#4285 - Upgrade dependencies

- Remove workaround for apache/uima-uimaj#345
inception-project · Nov 7, 2023 · 10d6be2 · 10d6be2
1 parent 28e2775
commit 10d6be2
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Showing 8 changed files with 32 additions and 149 deletions.
diff --git a/...tation/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanRenderer.java b/...tation/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanRenderer.java
@@ -30,7 +30,6 @@
 import java.util.Optional;
 
 import org.apache.uima.cas.CAS;
-import org.apache.uima.cas.FSIterator;
 import org.apache.uima.cas.FeatureStructure;
 import org.apache.uima.cas.Type;
 import org.apache.uima.cas.TypeSystem;
@@ -93,40 +92,9 @@ protected boolean typeSystemInit(TypeSystem aTypeSystem)
     @Override
     public List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin, int aWindowEnd)
     {
-        // https://github.com/apache/uima-uimaj/issues/345
-        // return aCas.select(type).coveredBy(0, aWindowEnd).includeAnnotationsWithEndBeyondBounds()
-        // .map(fs -> (AnnotationFS) fs)
-        // .filter(ann -> AnnotationPredicates.overlapping(ann, aWindowBegin, aWindowEnd))
-        // .collect(toList());
-
-        List<AnnotationFS> list = new ArrayList<AnnotationFS>();
-
-        // withSnapshotIterators() not needed here since we copy the FSes to a list anyway
-        FSIterator<AnnotationFS> it = aCas.getAnnotationIndex(type).iterator();
-
-        // Skip annotations whose start is before the start parameter.
-        while (it.isValid() && (it.get()).getBegin() < 0) {
-            it.moveToNext();
-        }
-
-        boolean strict = false;
-        while (it.isValid()) {
-            AnnotationFS a = it.get();
-            // If the start of the current annotation is past the end parameter, we're done.
-            if (a.getBegin() > aWindowEnd) {
-                break;
-            }
-            it.moveToNext();
-            if (strict && a.getEnd() > aWindowEnd) {
-                continue;
-            }
-
-            list.add(a);
-        }
-
-        return list.stream() //
-                .map(fs -> (AnnotationFS) fs) //
-                .filter(ann -> AnnotationPredicates.overlapping(ann, aWindowBegin, aWindowEnd)) //
+        return aCas.select(type).coveredBy(0, aWindowEnd).includeAnnotationsWithEndBeyondBounds()
+                .map(fs -> (AnnotationFS) fs)
+                .filter(ann -> AnnotationPredicates.overlapping(ann, aWindowBegin, aWindowEnd))
                 .collect(toList());
     }
 

diff --git a/...rc/main/java/de/tudarmstadt/ukp/clarin/webanno/curation/casdiff/span/SpanDiffAdapter.java b/...rc/main/java/de/tudarmstadt/ukp/clarin/webanno/curation/casdiff/span/SpanDiffAdapter.java
@@ -20,17 +20,14 @@
 import static java.util.Arrays.asList;
 import static java.util.stream.Collectors.toList;
 
-import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
 import org.apache.uima.cas.CAS;
-import org.apache.uima.cas.FSIterator;
 import org.apache.uima.cas.FeatureStructure;
 import org.apache.uima.cas.text.AnnotationFS;
 import org.apache.uima.cas.text.AnnotationPredicates;
-import org.apache.uima.fit.util.CasUtil;
 import org.apache.uima.fit.util.FSUtil;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil;
@@ -74,41 +71,9 @@ public SpanDiffAdapter(String aType, Set<String> aLabelFeatures)
     @Override
     public List<AnnotationFS> selectAnnotationsInWindow(CAS aCas, int aWindowBegin, int aWindowEnd)
     {
-        // https://github.com/apache/uima-uimaj/issues/345
-        // return aCas.select(type).coveredBy(0, aWindowEnd).includeAnnotationsWithEndBeyondBounds()
-        // .map(fs -> (AnnotationFS) fs)
-        // .filter(ann -> AnnotationPredicates.overlapping(ann, aWindowBegin, aWindowEnd))
-        // .collect(toList());
-
-        List<AnnotationFS> list = new ArrayList<AnnotationFS>();
-
-        // withSnapshotIterators() not needed here since we copy the FSes to a list anyway
-        FSIterator<AnnotationFS> it = aCas.getAnnotationIndex(CasUtil.getType(aCas, getType()))
-                .iterator();
-
-        // Skip annotations whose start is before the start parameter.
-        while (it.isValid() && (it.get()).getBegin() < aWindowBegin) {
-            it.moveToNext();
-        }
-
-        boolean strict = false;
-        while (it.isValid()) {
-            AnnotationFS a = it.get();
-            // If the start of the current annotation is past the end parameter, we're done.
-            if (a.getBegin() > aWindowEnd) {
-                break;
-            }
-            it.moveToNext();
-            if (strict && a.getEnd() > aWindowEnd) {
-                continue;
-            }
-
-            list.add(a);
-        }
-
-        return list.stream() //
-                .map(fs -> (AnnotationFS) fs) //
-                .filter(ann -> AnnotationPredicates.overlapping(ann, aWindowBegin, aWindowEnd)) //
+        return aCas.select(getType()).coveredBy(0, aWindowEnd)
+                .includeAnnotationsWithEndBeyondBounds().map(fs -> (AnnotationFS) fs)
+                .filter(ann -> AnnotationPredicates.overlapping(ann, aWindowBegin, aWindowEnd))
                 .collect(toList());
     }
 

diff --git a/...rmstadt/ukp/clarin/webanno/diag/checks/AllAnnotationsStartAndEndWithinSentencesCheck.java b/...rmstadt/ukp/clarin/webanno/diag/checks/AllAnnotationsStartAndEndWithinSentencesCheck.java
@@ -27,7 +27,6 @@
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.Type;
 import org.apache.uima.cas.text.AnnotationFS;
-import org.apache.uima.fit.util.CasUtil;
 import org.springframework.util.CollectionUtils;
 
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
@@ -77,19 +76,10 @@ public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages)
             }
 
             for (AnnotationFS ann : select(aCas, type)) {
-                // https://github.com/apache/uima-uimaj/issues/345
-                // var startsOutside = aCas.select(Sentence._TypeName)
-                // .covering(ann.getBegin(), ann.getBegin()).isEmpty();
-                var startsOutside = CasUtil
-                        .selectCovering(ann.getCAS(), CasUtil.getType(ann.getCAS(), Sentence.class),
-                                ann.getBegin(), ann.getBegin())
-                        .isEmpty();
-                // https://github.com/apache/uima-uimaj/issues/345
-                // var endsOutside = aCas.select(Sentence._TypeName)
-                // .covering(ann.getEnd(), ann.getEnd()).isEmpty();
-                var endsOutside = CasUtil.selectCovering(ann.getCAS(),
-                        CasUtil.getType(ann.getCAS(), Sentence.class), ann.getEnd(), ann.getEnd())
-                        .isEmpty();
+                var startsOutside = aCas.select(Sentence._TypeName)
+                        .covering(ann.getBegin(), ann.getBegin()).isEmpty();
+                var endsOutside = aCas.select(Sentence._TypeName)
+                        .covering(ann.getEnd(), ann.getEnd()).isEmpty();
 
                 if (!startsOutside && !endsOutside) {
                     continue;

diff --git a/...inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/CasToBioC.java b/...inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/CasToBioC.java
@@ -40,7 +40,6 @@
 
 import org.apache.uima.cas.text.AnnotationFS;
 import org.apache.uima.fit.util.FSUtil;
-import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.dkpro.core.api.xml.type.XmlElement;
@@ -82,12 +81,8 @@ public void convert(JCas aJCas, BioCCollection aCollection)
                 bioCPassage.addInfon(I_TYPE, div.getDivType());
             }
 
-            // https://github.com/apache/uima-uimaj/issues/345
-            // var sentences = aJCas.select(Sentence.class).coveredBy(div).asList();
-            var sentences = JCasUtil.selectCovered(Sentence.class, div);
-            // https://github.com/apache/uima-uimaj/issues/345
-            // var annotations = aJCas.select(Annotation.class).coveredBy(div);
-            var annotations = JCasUtil.selectCovered(Annotation.class, div);
+            var sentences = aJCas.select(Sentence.class).coveredBy(div).asList();
+            var annotations = aJCas.select(Annotation.class).coveredBy(div);
             if (sentences.isEmpty()) {
                 bioCPassage.setText(div.getCoveredText());
                 processAnnotations(bioCPassage, bioCPassage.getOffset(), annotations);
@@ -96,10 +91,7 @@ public void convert(JCas aJCas, BioCCollection aCollection)
                 var bioCSentences = processSentences(div.getBegin(), sentences);
                 bioCPassage.setSentences(bioCSentences);
                 processAnnotations(bioCPassage, bioCPassage.getOffset(),
-                        annotations.stream().filter(a ->
-                        // https://github.com/apache/uima-uimaj/issues/345
-                        // aJCas.select(Sentence.class).covering(a).isEmpty()
-                        JCasUtil.selectCovering(Sentence.class, a).isEmpty())
+                        annotations.filter(a -> aJCas.select(Sentence.class).covering(a).isEmpty())
                                 .collect(Collectors.toList()));
             }
         }
@@ -136,9 +128,7 @@ private List<BioCSentence> processSentences(int aPassageOffset, List<Sentence> s
             bioCSentence.setText(sentence.getCoveredText());
 
             processAnnotations(bioCSentence, sentence.getBegin(),
-                    // https://github.com/apache/uima-uimaj/issues/345
-                    // sentence.getCAS().select(Annotation.class).coveredBy(sentence)
-                    JCasUtil.selectCovered(Annotation.class, sentence));
+                    sentence.getCAS().select(Annotation.class).coveredBy(sentence));
 
             bioCSentences.add(bioCSentence);
         }

diff --git a/...ion-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/Cas2BioCSaxEvents.java b/...ion-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/Cas2BioCSaxEvents.java
@@ -58,7 +58,6 @@
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.text.AnnotationFS;
 import org.apache.uima.fit.util.FSUtil;
-import org.apache.uima.fit.util.JCasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.tcas.Annotation;
 import org.dkpro.core.api.xml.type.XmlElement;
@@ -140,10 +139,8 @@ private void processSentenceElement(XmlElement aSentenceElement) throws SAXExcep
             return;
         }
 
-        // https://github.com/apache/uima-uimaj/issues/345
-        // var annotations = aSentenceElement.getCAS().select(Annotation.class)
-        // .coveredBy(aSentenceElement);
-        var annotations = JCasUtil.selectCovered(Annotation.class, aSentenceElement);
+        var annotations = aSentenceElement.getCAS().select(Annotation.class)
+                .coveredBy(aSentenceElement);
         for (var annotation : annotations) {
             serializeAnnotation(sentenceTextElement.get().getBegin(), annotation);
         }

diff --git a/...editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/format/VisualPdfReader.java b/...editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/format/VisualPdfReader.java
@@ -27,7 +27,6 @@
 import org.apache.uima.cas.CAS;
 import org.apache.uima.collection.CollectionException;
 import org.apache.uima.fit.descriptor.ConfigurationParameter;
-import org.apache.uima.fit.util.CasUtil;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FloatArray;
 import org.apache.uima.jcas.cas.IntegerArray;
@@ -117,11 +116,8 @@ public static VModel visualModelFromCas(CAS cas, List<PdfPage> pdfPages)
         VModel vModel;
         List<VPage> vPages = new ArrayList<>();
         for (PdfPage pdfPage : pdfPages) {
-            List<VChunk> vChunks = new ArrayList<>();
-            // https://github.com/apache/uima-uimaj/issues/345
-            // SelectFSs<PdfChunk> coveredBy = cas.select(PdfChunk.class).coveredBy(pdfPage);
-            List<PdfChunk> coveredBy = (List) CasUtil
-                    .selectCovered(CasUtil.getType(cas, PdfChunk.class), pdfPage);
+            var vChunks = new ArrayList<VChunk>();
+            var coveredBy = cas.select(PdfChunk.class).coveredBy(pdfPage);
             for (var pdfChunk : coveredBy) {
                 float d = pdfChunk.getD();
                 List<VGlyph> vGlyphs = new ArrayList<>();

diff --git a/...n/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImpl.java b/...n/java/de/tudarmstadt/ukp/inception/recommendation/service/RecommendationServiceImpl.java
@@ -1081,12 +1081,9 @@ private AnnotationFS acceptOrCorrectSuggestion(String aSessionOwner, SourceDocum
         var aEnd = aSuggestion.getEnd();
         var aValue = aSuggestion.getLabel();
 
-        // https://github.com/apache/uima-uimaj/issues/345
-        // var candidates = aCas.<Annotation> select(aAdapter.getAnnotationTypeName()) //
-        // .at(aBegin, aEnd) //
-        // .asList();
-        var candidates = CasUtil.selectAt(aCas,
-                CasUtil.getType(aCas, aAdapter.getAnnotationTypeName()), aBegin, aEnd);
+        var candidates = aCas.<Annotation> select(aAdapter.getAnnotationTypeName()) //
+                .at(aBegin, aEnd) //
+                .asList();
 
         var candidateWithEmptyLabel = candidates.stream() //
                 .filter(c -> aAdapter.getFeatureValue(aFeature, c) == null) //
@@ -2087,15 +2084,9 @@ private static Optional<Offset> getOffsetsAnchoredOnSingleTokens(CAS aOriginalCa
             Annotation aPredictedAnnotation)
     {
         Type tokenType = getType(aOriginalCas, Token.class);
-        // https://github.com/apache/uima-uimaj/issues/345
-        // var tokens = aOriginalCas.<Annotation> select(tokenType) //
-        // .coveredBy(aPredictedAnnotation) //
-        // .limit(2).asList();
-        var tokens = CasUtil
-                .selectCovered(aOriginalCas, tokenType, aPredictedAnnotation.getBegin(),
-                        aPredictedAnnotation.getEnd())
-                .stream() //
-                .limit(2).collect(toList());
+        var tokens = aOriginalCas.<Annotation> select(tokenType) //
+                .coveredBy(aPredictedAnnotation) //
+                .limit(2).asList();
 
         if (tokens.isEmpty()) {
             // This can happen if a recommender uses different token boundaries (e.g. if a
@@ -2122,13 +2113,9 @@ private static Optional<Offset> getOffsetsAnchoredOnSingleTokens(CAS aOriginalCa
     private static Optional<Offset> getOffsetsAnchoredOnSentences(CAS aOriginalCas,
             Annotation aPredictedAnnotation)
     {
-        // https://github.com/apache/uima-uimaj/issues/345
-        // var sentences = aOriginalCas.select(Sentence.class) //
-        // .coveredBy(aPredictedAnnotation) //
-        // .asList();
-        var sentences = CasUtil.selectCovered(aOriginalCas,
-                CasUtil.getType(aOriginalCas, Sentence.class), aPredictedAnnotation.getBegin(),
-                aPredictedAnnotation.getEnd());
+        var sentences = aOriginalCas.select(Sentence.class) //
+                .coveredBy(aPredictedAnnotation) //
+                .asList();
 
         if (sentences.isEmpty()) {
             // This can happen if a recommender uses different token boundaries (e.g. if a
@@ -2147,12 +2134,9 @@ private static Optional<Offset> getOffsetsAnchoredOnSentences(CAS aOriginalCas,
     static Optional<Offset> getOffsetsAnchoredOnTokens(CAS aOriginalCas,
             Annotation aPredictedAnnotation)
     {
-        // https://github.com/apache/uima-uimaj/issues/345
-        // var tokens = aOriginalCas.select(Token.class) //
-        // .coveredBy(aPredictedAnnotation) //
-        // .asList();
-        var tokens = CasUtil.selectCovered(aOriginalCas, CasUtil.getType(aOriginalCas, Token.class),
-                aPredictedAnnotation.getBegin(), aPredictedAnnotation.getEnd());
+        var tokens = aOriginalCas.select(Token.class) //
+                .coveredBy(aPredictedAnnotation) //
+                .asList();
 
         if (tokens.isEmpty()) {
             if (aPredictedAnnotation.getBegin() == aPredictedAnnotation.getEnd()) {

diff --git a/...a/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java b/...a/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java
@@ -1235,15 +1235,8 @@ public void onBulkAnnotationEvent(BulkAnnotationEvent aEvent)
         try {
             var selection = getModelObject().getSelection();
             int id = selection.getAnnotation().getId();
-            // https://github.com/apache/uima-uimaj/issues/345
-            // boolean annotationStillExists = getEditorCas().select(Annotation.class) //
-            // .at(selection.getBegin(), selection.getEnd()) //
-            // .anyMatch(ann -> ann._id() == id);
-            var cas = getEditorCas();
-            boolean annotationStillExists = CasUtil
-                    .selectAt(cas, CasUtil.getType(cas, Annotation.class), selection.getBegin(),
-                            selection.getEnd())
-                    .stream() //
+            boolean annotationStillExists = getEditorCas().select(Annotation.class) //
+                    .at(selection.getBegin(), selection.getEnd()) //
                     .anyMatch(ann -> ann._id() == id);
 
             if (!annotationStillExists) {