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Siedlerchrkoppor
Siedlerchr
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koppor
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Convert to jackson 3 (#14259)
* convert to jackson 3 * checkstyle * checkstyle * fix jbang and checkstlye * fix typo * fix jbang * fix jbang * fix jbang * fix jbang * fix artifat id * add jackson annotations * fix imports * fix imports * Add debug * fix imports * add jackson deps to jbang * fix import * fix imports * reveRT CSL CHANGE * fix imports * add to example * cahnge mscocde utils * fix lsp import * ad jackson annotaitons * ad jackson annotaitons * Try to fix .. * Fix variable --------- Co-authored-by: Oliver Kopp <[email protected]>
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‎.github/workflows/tests-code.yml‎

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@@ -576,6 +576,7 @@ jobs:
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echo "//SOURCES ../../$f" >> "${{ matrix.script }}"
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fi
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done
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- run: cat ${{ matrix.script }}
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- run: jbang build "${{ matrix.script }}"
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shell: bash
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- run: jbang "${{ matrix.script }}" --help

‎.jbang/JabLsLauncher.java‎

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//DEPS org.jspecify:jspecify:1.0.0
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// from jabls
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//DEPS com.fasterxml.jackson.core:jackson-databind:2.20.1
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//DEPS com.fasterxml.jackson.core:jackson-annotations:2.20
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//DEPS tools.jackson.core:jackson-core:3.0.2
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//DEPS tools.jackson.core:jackson-databind:3.0.2
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//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
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//DEPS info.picocli:picocli:4.7.7
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//DEPS org.apache.logging.log4j:log4j-to-slf4j:2.25.2
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//DEPS org.eclipse.lsp4j:org.eclipse.lsp4j:0.24.0

‎.jbang/JabSrvLauncher.java‎

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//DEPS org.jabref:afterburner.fx:2.0.0
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//DEPS net.harawata:appdirs:1.5.0
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//DEPS de.undercouch:citeproc-java:3.4.0
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//DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
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//DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
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//DEPS tools.jackson.core:jackson-core:3.0.2
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//DEPS tools.jackson.core:jackson-databind:3.0.2
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//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
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//DEPS org.apache.commons:commons-lang3:3.20.0
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/// This class is required for [jbang](https://www.jbang.dev/)

‎jablib-examples/jbang/ieee_pdf_references_to_bibtex.java‎

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//DEPS org.jabref:jablib:6.0-SNAPSHOT
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// JabRef relies on PR https://github.com/unicode-org/icu/pull/2127; for experiments the release version is OK.
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//DEPS com.ibm.icu:icu4j:78.1
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//DEPS com.fasterxml.jackson.core:jackson-annotations:2.20
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//DEPS tools.jackson.core:jackson-core:3.0.2
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//DEPS tools.jackson.core:jackson-databind:3.0.2
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//DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
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void main() throws Exception {
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var preferences = JabRefCliPreferences.getInstance();

‎jablib/build.gradle.kts‎

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@@ -103,8 +103,8 @@ dependencies {
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implementation("org.eclipse.jgit:org.eclipse.jgit")
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implementation("com.fasterxml.jackson.dataformat:jackson-dataformat-yaml")
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implementation("com.fasterxml.jackson.datatype:jackson-datatype-jsr310")
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implementation("tools.jackson.dataformat:jackson-dataformat-yaml")
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implementation("tools.jackson.core:jackson-databind")
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// TODO: Somwewhere we get a warning: unknown enum constant Id.CLASS reason: class file for com.fasterxml.jackson.annotation.JsonTypeInfo$Id not found
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// implementation("com.fasterxml.jackson.core:jackson-annotations:2.19.1")
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‎jablib/src/main/java/module-info.java‎

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// region: data mapping
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requires jdk.xml.dom;
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requires com.google.gson;
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requires com.fasterxml.jackson.databind;
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requires com.fasterxml.jackson.dataformat.yaml;
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requires com.fasterxml.jackson.datatype.jsr310;
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requires tools.jackson.databind;
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requires tools.jackson.dataformat.yaml;
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requires tools.jackson.core;
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// endregion
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// region HTTP clients

‎jablib/src/main/java/org/jabref/logic/citationstyle/CSLStyleLoader.java‎

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import org.jabref.logic.openoffice.OpenOfficePreferences;
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import com.fasterxml.jackson.core.type.TypeReference;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import org.jspecify.annotations.NonNull;
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import org.jspecify.annotations.Nullable;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import tools.jackson.core.type.TypeReference;
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import tools.jackson.databind.ObjectMapper;
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/**
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* Manages the loading of CitationStyles from both internal resources and external files.

‎jablib/src/main/java/org/jabref/logic/crawler/StudyYamlParser.java‎

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import org.jabref.model.study.Study;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
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import com.fasterxml.jackson.dataformat.yaml.YAMLGenerator;
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import tools.jackson.databind.ObjectMapper;
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import tools.jackson.dataformat.yaml.YAMLFactory;
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import tools.jackson.dataformat.yaml.YAMLMapper;
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import tools.jackson.dataformat.yaml.YAMLWriteFeature;
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/**
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* Example use: <code>new StudyYamlParser().parseStudyYamlFile(studyDefinitionFile);</code>
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* Writes the given study instance into a yaml file to the given path
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*/
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public void writeStudyYamlFile(Study study, Path studyYamlFile) throws IOException {
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ObjectMapper yamlMapper = new ObjectMapper(new YAMLFactory().disable(YAMLGenerator.Feature.WRITE_DOC_START_MARKER)
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.enable(YAMLGenerator.Feature.MINIMIZE_QUOTES));
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ObjectMapper yamlMapper = new YAMLMapper(YAMLFactory.builder()
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.disable(YAMLWriteFeature.WRITE_DOC_START_MARKER)
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.enable(YAMLWriteFeature.MINIMIZE_QUOTES).build());
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yamlMapper.writeValue(studyYamlFile.toFile(), study);
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}
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}

‎jablib/src/main/java/org/jabref/logic/importer/fileformat/CffImporter.java‎

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import com.fasterxml.jackson.annotation.JsonAnySetter;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
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import com.google.common.collect.HashBiMap;
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import org.jspecify.annotations.NonNull;
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import tools.jackson.core.JacksonException;
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import tools.jackson.databind.ObjectMapper;
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import tools.jackson.dataformat.yaml.YAMLFactory;
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import tools.jackson.dataformat.yaml.YAMLMapper;
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public class CffImporter extends Importer {
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@Override
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public ParserResult importDatabase(@NonNull BufferedReader reader) throws IOException {
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ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
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ObjectMapper mapper = new YAMLMapper(new YAMLFactory());
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CffFormat citation = mapper.readValue(reader, CffFormat.class);
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List<BibEntry> entriesList = new ArrayList<>();
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@Override
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public boolean isRecognizedFormat(@NonNull BufferedReader reader) throws IOException {
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ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
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ObjectMapper mapper = new YAMLMapper(new YAMLFactory());
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CffFormat citation;
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try {
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citation = mapper.readValue(reader, CffFormat.class);
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return (citation != null) && (citation.values.get("title") != null);
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} catch (IOException e) {
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} catch (JacksonException e) {
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return false;
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}
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}

‎jablib/src/main/java/org/jabref/logic/util/MscCodeUtils.java‎

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import org.jabref.logic.shared.exception.MscCodeLoadingException;
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import com.fasterxml.jackson.core.JsonParseException;
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import com.fasterxml.jackson.core.type.TypeReference;
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import com.fasterxml.jackson.databind.JsonMappingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.HashBiMap;
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import org.jspecify.annotations.NonNull;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import tools.jackson.core.exc.StreamReadException;
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import tools.jackson.core.type.TypeReference;
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import tools.jackson.databind.DatabindException;
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import tools.jackson.databind.ObjectMapper;
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import tools.jackson.databind.json.JsonMapper;
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public class MscCodeUtils {
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private static final Logger LOGGER = LoggerFactory.getLogger(MscCodeUtils.class);
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@NonNull
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public static Optional<HashBiMap<String, String>> loadMscCodesFromJson(URL resourceUrl) throws MscCodeLoadingException {
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ObjectMapper mapper = new ObjectMapper();
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ObjectMapper mapper = new JsonMapper();
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try {
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Map<String, String> mapping =
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mapper.readValue(resourceUrl, new TypeReference<>() {
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mapper.readValue(resourceUrl.openStream(), new TypeReference<>() {
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});
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HashBiMap<String, String> result = HashBiMap.create(mapping);
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}
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return Optional.of(result);
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} catch (JsonParseException | JsonMappingException e) {
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} catch (StreamReadException | DatabindException e) {
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LOGGER.error("Error parsing MSC codes from JSON", e);
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throw new MscCodeLoadingException("Failed to parse MSC codes from JSON", e);
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} catch (IOException e) {

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