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#4150 - Upgrade dependencies #4287

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merged 11 commits into from
Nov 7, 2023
Merged

#4150 - Upgrade dependencies #4287

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28e2775
#4285 - Upgrade dependencies
reckart Nov 7, 2023
10d6be2
#4285 - Upgrade dependencies
reckart Nov 7, 2023
8c33a2a
Merge branch 'refactoring/4285-Upgrade-dependencies' into refactoring…
reckart Nov 7, 2023
9d74fa4
Revert "#4285 - Upgrade dependencies"
reckart Nov 7, 2023
5031e72
Empty merge of branch 'refactoring/4285-Upgrade-dependencies' into re…
reckart Nov 7, 2023
565fe5f
#4285 - Upgrade dependencies
reckart Nov 7, 2023
58fcaca
Empty merge of branch 'refactoring/4285-Upgrade-dependencies' into re…
reckart Nov 7, 2023
03ef3d4
#4285 - Upgrade dependencies
reckart Nov 7, 2023
7889faa
Empty merge of branch 'refactoring/4285-Upgrade-dependencies' into re…
reckart Nov 7, 2023
58bbac1
Merge branch 'main' into refactoring/4150-Upgrade-dependencies
reckart Nov 7, 2023
a372d29
Merge branch 'refactoring/4150-Upgrade-dependencies' of https://githu…
reckart Nov 7, 2023
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38 changes: 3 additions & 35 deletions ...tation/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/span/SpanRenderer.java
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Expand Up @@ -32,7 +32,6 @@
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;
Expand Down Expand Up @@ -100,40 +99,9 @@ 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());
}

Expand Down
41 changes: 3 additions & 38 deletions ...rc/main/java/de/tudarmstadt/ukp/clarin/webanno/curation/casdiff/span/SpanDiffAdapter.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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());
}

Expand Down
118 changes: 48 additions & 70 deletions inception/inception-dependencies/pom.xml
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Expand Up @@ -32,28 +32,10 @@
<dependencies>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
<version>${uima.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-cpe</artifactId>
<version>${uima.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-tools</artifactId>
<version>${uima.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-json</artifactId>
<version>${uima.version}</version>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-document-annotation</artifactId>
<artifactId>uimaj-bom</artifactId>
<version>${uima.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>org.apache.uima</groupId>
Expand All @@ -76,6 +58,49 @@
<version>${json.version}</version>
</dependency>

<!-- JAXB DEPENDENCIES -->
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-bom</artifactId>
<version>2.3.9</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.1</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>2.3.0.1</version>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>javax.activation-api</artifactId>
<version>1.2.0</version>
</dependency>
<dependency>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
<version>1.2.0</version>
<exclusions>
<exclusion>
<artifactId>dom4j</artifactId>
<groupId>dom4j</groupId>
</exclusion>
<exclusion>
<artifactId>xom</artifactId>
<groupId>xom</groupId>
</exclusion>
<exclusion>
<artifactId>jdom</artifactId>
<groupId>jdom</groupId>
</exclusion>
</exclusions>
</dependency>

<!-- Testing -->
<dependency>
<groupId>org.junit</groupId>
Expand Down Expand Up @@ -587,7 +612,7 @@
<dependency>
<groupId>org.codehaus.woodstox</groupId>
<artifactId>stax2-api</artifactId>
<version>4.2.1</version>
<version>4.2.2</version>
</dependency>

<dependency>
Expand Down Expand Up @@ -974,53 +999,6 @@
<version>1.1.10.5</version>
</dependency>

<!-- JAXB DEPENDENCIES -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.1</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>2.3.0.1</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.3.8</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>2.3.8</version>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>javax.activation-api</artifactId>
<version>1.2.0</version>
</dependency>

<dependency>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
<version>1.2.0</version>
<exclusions>
<exclusion>
<artifactId>dom4j</artifactId>
<groupId>dom4j</groupId>
</exclusion>
<exclusion>
<artifactId>xom</artifactId>
<groupId>xom</groupId>
</exclusion>
<exclusion>
<artifactId>jdom</artifactId>
<groupId>jdom</groupId>
</exclusion>
</exclusions>
</dependency>

<dependency>
<groupId>org.dkpro.core</groupId>
<artifactId>dkpro-core-testing-asl</artifactId>
Expand Down Expand Up @@ -1081,7 +1059,7 @@
<dependency>
<groupId>com.github.jsonld-java</groupId>
<artifactId>jsonld-java</artifactId>
<version>0.13.4</version>
<version>0.13.6</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
Expand Down
18 changes: 4 additions & 14 deletions ...rmstadt/ukp/clarin/webanno/diag/checks/AllAnnotationsStartAndEndWithinSentencesCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
18 changes: 4 additions & 14 deletions ...inception-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/model/CasToBioC.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
Expand All @@ -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()));
}
}
Expand Down Expand Up @@ -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);
}
Expand Down
7 changes: 2 additions & 5 deletions ...ion-io-bioc/src/main/java/de/tudarmstadt/ukp/inception/io/bioc/xml/Cas2BioCSaxEvents.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
}
Expand Down
8 changes: 2 additions & 6 deletions ...editor2/src/main/java/de/tudarmstadt/ukp/inception/pdfeditor2/format/VisualPdfReader.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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<>();
Expand Down
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