Merge remote-tracking branch 'upstream/main' into newGlobalSearch

* upstream/main:
  Switch to archive.org for site.icu-project.org
  Add Java Profiler
  Fix output when closing JabRef while indexing (#8043)
  Remove explicit XMP import for PDFs (#8040)
  Fix crosses
  Stop indexing on cancel (#8039)
  Write embedded bib in addition to XMP metadata (#8037)
  Cleanup preferences (#8036)
  Fix Search dark mode theme (#8028)
  Allow the search to return multiple entries. (#8038)
  Refactored GroupTree.fxml to plain java (#8035)

Author: Siedlerchr

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,8 +11,8 @@ The title of the PR must not reference an issue, because GitHub does not support
 - [x] done; [ ] not done / not applicable
 -->
 
-- [] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
-- [] Tests created for changes (if applicable)
-- [] Manually tested changed features in running JabRef (always required)
-- [] Screenshots added in PR description (for UI changes)
-- [] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, submitted a pull request to the documentation repository.
+- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
+- [ ] Tests created for changes (if applicable)
+- [ ] Manually tested changed features in running JabRef (always required)
+- [ ] Screenshots added in PR description (for UI changes)
+- [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not, I created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, I submitted a pull request to the documentation repository.

CHANGELOG.md

@@ -27,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We merged the barely used ImportSettingsTab and the CustomizationTab in the preferences into one single tab and moved the option to allow Integers in Edition Fields in Bibtex-Mode to the EntryEditor tab. [#7849](https://github.com/JabRef/jabref/pull/7849)
 - We moved the export order in the preferences from `File` to `Import and Export`. [#7935](https://github.com/JabRef/jabref/pull/7935)
 - We reworked the export order in the preferences and the save order in the library preferences. You can now set more than three sort criteria in your library preferences. [#7935](https://github.com/JabRef/jabref/pull/7935)
+- The metadata-to-pdf actions now also embeds the bibfile to the PDF. [#8037](https://github.com/JabRef/jabref/pull/8037)
 
 ### Fixed
 

README.md

@@ -96,4 +96,9 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th
 
 `gradlew test` executes all tests. We use [Github Actions](https://github.com/JabRef/jabref/actions) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Github will report any other failure.
 
+## Sponsoring
+
+JabRef development is powered by YourKit Java Profiler [![YourKit Java Profiler](https://www.yourkit.com/images/yk_logo.png)](https://www.yourkit.com/java/profiler/)
+
+
 [JabRef]: https://www.jabref.org

docs/adr/0018-use-regular-expression-to-split-multiple-sentence-titles.md

@@ -8,7 +8,7 @@ Some entry titles are composed of multiple sentences, for example: "Whose Music?
 
 * [Regular expression](https://docs.oracle.com/javase/tutorial/essential/regex/)
 * [OpenNLP](https://opennlp.apache.org/)
-* [ICU4J](http://site.icu-project.org/home)
+* [ICU4J](https://web.archive.org/web/20210413013221/http://site.icu-project.org/home)
 
 ## Decision Outcome
 

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -18,10 +18,12 @@
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.JabRefException;
+import org.jabref.logic.bibtex.FieldWriterPreferences;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.exporter.AtomicFileWriter;
 import org.jabref.logic.exporter.BibDatabaseWriter;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
+import org.jabref.logic.exporter.EmbeddedBibFilePdfExporter;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SavePreferences;
@@ -51,6 +53,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileHelper;
@@ -224,13 +227,22 @@ private List<ParserResult> processArguments() {
             automaticallySetFileLinks(loaded);
         }
 
-        if (cli.isWriteXMPtoPdf()) {
+        if (cli.isWriteXMPtoPdf() && cli.isEmbeddBibfileInPdf() || cli.isWriteMetadatatoPdf() && (cli.isWriteXMPtoPdf() || cli.isEmbeddBibfileInPdf())) {
+            System.err.println("Give only one of [writeXMPtoPdf, embeddBibfileInPdf, writeMetadatatoPdf]");
+        }
+
+        if (cli.isWriteMetadatatoPdf() || cli.isWriteXMPtoPdf() || cli.isEmbeddBibfileInPdf()) {
             if (!loaded.isEmpty()) {
-                writeXMPtoPdf(loaded,
-                        cli.getWriteXMPtoPdf(),
+                writeMetadatatoPdf(loaded,
+                        cli.getWriteMetadatatoPdf(),
                         preferencesService.getDefaultEncoding(),
                         preferencesService.getXmpPreferences(),
-                        preferencesService.getFilePreferences());
+                        preferencesService.getFilePreferences(),
+                        preferencesService.getDefaultBibDatabaseMode(),
+                        Globals.entryTypesManager,
+                        preferencesService.getFieldWriterPreferences(),
+                        cli.isWriteXMPtoPdf() || cli.isWriteMetadatatoPdf(),
+                        cli.isEmbeddBibfileInPdf() || cli.isWriteMetadatatoPdf());
             }
         }
 
@@ -258,7 +270,7 @@ private List<ParserResult> processArguments() {
         return loaded;
     }
 
-    private void writeXMPtoPdf(List<ParserResult> loaded, String filesAndCitekeys, Charset encoding, XmpPreferences xmpPreferences, FilePreferences filePreferences) {
+    private void writeMetadatatoPdf(List<ParserResult> loaded, String filesAndCitekeys, Charset encoding, XmpPreferences xmpPreferences, FilePreferences filePreferences, BibDatabaseMode databaseMode, BibEntryTypesManager entryTypesManager, FieldWriterPreferences fieldWriterPreferences, boolean writeXMP, boolean embeddBibfile) {
         if (loaded.isEmpty()) {
             LOGGER.error("The write xmp option depends on a valid import option.");
             return;
@@ -268,10 +280,11 @@ private void writeXMPtoPdf(List<ParserResult> loaded, String filesAndCitekeys, C
         BibDatabase dataBase = pr.getDatabase();
 
         XmpPdfExporter xmpPdfExporter = new XmpPdfExporter(xmpPreferences);
+        EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter = new EmbeddedBibFilePdfExporter(databaseMode, entryTypesManager, fieldWriterPreferences);
 
         if ("all".equals(filesAndCitekeys)) {
             for (BibEntry entry : dataBase.getEntries()) {
-                writeXMPtoPDFsOfEntry(databaseContext, entry.getCitationKey().orElse("<no cite key defined>"), entry, encoding, filePreferences, xmpPdfExporter);
+                writeMetadatatoPDFsOfEntry(databaseContext, entry.getCitationKey().orElse("<no cite key defined>"), entry, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
             }
             return;
         }
@@ -286,48 +299,66 @@ private void writeXMPtoPdf(List<ParserResult> loaded, String filesAndCitekeys, C
             }
         }
 
-        writeXMPtoPdfByCitekey(databaseContext, dataBase, citeKeys, encoding, filePreferences, xmpPdfExporter);
-        writeXMPtoPdfByFileNames(databaseContext, dataBase, pdfs, encoding, filePreferences, xmpPdfExporter);
+        writeMetadatatoPdfByCitekey(databaseContext, dataBase, citeKeys, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
+        writeMetadatatoPdfByFileNames(databaseContext, dataBase, pdfs, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
 
     }
 
-    private void writeXMPtoPDFsOfEntry(BibDatabaseContext databaseContext, String citeKey, BibEntry entry, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+    private void writeMetadatatoPDFsOfEntry(BibDatabaseContext databaseContext, String citeKey, BibEntry entry, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         try {
-            if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, List.of(entry))) {
-                LOGGER.info(String.format("Successfully written XMP metadata on at least one linked file of %s", citeKey));
-            } else {
-                LOGGER.error(String.format("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
+            if (writeXMP) {
+                if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, List.of(entry))) {
+                    System.out.println(String.format("Successfully written XMP metadata on at least one linked file of %s", citeKey));
+                } else {
+                    System.err.println(String.format("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
+                }
+            }
+            if (embeddBibfile) {
+                if (embeddedBibFilePdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, List.of(entry))) {
+                    System.out.println(String.format("Successfully embedded metadata on at least one linked file of %s", citeKey));
+                } else {
+                    System.out.println(String.format("Cannot embedd metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
+                }
             }
         } catch (Exception e) {
-            LOGGER.error(String.format("Failed writing XMP metadata on a linked file of %s.", citeKey));
+            LOGGER.error(String.format("Failed writing metadata on a linked file of %s.", citeKey));
         }
     }
 
-    private void writeXMPtoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+    private void writeMetadatatoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         for (String citeKey : citeKeys) {
             List<BibEntry> bibEntryList = dataBase.getEntriesByCitationKey(citeKey);
             if (bibEntryList.isEmpty()) {
-                LOGGER.error(String.format("Skipped - Cannot find %s in library.", citeKey));
+                System.err.println(String.format("Skipped - Cannot find %s in library.", citeKey));
                 continue;
             }
             for (BibEntry entry : bibEntryList) {
-                writeXMPtoPDFsOfEntry(databaseContext, citeKey, entry, encoding, filePreferences, xmpPdfExporter);
+                writeMetadatatoPDFsOfEntry(databaseContext, citeKey, entry, encoding, filePreferences, xmpPdfExporter, embeddedBibFilePdfExporter, writeXMP, embeddBibfile);
             }
         }
     }
 
-    private void writeXMPtoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> fileNames, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+    private void writeMetadatatoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> fileNames, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         for (String fileName : fileNames) {
             Path filePath = Path.of(fileName);
             if (!filePath.isAbsolute()) {
                 filePath = FileHelper.find(fileName, databaseContext.getFileDirectories(filePreferences)).orElse(FileHelper.find(fileName, List.of(Path.of("").toAbsolutePath())).orElse(filePath));
             }
             if (Files.exists(filePath)) {
                 try {
-                    if (xmpPdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
-                        LOGGER.info(String.format("Successfully written XMP metadata of at least one entry to %s", fileName));
-                    } else {
-                        LOGGER.error(String.format("File %s is not linked to any entry in database.", fileName));
+                    if (writeXMP) {
+                        if (xmpPdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
+                            System.out.println(String.format("Successfully written XMP metadata of at least one entry to %s", fileName));
+                        } else {
+                            System.out.println(String.format("File %s is not linked to any entry in database.", fileName));
+                        }
+                    }
+                    if (embeddBibfile) {
+                        if (embeddedBibFilePdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
+                            System.out.println(String.format("Successfully embedded XMP metadata of at least one entry to %s", fileName));
+                        } else {
+                            System.out.println(String.format("File %s is not linked to any entry in database.", fileName));
+                        }
                     }
                 } catch (IOException e) {
                     LOGGER.error("Error accessing file '{}'.", fileName);
@@ -567,7 +598,8 @@ private void importPreferences() {
                     preferencesService.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);
             SavePreferences savePreferences = preferencesService.getSavePreferencesForExport();
             XmpPreferences xmpPreferences = preferencesService.getXmpPreferences();
-            Globals.exportFactory = ExporterFactory.create(customExporters, layoutPreferences, savePreferences, xmpPreferences);
+            BibDatabaseMode bibDatabaseMode = preferencesService.getDefaultBibDatabaseMode();
+            Globals.exportFactory = ExporterFactory.create(customExporters, layoutPreferences, savePreferences, xmpPreferences, bibDatabaseMode, Globals.entryTypesManager);
         } catch (JabRefException ex) {
             LOGGER.error("Cannot import preferences", ex);
         }

src/main/java/org/jabref/cli/JabRefCLI.java

@@ -151,8 +151,18 @@ public boolean isWriteXMPtoPdf() {
         return cl.hasOption("writeXMPtoPdf");
     }
 
-    public String getWriteXMPtoPdf() {
-        return cl.getOptionValue("writeXMPtoPdf");
+    public boolean isEmbeddBibfileInPdf() {
+        return cl.hasOption("embeddBibfileInPdf");
+    }
+
+    public boolean isWriteMetadatatoPdf() {
+        return cl.hasOption("writeMetadatatoPdf");
+    }
+
+    public String getWriteMetadatatoPdf() {
+        return cl.hasOption("writeMetadatatoPdf") ? cl.getOptionValue("writeMetadatatoPdf") :
+                cl.hasOption("writeXMPtoPdf") ? cl.getOptionValue("writeXMPtoPdf") :
+                cl.hasOption("embeddBibfileInPdf") ? cl.getOptionValue("embeddBibfileInPdf") : null;
     }
 
     private static Options getOptions() {
@@ -251,13 +261,29 @@ private static Options getOptions() {
                 .build());
 
         options.addOption(Option
-                .builder("w")
+                .builder()
                 .longOpt("writeXMPtoPdf")
                 .desc(String.format("%s: '%s'", Localization.lang("Write BibTeXEntry as XMP metadata to PDF."), "-w pathToMyOwnPaper.pdf"))
                 .hasArg()
                 .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
                 .build());
 
+        options.addOption(Option
+                .builder()
+                .longOpt("embeddBibfileInPdf")
+                .desc(String.format("%s: '%s'", Localization.lang("Embedd BibTeXEntry in PDF."), "-w pathToMyOwnPaper.pdf"))
+                .hasArg()
+                .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
+                .build());
+
+        options.addOption(Option
+                .builder("w")
+                .longOpt("writeMetadatatoPdf")
+                .desc(String.format("%s: '%s'", Localization.lang("Write BibTeXEntry as metadata to PDF."), "-w pathToMyOwnPaper.pdf"))
+                .hasArg()
+                .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
+                .build());
+
         return options;
     }
 

src/main/java/org/jabref/gui/Dark.css

@@ -66,11 +66,11 @@
     -fx-background-color: -fx-control-inner-background;
 }
 
-.table-row-cell: odd{
+.table-row-cell:odd{
     -fx-background-color:#272b38;
 }
 
-.table-row-cell: even{
+.table-row-cell:even{
     -fx-background-color: #212330;
 }
 
@@ -108,12 +108,15 @@
     -fx-background-color: -jr-background;
 }
 
+
 .mainToolbar .search-field .toggle-button .glyph-icon {
     -fx-fill: -jr-search-text;
     -fx-text-fill: -jr-search-text;
+    -fx-icon-color:-jr-search-text;
 }
 
 .mainToolbar .search-field .toggle-button:selected .glyph-icon {
-    -fx-fill: derive(-jr-search-text, 80%);
-    -fx-text-fill: derive(-jr-search-text, 80%);
+    -fx-fill: derive(-fx-light-text-color, 80%);
+    -fx-text-fill: derive(-fx-light-text-color, 80%);
+    -fx-icon-color: derive(-fx-light-text-color, 80%);
 }