Initial framework for jablib-examples

.github/workflows/binaries.yml

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

.github/workflows/tests-code.yml

@@ -56,7 +56,7 @@ jobs:
           distribution: 'corretto'
           check-latest: true
       - name: Run checkstyle reporter
-        uses: dbelyaev/action-checkstyle@master
+        uses: dbelyaev/action-checkstyle@v3
         with:
           reporter: github-pr-review
           github_token: ${{ secrets.GITHUB_TOKEN }}
@@ -119,7 +119,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-      - uses: koppor/intellij-idea-format@update-to-latest-intellij
+      - uses: leventeBajczi/intellij-idea-format@master
         with:
           file-mask: "*.java"
           settings-file: ".idea/codeStyles/Project.xml"
@@ -438,13 +438,25 @@ jobs:
         with:
           submodules: 'false'
           show-progress: 'false'
+      - name: Detect changed jablib classes
+        id: changed-jablib-files
+        uses: tj-actions/changed-files@v47
+        with:
+          files: |
+            .jbang/*.java
+            jablib/src/main/java/**/*.java
+            jablib-examples/**/*.java
+          files_ignore: |
+            jablib/src/main/java/**/*-*.java
       - name: Set up JDK
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
         uses: actions/setup-java@v5
         with:
           java-version: 24
           distribution: 'corretto'
           check-latest: true
       - name: Generate JBang cache key
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
         id: cache-key
         shell: bash
         run: |
@@ -457,15 +469,26 @@ jobs:
           restore-keys:
             jbang-
       - name: Setup JBang
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
         uses: jbangdev/setup-jbang@main
       - run: jbang build .jbang/CheckoutPR.java
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: jbang build .jbang/CloneJabRef.java
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: jbang build --fresh .jbang/JabKitLauncher.java
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: jbang build --fresh .jbang/JabLsLauncher.java
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: jbang build --fresh .jbang/JabSrvLauncher.java
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
+      - run: jbang build --fresh jablib-examples/*.java
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: jbang run .jbang/JabKitLauncher.java --help
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: jbang run .jbang/JabLsLauncher.java --help
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
       - run: jbang run .jbang/JabSrvLauncher.java --help
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
 
   jbang-pr:
     name: JBang (PR)
@@ -475,13 +498,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        launcher: [JabKitLauncher, JabLsLauncher, JabSrvLauncher]
+        script: [.jbang/JabKitLauncher.java, .jbang/JabLsLauncher.java, .jbang/JabSrvLauncher.java, jablib-examples/ieee_pdf_references_to_bibtex.java]
     steps:
       - name: Checkout source
         uses: actions/checkout@v5
         with:
           submodules: 'false'
           show-progress: 'false'
+      - name: Detect changed jablib classes
+        id: changed-jablib-files
+        uses: tj-actions/changed-files@v47
+        with:
+          files: |
+            .jbang/*.java
+            jablib/src/main/java/**/*.java
+            jablib-examples/**/*.java
+          files_ignore: |
+            jablib/src/main/java/**/*-*.java
+          base_sha: ${{ github.event.pull_request.base.sha }
+          write_output_files: true
+      - run: cat .github/outputs/*.txt
       - name: Set up JDK
         uses: actions/setup-java@v5
         with:
@@ -502,24 +538,16 @@ jobs:
             jbang-
       - name: Setup JBang
         uses: jbangdev/setup-jbang@main
-      - name: Detect changed jablib classes
-        id: changed-jablib-files
-        uses: tj-actions/changed-files@v47
-        with:
-          files: |
-            jablib/src/main/java/**/*.java
-          files_ignore: |
-            jablib/src/main/java/**/*-*.java
-      - name: Build ${{ matrix.launcher }} launcher including changed classes
+      - name: Build ${{ matrix.script }} including changed classes
         shell: bash
         # We always run, because changes in jabls, jabsrv also could cause JBang to fail
         run: |
           # We modify the JBang scripts directly to avoid issues with relative paths
           for f in ${{ steps.changed-jablib-files.outputs.all_changed_files }}; do
-            echo "//SOURCES ../$f" >> ".jbang/${{ matrix.launcher }}.java"
+            echo "//SOURCES ../$f" >> "${{ matrix.script }}.java"
           done
-          jbang build --fresh ".jbang/${{ matrix.launcher }}.java"
-      - run: jbang ".jbang/${{ matrix.launcher }}.java" --help
+          jbang build --fresh "${{ matrix.script }}"
+      - run: jbang "${{ matrix.script }}" --help
         shell: bash
 
   codecoverage:

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added "IEEE" as another option for parsing plain text citations. [#14233](github.com/JabRef/jabref/pull/14233)
 - 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)
 
 ### Changed

config/checkstyle/checkstyle.xml

@@ -6,16 +6,38 @@
 <module name="Checker">
     <property name="charset" value="UTF-8"/>
 
-    <module name="Header">
-        <property name="header" value=""/>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]\.idea[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]\.jbang[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]build-support[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]generated(-sources|-src)?[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]jablib-examples[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]src-gen[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <!-- 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 -->
+        <property name="fileNamePattern" value="CustomTitledPaneSkin\.java$" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="module\-info\.java$"/>
     </module>
 
     <module name="SuppressionFilter">
         <property name="file" value="${config_loc}/suppressions.xml"/>
     </module>
 
-    <module name="BeforeExecutionExclusionFileFilter">
-        <property name="fileNamePattern" value="module\-info\.java$"/>
+    <module name="Header">
+        <property name="header" value=""/>
     </module>
 
     <module name="FileTabCharacter"/>

config/checkstyle/checkstyle_reviewdog.xml

@@ -6,16 +6,38 @@
 <module name="Checker">
     <property name="charset" value="UTF-8"/>
 
-    <module name="Header">
-        <property name="header" value=""/>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]\.idea[/\\]" />
     </module>
-
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]\.jbang[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]build-support[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]generated(-sources|-src)?[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]jablib-examples[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="[/\\]src-gen[/\\]" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <!-- 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 -->
+        <property name="fileNamePattern" value="CustomTitledPaneSkin\.java$" />
+    </module>
+    <module name="BeforeExecutionExclusionFileFilter">
+        <property name="fileNamePattern" value="(module\-info|heylogs)\.java$"/>
+    </module>
+
     <module name="SuppressionFilter">
         <property name="file" value="config/checkstyle/suppressions.xml"/>
     </module>
 
-    <module name="BeforeExecutionExclusionFileFilter">
-        <property name="fileNamePattern" value="(module\-info|heylogs)\.java$"/>
+    <module name="Header">
+        <property name="header" value=""/>
     </module>
 
     <module name="FileTabCharacter"/>

config/checkstyle/suppressions.xml

@@ -5,15 +5,6 @@
         "http://www.checkstyle.org/dtds/suppressions_1_1.dtd">
 
 <suppressions>
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/].jbang[\\/]" />
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/]build-support[\\/]" />
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/]generated[\\/]" />
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/]generated-sources[\\/]" />
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/]generated-src[\\/]" />
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/]src-gen[\\/]" />
-    <suppress checks="[a-zA-Z0-9]*" files="[\\/].idea[\\/]" />
-    <!-- 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 -->
-    <suppress checks="[a-zA-Z0-9]*" files="CustomTitledPaneSkin.java" />
     <!-- Following contain examples or comments with "}}" that are necessary -->
     <suppress id="NoMultipleClosingBracesAtEndOfLine" files="(BibtexParserTest|StringUtil).java" />
 </suppressions>

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

@@ -168,6 +168,6 @@ private String serializeEntries(List<BibEntry> entries, BibEntryTypesManager ent
         // 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
         // Furthermore, storing a string also enables other applications to work with the data
         BibEntryWriter writer = new BibEntryWriter(new FieldWriter(preferences.getFieldPreferences()), entryTypesManager);
-        return writer.serializeAll(entries, BibDatabaseMode.BIBTEX);
+        return writer.write(entries, BibDatabaseMode.BIBTEX);
     }
 }

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

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

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

@@ -60,7 +60,7 @@
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.EntryBasedFetcher;
 import org.jabref.logic.importer.WebFetchers;
-import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
+import org.jabref.logic.importer.fileformat.pdf.PdfMergeMetadataImporter;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.logic.util.TaskExecutor;

jabgui/src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -271,9 +271,9 @@ private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding,
                         entryTypesManager);
 
                 if (selectedOnly) {
-                    databaseWriter.savePartOfDatabase(bibDatabaseContext, libraryTab.getSelectedEntries());
+                    databaseWriter.writePartOfDatabase(bibDatabaseContext, libraryTab.getSelectedEntries());
                 } else {
-                    databaseWriter.saveDatabase(bibDatabaseContext);
+                    databaseWriter.writeDatabase(bibDatabaseContext);
                 }
 
                 libraryTab.registerUndoableChanges(databaseWriter.getSaveActionsFieldChanges());

jabgui/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java

@@ -37,7 +37,7 @@
 import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fileformat.BibtexParser;
-import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
+import org.jabref.logic.importer.fileformat.pdf.PdfMergeMetadataImporter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLDownload;
 import org.jabref.logic.util.BackgroundTask;

jabgui/src/main/java/org/jabref/gui/importer/ImportCommand.java

@@ -23,8 +23,8 @@
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.Importer;
 import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
 import org.jabref.logic.importer.fileformat.pdf.PdfGrobidImporter;
+import org.jabref.logic.importer.fileformat.pdf.PdfMergeMetadataImporter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.BackgroundTask;

jabgui/src/main/java/org/jabref/gui/maintable/ExtractReferencesAction.java

@@ -15,7 +15,7 @@
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.importer.ImportEntriesDialog;
 import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.importer.fileformat.BibliographyFromPdfImporter;
+import org.jabref.logic.importer.fileformat.pdf.RuleBasedBibliographyPdfImporter;
 import org.jabref.logic.importer.util.GrobidService;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.CliPreferences;
@@ -48,7 +48,7 @@ public class ExtractReferencesAction extends SimpleCommand {
     private final BibEntry entry;
     private final LinkedFile linkedFile;
 
-    private final BibliographyFromPdfImporter bibliographyFromPdfImporter;
+    private final RuleBasedBibliographyPdfImporter ruleBasedBibliographyPdfImporter;
 
     public ExtractReferencesAction(DialogService dialogService,
                                    StateManager stateManager,
@@ -72,7 +72,7 @@ private ExtractReferencesAction(@NonNull DialogService dialogService,
         this.preferences = preferences;
         this.entry = entry;
         this.linkedFile = linkedFile;
-        bibliographyFromPdfImporter = new BibliographyFromPdfImporter(preferences.getCitationKeyPatternPreferences());
+        ruleBasedBibliographyPdfImporter = new RuleBasedBibliographyPdfImporter(preferences.getCitationKeyPatternPreferences());
 
         if (this.linkedFile == null) {
             this.executable.bind(
@@ -132,7 +132,7 @@ private void extractReferences() {
             List<Path> fileList = FileUtil.getListOfLinkedFiles(selectedEntries, databaseContext.getFileDirectories(preferences.getFilePreferences()));
 
             // We need to have ParserResult handled at the importer, because it imports the meta data (library type, encoding, ...)
-            ParserResult result = bibliographyFromPdfImporter.importDatabase(fileList.getFirst());
+            ParserResult result = ruleBasedBibliographyPdfImporter.importDatabase(fileList.getFirst());
 
             // subsequent files are just appended to result
             Iterator<Path> fileListIterator = fileList.iterator();
@@ -155,7 +155,7 @@ private void extractReferences() {
 
     private void extractReferences(Iterator<Path> fileListIterator, ParserResult result, BibEntry currentEntry) {
         while (fileListIterator.hasNext()) {
-            result.getDatabase().insertEntries(bibliographyFromPdfImporter.importDatabase(fileListIterator.next()).getDatabase().getEntries());
+            result.getDatabase().insertEntries(ruleBasedBibliographyPdfImporter.importDatabase(fileListIterator.next()).getDatabase().getEntries());
         }
 
         String cites = getCites(result.getDatabase().getEntries(), currentEntry);

jabgui/src/main/java/org/jabref/gui/maintable/NewLibraryFromPdfActionOffline.java

@@ -7,23 +7,23 @@
 import org.jabref.gui.LibraryTabContainer;
 import org.jabref.gui.StateManager;
 import org.jabref.logic.importer.ParserResult;
-import org.jabref.logic.importer.fileformat.BibliographyFromPdfImporter;
+import org.jabref.logic.importer.fileformat.pdf.RuleBasedBibliographyPdfImporter;
 import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.TaskExecutor;
 
 public class NewLibraryFromPdfActionOffline extends NewLibraryFromPdfAction {
 
-    private final BibliographyFromPdfImporter bibliographyFromPdfImporter;
+    private final RuleBasedBibliographyPdfImporter ruleBasedBibliographyPdfImporter;
 
     public NewLibraryFromPdfActionOffline(LibraryTabContainer libraryTabContainer, StateManager stateManager, DialogService dialogService, CliPreferences preferences, TaskExecutor taskExecutor) {
         super(libraryTabContainer, stateManager, dialogService, preferences, taskExecutor);
 
         // Use the importer keeping the numbers (instead of generating keys; which is the other constructor)
-        this.bibliographyFromPdfImporter = new BibliographyFromPdfImporter();
+        this.ruleBasedBibliographyPdfImporter = new RuleBasedBibliographyPdfImporter();
     }
 
     @Override
     protected Callable<ParserResult> getParserResultCallable(Path path) {
-        return () -> bibliographyFromPdfImporter.importDatabase(path);
+        return () -> ruleBasedBibliographyPdfImporter.importDatabase(path);
     }
 }

jabgui/src/main/java/org/jabref/gui/newentry/NewEntryView.java

@@ -345,7 +345,7 @@ private void initializeInterpretCitations() {
         interpretParser.valueProperty().bindBidirectional(viewModel.interpretParserProperty());
         PlainCitationParserChoice initialParser = parserFromName(preferences.getLatestInterpretParser(), interpretParser.getItems());
         if (initialParser == null) {
-            final PlainCitationParserChoice defaultParser = PlainCitationParserChoice.RULE_BASED;
+            final PlainCitationParserChoice defaultParser = PlainCitationParserChoice.RULE_BASED_GENERAL;
             initialParser = parserFromName(defaultParser.getLocalizedName(), interpretParser.getItems());
         }
         interpretParser.setValue(initialParser);