Merge branch 'main' into refactoring/Upgrade-to-Spring-Boot-3

inception-project · Mar 2, 2024 · 8822a49 · 8822a49
2 parents e4fc794 + 8077d7d
commit 8822a49
Show file tree

Hide file tree

Showing 83 changed files with 7,584 additions and 347 deletions.
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -20,9 +20,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up JDK 17
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         java-version: '17'
         distribution: 'temurin'

diff --git a/...orage/src/main/java/de/tudarmstadt/ukp/inception/annotation/storage/CasMetadataUtils.java b/...orage/src/main/java/de/tudarmstadt/ukp/inception/annotation/storage/CasMetadataUtils.java
@@ -19,18 +19,14 @@
 
 import static org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription;
 import static org.apache.uima.fit.util.CasUtil.getType;
+import static org.apache.uima.fit.util.FSUtil.setFeature;
 
 import java.io.IOException;
 import java.lang.invoke.MethodHandles;
-import java.util.ArrayList;
-import java.util.List;
 import java.util.Optional;
 
 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.cas.text.AnnotationFS;
 import org.apache.uima.fit.util.CasUtil;
 import org.apache.uima.fit.util.FSUtil;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
@@ -58,8 +54,7 @@ public static void clearCasMetadata(CAS aCas) throws IllegalStateException
             return;
         }
 
-        List<AnnotationFS> cmds = new ArrayList<>(
-                CasUtil.select(aCas, getType(aCas, CASMetadata.class)));
+        var cmds = aCas.select(CASMetadata.class).toList();
         if (cmds.size() > 1) {
             throw new IllegalStateException("CAS contains more than one CASMetadata instance");
         }
@@ -82,41 +77,42 @@ public static void addOrUpdateCasMetadata(CAS aCas, long aTimeStamp, SourceDocum
             return;
         }
 
-        Type casMetadataType = getType(aCas, CASMetadata.class);
+        var casMetadataType = getType(aCas, CASMetadata.class);
         FeatureStructure cmd;
-        List<AnnotationFS> cmds = new ArrayList<>(CasUtil.select(aCas, casMetadataType));
+        var cmds = aCas.select(CASMetadata.class).toList();
         if (cmds.size() > 1) {
             throw new IOException("CAS contains more than one CASMetadata instance!");
         }
-        else if (cmds.size() == 1) {
+
+        if (cmds.size() == 1) {
             cmd = cmds.get(0);
         }
         else {
             cmd = aCas.createAnnotation(casMetadataType, 0, 0);
         }
 
-        if (cmd.getType().getFeatureByBaseName("username") != null) {
-            FSUtil.setFeature(cmd, "username", aUsername);
+        if (cmd.getType().getFeatureByBaseName(CASMetadata._FeatName_username) != null) {
+            setFeature(cmd, CASMetadata._FeatName_username, aUsername);
         }
 
-        if (cmd.getType().getFeatureByBaseName("sourceDocumentId") != null) {
-            FSUtil.setFeature(cmd, "sourceDocumentId", aDocument.getId());
+        if (cmd.getType().getFeatureByBaseName(CASMetadata._FeatName_sourceDocumentId) != null) {
+            setFeature(cmd, CASMetadata._FeatName_sourceDocumentId, aDocument.getId());
         }
 
-        if (cmd.getType().getFeatureByBaseName("sourceDocumentName") != null) {
-            FSUtil.setFeature(cmd, "sourceDocumentName", aDocument.getName());
+        if (cmd.getType().getFeatureByBaseName(CASMetadata._FeatName_sourceDocumentName) != null) {
+            setFeature(cmd, CASMetadata._FeatName_sourceDocumentName, aDocument.getName());
         }
 
-        if (cmd.getType().getFeatureByBaseName("projectId") != null) {
-            FSUtil.setFeature(cmd, "projectId", aDocument.getProject().getId());
+        if (cmd.getType().getFeatureByBaseName(CASMetadata._FeatName_projectId) != null) {
+            setFeature(cmd, CASMetadata._FeatName_projectId, aDocument.getProject().getId());
         }
 
-        if (cmd.getType().getFeatureByBaseName("projectName") != null) {
-            FSUtil.setFeature(cmd, "projectName", aDocument.getProject().getName());
+        if (cmd.getType().getFeatureByBaseName(CASMetadata._FeatName_projectName) != null) {
+            setFeature(cmd, CASMetadata._FeatName_projectName, aDocument.getProject().getName());
         }
 
-        if (cmd.getType().getFeatureByBaseName("lastChangedOnDisk") != null) {
-            FSUtil.setFeature(cmd, "lastChangedOnDisk", aTimeStamp);
+        if (cmd.getType().getFeatureByBaseName(CASMetadata._FeatName_lastChangedOnDisk) != null) {
+            setFeature(cmd, CASMetadata._FeatName_lastChangedOnDisk, aTimeStamp);
             LOG.trace("CAS [{}] for [{}]@[{}]({}): set lastChangedOnDisk: {}", aCas.hashCode(),
                     aUsername, aDocument.getName(), aDocument.getId(), aTimeStamp);
         }
@@ -131,17 +127,18 @@ public static Optional<FeatureStructure> getCasMetadataFS(CAS aCas)
 
     public static long getLastChanged(CAS aCas)
     {
-        Type casMetadataType = getType(aCas, CASMetadata.class);
-        Feature feature = casMetadataType.getFeatureByBaseName("lastChangedOnDisk");
+        var casMetadataType = getType(aCas, CASMetadata.class);
+        var feature = casMetadataType.getFeatureByBaseName(CASMetadata._FeatName_lastChangedOnDisk);
         return aCas.select(casMetadataType).map(cmd -> cmd.getLongValue(feature)).findFirst()
                 .orElse(-1l);
     }
 
     public static Optional<String> getUsername(CAS aCas)
     {
         try {
-            FeatureStructure fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
-            return Optional.ofNullable(FSUtil.getFeature(fs, "username", String.class));
+            var fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
+            return Optional.ofNullable(
+                    FSUtil.getFeature(fs, CASMetadata._FeatName_username, String.class));
         }
         catch (IllegalArgumentException e) {
             return Optional.empty();
@@ -151,8 +148,9 @@ public static Optional<String> getUsername(CAS aCas)
     public static Optional<Long> getSourceDocumentId(CAS aCas)
     {
         try {
-            FeatureStructure fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
-            return Optional.ofNullable(FSUtil.getFeature(fs, "sourceDocumentId", Long.class));
+            var fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
+            return Optional.ofNullable(
+                    FSUtil.getFeature(fs, CASMetadata._FeatName_sourceDocumentId, Long.class));
         }
         catch (IllegalArgumentException e) {
             return Optional.empty();
@@ -162,8 +160,9 @@ public static Optional<Long> getSourceDocumentId(CAS aCas)
     public static Optional<String> getSourceDocumentName(CAS aCas)
     {
         try {
-            FeatureStructure fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
-            return Optional.ofNullable(FSUtil.getFeature(fs, "sourceDocumentName", String.class));
+            var fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
+            return Optional.ofNullable(
+                    FSUtil.getFeature(fs, CASMetadata._FeatName_sourceDocumentName, String.class));
         }
         catch (IllegalArgumentException e) {
             return Optional.empty();
@@ -173,8 +172,9 @@ public static Optional<String> getSourceDocumentName(CAS aCas)
     public static Optional<Long> getProjectId(CAS aCas)
     {
         try {
-            FeatureStructure fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
-            return Optional.ofNullable(FSUtil.getFeature(fs, "projectId", Long.class));
+            var fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
+            return Optional
+                    .ofNullable(FSUtil.getFeature(fs, CASMetadata._FeatName_projectId, Long.class));
         }
         catch (IllegalArgumentException e) {
             return Optional.empty();
@@ -184,8 +184,9 @@ public static Optional<Long> getProjectId(CAS aCas)
     public static Optional<String> getProjectName(CAS aCas)
     {
         try {
-            FeatureStructure fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
-            return Optional.ofNullable(FSUtil.getFeature(fs, "projectName", String.class));
+            var fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
+            return Optional.ofNullable(
+                    FSUtil.getFeature(fs, CASMetadata._FeatName_projectName, String.class));
         }
         catch (IllegalArgumentException e) {
             return Optional.empty();

diff --git a/.../src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/chain/ChainLayerSupport.java b/.../src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/chain/ChainLayerSupport.java
@@ -21,14 +21,16 @@
 
 import java.lang.invoke.MethodHandles;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
+import java.util.Set;
 import java.util.function.Supplier;
 
 import org.apache.uima.cas.CAS;
-import org.apache.uima.resource.metadata.TypeDescription;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.wicket.markup.html.panel.Panel;
 import org.apache.wicket.model.IModel;
+import org.apache.wicket.validation.ValidationError;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
@@ -55,6 +57,13 @@ public class ChainLayerSupport
     extends LayerSupport_ImplBase<ChainAdapter, ChainLayerTraits>
     implements InitializingBean
 {
+    public static final String FEATURE_NAME_FIRST = "first";
+    public static final String FEATURE_NAME_NEXT = "next";
+    public static final String FEATURE_NAME_REFERENCE_RELATION = "referenceRelation";
+    public static final String FEATURE_NAME_REFERENCE = "referenceType";
+    private static final String TYPE_SUFFIX_LINK = "Link";
+    private static final String TYPE_SUFFIX_CHAIN = "Chain";
+
     private final static Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 
     @SuppressWarnings("deprecation")
@@ -91,7 +100,7 @@ public void setBeanName(String aBeanName)
     @Override
     public void afterPropertiesSet() throws Exception
     {
-        types = asList(new LayerType(TYPE, "Chain", layerSupportId));
+        types = asList(new LayerType(TYPE, TYPE_SUFFIX_CHAIN, layerSupportId));
     }
 
     @Override
@@ -110,35 +119,33 @@ public boolean accepts(AnnotationLayer aLayer)
     public ChainAdapter createAdapter(AnnotationLayer aLayer,
             Supplier<Collection<AnnotationFeature>> aFeatures)
     {
-        ChainAdapter adapter = new ChainAdapter(getLayerSupportRegistry(), featureSupportRegistry,
-                eventPublisher, aLayer, aFeatures,
+        return new ChainAdapter(getLayerSupportRegistry(), featureSupportRegistry, eventPublisher,
+                aLayer, aFeatures,
                 layerBehaviorsRegistry.getLayerBehaviors(this, SpanLayerBehavior.class));
-
-        return adapter;
     }
 
     @Override
     public void generateTypes(TypeSystemDescription aTsd, AnnotationLayer aLayer,
             List<AnnotationFeature> aAllFeaturesInProject)
     {
-        TypeDescription tdChains = aTsd.addType(aLayer.getName() + "Chain", aLayer.getDescription(),
+        var tdChain = aTsd.addType(aLayer.getName() + TYPE_SUFFIX_CHAIN, aLayer.getDescription(),
                 CAS.TYPE_NAME_ANNOTATION_BASE);
-        tdChains.addFeature("first", "", aLayer.getName() + "Link");
+        tdChain.addFeature(FEATURE_NAME_FIRST, "", aLayer.getName() + TYPE_SUFFIX_LINK);
 
         // Custom features on chain layers are currently not supported
         // generateFeatures(aTsd, tdChains, type);
 
-        TypeDescription tdLink = aTsd.addType(aLayer.getName() + "Link", "",
+        var tdLink = aTsd.addType(aLayer.getName() + TYPE_SUFFIX_LINK, "",
                 CAS.TYPE_NAME_ANNOTATION);
-        tdLink.addFeature("next", "", aLayer.getName() + "Link");
-        tdLink.addFeature("referenceType", "", CAS.TYPE_NAME_STRING);
-        tdLink.addFeature("referenceRelation", "", CAS.TYPE_NAME_STRING);
+        tdLink.addFeature(FEATURE_NAME_NEXT, "", aLayer.getName() + TYPE_SUFFIX_LINK);
+        tdLink.addFeature(FEATURE_NAME_REFERENCE, "", CAS.TYPE_NAME_STRING);
+        tdLink.addFeature(FEATURE_NAME_REFERENCE_RELATION, "", CAS.TYPE_NAME_STRING);
     }
 
     @Override
     public List<String> getGeneratedTypeNames(AnnotationLayer aLayer)
     {
-        return asList(aLayer.getName() + "Chain", aLayer.getName() + "Link");
+        return asList(aLayer.getName() + TYPE_SUFFIX_CHAIN, aLayer.getName() + TYPE_SUFFIX_LINK);
     }
 
     @Override
@@ -153,7 +160,7 @@ public Renderer createRenderer(AnnotationLayer aLayer,
     @Override
     public Panel createTraitsEditor(String aId, IModel<AnnotationLayer> aLayerModel)
     {
-        AnnotationLayer layer = aLayerModel.getObject();
+        var layer = aLayerModel.getObject();
 
         if (!accepts(layer)) {
             throw unsupportedLayerTypeException(layer);
@@ -167,4 +174,18 @@ public ChainLayerTraits createTraits()
     {
         return new ChainLayerTraits();
     }
+
+    @Override
+    public List<ValidationError> validateFeatureName(AnnotationFeature aFeature)
+    {
+        var name = aFeature.getName();
+
+        if (Set.of(FEATURE_NAME_FIRST, FEATURE_NAME_NEXT, FEATURE_NAME_REFERENCE,
+                FEATURE_NAME_REFERENCE_RELATION).contains(name)) {
+            return asList(new ValidationError("[" + name + "] is a reserved feature name on "
+                    + "chain layers. Please use a different name for the feature."));
+        }
+
+        return Collections.emptyList();
+    }
 }
diff --git a/...ain/java/de/tudarmstadt/ukp/inception/annotation/layer/relation/RelationLayerSupport.java b/...ain/java/de/tudarmstadt/ukp/inception/annotation/layer/relation/RelationLayerSupport.java
@@ -17,20 +17,20 @@
  */
 package de.tudarmstadt.ukp.inception.annotation.layer.relation;
 
-import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.FEAT_REL_SOURCE;
-import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.FEAT_REL_TARGET;
 import static java.util.Arrays.asList;
 import static java.util.stream.Collectors.toList;
 import static org.apache.uima.cas.CAS.TYPE_NAME_ANNOTATION;
 
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 import java.util.function.Supplier;
 
 import org.apache.uima.resource.metadata.TypeDescription;
 import org.apache.uima.resource.metadata.TypeSystemDescription;
 import org.apache.wicket.markup.html.panel.Panel;
 import org.apache.wicket.model.IModel;
+import org.apache.wicket.validation.ValidationError;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationEventPublisher;
@@ -54,6 +54,12 @@ public class RelationLayerSupport
     extends LayerSupport_ImplBase<RelationAdapter, RelationLayerTraits>
     implements InitializingBean
 {
+    @SuppressWarnings("deprecation")
+    public static final String FEAT_REL_TARGET = WebAnnoConst.FEAT_REL_TARGET;
+
+    @SuppressWarnings("deprecation")
+    public static final String FEAT_REL_SOURCE = WebAnnoConst.FEAT_REL_SOURCE;
+
     @SuppressWarnings("deprecation")
     public static final String TYPE = WebAnnoConst.RELATION_TYPE;
 
@@ -157,4 +163,16 @@ public RelationLayerTraits createTraits()
     {
         return new RelationLayerTraits();
     }
+
+    @Override
+    public List<ValidationError> validateFeatureName(AnnotationFeature aFeature)
+    {
+        var name = aFeature.getName();
+        if (name.equals(FEAT_REL_SOURCE) || name.equals(FEAT_REL_TARGET)) {
+            return asList(new ValidationError("[" + name + "] is a reserved feature name on "
+                    + "relation layers. Please use a different name for the feature."));
+        }
+
+        return Collections.emptyList();
+    }
 }
diff --git a/...on/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanLayerSupport.java b/...on/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanLayerSupport.java
@@ -102,11 +102,9 @@ public boolean accepts(AnnotationLayer aLayer)
     public SpanAdapter createAdapter(AnnotationLayer aLayer,
             Supplier<Collection<AnnotationFeature>> aFeatures)
     {
-        var adapter = new SpanAdapter(getLayerSupportRegistry(), featureSupportRegistry,
-                eventPublisher, aLayer, aFeatures,
+        return new SpanAdapter(getLayerSupportRegistry(), featureSupportRegistry, eventPublisher,
+                aLayer, aFeatures,
                 layerBehaviorsRegistry.getLayerBehaviors(this, SpanLayerBehavior.class));
-
-        return adapter;
     }
 
     @Override
@@ -134,7 +132,7 @@ public SpanRenderer createRenderer(AnnotationLayer aLayer,
     @Override
     public Panel createTraitsEditor(String aId, IModel<AnnotationLayer> aLayerModel)
     {
-        AnnotationLayer layer = aLayerModel.getObject();
+        var layer = aLayerModel.getObject();
 
         if (!accepts(layer)) {
             throw unsupportedLayerTypeException(layer);