 @@ search=Search
preferences=Preferences
undo=Undo
redo=Redo
+moveUp=Up
+moveDown=Down
busy=Busy...
enabled=Enabled
diff --git a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterItem.java b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterItem.java
index ac73bc827ff..4f9730d7ded 100644
--- a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterItem.java
+++ b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterItem.java
@@ -21,7 +21,6 @@
import org.springframework.core.annotation.Order;
@Order(FooterItem.ORDER_CENTER)
-@org.springframework.stereotype.Component
public class VersionFooterItem
implements FooterItem
{
diff --git a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterPanel.html b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterPanel.html
index adc1f9f526d..110e502c796 100644
--- a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterPanel.html
+++ b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterPanel.html
@@ -19,7 +19,7 @@
-
+
Technische Universität Darmstadt --
Computer Science Department --
--
diff --git a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterItem.java b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterItem.java
index dcf95f280d6..924da7589f5 100644
--- a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterItem.java
+++ b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterItem.java
@@ -21,7 +21,6 @@
import org.springframework.core.annotation.Order;
@Order(FooterItem.ORDER_RIGHT)
-@org.springframework.stereotype.Component
public class WarningsFooterItem
implements FooterItem
{
diff --git a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterPanel.html b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterPanel.html
index 121052193c4..04fb1ada14f 100644
--- a/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterPanel.html
+++ b/inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterPanel.html
@@ -20,7 +20,7 @@
-
`
+ norminfo += `