#1602 - Upgrade dependencies

[reckart]

What's in the PR

• corenlp 4.5.7 -> 4.5.10
• gate 8.6.1 -> 9.0.1
• annie 8.6 -> 9.1
• gate-tools 8.6 -> 9.0.1
• jsoup 1.21.2 -> 1.22.1
• solr-solrj 9.6.1 -> 9.10.0
• jaxen 1.2.0 -> 2.0.0
• jakarta.xml.bind-api 4.0.2 -> 4.0.4
• dkpro-parent-pom 32 -> 34

How to test manually

• No specific test procedure

Automatic testing

• PR includes unit tests

Documentation

• PR updates documentation

[Copilot]

Pull request overview

This PR upgrades multiple dependencies and refactors the BioC and XCES modules to use Jackson instead of JAXB for XML processing.

Key Changes:

• Upgraded parent POM (dkpro-parent-pom 32 → 34) and multiple library versions (CoreNLP, GATE, jsoup, Solr, jaxen, jakarta.xml.bind-api)
• Migrated BioC and XCES modules from JAXB to Jackson for XML serialization/deserialization
• Updated license headers to new format across XCES module files

Reviewed changes

Copilot reviewed 35 out of 36 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
pom.xml	Upgraded dkpro-parent-pom from version 32 to 34
dkpro-core-parent-common/pom.xml	Updated jaxen (1.2.0 → 2.0.0) and jakarta.xml.bind-api (4.0.2 → 4.0.4) versions
dkpro-core-io-xces-asl/pom.xml	Replaced JAXB dependencies with Jackson databind and dataformat-xml
dkpro-core-io-xces-asl/src/main/java/org/dkpro/core/io/xces/models/*.java	Replaced JAXB annotations with Jackson XML annotations in model classes
dkpro-core-io-xces-asl/src/main/java/org/dkpro/core/io/xces/XcesXmlReader.java	Migrated from JAXB Unmarshaller to Jackson XmlMapper with XMLStreamReader
dkpro-core-io-xces-asl/src/main/java/org/dkpro/core/io/xces/XcesBasicXmlReader.java	Migrated from JAXB Unmarshaller to Jackson XmlMapper with XMLStreamReader
dkpro-core-io-xces-asl/src/main/java/org/dkpro/core/io/xces/XcesXmlWriter.java	Migrated from JAXB Marshaller to Jackson XmlMapper with string-based intermediate serialization
dkpro-core-io-xces-asl/src/main/java/org/dkpro/core/io/xces/XcesBasicXmlWriter.java	Migrated from JAXB Marshaller to Jackson XmlMapper with string-based intermediate serialization
dkpro-core-io-xces-asl/src/test/java/org/dkpro/core/io/xces/*.java	Updated license headers and modernized test code with var declarations and static imports
dkpro-core-io-bioc-asl/pom.xml	Replaced JAXB dependencies with Jackson databind, annotations, and dataformat-xml
dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/internal/model/*.java	Replaced JAXB annotations with Jackson XML annotations in model classes
dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/BioCReader.java	Migrated from JAXB to Jackson with StringWriter-based intermediate parsing
dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/BioCWriter.java	Migrated from JAXB to Jackson with custom indentation handling via regex
dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/internal/BioCToCas.java	Updated to use Jackson XmlMapper with StringWriter-based parsing approach
dkpro-core-io-solr-asl/pom.xml	Updated solr-solrj from 9.6.1 to 9.10.0
dkpro-core-io-html-asl/pom.xml	Updated jsoup from 1.21.2 to 1.22.1
dkpro-core-gate-asl/pom.xml	Updated GATE (8.6.1 → 9.0.1), ANNIE (8.6 → 9.1), and tools (8.6 → 9.0.1) versions
dkpro-core-gate-asl/src/scripts/build.xml	Removed trailing whitespace from XML pattern includes
dkpro-core-corenlp-gpl/pom.xml	Updated CoreNLP from 4.5.7 to 4.5.10

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[Copilot]

Pull request overview

Copilot reviewed 37 out of 39 changed files in this pull request and generated 6 comments.

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Pull request overview

Copilot reviewed 37 out of 39 changed files in this pull request and generated 5 comments.

Comments suppressed due to low confidence (1)

dkpro-core-io-bioc-asl/src/main/java/org/dkpro/core/io/bioc/BioCWriter.java:114

• The Marshaller is now created once during initialization and reused across all process() calls. However, Marshaller instances are not thread-safe. If this component can be called concurrently from multiple threads, reusing the same Marshaller instance could lead to race conditions and corrupted output. Consider creating a new Marshaller instance for each process() call, or ensure this component is only used in single-threaded contexts.

    private Marshaller marshaller;

    @Override
    public void initialize(UimaContext aContext) throws ResourceInitializationException
    {
        super.initialize(aContext);
        try {
            context = JAXBContext.newInstance(BioCCollection.class);
            marshaller = context.createMarshaller();
            marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, indent);
            marshaller.setProperty(Marshaller.JAXB_ENCODING, targetEncoding);
        }
        catch (JAXBException e) {
            throw new ResourceInitializationException(e);
        }
    }

    @Override
    public void process(JCas aJCas) throws AnalysisEngineProcessException
    {
        try (var docOS = getOutputStream(aJCas, filenameSuffix)) {
            var bioCCollection = new BioCCollection();

            // Base-information - may be overwritten by the metadata fields below
            var dmd = DocumentMetaData.get(aJCas);
            bioCCollection.setSource(dmd.getCollectionId());

            // Use BioC metadata fields if available
            getCollectionMetadataField(aJCas.getCas(), E_SOURCE)
                    .ifPresent($ -> bioCCollection.setSource($.getValue()));
            getCollectionMetadataField(aJCas.getCas(), E_KEY)
                    .ifPresent($ -> bioCCollection.setKey($.getValue()));
            getCollectionMetadataField(aJCas.getCas(), E_DATE)
                    .ifPresent($ -> bioCCollection.setDate($.getValue()));

            new CasToBioC().convert(aJCas, bioCCollection);

            marshaller.marshal(bioCCollection, docOS);

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Pull request overview

Copilot reviewed 37 out of 39 changed files in this pull request and generated no new comments.

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