Merge pull request #6 from JabRef/main

updates

.github/workflows/on-labeled.yml → .github/workflows/on-labeled-issue.yml

@@ -1,12 +1,9 @@
-name: On labeled
+name: On labeled issue
 
 on:
   issues:
      types:
        - labeled
-  pull_request_target:
-    types:
-       - labeled
 
 jobs:
   FirstTimeCodeContribution:
@@ -28,17 +25,21 @@ jobs:
 
           Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on [JabRef's Gitter chat](https://gitter.im/JabRef/jabref). And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.
 
+          ⚠ Note that this issue will become unassigned if it isn't closed within **30 days**.
+
+          🔧 A maintainer can also add the **`Pinned`** label to prevent it from being unassigned automatically.
+
           Happy coding! 🚀
     - name: Move Issue to "Assigned" Column in "Candidates for University Projects"
-      uses: m7kvqbe1/github-action-move-issues@v1.0.9
+      uses: m7kvqbe1/github-action-move-issues@v1.1.1
       with:
        github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
        project-url: "https://github.com/orgs/JabRef/projects/3"
        target-labels: "FirstTimeCodeContribution"
        target-column: "Assigned"
        ignored-columns: ""
     - name: Move Issue to "Assigned" Column in "Good First Issues"
-      uses: m7kvqbe1/github-action-move-issues@v1.0.9
+      uses: m7kvqbe1/github-action-move-issues@v1.1.1
       with:
        github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
        project-url: "https://github.com/orgs/JabRef/projects/5"
@@ -53,15 +54,15 @@ jobs:
       issues: write
     steps:
     - name: Move Issue to "Assigned" Column in "Candidates for University Projects"
-      uses: m7kvqbe1/github-action-move-issues@v1.0.9
+      uses: m7kvqbe1/github-action-move-issues@v1.1.1
       with:
        github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
        project-url: "https://github.com/orgs/JabRef/projects/3"
        target-labels: "📍 Assigned"
        target-column: "Assigned"
        ignored-columns: ""
     - name: Move Issue to "Assigned" Column in "Good First Issues"
-      uses: m7kvqbe1/github-action-move-issues@v1.0.9
+      uses: m7kvqbe1/github-action-move-issues@v1.1.1
       with:
        github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
        project-url: "https://github.com/orgs/JabRef/projects/5"

.github/workflows/on-labeled-pr.yml

@@ -0,0 +1,23 @@
+name: On labeled PR
+
+on:
+  pull_request:
+     types:
+       - labeled
+
+jobs:
+  automerge:
+    name: Auto Merge
+    if: "${{ github.event.label.name == 'automerge' }}"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Approve PR
+        run: gh pr review --approve "$PR_URL"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GITHUB_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
+      - name: Merge PR
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GITHUB_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}

.github/workflows/on-unlabeled.yml → .github/workflows/on-unlabeled-issue.yml

@@ -1,12 +1,9 @@
-name: On unlabeled
+name: On unlabeled issue
 
 on:
   issues:
      types:
        - unlabeled
-  pull_request_target:
-    types:
-       - unlabeled
 
 jobs:
   FirstTimeCodeContribution_or_Assigned:
@@ -16,7 +13,7 @@ jobs:
       issues: write
     steps:
     - name: Move Issue to "Free to take" Column in "Candidates for University Projects"
-      uses: m7kvqbe1/github-action-move-issues@feat/default-column-label-remove
+      uses: m7kvqbe1/github-action-move-issues@v1.1.1
       with:
        github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
        project-url: "https://github.com/orgs/JabRef/projects/3"
@@ -25,7 +22,7 @@ jobs:
        ignored-columns: ""
        default-column: "Free to take"
     - name: Move Issue to "Free to take" Column in "Good First Issues"
-      uses: m7kvqbe1/github-action-move-issues@feat/default-column-label-remove
+      uses: m7kvqbe1/github-action-move-issues@v1.1.1
       with:
        github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
        project-url: "https://github.com/orgs/JabRef/projects/5"

CHANGELOG.md

@@ -34,6 +34,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 - We added a setting which always adds the literal "Cited on pages" text before each JStyle citation. [#11691](https://github.com/JabRef/jabref/pull/11732)
 - We added a new plain citation parser that uses LLMs. [#11825](https://github.com/JabRef/jabref/issues/11825)
+- We added a compare button to the duplicates in the citation relations tab to open the "Possible duplicate entries" window. [#11192](https://github.com/JabRef/jabref/issues/11192)
 - We added automatic browser extension install on Windows for Chrome and Edge. [#6076](https://github.com/JabRef/jabref/issues/6076)
 - We added a search bar for filtering keyboard shortcuts. [#11686](https://github.com/JabRef/jabref/issues/11686)
 - By double clicking on a local citation in the Citation Relations Tab you can now jump the the linked entry. [#11955](https://github.com/JabRef/jabref/pull/11955)
@@ -52,6 +53,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - ⚠️ Renamed command line parameters `embeddBibfileInPdf` to `embedBibFileInPdf`, `writeMetadatatoPdf` to `writeMetadataToPdf`, and `writeXMPtoPdf` to `writeXmpToPdf`. [#11575](https://github.com/JabRef/jabref/pull/11575)
 - The browse button for a Custom theme now opens in the directory of the current used CSS file. [#11597](https://github.com/JabRef/jabref/pull/11597)
 - The browse button for a Custom exporter now opens in the directory of the current used exporter file. [#11717](https://github.com/JabRef/jabref/pull/11717)
+- ⚠️ We relaxed the escaping requirements for [bracketed patterns](https://docs.jabref.org/setup/citationkeypatterns), which are used for the [citaton key generator](https://docs.jabref.org/advanced/entryeditor#autogenerate-citation-key) and [filename and directory patterns](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#auto-linking-files). One only needs to write `\"` if a quote sign should be escaped. All other escapings are not necessary (and working) any more. [#11967](https://github.com/JabRef/jabref/pull/11967)
 - JabRef now uses TLS 1.2 for all HTTPS connections. [#11852](https://github.com/JabRef/jabref/pull/11852)
 - We improved the display of long messages in the integrity check dialog. [#11619](https://github.com/JabRef/jabref/pull/11619)
 - We improved the undo/redo buttons in the main toolbar and main menu to be disabled when there is nothing to undo/redo. [#8807](https://github.com/JabRef/jabref/issues/8807)
@@ -89,6 +91,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where unescaped braces in the arXiv fetcher were not treated. [#11704](https://github.com/JabRef/jabref/issues/11704)
 - We fixed an issue where HTML instead of the fulltext pdf was downloaded when importing arXiv entries. [#4913](https://github.com/JabRef/jabref/issues/4913)
 - We fixed an issue where the keywords and crossref fields were not properly focused. [#11177](https://github.com/JabRef/jabref/issues/11177)
+- We fixed handling of `\"` in [bracketed patterns](https://docs.jabref.org/setup/citationkeypatterns) containing a RegEx. [#11967](https://github.com/JabRef/jabref/pull/11967)
 - We fixed an issue where the Undo/Redo buttons were active even when all libraries are closed. [#11837](https://github.com/JabRef/jabref/issues/11837)
 - We fixed an issue where recently opened files were not displayed in the main menu properly. [#9042](https://github.com/JabRef/jabref/issues/9042)
 - We fixed an issue where the DOI lookup would show an error when a DOI was found for an entry. [#11850](https://github.com/JabRef/jabref/issues/11850)

CONTRIBUTING.md

@@ -53,7 +53,6 @@ Check out the [documentation for developers](https://devdocs.jabref.org/contribu
 
 For improving developer's documentation, go on at the [docs/ subdirectory of JabRef's code](https://github.com/JabRef/jabref/tree/main/docs) and edit the file.
 GitHub offers a good guide at [Editing files in another user's repository](https://help.github.com/en/github/managing-files-in-a-repository/editing-files-in-another-users-repository).
-
 One can also add [callouts](https://just-the-docs.github.io/just-the-docs-tests/components/callouts/).
 
 ## Getting a task assigned
@@ -63,20 +62,23 @@ GitHub will then automatically assign you.
 
 ## Pull Request Process
 
-1. **Create a new branch** (such as `fix-for-issue-121`). Be sure to create a **separate branch** for each improvement you implement.
-2. Work on the **new branch — not the `main` branch.** Refer to our [code how-tos](https://devdocs.jabref.org/code-howtos) if you have questions about your implementation.
-3. Create a pull request. For an overview of pull requests, take a look at GitHub's [pull request help documentation](https://help.github.com/articles/about-pull-requests/).
+1. Follow the steps at [Pre Condition 3: Code on the local machine](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/pre-03-code.html) to a) create a fork and b) have the fork checked out on your local machine
+2. Ensure that you followed the [steps to set up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/) to have the code running properly in IntelliJ.
+3. **Create a new branch** (such as `fix-for-issue-121`). Be sure to create a **separate branch** for each improvement you implement.
+4. Work on the **new branch — not the `main` branch.** Refer to our [code how-tos](https://devdocs.jabref.org/code-howtos) if you have questions about your implementation.
+5. Create a [pull request to JabRef main repository](https://github.com/JabRef/jabref/pulls).
+   For an overview on the concept of pull requests, take a look at GitHub's [pull request help documentation](https://help.github.com/articles/about-pull-requests/).
    1. Ensure that you followed the requirements listed below. They are not too hard, they merely support the maintainers to focus on supportive feedback than just stating the obvious.
    2. For text inspirations, consider [How to write the perfect pull request](https://github.com/blog/1943-how-to-write-the-perfect-pull-request).
    3. In case your pull request is not yet complete or not yet ready for review, create a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/) instead.
-4. Wait for feedback of the developers
-5. Address the feedback of the developers
-6. After two developers gave their green flag, the pull request will be merged.
+6. Wait for feedback of the developers
+7. Address the feedback of the developers
+8. After two developers gave their green flag, the pull request will be merged.
 
 In case you have any questions, please
 
 1. comment on the issue,
-2. show up in our [gitter chat](https://gitter.im/JabRef/jabref), or
+2. show up in our [Gitter chat](https://gitter.im/JabRef/jabref), or
 3. show your current code using a draft pull request and ask questions.
 
 We favor looking into your code using a draft pull request, because we can then also load the code into our IDE.

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md

@@ -50,7 +50,7 @@ If that does not exist, just select JDK 21.
 ![Gradle JVM is project SDK](guidelines-intellij-settings-gradle-gradlejvm-is-projectjvm.png)
 {% endfigure %}
 
-## Enable compiliation by IntelliJ
+## Enable compilation by IntelliJ
 
 To prepare IntelliJ's build system additional steps are required:
 

src/main/java/org/jabref/Launcher.java

@@ -2,7 +2,7 @@
 
 import java.util.List;
 
-import org.jabref.cli.JabRefCli;
+import org.jabref.cli.JabKit;
 import org.jabref.gui.JabRefGUI;
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.gui.preferences.JabRefGuiPreferences;
@@ -23,7 +23,7 @@
 public class Launcher {
 
     public static void main(String[] args) {
-        JabRefCli.initLogging(args);
+        JabKit.initLogging(args);
 
         // Initialize preferences
         final JabRefGuiPreferences preferences = JabRefGuiPreferences.getInstance();
@@ -33,7 +33,7 @@ public static void main(String[] args) {
         DefaultFileUpdateMonitor fileUpdateMonitor = new DefaultFileUpdateMonitor();
         HeadlessExecutorService.INSTANCE.executeInterruptableTask(fileUpdateMonitor, "FileUpdateMonitor");
 
-        List<UiCommand> uiCommands = JabRefCli.processArguments(args, preferences, fileUpdateMonitor);
+        List<UiCommand> uiCommands = JabKit.processArguments(args, preferences, fileUpdateMonitor);
         // The method `processArguments` quites the whole JVM if no GUI is needed.
 
         PreferencesMigrations.runMigrations(preferences);

src/main/java/org/jabref/cli/JabRefCli.java → src/main/java/org/jabref/cli/JabKit.java

@@ -37,12 +37,16 @@
 import org.slf4j.bridge.SLF4JBridgeHandler;
 import org.tinylog.configuration.Configuration;
 
-/**
- * Entrypoint for a command-line only version of JabRef.
- *
- * Does not do any preference migrations
- */
-public class JabRefCli {
+/// Entrypoint for a command-line only version of JabRef.
+/// It does not open any dialogs, just parses the command line arguments and outputs text and creates/modifies files.
+///
+/// See [Command Line Interface Guidelines](https://clig.dev/) for general guidelines how to design a good CLI interface.
+///
+/// It does not open any GUI.
+/// For the GUI application see {@link org.jabref.Launcher}.
+///
+/// Does not do any preference migrations.
+public class JabKit {
     private static Logger LOGGER;
 
     public static void main(String[] args) {
@@ -144,7 +148,7 @@ public static void initLogging(String[] args) {
         try {
             Files.createDirectories(directory);
         } catch (IOException e) {
-            LOGGER = LoggerFactory.getLogger(JabRefCli.class);
+            LOGGER = LoggerFactory.getLogger(JabKit.class);
             LOGGER.error("Could not create log directory {}", directory, e);
             return;
         }
@@ -162,7 +166,7 @@ public static void initLogging(String[] args) {
                 "writerFile.backups", "30");
         configuration.forEach(Configuration::set);
 
-        LOGGER = LoggerFactory.getLogger(JabRefCli.class);
+        LOGGER = LoggerFactory.getLogger(JabKit.class);
     }
 
     /**

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

@@ -5,6 +5,7 @@
 import java.net.URI;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Optional;
 
 import javax.swing.undo.UndoManager;
 
@@ -39,7 +40,12 @@
 import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.CitationFetcher;
 import org.jabref.gui.entryeditor.citationrelationtab.semanticscholar.SemanticScholarFetcher;
 import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.mergeentries.EntriesMergeResult;
+import org.jabref.gui.mergeentries.MergeEntriesDialog;
 import org.jabref.gui.preferences.GuiPreferences;
+import org.jabref.gui.undo.NamedCompound;
+import org.jabref.gui.undo.UndoableInsertEntries;
+import org.jabref.gui.undo.UndoableRemoveEntries;
 import org.jabref.gui.util.NoSelectionModel;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.logic.bibtex.BibEntryWriter;
@@ -51,6 +57,7 @@
 import org.jabref.logic.os.OS;
 import org.jabref.logic.util.BackgroundTask;
 import org.jabref.logic.util.TaskExecutor;
+import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.database.BibDatabaseModeDetection;
@@ -89,6 +96,8 @@ public class CitationRelationsTab extends EntryEditorTab {
     private final CitationsRelationsTabViewModel citationsRelationsTabViewModel;
     private final DuplicateCheck duplicateCheck;
     private final BibEntryTypesManager entryTypesManager;
+    private final StateManager stateManager;
+    private final UndoManager undoManager;
 
     public CitationRelationsTab(DialogService dialogService,
                                 BibDatabaseContext databaseContext,
@@ -104,6 +113,8 @@ public CitationRelationsTab(DialogService dialogService,
         this.preferences = preferences;
         this.libraryTab = libraryTab;
         this.taskExecutor = taskExecutor;
+        this.undoManager = undoManager;
+        this.stateManager = stateManager;
         setText(Localization.lang("Citation relations"));
         setTooltip(new Tooltip(Localization.lang("Show articles related by citation")));
 
@@ -238,6 +249,13 @@ private void styleFetchedListView(CheckListView<CitationRelationItem> listView)
                                 }
                         });
                         vContainer.getChildren().add(jumpTo);
+
+                        Button compareButton = IconTheme.JabRefIcons.MERGE_ENTRIES.asButton();
+                        compareButton.setTooltip(new Tooltip(Localization.lang("Compare with existing entry")));
+                        compareButton.setOnMouseClicked(event -> {
+                            openPossibleDuplicateEntriesWindow(entry, listView);
+                        });
+                        vContainer.getChildren().add(compareButton);
                     } else {
                         ToggleButton addToggle = IconTheme.JabRefIcons.ADD.asToggleButton();
                         addToggle.setTooltip(new Tooltip(Localization.lang("Select entry")));
@@ -511,4 +529,43 @@ private void importEntries(List<CitationRelationItem> entriesToImport, CitationF
 
         dialogService.notify(Localization.lang("Number of entries successfully imported") + ": " + entriesToImport.size());
     }
+
+    /**
+     * Function to open possible duplicate entries window to compare duplicate entries
+     *
+     * @param citationRelationItem duplicate in the citation relations tab
+     * @param listView CheckListView to display citations
+     */
+    private void openPossibleDuplicateEntriesWindow(CitationRelationItem citationRelationItem, CheckListView<CitationRelationItem> listView) {
+        BibEntry libraryEntry = citationRelationItem.localEntry();
+        BibEntry citationEntry = citationRelationItem.entry();
+        String leftHeader = Localization.lang("Library Entry");
+        String rightHeader = Localization.lang("Citation Entry");
+
+        MergeEntriesDialog dialog = new MergeEntriesDialog(libraryEntry, citationEntry, leftHeader, rightHeader, preferences);
+        dialog.setTitle(Localization.lang("Possible duplicate entries"));
+
+        Optional<EntriesMergeResult> entriesMergeResult = dialogService.showCustomDialogAndWait(dialog);
+        entriesMergeResult.ifPresentOrElse(mergeResult -> {
+
+            BibEntry mergedEntry = mergeResult.mergedEntry();
+            // update local entry of selected citation relation item
+            listView.getItems().set(listView.getItems().indexOf(citationRelationItem), new CitationRelationItem(citationRelationItem.entry(), mergedEntry, true));
+
+            // Merge method is similar to MergeTwoEntriesAction#execute
+            BibDatabase database = stateManager.getActiveDatabase().get().getDatabase();
+            database.removeEntry(mergeResult.originalLeftEntry());
+            libraryTab.getMainTable().setCitationMergeMode(true);
+            database.insertEntry(mergedEntry);
+
+            NamedCompound ce = new NamedCompound(Localization.lang("Merge entries"));
+            ce.addEdit(new UndoableRemoveEntries(database, mergeResult.originalLeftEntry()));
+            ce.addEdit(new UndoableInsertEntries(stateManager.getActiveDatabase().get().getDatabase(), mergedEntry));
+            ce.end();
+
+            undoManager.addEdit(ce);
+
+            dialogService.notify(Localization.lang("Merged entries"));
+        }, () -> dialogService.notify(Localization.lang("Canceled merging entries")));
+    }
 }

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationsRelationsTabViewModel.java

@@ -64,6 +64,7 @@ private void importCites(List<BibEntry> entries, BibEntry existingEntry, ImportH
 
         List<String> citeKeys = getExistingEntriesFromCiteField(existingEntry);
         citeKeys.removeIf(String::isEmpty);
+
         for (BibEntry entryToCite : entries) {
             if (generateNewKeyOnImport || entryToCite.getCitationKey().isEmpty()) {
                 String key = generator.generateKey(entryToCite);