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reckartreckart
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Merge pull request #1614 from dkpro/refactoring/1602-Upgrade-dependencies
#1602 - Upgrade dependencies
2 parents 173c761 + 635825e commit d03a63a

39 files changed

Lines changed: 278 additions & 246 deletions

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‎dkpro-core-corenlp-gpl/pom.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@
3333
<url>https://dkpro.github.io/dkpro-core/</url>
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<properties>
36-
<corenlp.version>4.5.7</corenlp.version>
36+
<corenlp.version>4.5.10</corenlp.version>
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</properties>
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<dependencies>

‎dkpro-core-gate-asl/pom.xml‎

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@@ -31,9 +31,9 @@
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<url>https://dkpro.github.io/dkpro-core/</url>
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<properties>
34-
<gate.version>8.6.1</gate.version>
35-
<annie.version>8.6</annie.version>
36-
<tools.version>8.6</tools.version>
34+
<gate.version>9.0.1</gate.version>
35+
<annie.version>9.1</annie.version>
36+
<tools.version>9.0.1</tools.version>
3737
</properties>
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<dependencies>

‎dkpro-core-gate-asl/src/scripts/build.xml‎

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@@ -46,7 +46,7 @@
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<mkdir dir="target/download/tmp"/>
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<unzip src="target/download/gate/gate-ALL.zip" dest="target/download/tmp">
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<patternset>
49-
<include name="**/plugins/Tools/resources/morph/default.rul"/>
49+
<include name="**/plugins/Tools/resources/morph/default.rul"/>
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</patternset>
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<chainedmapper>
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<mapper type="flatten"/>
@@ -75,8 +75,8 @@
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<mkdir dir="target/download/tmp"/>
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<unzip src="target/download/gate/gate-ALL.zip" dest="target/download/tmp">
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<patternset>
78-
<include name="**/plugins/ANNIE/resources/heptag/lexicon"/>
79-
<include name="**/plugins/ANNIE/resources/heptag/ruleset"/>
78+
<include name="**/plugins/ANNIE/resources/heptag/lexicon"/>
79+
<include name="**/plugins/ANNIE/resources/heptag/ruleset"/>
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</patternset>
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<chainedmapper>
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<mapper type="flatten"/>

‎dkpro-core-io-bioc-asl/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -28,20 +28,12 @@
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<url>https://dkpro.github.io/dkpro-core/</url>
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<dependencies>
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<dependency>
31-
<groupId>javax.xml.bind</groupId>
32-
<artifactId>jaxb-api</artifactId>
31+
<groupId>jakarta.xml.bind</groupId>
32+
<artifactId>jakarta.xml.bind-api</artifactId>
3333
</dependency>
3434
<dependency>
35-
<groupId>com.sun.xml.bind</groupId>
36-
<artifactId>jaxb-core</artifactId>
37-
</dependency>
38-
<dependency>
39-
<groupId>com.sun.xml.bind</groupId>
40-
<artifactId>jaxb-impl</artifactId>
41-
</dependency>
42-
<dependency>
43-
<groupId>javax.activation</groupId>
44-
<artifactId>javax.activation-api</artifactId>
35+
<groupId>org.glassfish.jaxb</groupId>
36+
<artifactId>jaxb-runtime</artifactId>
4537
</dependency>
4638
<dependency>
4739
<groupId>org.apache.uima</groupId>

‎dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/BioCReader.java‎

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Original file line numberDiff line numberDiff line change
@@ -22,9 +22,6 @@
2222
import java.io.IOException;
2323
import java.util.Optional;
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25-
import javax.xml.bind.JAXBContext;
26-
import javax.xml.bind.JAXBException;
27-
import javax.xml.bind.Unmarshaller;
2825
import javax.xml.stream.XMLStreamException;
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import org.apache.uima.UimaContext;
@@ -40,6 +37,9 @@
4037
import org.dkpro.core.io.bioc.internal.model.BioCDocument;
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4239
import eu.openminted.share.annotations.api.DocumentationResource;
40+
import jakarta.xml.bind.JAXBContext;
41+
import jakarta.xml.bind.JAXBException;
42+
import jakarta.xml.bind.Unmarshaller;
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/**
4545
* Reader for the BioC format.

‎dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/BioCWriter.java‎

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Original file line numberDiff line numberDiff line change
@@ -19,10 +19,6 @@
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2020
import static org.dkpro.core.io.bioc.BioCComponent.getCollectionMetadataField;
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22-
import javax.xml.bind.JAXBContext;
23-
import javax.xml.bind.JAXBException;
24-
import javax.xml.bind.Marshaller;
25-
2622
import org.apache.uima.UimaContext;
2723
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
2824
import org.apache.uima.fit.descriptor.ConfigurationParameter;
@@ -39,6 +35,9 @@
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4036
import de.tudarmstadt.ukp.dkpro.core.api.metadata.type.DocumentMetaData;
4137
import eu.openminted.share.annotations.api.DocumentationResource;
38+
import jakarta.xml.bind.JAXBContext;
39+
import jakarta.xml.bind.JAXBException;
40+
import jakarta.xml.bind.Marshaller;
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4342
/**
4443
* Writer for the BioC format.
@@ -75,14 +74,17 @@ public class BioCWriter
7574
private String targetEncoding;
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7776
private JAXBContext context;
77+
private Marshaller marshaller;
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7979
@Override
8080
public void initialize(UimaContext aContext) throws ResourceInitializationException
8181
{
8282
super.initialize(aContext);
83-
8483
try {
8584
context = JAXBContext.newInstance(BioCCollection.class);
85+
marshaller = context.createMarshaller();
86+
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, indent);
87+
marshaller.setProperty(Marshaller.JAXB_ENCODING, targetEncoding);
8688
}
8789
catch (JAXBException e) {
8890
throw new ResourceInitializationException(e);
@@ -93,11 +95,6 @@ public void initialize(UimaContext aContext) throws ResourceInitializationExcept
9395
public void process(JCas aJCas) throws AnalysisEngineProcessException
9496
{
9597
try (var docOS = getOutputStream(aJCas, filenameSuffix)) {
96-
Marshaller marshaller = context.createMarshaller();
97-
marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
98-
// Set to fragment mode to omit XML declaration
99-
marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
100-
10198
var bioCCollection = new BioCCollection();
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103100
// Base-information - may be overwritten by the metadata fields below

‎dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/internal/BioCToCas.java‎

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@@ -39,8 +39,6 @@
3939
import java.util.List;
4040
import java.util.Map;
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42-
import javax.xml.bind.JAXBContext;
43-
import javax.xml.bind.JAXBException;
4442
import javax.xml.stream.XMLStreamException;
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4644
import org.apache.uima.cas.Type;
@@ -59,12 +57,14 @@
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6058
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Div;
6159
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence;
60+
import jakarta.xml.bind.JAXBContext;
61+
import jakarta.xml.bind.JAXBException;
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6363
public class BioCToCas
6464
{
6565
private static final Logger LOG = getLogger(lookup().lookupClass());
6666

67-
public void parseXml(InputStream aReader, JCas aJCas) throws JAXBException, XMLStreamException
67+
public void parseXml(InputStream aReader, JCas aJCas) throws XMLStreamException, JAXBException
6868
{
6969
var collection = loadBioCCollection(aReader);
7070

‎dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/internal/model/BioCAnnotation.java‎

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Original file line numberDiff line numberDiff line change
@@ -19,46 +19,48 @@
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2020
import java.util.List;
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22-
import javax.xml.bind.annotation.XmlAttribute;
23-
import javax.xml.bind.annotation.XmlElement;
22+
import jakarta.xml.bind.annotation.XmlAttribute;
23+
import jakarta.xml.bind.annotation.XmlElement;
24+
import jakarta.xml.bind.annotation.XmlType;
2425

26+
@XmlType(propOrder = { "locations", "text" })
2527
public class BioCAnnotation
2628
extends BioCObject
2729
{
2830
private String id;
29-
private String text;
3031
private List<BioCLocation> locations;
32+
private String text;
3133

34+
@XmlAttribute(name = "id")
3235
public String getId()
3336
{
3437
return id;
3538
}
3639

37-
@XmlAttribute(name = "id")
3840
public void setId(String aId)
3941
{
4042
id = aId;
4143
}
4244

43-
public String getText()
45+
@XmlElement(name = "location")
46+
public List<BioCLocation> getLocations()
4447
{
45-
return text;
48+
return locations;
4649
}
4750

48-
@XmlElement(name = "text")
49-
public void setText(String aText)
51+
public void setLocations(List<BioCLocation> aLocations)
5052
{
51-
text = aText;
53+
locations = aLocations;
5254
}
5355

54-
public List<BioCLocation> getLocations()
56+
@XmlElement(name = "text")
57+
public String getText()
5558
{
56-
return locations;
59+
return text;
5760
}
5861

59-
@XmlElement(name = "location")
60-
public void setLocations(List<BioCLocation> aLocations)
62+
public void setText(String aText)
6163
{
62-
locations = aLocations;
64+
text = aText;
6365
}
6466
}

‎dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/internal/model/BioCAnnotationContainer.java‎

Lines changed: 14 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -20,41 +20,24 @@
2020
import java.util.ArrayList;
2121
import java.util.List;
2222

23-
import javax.xml.bind.annotation.XmlElement;
24-
import javax.xml.bind.annotation.XmlTransient;
23+
import jakarta.xml.bind.annotation.XmlAccessType;
24+
import jakarta.xml.bind.annotation.XmlAccessorType;
25+
import jakarta.xml.bind.annotation.XmlElement;
26+
import jakarta.xml.bind.annotation.XmlType;
2527

26-
@XmlTransient
28+
@XmlAccessorType(XmlAccessType.NONE)
29+
@XmlType(propOrder = { "relations" })
2730
public abstract class BioCAnnotationContainer
2831
extends BioCObject
2932
{
30-
private List<BioCAnnotation> annotations;
3133
private List<BioCRelation> relations;
3234

33-
public List<BioCAnnotation> getAnnotations()
34-
{
35-
return annotations;
36-
}
37-
38-
@XmlElement(name = "annotation")
39-
public void setAnnotations(List<BioCAnnotation> aAnnotations)
40-
{
41-
annotations = aAnnotations;
42-
}
43-
44-
public void addAnnotation(BioCAnnotation aAnnotation)
45-
{
46-
if (annotations == null) {
47-
annotations = new ArrayList<>();
48-
}
49-
annotations.add(aAnnotation);
50-
}
51-
35+
@XmlElement(name = "relation")
5236
public List<BioCRelation> getRelations()
5337
{
5438
return relations;
5539
}
5640

57-
@XmlElement(name = "relation")
5841
public void setRelations(List<BioCRelation> aRelations)
5942
{
6043
relations = aRelations;
@@ -67,4 +50,11 @@ public void addRelation(BioCRelation aRelation)
6750
}
6851
relations.add(aRelation);
6952
}
53+
54+
// Methods for annotations - subclasses must implement
55+
public abstract List<BioCAnnotation> getAnnotations();
56+
57+
public abstract void setAnnotations(List<BioCAnnotation> aAnnotations);
58+
59+
public abstract void addAnnotation(BioCAnnotation aAnnotation);
7060
}

‎dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/internal/model/BioCCollection.java‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -25,12 +25,12 @@
2525
import java.util.ArrayList;
2626
import java.util.List;
2727

28-
import javax.xml.bind.annotation.XmlElement;
29-
import javax.xml.bind.annotation.XmlRootElement;
30-
import javax.xml.bind.annotation.XmlType;
28+
import jakarta.xml.bind.annotation.XmlElement;
29+
import jakarta.xml.bind.annotation.XmlRootElement;
30+
import jakarta.xml.bind.annotation.XmlType;
3131

3232
@XmlRootElement(name = "collection")
33-
@XmlType(propOrder = { "source", "date", "key", "infons", "documents" })
33+
@XmlType(propOrder = { "source", "date", "key", "documents" })
3434
public class BioCCollection
3535
extends BioCObject
3636
{
@@ -39,45 +39,45 @@ public class BioCCollection
3939
private String key;
4040
private List<BioCDocument> documents;
4141

42+
@XmlElement(name = E_SOURCE)
4243
public String getSource()
4344
{
4445
return source;
4546
}
4647

47-
@XmlElement(name = E_SOURCE)
4848
public void setSource(String aSource)
4949
{
5050
source = aSource;
5151
}
5252

53+
@XmlElement(name = E_DATE)
5354
public String getDate()
5455
{
5556
return date;
5657
}
5758

58-
@XmlElement(name = E_DATE)
5959
public void setDate(String aDate)
6060
{
6161
date = aDate;
6262
}
6363

64+
@XmlElement(name = E_KEY)
6465
public String getKey()
6566
{
6667
return key;
6768
}
6869

69-
@XmlElement(name = E_KEY)
7070
public void setKey(String aKey)
7171
{
7272
key = aKey;
7373
}
7474

75+
@XmlElement(name = E_DOCUMENT)
7576
public List<BioCDocument> getDocuments()
7677
{
7778
return documents;
7879
}
7980

80-
@XmlElement(name = E_DOCUMENT)
8181
public void setDocuments(List<BioCDocument> aDocuments)
8282
{
8383
documents = aDocuments;

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