#2696 - Document-level recommendations

- Removed a bunch of unused methods - Moved a bunch of methods only used once to the classes where they are used
inception-project · Dec 26, 2023 · eb66783 · eb66783
1 parent bf47a1f
commit eb66783
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Showing 8 changed files with 99 additions and 181 deletions.
diff --git a/...r/src/test/java/de/tudarmstadt/ukp/clarin/webanno/brat/render/BratSerializerImplTest.java b/...r/src/test/java/de/tudarmstadt/ukp/clarin/webanno/brat/render/BratSerializerImplTest.java
@@ -23,6 +23,8 @@
 import static java.util.Arrays.asList;
 import static org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine;
 import static org.apache.uima.fit.factory.CollectionReaderFactory.createReader;
+import static org.apache.uima.fit.util.CasUtil.getType;
+import static org.apache.uima.fit.util.CasUtil.select;
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.assertj.core.api.Assertions.contentOf;
 import static org.mockito.ArgumentMatchers.any;
@@ -32,6 +34,7 @@
 
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.text.AnnotationFS;
 import org.apache.uima.collection.CollectionReader;
 import org.apache.uima.fit.factory.JCasFactory;
 import org.dkpro.core.io.tcf.TcfReader;
@@ -59,6 +62,7 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
 import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
 import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS;
+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.bool.BooleanFeatureSupport;
 import de.tudarmstadt.ukp.inception.annotation.feature.link.LinkFeatureSupport;
@@ -76,7 +80,6 @@
 import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
 import de.tudarmstadt.ukp.inception.schema.service.FeatureSupportRegistryImpl;
 import de.tudarmstadt.ukp.inception.support.json.JSONUtil;
-import de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil;
 
 @ExtendWith(MockitoExtension.class)
 public class BratSerializerImplTest
@@ -180,7 +183,7 @@ public void thatSentenceOrientedStrategyRenderCorrectly() throws Exception
         state.setAllAnnotationLayers(schemaService.listAnnotationLayer(project));
         state.setPagingStrategy(new SentenceOrientedPagingStrategy());
         state.getPreferences().setWindowSize(10);
-        state.setFirstVisibleUnit(WebAnnoCasUtil.getFirstSentence(cas));
+        state.setFirstVisibleUnit(getFirstSentence(cas));
         state.setProject(project);
         state.setDocument(sourceDocument, asList(sourceDocument));
 
@@ -219,7 +222,7 @@ public void thatLineOrientedStrategyRenderCorrectly() throws Exception
         AnnotatorState state = new AnnotatorStateImpl(Mode.ANNOTATION);
         state.setPagingStrategy(new LineOrientedPagingStrategy());
         state.getPreferences().setWindowSize(10);
-        state.setFirstVisibleUnit(WebAnnoCasUtil.getFirstSentence(cas));
+        state.setFirstVisibleUnit(getFirstSentence(cas));
         state.setProject(project);
         state.setDocument(sourceDocument, asList(sourceDocument));
 
@@ -258,7 +261,7 @@ public void thatTokenWrappingStrategyRenderCorrectly() throws Exception
         AnnotatorState state = new AnnotatorStateImpl(Mode.ANNOTATION);
         state.setPagingStrategy(new TokenWrappingPagingStrategy(80));
         state.getPreferences().setWindowSize(10);
-        state.setFirstVisibleUnit(WebAnnoCasUtil.getFirstSentence(cas));
+        state.setFirstVisibleUnit(getFirstSentence(cas));
         state.setProject(project);
         state.setDocument(sourceDocument, asList(sourceDocument));
 
@@ -281,4 +284,22 @@ public void thatTokenWrappingStrategyRenderCorrectly() throws Exception
         assertThat(contentOf(new File("src/test/resources/longlines.json"), UTF_8))
                 .isEqualToNormalizingNewlines(contentOf(new File(jsonFilePath), UTF_8));
     }
+
+    /**
+     * Get the internal address of the first sentence annotation from CAS. This will be used as a
+     * reference for moving forward/backward sentences positions
+     *
+     * @param aCas
+     *            The CAS object assumed to contains some sentence annotations
+     * @return the sentence number or -1 if aCas don't have sentence annotation
+     */
+    private static AnnotationFS getFirstSentence(CAS aCas)
+    {
+        AnnotationFS firstSentence = null;
+        for (AnnotationFS s : select(aCas, getType(aCas, Sentence.class))) {
+            firstSentence = s;
+            break;
+        }
+        return firstSentence;
+    }
 }
diff --git a/...n/java/de/tudarmstadt/ukp/inception/conceptlinking/service/ConceptLinkingServiceImpl.java b/...n/java/de/tudarmstadt/ukp/inception/conceptlinking/service/ConceptLinkingServiceImpl.java
@@ -24,13 +24,13 @@
 import static de.tudarmstadt.ukp.inception.conceptlinking.model.CandidateEntity.KEY_QUERY;
 import static de.tudarmstadt.ukp.inception.conceptlinking.model.CandidateEntity.KEY_QUERY_BEST_MATCH_TERM_NC;
 import static de.tudarmstadt.ukp.inception.conceptlinking.model.CandidateEntity.KEY_QUERY_NC;
-import static de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil.selectSentenceCovering;
-import static de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil.selectTokensCovered;
 import static java.lang.System.currentTimeMillis;
 import static java.util.Arrays.asList;
 import static java.util.Collections.unmodifiableList;
 import static java.util.Comparator.comparingInt;
 import static java.util.stream.Collectors.toCollection;
+import static org.apache.uima.fit.util.CasUtil.getType;
+import static org.apache.uima.fit.util.CasUtil.select;
 
 import java.io.File;
 import java.net.URISyntaxException;
@@ -47,6 +47,7 @@
 import org.apache.commons.lang3.Validate;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.fit.util.CasUtil;
 import org.eclipse.rdf4j.common.net.ParsedIRI;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -58,6 +59,8 @@
 import org.springframework.core.annotation.AnnotationAwareOrderComparator;
 
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+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.conceptlinking.config.EntityLinkingProperties;
 import de.tudarmstadt.ukp.inception.conceptlinking.config.EntityLinkingPropertiesImpl;
 import de.tudarmstadt.ukp.inception.conceptlinking.config.EntityLinkingServiceAutoConfiguration;
@@ -513,4 +516,31 @@ public List<KBHandle> searchItems(KnowledgeBase aKB, String aQuery)
     {
         return disambiguate(aKB, null, ConceptFeatureValueType.ANY_OBJECT, aQuery, null, 0, null);
     }
+
+    /**
+     * Get the sentence based on the annotation begin offset
+     *
+     * @param aCas
+     *            the CAS.
+     * @param aBegin
+     *            the begin offset.
+     * @return the sentence.
+     */
+    private static AnnotationFS selectSentenceCovering(CAS aCas, int aBegin)
+    {
+        AnnotationFS currentSentence = null;
+        for (AnnotationFS sentence : select(aCas, getType(aCas, Sentence.class))) {
+            if (sentence.getBegin() <= aBegin && sentence.getEnd() > aBegin) {
+                currentSentence = sentence;
+                break;
+            }
+        }
+        return currentSentence;
+    }
+
+    private static Collection<AnnotationFS> selectTokensCovered(AnnotationFS aCover)
+    {
+        return CasUtil.selectCovered(aCover.getCAS(), getType(aCover.getCAS(), Token.class),
+                aCover);
+    }
 }
diff --git a/.../main/java/de/tudarmstadt/ukp/clarin/webanno/diag/checks/UnreachableAnnotationsCheck.java b/.../main/java/de/tudarmstadt/ukp/clarin/webanno/diag/checks/UnreachableAnnotationsCheck.java
@@ -24,10 +24,13 @@
 import static org.apache.uima.cas.impl.Serialization.deserializeCASComplete;
 import static org.apache.uima.cas.impl.Serialization.serializeCASComplete;
 
+import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.FeatureStructure;
 import org.apache.uima.cas.impl.CASImpl;
 import org.apache.uima.resource.ResourceInitializationException;
 
@@ -93,8 +96,15 @@ public static CASImpl makeDummyCas()
 
     public static Map<String, Long> countFeatureStructures(CASImpl casImpl)
     {
-        return WebAnnoCasUtil.findAllFeatureStructures(casImpl).stream() //
+        return findAllFeatureStructures(casImpl).stream() //
                 .map(fs -> fs.getType().getName()) //
                 .collect(groupingBy(identity(), counting()));
     }
+
+    public static Set<FeatureStructure> findAllFeatureStructures(CAS aCas)
+    {
+        Set<FeatureStructure> allFSes = new LinkedHashSet<>();
+        ((CASImpl) aCas).walkReachablePlusFSsSorted(allFSes::add, null, null, null);
+        return allFSes;
+    }
 }
diff --git a/inception/inception-pdf-editor/pom.xml b/inception/inception-pdf-editor/pom.xml
@@ -87,6 +87,10 @@
       <groupId>org.dkpro.core</groupId>
       <artifactId>dkpro-core-io-pdf-asl</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.dkpro.core</groupId>
+      <artifactId>dkpro-core-api-segmentation-asl</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.dkpro.core</groupId>
       <artifactId>dkpro-core-api-resources-asl</artifactId>
@@ -168,11 +172,6 @@
       <artifactId>dkpro-core-api-lexmorph-asl</artifactId>
       <scope>test</scope>
     </dependency>
-    <dependency>
-      <groupId>org.dkpro.core</groupId>
-      <artifactId>dkpro-core-api-segmentation-asl</artifactId>
-      <scope>test</scope>
-    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-schema</artifactId>

diff --git a/...-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditor.java b/...-pdf-editor/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor/PdfAnnotationEditor.java
@@ -20,10 +20,10 @@
 import static de.tudarmstadt.ukp.inception.pdfeditor.pdfanno.render.PdfAnnoSerializer.convertToDocumentOffset;
 import static de.tudarmstadt.ukp.inception.pdfeditor.pdfanno.render.PdfAnnoSerializer.convertToDocumentOffsets;
 import static de.tudarmstadt.ukp.inception.rendering.vmodel.VID.NONE_ID;
-import static de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil.selectSentenceAt;
 import static de.tudarmstadt.ukp.inception.support.wicket.ServletContextUtils.referenceToUrl;
 import static java.lang.String.join;
 import static java.util.Arrays.asList;
+import static org.apache.uima.fit.util.CasUtil.getType;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -37,6 +37,7 @@
 import org.apache.commons.lang3.exception.ExceptionUtils;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.text.AnnotationFS;
+import org.apache.uima.fit.util.CasUtil;
 import org.apache.wicket.Component;
 import org.apache.wicket.ajax.AjaxRequestTarget;
 import org.apache.wicket.feedback.IFeedback;
@@ -48,6 +49,7 @@
 import org.slf4j.LoggerFactory;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasProvider;
+import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
 import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
 import de.tudarmstadt.ukp.inception.editor.AnnotationEditorExtensionRegistry;
 import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
@@ -314,4 +316,20 @@ private String getAnnotationsJS(PdfAnnoModel aPdfAnnoModel)
                 "'colorMap': {},", //
                 "'annotations':[annoFile]}, true);");
     }
+
+    /**
+     * Get the sentence for this CAS based on the begin and end offsets. This is basically used to
+     * transform sentence address in one CAS to other sentence address for different CAS
+     *
+     * @param aCas
+     *            the CAS.
+     * @param aBegin
+     *            the begin offset.
+     * @return the sentence.
+     */
+    private static AnnotationFS selectSentenceAt(CAS aCas, int aBegin)
+    {
+        return CasUtil.select(aCas, getType(aCas, Sentence.class)).stream()
+                .filter(s -> s.getBegin() == aBegin).findFirst().orElse(null);
+    }
 }
diff --git a/.../java/de/tudarmstadt/ukp/inception/recommendation/relation/RelationSuggestionSupport.java b/.../java/de/tudarmstadt/ukp/inception/recommendation/relation/RelationSuggestionSupport.java
@@ -20,7 +20,6 @@
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion.FLAG_OVERLAP;
 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.stream.Collectors.toList;
 import static org.apache.uima.cas.text.AnnotationPredicates.colocated;
 import static org.apache.uima.fit.util.CasUtil.select;
 import static org.apache.uima.fit.util.CasUtil.selectAt;
@@ -243,8 +242,8 @@ public <T extends AnnotationSuggestion> void calculateSuggestionVisibility(Strin
         // Collect all suggestions of the given layer
         var groupedSuggestions = aRecommendations.stream()
                 .filter(group -> group.getLayerId() == aLayer.getId()) //
-                .map(group -> (SuggestionGroup) group) //
-                .collect(toList());
+                .map(group -> (SuggestionGroup<RelationSuggestion>) group) //
+                .toList();
 
         // Get previously rejected suggestions
         var groupedRecordedAnnotations = new ArrayListValuedHashMap<Position, LearningRecord>();
@@ -267,7 +266,7 @@ public <T extends AnnotationSuggestion> void calculateSuggestionVisibility(Strin
                 return;
             }
 
-            for (SuggestionGroup<RelationSuggestion> group : groupedSuggestions) {
+            for (var group : groupedSuggestions) {
                 if (!feature.getName().equals(group.getFeature())) {
                     continue;
                 }

diff --git a/...dt/ukp/inception/recommendation/relation/RelationSuggestionVisibilityCalculationTest.java b/...dt/ukp/inception/recommendation/relation/RelationSuggestionVisibilityCalculationTest.java
@@ -21,14 +21,13 @@
 import static de.tudarmstadt.ukp.inception.recommendation.service.Fixtures.getVisibleSuggestions;
 import static de.tudarmstadt.ukp.inception.recommendation.service.Fixtures.makeRelationSuggestionGroup;
 import static java.util.Arrays.asList;
+import static java.util.Collections.emptyList;
 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.when;
 
-import java.util.ArrayList;
-
 import org.apache.uima.cas.CAS;
 import org.apache.uima.fit.factory.JCasFactory;
 import org.junit.jupiter.api.BeforeEach;
@@ -82,8 +81,8 @@ public void setUp() throws Exception
     @Test
     public void testCalculateVisibilityNoRecordsAllHidden() throws Exception
     {
-        doReturn(new ArrayList<>()).when(learningRecordService).listLearningRecords(TEST_USER,
-                TEST_USER, layer);
+        doReturn(emptyList()).when(learningRecordService).listLearningRecords(TEST_USER, TEST_USER,
+                layer);
 
         var cas = getTestCas();
         var suggestions = makeRelationSuggestionGroup(doc, feature,
@@ -105,8 +104,8 @@ public void testCalculateVisibilityNoRecordsAllHidden() throws Exception
     @Test
     public void thatVisibilityIsRestoredWhenOverlappingAnnotationIsRemoved() throws Exception
     {
-        doReturn(new ArrayList<>()).when(learningRecordService).listLearningRecords(TEST_USER,
-                TEST_USER, layer);
+        doReturn(emptyList()).when(learningRecordService).listLearningRecords(TEST_USER, TEST_USER,
+                layer);
 
         var cas = getTestCas();
         var suggestions = makeRelationSuggestionGroup(doc, feature,