Merge branch 'main' into feature/3944-Ability-to-use-recommenders-as-…

…curator * main: [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-27.6 #3958 - Dynamically sized multi-line string fields no resize automatically #3957 - Cannot create project using project-creator role [maven-release-plugin] prepare for next development iteration [maven-release-plugin] prepare release inception-27.5 #3932 - Upgrade dependencies #3953 - Switch core footer items to auto-configuration #3951 - Lots of errors and warnings from logging system during startup No issue: Demote some logged message to debug level #3940 - Merge label into eligible existing annotation even when stacking is enabled % Conflicts: % inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImpl.java % inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java
inception-project · Apr 18, 2023 · 8370acb · 8370acb
2 parents d7c6741 + 6144292
commit 8370acb
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diff --git a/.../de/tudarmstadt/ukp/inception/annotation/feature/string/DynamicTextAreaFeatureEditor.html b/.../de/tudarmstadt/ukp/inception/annotation/feature/string/DynamicTextAreaFeatureEditor.html
@@ -26,7 +26,7 @@
       </span>
     </label>
     <div class="feature-editor-value">
-      <textarea wicket:id="value" class="form-control dynamic-textarea" style="resize: none;"  onfocus="resizeDynamicTextArea(this)" oninput="resizeDynamicTextArea(this)" onblur="resizeDynamicTextArea(this)"></textarea>
+      <textarea wicket:id="value" class="form-control dynamic-textarea" style="resize: none;"/>
     </div>
   </div>
 </wicket:panel>

diff --git a/.../de/tudarmstadt/ukp/inception/annotation/feature/string/DynamicTextAreaFeatureEditor.java b/.../de/tudarmstadt/ukp/inception/annotation/feature/string/DynamicTextAreaFeatureEditor.java
@@ -51,8 +51,11 @@ protected AbstractTextComponent<String> createInputField()
     public void renderHead(IHeaderResponse aResponse)
     {
         aResponse.render(JavaScriptHeaderItem.forReference(DynamicTextAreaScriptReference.get()));
-        aResponse.render(OnDomReadyHeaderItem.forScript(
-                "window.addEventListener('load', function(){resizeDynamicTextArea(document.getElementById('"
-                        + textarea.getMarkupId() + "'));});"));
+        aResponse.render(OnDomReadyHeaderItem.forScript(String.join("\n", //
+                "let ta = document.getElementById('" + textarea.getMarkupId() + "');", //
+                "ta && window.addEventListener('load', () => resizeDynamicTextArea(ta));", //
+                "ta?.addEventListener('focus', ev => resizeDynamicTextArea(ta));", //
+                "ta?.addEventListener('input', ev => resizeDynamicTextArea(ta));", //
+                "ta?.addEventListener('blur', ev => resizeDynamicTextArea(ta));")));
     }
 }
diff --git a/...ion/src/test/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanAdapterTest.java b/...ion/src/test/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanAdapterTest.java
@@ -27,7 +27,6 @@
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.assertj.core.api.Assertions.assertThatCode;
 import static org.assertj.core.api.Assertions.assertThatExceptionOfType;
-import static org.mockito.Mockito.mock;
 
 import java.util.List;
 
@@ -38,6 +37,7 @@
 import org.junit.jupiter.api.BeforeEach;
 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.clarin.webanno.api.annotation.exception.MultipleSentenceCoveredException;
@@ -56,8 +56,9 @@
 @ExtendWith(MockitoExtension.class)
 public class SpanAdapterTest
 {
+    private @Mock FeatureSupportRegistry featureSupportRegistry;
+
     private LayerSupportRegistry layerSupportRegistry;
-    private FeatureSupportRegistry featureSupportRegistry;
     private Project project;
     private AnnotationLayer neLayer;
     private JCas jcas;
@@ -89,7 +90,6 @@ public void setup() throws Exception
         neLayer.setId(1l);
 
         layerSupportRegistry = new LayerSupportRegistryImpl(asList());
-        featureSupportRegistry = mock(FeatureSupportRegistry.class);
 
         behaviors = asList(new SpanOverlapBehavior(), new SpanCrossSentenceBehavior(),
                 new SpanAnchoringModeBehavior());

diff --git a/...-app-webapp/src/main/resources/log4j2.xml → ...bapp/src/main/resources/log4j2-spring.xml b/...-app-webapp/src/main/resources/log4j2.xml → ...bapp/src/main/resources/log4j2-spring.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="WARN" packages="de.tudarmstadt.ukp">
+<Configuration status="WARN">
   <properties>
     <SpringProfile name="!app &amp; !cli"> <!-- While booting before Spring is there-->
       <property name="pattern">%d{yyyy-MM-dd HH:mm:ss} %level{length=5} [%encode{$${ctx:username:-SYSTEM}}{CRLF}] %logger{1} - %encode{%msg}{CRLF}%n</property>

diff --git a/...ion/inception-doc/src/main/resources/META-INF/asciidoc/admin-guide/logging.adoc b/...ion/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.
+`-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.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-js-api/src/main/ts/src/util/ViewportTracker.ts b/inception/inception-js-api/src/main/ts/src/util/ViewportTracker.ts
@@ -100,7 +100,7 @@ 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 {
@@ -117,7 +117,7 @@ export class ViewportTracker {
     })
 
     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 +143,7 @@ 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/...n/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImpl.java b/...n/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImpl.java
@@ -1035,7 +1035,11 @@ public int upsertSpanFeature(SourceDocument aDocument, String aDocumentOwner, CA
                 .at(aBegin, aEnd).nullOK().get();
 
         int address;
-        if (annoFS == null || aLayer.isAllowStacking()) {
+        if (annoFS != null && adapter.getFeatureValue(aFeature, annoFS) == null) {
+            // If there is an annotation where the predicted feature is unset, use it ...
+            address = ICasUtil.getAddr(annoFS);
+        }
+        else if (annoFS == null || aLayer.isAllowStacking()) {
             // ... if not or if stacking is allowed, then we create a new annotation - this also
             // takes care of attaching to an annotation if necessary
             var newAnnotation = adapter.add(aDocument, aDocumentOwner, aCas, aBegin, aEnd);

diff --git a/...ation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java b/...ation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/tasks/PredictionTask.java
@@ -99,7 +99,7 @@ public void execute()
 
             appEventPublisher.publishEvent(RecommenderTaskNotificationEvent
                     .builder(this, project, sessionOwner.getUsername()) //
-                    .withMessage(LogMessage.info(this, "New preditions available")) //
+                    .withMessage(LogMessage.info(this, "New predictions available")) //
                     .build());
 
             // We reset this in case the state was not properly cleared, e.g. the AL session

diff --git a/...mstadt/ukp/inception/recommendation/service/RecommendationServiceImplIntegrationTest.java b/...mstadt/ukp/inception/recommendation/service/RecommendationServiceImplIntegrationTest.java
@@ -17,6 +17,8 @@
  */
 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;
@@ -27,6 +29,7 @@
 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;
@@ -60,15 +63,20 @@
 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.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.Offset;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
 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)
@@ -80,10 +88,13 @@ public class RecommendationServiceImplIntegrationTest
 
     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;
@@ -93,7 +104,10 @@ public class RecommendationServiceImplIntegrationTest
     public void setUp() throws Exception
     {
         sut = new RecommendationServiceImpl(null, null, null, recommenderFactoryRegistry, null,
-                annoService, null, null, testEntityManager.getEntityManager());
+                schemaService, null, null, testEntityManager.getEntityManager());
+
+        featureSupportRegistry = new FeatureSupportRegistryImpl(asList(new StringFeatureSupport()));
+        featureSupportRegistry.init();
 
         project = createProject(PROJECT_NAME);
         layer = createAnnotationLayer();
@@ -190,10 +204,10 @@ 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.listAnnotationLayer(project)).thenReturn(asList(layer));
+            doCallRealMethod().when(schemaService).upgradeCas(any(CAS.class), any(CAS.class),
                     any(TypeSystemDescription.class));
 
             sut.cloneAndMonkeyPatchCAS(project, jCas.getCas(), jCas.getCas());
@@ -236,6 +250,88 @@ void thatZeroWithAnnotationsAreCorrectlyAnchoredOnTokens() 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());
+
+        when(schemaService.getAdapter(layer)).thenReturn(adapter);
+
+        layer.setOverlapMode(NO_OVERLAP);
+        var cas = createJCas();
+        var targetFS = new NamedEntity(cas, 0, 10);
+        targetFS.addToIndexes();
+        assertThat(targetFS.getValue()).isNull();
+
+        sut.upsertSpanFeature(doc, docOwner, cas.getCas(), layer, feature, "V1",
+                targetFS.getBegin(), targetFS.getEnd());
+
+        assertThat(targetFS.getValue()) //
+                .as("Label was merged into existing annotation replacing unset label") //
+                .isEqualTo("V1");
+
+        sut.upsertSpanFeature(doc, docOwner, cas.getCas(), layer, feature, "V2",
+                targetFS.getBegin(), targetFS.getEnd());
+
+        assertThat(targetFS.getValue()) //
+                .as("Label was merged into existing annotation replacing previous label") //
+                .isEqualTo("V2");
+
+        sut.upsertSpanFeature(doc, docOwner, cas.getCas(), layer, feature, "V3", 10, 20);
+
+        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();
+
+        sut.upsertSpanFeature(doc, docOwner, cas.getCas(), layer, feature, "V1",
+                targetFS.getBegin(), targetFS.getEnd());
+
+        assertThat(targetFS.getValue()) //
+                .as("Label was merged into existing annotation replacing unset label") //
+                .isEqualTo("V1");
+
+        sut.upsertSpanFeature(doc, docOwner, cas.getCas(), layer, feature, "V2",
+                targetFS.getBegin(), targetFS.getEnd());
+
+        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"));
+
+        sut.upsertSpanFeature(doc, docOwner, cas.getCas(), layer, feature, "V3", 10, 20);
+
+        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"));
+    }
+
     // Helper
 
     private Project createProject(String aName)

diff --git a/inception/inception-ui-core/pom.xml b/inception/inception-ui-core/pom.xml
@@ -76,6 +76,10 @@
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-autoconfigure</artifactId>
+    </dependency>
 
     <!-- Spring security dependencies -->
     <dependency>

diff --git a/...ore/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/VersionFooterItem.java b/...ore/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/...re/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/footer/WarningsFooterItem.java b/...re/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/...ion-ui-core/src/main/java/de/tudarmstadt/ukp/inception/ui/core/about/AboutFooterItem.java b/...ion-ui-core/src/main/java/de/tudarmstadt/ukp/inception/ui/core/about/AboutFooterItem.java
@@ -23,7 +23,6 @@
 import de.tudarmstadt.ukp.clarin.webanno.ui.core.footer.FooterItem;
 
 @Order(FooterItem.ORDER_RIGHT + 100)
-@org.springframework.stereotype.Component
 public class AboutFooterItem
     implements FooterItem
 {

diff --git a/...re/src/main/java/de/tudarmstadt/ukp/inception/ui/core/config/CoreUiAutoConfiguration.java b/...re/src/main/java/de/tudarmstadt/ukp/inception/ui/core/config/CoreUiAutoConfiguration.java
@@ -17,12 +17,35 @@
  */
 package de.tudarmstadt.ukp.inception.ui.core.config;
 
+import org.springframework.boot.autoconfigure.condition.ConditionalOnMissingBean;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
+import de.tudarmstadt.ukp.clarin.webanno.ui.core.footer.VersionFooterItem;
+import de.tudarmstadt.ukp.clarin.webanno.ui.core.footer.WarningsFooterItem;
+import de.tudarmstadt.ukp.inception.ui.core.about.AboutFooterItem;
+
 @Configuration
 @EnableConfigurationProperties(CspPropertiesImpl.class)
 public class CoreUiAutoConfiguration
 {
-    // No beans yet
+    @ConditionalOnMissingBean(value = VersionFooterItem.class)
+    @Bean
+    public VersionFooterItem versionFooterItem()
+    {
+        return new VersionFooterItem();
+    }
+
+    @Bean
+    public WarningsFooterItem warningsFooterItem()
+    {
+        return new WarningsFooterItem();
+    }
+
+    @Bean
+    public AboutFooterItem aboutFooterItem()
+    {
+        return new AboutFooterItem();
+    }
 }
diff --git a/...tion-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/menubar/MenuBar.java b/...tion-ui-dashboard/src/main/java/de/tudarmstadt/ukp/inception/ui/core/menubar/MenuBar.java
@@ -157,10 +157,18 @@ private boolean isMenubarVisibleToCurrentUser()
             return true;
         }
 
-        if (userRepository.isAdministrator(user.getObject())) {
+        if (userRepository.isAdministrator(user.getObject())
+                || userRepository.isProjectCreator(user.getObject())) {
             return true;
         }
 
+        // The project might be null if it is in the process of being created. Normally, this can
+        // only be done by admisn and project creators that are handled above - so returning false
+        // here is really just a sanity fallback that should never kick in.
+        if (project.getObject().getId() == null) {
+            return false;
+        }
+
         var roles = dashboardProperties.getAccessibleByRoles().toArray(PermissionLevel[]::new);
         return projectService.hasRole(user.getObject(), project.getObject(), MANAGER, roles);
     }