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Merge branch 'main' into feature/4907-Support-for-DocX
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* main:
  #5047 - Clean up layer detail UI a bit
  #4949 - Showing the start and end points of relations in left side bar
  No issue: Minor cleaning up
  #5043 - Ability to specify token breaking zones when calling tokenizer
  #4904 - Upgrade to RDF4J 5.x
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@reckart
reckart committed Sep 8, 2024
2 parents 4c607bf + ccd189e commit 160abac
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Showing 28 changed files with 302 additions and 225 deletions.
30 changes: 14 additions & 16 deletions ...api-formats/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/format/FormatSupport.java
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Expand Up @@ -19,9 +19,13 @@

import static de.tudarmstadt.ukp.inception.support.io.ZipUtils.zipFolder;
import static java.io.File.createTempFile;
import static java.util.Collections.emptyList;
import static java.util.Collections.unmodifiableSet;
import static java.util.Optional.empty;
import static org.apache.commons.io.FileUtils.copyFile;
import static org.apache.commons.io.FilenameUtils.getBaseName;
import static org.apache.commons.io.FilenameUtils.getExtension;
import static org.apache.commons.lang3.StringUtils.rightPad;
import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine;
import static org.apache.uima.fit.factory.CollectionReaderFactory.createReader;
import static org.apache.uima.fit.factory.ConfigurationParameterFactory.addConfigurationParameters;
Expand All @@ -32,13 +36,10 @@
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import java.util.Set;

import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
Expand Down Expand Up @@ -124,20 +125,20 @@ default InputStream openResourceStream(File aDocFile, String aResourcePath) thro
*/
default List<ResourceReference> getCssStylesheets()
{
return Collections.emptyList();
return emptyList();
}

/**
* @return format-specific section elements
*/
default List<String> getSectionElements()
{
return Collections.emptyList();
return emptyList();
}

default Optional<PolicyCollection> getPolicy() throws IOException
{
return Optional.empty();
return empty();
}

/**
Expand Down Expand Up @@ -203,7 +204,7 @@ default File write(SourceDocument aDocument, CAS aCas, File aTargetFolder,
boolean aStripExtension)
throws ResourceInitializationException, AnalysisEngineProcessException, IOException
{
AnalysisEngineDescription writer = getWriterDescription(aDocument.getProject(), null, aCas);
var writer = getWriterDescription(aDocument.getProject(), null, aCas);
addConfigurationParameters(writer, //
JCasFileWriter_ImplBase.PARAM_USE_DOCUMENT_ID, true,
JCasFileWriter_ImplBase.PARAM_ESCAPE_FILENAME, false,
Expand All @@ -225,21 +226,18 @@ default File write(SourceDocument aDocument, CAS aCas, File aTargetFolder,

// If the writer produced more than one file, we package it up as a ZIP file
if (aTargetFolder.listFiles().length > 1) {
File exportFile = createTempFile("inception-document", ".zip");
// File exportFile = new File(aTargetFolder.getAbsolutePath() + ".zip");
var exportFile = createTempFile("inception-document", ".zip");
zipFolder(aTargetFolder, exportFile);
return exportFile;
}

// If the writer produced only a single file, then that is the result
String filename = FilenameUtils.getBaseName(aTargetFolder.listFiles()[0].getName());
var exportedFile = aTargetFolder.listFiles()[0];
// temp-file prefix must be at least 3 chars
filename = StringUtils.rightPad(filename, 3, "_");
File exportFile = createTempFile(filename,
"." + FilenameUtils.getExtension(aTargetFolder.listFiles()[0].getName()));
// File exportFile = new File(aTargetFolder.getParent(),
// aTargetFolder.listFiles()[0].getName());
copyFile(aTargetFolder.listFiles()[0], exportFile);
var baseName = rightPad(getBaseName(exportedFile.getName()), 3, "_");
var extension = getExtension(exportedFile.getName());
var exportFile = createTempFile(baseName, "." + extension);
copyFile(exportedFile, exportFile);
return exportFile;
}
}
30 changes: 4 additions & 26 deletions inception/inception-dependencies/pom.xml
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Expand Up @@ -1182,39 +1182,17 @@

<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-api</artifactId>
<artifactId>owlapi-bom</artifactId>
<version>${owlapi-version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<!-- See https://github.com/owlcs/owlapi/issues/1154 -->
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>${owlapi-version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-impl</artifactId>
<version>${owlapi-version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-oboformat</artifactId>
<version>${owlapi-version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-parsers</artifactId>
<version>${owlapi-version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-rio</artifactId>
<version>${owlapi-version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-tools</artifactId>
<version>${owlapi-version}</version>
</dependency>

<dependency>
<groupId>com.github.jsonld-java</groupId>
Expand Down
9 changes: 8 additions & 1 deletion ...mpactv2/src/main/java/de/tudarmstadt/ukp/inception/diam/model/compactv2/CompactLayer.java
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Expand Up @@ -21,11 +21,13 @@ public class CompactLayer
{
private final long id;
private final String name;
private final String type;

public CompactLayer(long aId, String aName)
public CompactLayer(long aId, String aName, String aType)
{
id = aId;
name = aName;
type = aType;
}

public long getId()
Expand All @@ -37,4 +39,9 @@ public String getName()
{
return name;
}

public String getType()
{
return type;
}
}
2 changes: 1 addition & 1 deletion .../main/java/de/tudarmstadt/ukp/inception/diam/model/compactv2/CompactSerializerV2Impl.java
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Expand Up @@ -99,7 +99,7 @@ private void renderLayers(RenderRequest aRequest, CompactAnnotatedText aResponse
continue;
}

layers.add(new CompactLayer(layer.getId(), layer.getUiName()));
layers.add(new CompactLayer(layer.getId(), layer.getUiName(), layer.getType()));

for (VSpan vspan : aVDoc.spans(layer.getId())) {
var cspan = renderSpan(aRequest, vspan);
Expand Down
6 changes: 4 additions & 2 deletions inception/inception-diam-compactv2/src/test/resources/compactv2/reference.json
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Expand Up @@ -2,10 +2,12 @@
"action" : "getAnnotatedDocument",
"layers" : [ {
"id" : 1,
"name" : "Span"
"name" : "Span",
"type" : "span"
}, {
"id" : 2,
"name" : "Relation"
"name" : "Relation",
"type" : "relation"
} ],
"text" : "This is a test.",
"window" : [ 0, 15 ],
Expand Down
4 changes: 3 additions & 1 deletion inception/inception-diam-editor/src/main/ts/src/AnnotationsByLabelList.svelte
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Expand Up @@ -88,7 +88,9 @@
return b.score - a.score;
}
return compareOffsets(targetA.offsets[0], targetB.offsets[0])
const targetA = a.arguments[0].target as Span
const targetB = b.arguments[0].target as Span
return compareOffsets(targetA.offsets[0], targetB.offsets[0]);
}
console.error("Unexpected annotation type combination", a, b);
Expand Down
131 changes: 95 additions & 36 deletions inception/inception-diam-editor/src/main/ts/src/AnnotationsByLayerList.svelte
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Expand Up @@ -30,12 +30,13 @@
import { compareOffsets } from "@inception-project/inception-js-api/src/model/Offsets";
import LabelBadge from "./LabelBadge.svelte";
import SpanText from "./SpanText.svelte";
import { compareSpanText, debounce, filterAnnotations, getCoveredText, groupBy, uniqueLayers } from "./Utils";
import { compareSpanText, debounce, filterAnnotations, groupRelationsBySource, groupBy, uniqueLayers } from "./Utils";
import { sortByScore, recommendationsFirst } from "./AnnotationBrowserState"
export let ajaxClient: DiamAjax;
export let data: AnnotatedText;
let groupedRelations: Record<string, Relation[]>;
let groupedAnnotations: Record<string, Annotation[]>;
let groups: { layer: Layer, collapsed: boolean }[]
let collapsedGroups = new Set<number>()
Expand All @@ -55,6 +56,8 @@
(s) => s.layer.name
)
groupedRelations = groupRelationsBySource(data);
for (let [key, items] of Object.entries(groupedAnnotations)) {
items = filterAnnotations(data, items, filter)
items.sort((a, b) => {
Expand Down Expand Up @@ -193,56 +196,112 @@
{#each groups as group}
<li class="list-group-item py-0 px-0 border-0">
<!-- svelte-ignore a11y-click-events-have-key-events -->
<!-- svelte-ignore a11y-no-static-element-interactions -->
<div
class="px-2 py-1 bg-light-subtle fw-bold sticky-top border-top border-bottom"
on:click={() => toggleCollapsed(group)}
>
<button class="btn btn-link p-0" style="color: var(--bs-body-color)">
<i class="fas fa-caret-down d-inline-block" class:group-collapsed={group.collapsed}/>
</button>
<span>{group.layer.name}</span>
<span>{group.layer.name} {group.layer.type}</span>
</div>
<ul class="px-0 list-group list-group-flush" class:d-none={group.collapsed}>
{#if groupedAnnotations[group.layer.name]}
{#each groupedAnnotations[group.layer.name] as ann}
<!-- svelte-ignore a11y-mouse-events-have-key-events -->
<li
class="list-group-item list-group-item-action p-0 d-flex"
on:mouseover={ev => mouseOverAnnotation(ev, ann)}
on:mouseout={ev => mouseOutAnnotation(ev, ann)}
>
<div
class="text-secondary bg-light-subtle border-end px-2 d-flex align-items-center"
{#if ann instanceof Span}
<li
class="list-group-item list-group-item-action p-0 d-flex"
on:mouseover={ev => mouseOverAnnotation(ev, ann)}
on:mouseout={ev => mouseOutAnnotation(ev, ann)}
>
{#if ann instanceof Span}
<div class="annotation-type-marker i7n-icon-span"/>
{:else if ann instanceof Relation}
<div class="annotation-type-marker i7n-icon-relation"/>
{/if}
</div>
<!-- svelte-ignore a11y-click-events-have-key-events -->
<div
class="flex-grow-1 my-1 mx-2 position-relative overflow-hidden"
on:click={() => scrollTo(ann)}
>
<div class="float-end labels">
<LabelBadge
annotation={ann}
{ajaxClient}
showText={true}
/>
<!-- svelte-ignore a11y-click-events-have-key-events -->
<!-- svelte-ignore a11y-no-static-element-interactions -->
<div class="flex-grow-1 my-1 mx-2 position-relative overflow-hidden" on:click={() => scrollTo(ann)}>
<div class="float-end labels me-1">
<LabelBadge
annotation={ann}
{ajaxClient}
showText={true}
/>
</div>
<SpanText {data} span={ann} />
</div>
</li>

{#if ann instanceof Span}
<SpanText {data} span={ann} />
{:else if ann instanceof Relation}
<SpanText
{data}
span={ann.arguments[0].target}
/>
{/if}
</div>
</li>
{@const relations = groupedRelations[`${ann.vid}`]}
{#if relations}
{#each relations as relation}
{@const target = relation.arguments[1].target}
<!-- svelte-ignore a11y-mouse-events-have-key-events -->
<li
class="list-group-item list-group-item-action p-0 d-flex"
on:mouseover={(ev) =>
mouseOverAnnotation(ev, relation)}
on:mouseout={(ev) =>
mouseOutAnnotation(ev, relation)}
>
<div
class="text-secondary bg-light-subtle border-end px-2 d-flex align-items-center"
>
<span>↳</span>
</div>
<!-- svelte-ignore a11y-click-events-have-key-events -->
<!-- svelte-ignore a11y-no-static-element-interactions -->
<div
class="flex-grow-1 my-1 mx-2 overflow-hidden"
on:click={() => scrollTo(target)}
>
<div class="float-end labels me-1">
<LabelBadge
annotation={relation}
{ajaxClient}
/>
</div>

<SpanText {data} span={target} />
</div>
</li>
{/each}
{/if}
{:else if ann instanceof Relation && group.layer.type === "relation"}
<li
class="list-group-item p-0 d-flex"
on:mouseover={ev => mouseOverAnnotation(ev, ann)}
on:mouseout={ev => mouseOutAnnotation(ev, ann)}
>
<!-- svelte-ignore a11y-click-events-have-key-events -->
<!-- svelte-ignore a11y-no-static-element-interactions -->
<div class="flex-grow-1 my-1 mx-0 position-relative overflow-hidden">
<div class="me-2">
<LabelBadge
annotation={ann}
{ajaxClient}
showText={true}
/>
</div>
<div class="d-flex flex-row list-group-item-action" on:click={() => scrollTo(ann.arguments[0].target)}>
<div class="text-secondary bg-light-subtle border-end px-2 d-flex align-items-center">
<span style="transform: rotate(90deg);">↳</span>
</div>
<SpanText
{data}
span={ann.arguments[0].target}
/>
</div>
<div class="d-flex flex-row list-group-item-action" on:click={() => scrollTo(ann.arguments[1].target)}>
<div class="text-secondary bg-light-subtle border-end px-2 d-flex align-items-center">
<span>↳</span>
</div>
<SpanText
{data}
span={ann.arguments[1].target}
/>
</div>
</div>
</li>
{/if}
{/each}
{:else}
<li class="list-group-item list-group-item-action p-2 text-center text-secondary bg-light">
Expand Down
6 changes: 3 additions & 3 deletions inception/inception-diam-editor/src/main/ts/src/AnnotationsByPositionList.svelte
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Expand Up @@ -29,7 +29,7 @@
import LabelBadge from "./LabelBadge.svelte";
import SpanText from "./SpanText.svelte";
import {
debounce,
debounce,
groupRelationsByPosition,
groupSpansByPosition,
uniqueOffsets,
Expand Down Expand Up @@ -103,7 +103,7 @@
class="flex-grow-1 my-1 mx-2 overflow-hidden"
on:click={() => scrollToSpan(firstSpan)}
>
<div class="float-end labels">
<div class="float-end labels me-1">
{#each spans as span}
<span
on:mouseover={(ev) =>
Expand Down Expand Up @@ -144,7 +144,7 @@
class="flex-grow-1 my-1 mx-2 overflow-hidden"
on:click={() => scrollToRelation(relation)}
>
<div class="float-end labels">
<div class="float-end labels me-1">
<LabelBadge
annotation={relation}
{ajaxClient}
Expand Down
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