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kopporSiedlerchrInAnYan
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Initial framework for jablib-examples (#14233)
* Initial framework for jablib-examples * Rename "serializeAll" to "writeAll" * Add some `@NonNull` annotations * Even more consistent * More renamings * Add convenience constructor * Add some nullable annotations * Add cross-links * Fix typo * Fix class name * Have BibliographyFromPdfImporter implementing PlainCitationParser * Add "IEEE" as another rule option * Fix method name (and visibility) * Compilefix * Fix casing in BibTeX * Enable LLM to be used to parse references * Refine code - BibliographyFromPdfImporter is also an PdfImporter - importDatabase returns ParserResult (for consistency) * Move pdf related importers to pdf sub package * Initial PdfImporterWithPlainCitationParser * WIP: ieee_pdf_references_to_bibtex * Add link to CHANGELOG.md * Refine PlainCitationParser interface * Move methods to PdfUtils * Make LlmPlainCitationParser a real importer (and fix BibligraphyFromPdfImporter method use) * Add missing class * Wire all availble importers * Rename BibliographyFromPdfImporter to RuleBasedBibliographyPdfImporter * Introdue intermediate class BibliographyFromPdfImporter * Fix PdfGrobitImporter (to really extract the references) * Add comment * Fix JavaFX graphics dependency in ProgressCounter * Remove routing method * Remove obsolete test file * Add development hint to README.md * First version of to BibTeX conversion * Adapt test to new behavior * Apply format * Fix NullAway warning * Fix Moderinzer * Refine checkstyle supressions * Fix typo * Use release version of action-checkstyle * Move complete file ignores to checkstyle.xml * Also run if jbang scripts themselves have changed * Add link * Update checkstyle version in checkstyle-idea.xml * Remove obsolete comment * Apply suggestions from code review Co-authored-by: Ruslan <[email protected]> * Fix checkstyle * Increase IntelliJ version * Switch to other formatter * Fix checkstyle * Fix reference * Apply renaming also in script * Fix jbang build command (double .java) * Workaround for formatter issue * Switch back to other formatter (better output) * Remove one more ".java" * Try to list all files * Rename "simple" to "general" * Debug: output modified files * Add missing } * Try other way for debugging * Ohter debug * Fix debug * Fix copy and paste error * Output script * Remove obsolete ".java" * Remove debug * Remove "build" * Fix source adaption * Refine tests * Better grouping --------- Co-authored-by: Christoph <[email protected]> Co-authored-by: Ruslan <[email protected]>
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‎.github/workflows/binaries.yml‎

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@@ -50,7 +50,7 @@ jobs:
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upload-to-builds-jabref-org: ${{ steps.binary.outputs.upload-to-builds-jabref-org }}
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secretspresent: ${{ steps.binary.outputs.secretspresent }}
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tagbuild: ${{ steps.binary.outputs.tagbuild }}
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# requried to avoid obsolete builds in case of labels != "dev: binaries"
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# required to avoid obsolete builds in case of labels != "dev: binaries"
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should-build: ${{ steps.binary.outputs.should-build }}
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should-notarize: ${{ steps.binary.outputs.should-notarize }}
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‎.github/workflows/tests-code.yml‎

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@@ -56,7 +56,7 @@ jobs:
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distribution: 'corretto'
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check-latest: true
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- name: Run checkstyle reporter
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uses: dbelyaev/action-checkstyle@master
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uses: dbelyaev/action-checkstyle@v3
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with:
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reporter: github-pr-review
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github_token: ${{ secrets.GITHUB_TOKEN }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5
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- uses: koppor/intellij-idea-format@update-to-latest-intellij
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- uses: leventeBajczi/intellij-idea-format@master
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with:
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file-mask: "*.java"
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settings-file: ".idea/codeStyles/Project.xml"
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with:
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submodules: 'false'
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show-progress: 'false'
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- name: Detect changed jablib classes
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id: changed-jablib-files
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uses: tj-actions/changed-files@v47
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with:
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files: |
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.jbang/*.java
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jablib/src/main/java/**/*.java
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jablib-examples/**/*.java
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files_ignore: |
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jablib/src/main/java/**/*-*.java
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- name: Set up JDK
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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uses: actions/setup-java@v5
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with:
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java-version: 24
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distribution: 'corretto'
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check-latest: true
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- name: Generate JBang cache key
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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id: cache-key
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shell: bash
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run: |
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restore-keys:
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jbang-
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- name: Setup JBang
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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uses: jbangdev/setup-jbang@main
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# Build all JBang scripts
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- run: jbang build .jbang/CheckoutPR.java
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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- run: jbang build .jbang/CloneJabRef.java
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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- run: jbang build --fresh .jbang/JabKitLauncher.java
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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- run: jbang build --fresh .jbang/JabLsLauncher.java
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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- run: jbang build --fresh .jbang/JabSrvLauncher.java
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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- run: jbang build --fresh jablib-examples/*.java
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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# *Launcher.java should support "--help"
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- run: jbang run .jbang/JabKitLauncher.java --help
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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- run: jbang run .jbang/JabLsLauncher.java --help
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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- run: jbang run .jbang/JabSrvLauncher.java --help
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if: steps.changed-jablib-files.outputs.any_changed != 'true'
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jbang-pr:
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name: JBang (PR)
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strategy:
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fail-fast: false
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matrix:
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launcher: [JabKitLauncher, JabLsLauncher, JabSrvLauncher]
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script: [.jbang/JabKitLauncher.java, .jbang/JabLsLauncher.java, .jbang/JabSrvLauncher.java, jablib-examples/ieee_pdf_references_to_bibtex.java]
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steps:
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- name: Checkout source
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uses: actions/checkout@v5
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with:
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submodules: 'false'
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show-progress: 'false'
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- name: Detect changed jablib classes
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id: changed-jablib-files
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uses: tj-actions/changed-files@v47
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with:
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files: |
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.jbang/*.java
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jablib/src/main/java/**/*.java
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jablib-examples/**/*.java
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files_ignore: |
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jablib/src/main/java/**/*-*.java
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- name: Set up JDK
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uses: actions/setup-java@v5
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with:
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jbang-
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- name: Setup JBang
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uses: jbangdev/setup-jbang@main
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- name: Detect changed jablib classes
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id: changed-jablib-files
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uses: tj-actions/changed-files@v47
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with:
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files: |
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jablib/src/main/java/**/*.java
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files_ignore: |
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jablib/src/main/java/**/*-*.java
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- name: Build ${{ matrix.launcher }} launcher including changed classes
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- name: Modify ${{ matrix.script }} to include changed classes
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shell: bash
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# We always run, because changes in jabls, jabsrv also could cause JBang to fail
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run: |
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# We modify the JBang scripts directly to avoid issues with relative paths
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for f in ${{ steps.changed-jablib-files.outputs.all_changed_files }}; do
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echo "//SOURCES ../$f" >> ".jbang/${{ matrix.launcher }}.java"
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case "$f" in
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jablib-examples/*) continue ;; # skip scripts
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esac
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echo "//SOURCES ../$f" >> "${{ matrix.script }}"
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done
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jbang build --fresh ".jbang/${{ matrix.launcher }}.java"
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- run: jbang ".jbang/${{ matrix.launcher }}.java" --help
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- run: jbang build "${{ matrix.script }}"
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shell: bash
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- run: jbang "${{ matrix.script }}" --help
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if: ${{ contains(matrix.script, 'Launcher.java') }}
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shell: bash
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codecoverage:

‎.idea/checkstyle-idea.xml‎

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‎CHANGELOG.md‎

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@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
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### Added
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- We added "IEEE" as another option for parsing plain text citations. [#14233](github.com/JabRef/jabref/pull/14233)
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- We added automatic date-based groups that create year/month/day subgroups from an entry’s date fields. [#10822](https://github.com/JabRef/jabref/issues/10822)
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### Changed

‎config/checkstyle/checkstyle.xml‎

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<module name="Checker">
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<property name="charset" value="UTF-8"/>
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<module name="Header">
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<property name="header" value=""/>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]\.idea[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]\.jbang[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]build-support[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]generated(-sources|-src)?[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]jablib-examples[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]src-gen[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<!-- We ignore this file because it's a modification of the original java code https://github.com/openjdk/jfx/blob/jfx15/modules/javafx.controls/src/main/java/javafx/scene/control/skin/TitledPaneSkin.java -->
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<property name="fileNamePattern" value="CustomTitledPaneSkin\.java$" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="module\-info\.java$"/>
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</module>
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<module name="SuppressionFilter">
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<property name="file" value="${config_loc}/suppressions.xml"/>
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="module\-info\.java$"/>
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<module name="Header">
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<property name="header" value=""/>
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</module>
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<module name="FileTabCharacter"/>

‎config/checkstyle/checkstyle_reviewdog.xml‎

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<module name="Checker">
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<property name="charset" value="UTF-8"/>
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<module name="Header">
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<property name="header" value=""/>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]\.idea[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]\.jbang[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]build-support[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]generated(-sources|-src)?[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]jablib-examples[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="[/\\]src-gen[/\\]" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<!-- We ignore this file because it's a modification of the original java code https://github.com/openjdk/jfx/blob/jfx15/modules/javafx.controls/src/main/java/javafx/scene/control/skin/TitledPaneSkin.java -->
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<property name="fileNamePattern" value="CustomTitledPaneSkin\.java$" />
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="(module\-info|heylogs)\.java$"/>
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</module>
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<module name="SuppressionFilter">
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<property name="file" value="config/checkstyle/suppressions.xml"/>
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</module>
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<module name="BeforeExecutionExclusionFileFilter">
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<property name="fileNamePattern" value="(module\-info|heylogs)\.java$"/>
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<module name="Header">
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<property name="header" value=""/>
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<module name="FileTabCharacter"/>

‎config/checkstyle/suppressions.xml‎

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"http://www.checkstyle.org/dtds/suppressions_1_1.dtd">
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<suppressions>
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<suppress checks="[a-zA-Z0-9]*" files="[\\/].jbang[\\/]" />
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<suppress checks="[a-zA-Z0-9]*" files="[\\/]build-support[\\/]" />
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<suppress checks="[a-zA-Z0-9]*" files="[\\/]generated[\\/]" />
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<suppress checks="[a-zA-Z0-9]*" files="[\\/]generated-sources[\\/]" />
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<suppress checks="[a-zA-Z0-9]*" files="[\\/]generated-src[\\/]" />
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<suppress checks="[a-zA-Z0-9]*" files="[\\/]src-gen[\\/]" />
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<suppress checks="[a-zA-Z0-9]*" files="[\\/].idea[\\/]" />
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<!-- We ignore this file because it's a modification of the original java code https://github.com/openjdk/jfx/blob/jfx15/modules/javafx.controls/src/main/java/javafx/scene/control/skin/TitledPaneSkin.java -->
16-
<suppress checks="[a-zA-Z0-9]*" files="CustomTitledPaneSkin.java" />
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<!-- Following contain examples or comments with "}}" that are necessary -->
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<suppress id="NoMultipleClosingBracesAtEndOfLine" files="(BibtexParserTest|StringUtil).java" />
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</suppressions>

‎jabgui/src/main/java/org/jabref/gui/ClipBoardManager.java‎

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@@ -168,6 +168,6 @@ private String serializeEntries(List<BibEntry> entries, BibEntryTypesManager ent
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// At reading of the clipboard in JabRef, we parse the plain string in all cases, so we don't need to flag we put BibEntries here
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// Furthermore, storing a string also enables other applications to work with the data
170170
BibEntryWriter writer = new BibEntryWriter(new FieldWriter(preferences.getFieldPreferences()), entryTypesManager);
171-
return writer.serializeAll(entries, BibDatabaseMode.BIBTEX);
171+
return writer.write(entries, BibDatabaseMode.BIBTEX);
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}
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}

‎jabgui/src/main/java/org/jabref/gui/autosaveandbackup/BackupManager.java‎

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@@ -285,7 +285,7 @@ void performBackup(Path backupPath) {
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preferences.getCitationKeyPatternPreferences(),
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entryTypesManager)
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// we save the clone to prevent the original database (and thus the UI) from being changed
288-
.saveDatabase(bibDatabaseContextClone);
288+
.writeDatabase(bibDatabaseContextClone);
289289
backupFilesQueue.add(backupPath);
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// We wrote the file successfully

‎jabgui/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java‎

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import org.jabref.logic.help.HelpFile;
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import org.jabref.logic.importer.EntryBasedFetcher;
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import org.jabref.logic.importer.WebFetchers;
63-
import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
63+
import org.jabref.logic.importer.fileformat.pdf.PdfMergeMetadataImporter;
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import org.jabref.logic.journals.JournalAbbreviationRepository;
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import org.jabref.logic.util.BuildInfo;
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import org.jabref.logic.util.TaskExecutor;

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