Merge remote-tracking branch 'upstream/main' into citation-relations-…

…link * upstream/main: Bump org.apache.pdfbox:fontbox from 3.0.1 to 3.0.2 (JabRef#11042) Bump com.dlsc.gemsfx:gemsfx from 2.2.0 to 2.4.0 (JabRef#11044) Bump org.apache.pdfbox:xmpbox from 3.0.1 to 3.0.2 (JabRef#11041) Bump com.googlecode.plist:dd-plist from 1.23 to 1.28 (JabRef#11040) Bump gittools/actions from 0.13.4 to 1.1.1 (JabRef#11039) Change copy-paste function to handle string constants (follow up PR) (JabRef#11037) Fixes Zotero file handling for absolute paths (JabRef#11038) Speed up failure reporting (JabRef#11030) Importing of BibDesk Groups and Linked Files (JabRef#10968) Convert RemoveBracesFormatterTest to @ParameterizedTest (JabRef#11033) Update teaching.md Remove non-existing recipe (JabRef#11029) Update CSL styles (JabRef#11031) Clean up defintions of entry types (JabRef#11013) Fix log file path on Windows (JabRef#11028) Change to rolling logs (JabRef#11023) chore: remove repetitive words (JabRef#11015) Fix test names (JabRef#11014)
ror3d · Mar 18, 2024 · 77edfcf · 77edfcf
2 parents dca1e65 + c9415ff
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diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -66,12 +66,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.13.4
+        uses: gittools/actions/gitversion/setup@v1.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.13.4
+        uses: gittools/actions/gitversion/execute@v1.1.1
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
@@ -87,12 +87,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.13.4
+        uses: gittools/actions/gitversion/setup@v1.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.13.4
+        uses: gittools/actions/gitversion/execute@v1.1.1
       - name: 'Set up JDK ${{ matrix.jdk }}'
         uses: oracle-actions/setup-java@v1
         with:

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -79,12 +79,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.13.4
+        uses: gittools/actions/gitversion/setup@v1.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.13.4
+        uses: gittools/actions/gitversion/execute@v1.1.1
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -171,11 +171,15 @@ jobs:
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
         env:
           CI: "true"
+      - name: Prepare format failed test results
+        if: failure()
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: xml-twig-tools xsltproc
+          version: 1.0
       - name: Format failed test results
         if: failure()
-        run: |
-          sudo apt-get install -qq -y xml-twig-tools xsltproc
-          scripts/after-failure.sh
+        run: scripts/after-failure.sh
   databasetests:
     name: Database tests
     runs-on: ubuntu-latest

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,11 +24,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When pasting HTML into the abstract or a comment field, the hypertext is automatically converted to Markdown. [#10558](https://github.com/JabRef/jabref/issues/10558)
 - We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
 - We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
+- We added importing of static groups and linked files from BibDesk .bib files. [#10381](https://github.com/JabRef/jabref/issues/10381)
 - We added ability to export in CFF (Citation File Format) [#10661](https://github.com/JabRef/jabref/issues/10661).
 - We added ability to push entries to TeXworks. [#3197](https://github.com/JabRef/jabref/issues/3197)
 - We added the ability to zoom in and out in the document viewer using <kbd>Ctrl</kbd> + <kbd>Scroll</kbd>. [#10964](https://github.com/JabRef/jabref/pull/10964)
 - We added a Cleanup for removing non-existent files and grouped the related options [#10929](https://github.com/JabRef/jabref/issues/10929)
 - We added the functionality to parse the bibliography of PDFs using the GROBID online service. [#10200](https://github.com/JabRef/jabref/issues/10200)
+- We added support for BibTeX String constants during copy & paste between libraries [#10872](https://github.com/JabRef/jabref/issues/10872)
 
 ### Changed
 
@@ -42,6 +44,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We changed the duplicate handling in the Import entries dialog. Potential duplicate entries are marked with an icon and importing will now trigger the merge dialog [#10914](https://github.com/JabRef/jabref/pull/10914)
 - We made the command "Push to TexShop" more robust to allow cite commands with a character before the first slash. [forum#2699](https://discourse.jabref.org/t/push-to-texshop-mac/2699/17?u=siedlerchr)
 - We only show the notification "Saving library..." if the library contains more than 2000 entries. [#9803](https://github.com/JabRef/jabref/issues/9803)
+- JabRef now keeps previous log files upon start. [#11023](https://github.com/JabRef/jabref/pull/11023)
 - We enhanced the dialog for adding new fields in the content selector with a selection box containing a list of standard fields. [#10912](https://github.com/JabRef/jabref/pull/10912)
 - We store the citation relations in an LRU cache to avoid bloating the memory and out-of-memory exceptions. [#10958](https://github.com/JabRef/jabref/issues/10958)
 - Keywords filed are now displayed as tags. [#10910](https://github.com/JabRef/jabref/pull/10910)
@@ -64,6 +67,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the `File -> Close library` menu item was not disabled when no library was open. [#10948](https://github.com/JabRef/jabref/issues/10948)
 - We fixed an issue where the Document Viewer would show the PDF in only half the window when maximized. [#10934](https://github.com/JabRef/jabref/issues/10934)
 - Clicking on the crossref and related tags in the entry editor jumps to the linked entry. [#5484](https://github.com/JabRef/jabref/issues/5484) [#9369](https://github.com/JabRef/jabref/issues/9369)
+- We fixed an issue where JabRef could not parse absolute file paths from Zotero exports [#10959](https://github.com/JabRef/jabref/issues/10959)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -114,8 +114,8 @@ dependencies {
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
     implementation 'org.apache.pdfbox:pdfbox:3.0.1'
-    implementation 'org.apache.pdfbox:fontbox:3.0.1'
-    implementation ('org.apache.pdfbox:xmpbox:3.0.1') {
+    implementation 'org.apache.pdfbox:fontbox:3.0.2'
+    implementation ('org.apache.pdfbox:xmpbox:3.0.2') {
         exclude group: 'org.junit.jupiter'
     }
 
@@ -177,7 +177,7 @@ dependencies {
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.2.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.4.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
@@ -242,6 +242,9 @@ dependencies {
     // Because of GraalVM quirks, we need to ship that. See https://github.com/jspecify/jspecify/issues/389#issuecomment-1661130973 for details
     implementation 'org.jspecify:jspecify:0.3.0'
 
+    // parse plist files
+    implementation 'com.googlecode.plist:dd-plist:1.28'
+
     testImplementation 'io.github.classgraph:classgraph:4.8.168'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'

diff --git a/config/README.md b/config/README.md
@@ -20,7 +20,7 @@ Style-checks are done for each pull request and installing this code style confi
 # Eclipse:
 
 The Eclipse code formatter style is stored in the `eclipse.gradle` file and gets imported automatically.
-In case the formatter style needs to be adapted, configure it and export in in eclipse.
+In case the formatter style needs to be adapted, configure it and export in eclipse.
 
 1. Right click on the eclipse project "JabRef"
 2. Select "Export > General > Preferences"

diff --git a/docs/teaching.md b/docs/teaching.md
@@ -83,8 +83,6 @@ Course: BSc Computer Science Individual Project
 * Summary: Students experience the procedure of finding and fixing small and medium issues in an open source project.
 * Successfully run in 2022/2023
 
-Do you have additions/suggestions for improvement?
-
 #### Northern Arizona University (NAU), USA
 
 Course [CS499 - Open Source Software Development](https://github.com/igorsteinmacher/CS499-OSS)
@@ -129,7 +127,7 @@ Course "Programming and Software Development" as part of the [BSc Software Engin
 Course [DD2480 Software Engineering Fundamentals](https://www.kth.se/student/kurser/kurs/DD2480?l=en)
 
 * Summary: Groups of students from three to five persons experienced the whole software engineering process within a week: From the requirements' specification to the final pull request.
-* Successfully run in 2020
+* Successfully run in 2020, 2024, and other years.
 
 ### Portuguese
 

diff --git a/licenses/com.googlecode.plist_ddplist.txt b/licenses/com.googlecode.plist_ddplist.txt
@@ -0,0 +1,20 @@
+dd-plist - An open source library to parse and generate property lists
+Copyright (C) 2016 Daniel Dreibrodt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/rewrite.yml b/rewrite.yml
@@ -103,8 +103,6 @@ recipeList:
   - org.openrewrite.java.migrate.lang.StringFormatted
   - org.openrewrite.java.migrate.util.SequencedCollection
 
-  - org.openrewrite.java.recipes.UseJavaParserBuilderInJavaTemplate
-
   - org.openrewrite.java.RemoveObjectsIsNull
   - org.openrewrite.java.ShortenFullyQualifiedTypeReferences
 

diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
@@ -144,4 +144,5 @@
     requires org.libreoffice.uno;
     requires de.saxsys.mvvmfx.validation;
     requires com.jthemedetector;
+    requires dd.plist;
 }
diff --git a/src/main/java/org/jabref/Launcher.java b/src/main/java/org/jabref/Launcher.java
@@ -11,15 +11,13 @@
 import java.util.List;
 import java.util.Map;
 
-import org.jabref.architecture.AllowedToUseStandardStreams;
 import org.jabref.cli.ArgumentProcessor;
 import org.jabref.cli.JabRefCLI;
 import org.jabref.gui.Globals;
 import org.jabref.gui.JabRefGUI;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.journals.predatory.PredatoryJournalListLoader;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ProxyAuthenticator;
 import org.jabref.logic.net.ProxyPreferences;
 import org.jabref.logic.net.ProxyRegisterer;
@@ -48,7 +46,6 @@
  * - Handle the command line arguments
  * - Start the JavaFX application (if not in cli mode)
  */
-@AllowedToUseStandardStreams("Direct output to the user")
 public class Launcher {
     private static Logger LOGGER;
     private static boolean isDebugEnabled;
@@ -140,11 +137,14 @@ private static void addLogToDisk() {
         // The "Shared File Writer" is explained at
         // https://tinylog.org/v2/configuration/#shared-file-writer
         Map<String, String> configuration = Map.of(
-                "writerFile", "shared file",
-                "writerFile.level", isDebugEnabled ? "debug" : "info",
                 "level", isDebugEnabled ? "debug" : "info",
-                "writerFile.file", directory.resolve("log.txt").toString(),
-                "writerFile.charset", "UTF-8");
+                "writerFile", "rolling file",
+                "writerFile.level", isDebugEnabled ? "debug" : "info",
+                // We need to manually join the path, because ".resolve" does not work on Windows, because ":" is not allowed in file names on Windows
+                "writerFile.file", directory + File.separator + "log_{date:yyyy-MM-dd_HH-mm-ss}.txt",
+                "writerFile.charset", "UTF-8",
+                "writerFile.policies", "startup",
+                "writerFile.backups", "30");
 
         configuration.forEach(Configuration::set);
         initializeLogger();
@@ -169,9 +169,8 @@ private static boolean handleMultipleAppInstances(String[] args, RemotePreferenc
                 LOGGER.debug("Passing arguments passed on to running JabRef...");
                 if (remoteClient.sendCommandLineArguments(args)) {
                     // So we assume it's all taken care of, and quit.
-                    LOGGER.debug("Arguments passed on to running JabRef instance.");
-                    // Used for script-use output etc. to the user
-                    System.out.println(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
+                    // Output to both to the log and the screen. Therefore, we do not have an additional System.out.println.
+                    LOGGER.info("Arguments passed on to running JabRef instance. Shutting down.");
                     return false;
                 } else {
                     LOGGER.warn("Could not communicate with other running JabRef instance.");

diff --git a/src/main/java/org/jabref/gui/ClipBoardManager.java b/src/main/java/org/jabref/gui/ClipBoardManager.java
@@ -21,6 +21,7 @@
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.BibtexString;
 import org.jabref.preferences.PreferencesService;
 
 import org.slf4j.Logger;
@@ -155,14 +156,23 @@ public void setContent(String string) {
     }
 
     public void setContent(List<BibEntry> entries, BibEntryTypesManager entryTypesManager) throws IOException {
-        final ClipboardContent content = new ClipboardContent();
-        BibEntryWriter writer = new BibEntryWriter(new FieldWriter(preferencesService.getFieldPreferences()), entryTypesManager);
-        String serializedEntries = writer.serializeAll(entries, BibDatabaseMode.BIBTEX);
+        String serializedEntries = serializeEntries(entries, entryTypesManager);
+        setContent(serializedEntries);
+    }
+
+    public void setContent(List<BibEntry> entries, BibEntryTypesManager entryTypesManager, List<BibtexString> stringConstants) throws IOException {
+        StringBuilder builder = new StringBuilder();
+        stringConstants.forEach(strConst -> builder.append(strConst.getParsedSerialization() == null ? "" : strConst.getParsedSerialization()));
+        String serializedEntries = serializeEntries(entries, entryTypesManager);
+        builder.append(serializedEntries);
+        setContent(builder.toString());
+    }
+
+    private String serializeEntries(List<BibEntry> entries, BibEntryTypesManager entryTypesManager) throws IOException {
         // BibEntry is not Java serializable. Thus, we need to do the serialization manually
         // 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
-        content.putString(serializedEntries);
-        clipboard.setContent(content);
-        setPrimaryClipboardContent(content);
+        BibEntryWriter writer = new BibEntryWriter(new FieldWriter(preferencesService.getFieldPreferences()), entryTypesManager);
+        return writer.serializeAll(entries, BibDatabaseMode.BIBTEX);
     }
 }
diff --git a/src/main/java/org/jabref/gui/edit/ReplaceStringAction.java b/src/main/java/org/jabref/gui/edit/ReplaceStringAction.java
@@ -15,7 +15,6 @@ public class ReplaceStringAction extends SimpleCommand {
     public ReplaceStringAction(Supplier<LibraryTab> tabSupplier, StateManager stateManager, DialogService dialogService) {
         this.tabSupplier = tabSupplier;
         this.dialogService = dialogService;
-
         this.executable.bind(ActionHelper.needsDatabase(stateManager));
     }
 

diff --git a/...f/gui/entryeditor/OptionalFields2Tab.java → .../entryeditor/DetailOptionalFieldsTab.java b/...f/gui/entryeditor/OptionalFields2Tab.java → .../entryeditor/DetailOptionalFieldsTab.java
@@ -14,21 +14,21 @@
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.preferences.PreferencesService;
 
-public class OptionalFields2Tab extends OptionalFieldsTabBase {
+public class DetailOptionalFieldsTab extends OptionalFieldsTabBase {
 
     public static final String NAME = "Optional fields 2";
 
-    public OptionalFields2Tab(BibDatabaseContext databaseContext,
-                              SuggestionProviders suggestionProviders,
-                              UndoManager undoManager,
-                              DialogService dialogService,
-                              PreferencesService preferences,
-                              StateManager stateManager,
-                              ThemeManager themeManager,
-                              IndexingTaskManager indexingTaskManager,
-                              BibEntryTypesManager entryTypesManager,
-                              TaskExecutor taskExecutor,
-                              JournalAbbreviationRepository journalAbbreviationRepository) {
+    public DetailOptionalFieldsTab(BibDatabaseContext databaseContext,
+                                   SuggestionProviders suggestionProviders,
+                                   UndoManager undoManager,
+                                   DialogService dialogService,
+                                   PreferencesService preferences,
+                                   StateManager stateManager,
+                                   ThemeManager themeManager,
+                                   IndexingTaskManager indexingTaskManager,
+                                   BibEntryTypesManager entryTypesManager,
+                                   TaskExecutor taskExecutor,
+                                   JournalAbbreviationRepository journalAbbreviationRepository) {
         super(
                 Localization.lang("Optional fields 2"),
                 false,