Merge branch 'main' into fix-for-issue-JabRef#12272

Author: oops-shlok

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Keep ALL the items. Mark them as follows:
 [/] not applicable
 -->
 
-- [x] I own the copyright of the code submitted and I licence it under the [MIT license](https://github.com/JabRef/jabref/blob/main/LICENSE)
+- [x] I own the copyright of the code submitted and I license it under the [MIT license](https://github.com/JabRef/jabref/blob/main/LICENSE)
 - [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if change is visible to the user)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)

.github/ghprcomment.yml

@@ -9,8 +9,8 @@
   message: >
     Your code does not compile.
     Please ensure your changes compile successfully before pushing changes.
-   
-    
+
+
     To verify compilation locally, run `./gradlew build` or try running JabRef.
 - jobName: 'Conflicts with target branch'
   message: >
@@ -64,7 +64,7 @@
     Force pushing is a very bad practice when working together on a project (mainly because it is [not supported well by GitHub itself](https://github.com/orgs/community/discussions/3478)).
     Commits are lost and comments on commits lose their context, thus making it harder to review changes.
     At the end, all commits will be [squashed](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-commits) anyway before being merged into the `main` branch.
-- jobName: 'Mark issue as in progress'
+- jobName: 'Determine issue number'
   message: |
     Your pull request needs to link an issue.
 

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

@@ -25,42 +25,59 @@ jobs:
           bodyRegex: '#(?<ticketNumber>\d+)'
           bodyURLRegex: 'http(s?):\/\/(github.com)(\/:owner)(\/:repo)(\/issues)\/(?<ticketNumber>\d+)'
           outputOnly: true
+      - uses: actions/checkout@v4
+      - name: Remove assignee
+        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-assignee ${{ github.event.pull_request.user.login }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Check assignees
+        id: check_assignee
+        run: |
+          issue=$(gh issue view ${{ steps.get_issue_number.outputs.ticketNumber }} --json assignees)
+          count=$(echo "$issue" | jq '.assignees | length')
+          if [ "$count" -gt 0 ]; then
+            echo "assigned=yes" >> $GITHUB_OUTPUT
+          else
+            echo "assigned=no" >> $GITHUB_OUTPUT
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Remove assigned label
+        if: steps.check_assignee.outputs.assigned == 'no'
+        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📍 Assigned"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Remove pinned label
+        if: steps.check_assignee.outputs.assigned == 'no'
+        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📌 Pinned"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Remove FirstTimeCodeContribution label
+        if: steps.check_assignee.outputs.assigned == 'no'
+        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "FirstTimeCodeContribution"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Move issue to "Free to take" in "Good First Issues"
+        if: steps.check_assignee.outputs.assigned == 'no'
         uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/5"
           target-labels: "📍 Assigned"
-          target-column: "Free to take"
+          target-column: "Assigned"
           ignored-columns: ""
           default-column: "Free to take"
           issue-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
           skip-if-not-in-project: true
       - name: Move issue to "Free to take" in "Candidates for University Projects"
+        if: steps.check_assignee.outputs.assigned == 'no'
         uses: m7kvqbe1/github-action-move-issues/@add-issue-parameter
         with:
           github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
           project-url: "https://github.com/orgs/JabRef/projects/3"
           target-labels: "📍 Assigned"
-          target-column: "Free to take"
+          target-column: "Assigned"
           ignored-columns: ""
           default-column: "Free to take"
           issue-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
           skip-if-not-in-project: true
-      - uses: actions/checkout@v4
-      - name: Remove assigned status
-        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-assignee ${{ github.event.pull_request.user.login }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Remove assigned label
-        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📍 Assigned"
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Remove pinned label
-        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📌 Pinned"
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Remove FirstTimeCodeContribution label
-        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "FirstTimeCodeContribution"
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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

@@ -5,6 +5,23 @@ on:
   pull_request_target:
 
 jobs:
+  determine_issue_number:
+    name: Determine issue number
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Determine issue number
+        uses: koppor/ticket-check-action@add-output
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ticketLink: 'https://github.com/:owner/:repo/issues/%ticketNumber%'
+          ticketPrefix: '#'
+          titleRegex: '^#(?<ticketNumber>\d+)'
+          branchRegex: '^(?<ticketNumber>\d+)'
+          bodyRegex: '#(?!12345\b)(?<ticketNumber>\d+)'
+          bodyURLRegex: 'http(s?):\/\/(github.com)(\/JabRef)(\/jabref)(\/issues)\/(?<ticketNumber>\d+)'
+          outputOnly: true
   move_issue:
     name: Mark issue as in progress
     runs-on: ubuntu-latest
@@ -20,7 +37,7 @@ jobs:
           ticketPrefix: '#'
           titleRegex: '^#(?<ticketNumber>\d+)'
           branchRegex: '^(?<ticketNumber>\d+)'
-          bodyRegex: '#(?<ticketNumber>\d+)'
+          bodyRegex: '#(?!12345\b)(?<ticketNumber>\d+)'
           bodyURLRegex: 'http(s?):\/\/(github.com)(\/JabRef)(\/jabref)(\/issues)\/(?<ticketNumber>\d+)'
           outputOnly: true
       - name: Move issue to "In Progress" in "Good First Issues"
@@ -45,18 +62,40 @@ jobs:
           default-column: "In Progress"
           issue-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
           skip-if-not-in-project: true
+  ensure_assignment:
+    name: Ensure that contributor is assigned (fails if not commented on issue)
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Determine issue number
+        id: get_issue_number
+        uses: koppor/ticket-check-action@add-output
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ticketLink: 'https://github.com/:owner/:repo/issues/%ticketNumber%'
+          ticketPrefix: '#'
+          titleRegex: '^#(?<ticketNumber>\d+)'
+          branchRegex: '^(?<ticketNumber>\d+)'
+          bodyRegex: '#(?!12345\b)(?<ticketNumber>\d+)'
+          bodyURLRegex: 'http(s?):\/\/(github.com)(\/JabRef)(\/jabref)(\/issues)\/(?<ticketNumber>\d+)'
+          outputOnly: true
       - uses: actions/checkout@v4
         with:
           show-progress: 'false'
       - name: Assign PR creator to issue
-        # "gh issue edit" cannot be used - workaround found at https://github.com/cli/cli/issues/9620#issuecomment-2703135049
-        run: gh api -X PATCH /repos/JabRef/jabref/issues/${{ steps.get_issue_number.outputs.ticketNumber }} -f assignee=${{ github.event.pull_request.user.login }}
+        run: |
+          # "gh issue edit" cannot be used - workaround found at https://github.com/cli/cli/issues/9620#issuecomment-2703135049
+          ASSIGNEES=$(gh api /repos/JabRef/jabref/issues/${{ steps.get_issue_number.outputs.ticketNumber }} --jq '[.assignees[].login] | @json')
+          UPDATED_ASSIGNEES=$(echo $ASSIGNEES | jq --arg new "${{ github.event.pull_request.user.login }}" '. + [$new] | @json')
+          gh api -X PATCH /repos/JabRef/jabref/issues/${{ steps.get_issue_number.outputs.ticketNumber }} --input <(echo "{\"assignees\": $UPDATED_ASSIGNEES}")
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Add label "📌 Pinned"
         run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --add-label "📌 Pinned"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
   conflicts_with_target:
     name: Conflicts with target branch
     runs-on: ubuntu-latest

.github/workflows/unassign-issues.yml

@@ -23,7 +23,7 @@ jobs:
           unassigned_comment: |
             ### 📋 Assignment Update
 
-            Hi @{{ handle }}, you are no longer assigned to this issue.
+            Hi @{{ handle }}, due to inactivity, you have been unassigned from this issue.
 
             <details open>
             <summary>Next steps</summary>

CHANGELOG.md

@@ -82,6 +82,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where JabRef displayed an incorrect deletion notification when canceling entry deletion [#12645](https://github.com/JabRef/jabref/issues/12645)
 - We fixed an issue where JabRef displayed an incorrect deletion notification when canceling entry deletion. [#12645](https://github.com/JabRef/jabref/issues/12645)
 - We fixed an issue where an exception would occur when running abbreviate journals for multiple entries. [#12634](https://github.com/JabRef/jabref/issues/12634)
+- We fixed an issue where JabRef displayed dropdown triangle in wrong place in "Search for unlinked local files" dialog [#12713](https://github.com/JabRef/jabref/issues/12713)
 
 ### Removed
 

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

@@ -2492,3 +2492,7 @@ journalInfo .grid-cell-b {
 #styleSelectDialog .currentStyleNameLabel {
     -fx-font-size: 1em; -fx-font-weight: bold; -fx-text-fill: -jr-theme;
 }
+
+.refresh {
+    -fx-background-color: transparent;
+}

src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogView.java

@@ -60,6 +60,8 @@
 
 public class UnlinkedFilesDialogView extends BaseDialog<Void> {
 
+    private static final String REFRESH_CLASS = "refresh";
+
     @FXML private TextField directoryPathField;
     @FXML private ComboBox<FileExtensionViewModel> fileTypeCombo;
     @FXML private ComboBox<DateRange> fileDateCombo;
@@ -272,6 +274,12 @@ void startImport() {
 
         // Already imported files should not be re-added at a second click on "Import". Therefore, all imported files are unchecked.
         unlinkedFilesList.getCheckModel().clearChecks();
+
+        // JavaFX does not re-render everything necessary after the file import, and hence it ends up with some misalignment (see https://github.com/JabRef/jabref/issues/12713). Thus, we remove and add the CSS property to force it to re-render.
+        Platform.runLater(() -> {
+            accordion.getStyleClass().remove(REFRESH_CLASS);
+            accordion.getStyleClass().add(REFRESH_CLASS);
+        });
     }
 
     @FXML

src/test/java/org/jabref/logic/importer/fetcher/ACMPortalFetcherTest.java

@@ -11,6 +11,7 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.types.StandardEntryType;
+import org.jabref.support.DisabledOnCIServer;
 import org.jabref.testutils.category.FetcherTest;
 
 import org.apache.lucene.queryparser.flexible.core.QueryNodeParseException;
@@ -23,6 +24,7 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 @FetcherTest
+@DisabledOnCIServer("ACM replied with 403 Forbidden on 2025-03-17")
 class ACMPortalFetcherTest {
     ACMPortalFetcher fetcher;
 

src/test/java/org/jabref/logic/importer/fetcher/CrossRefTest.java

@@ -131,7 +131,7 @@ void performSearchByIdFindsPaperWithoutTitle() throws Exception {
         entry.setField(StandardField.YEAR, "1999");
         entry.setField(StandardField.JOURNAL, "Indo-Iranian Journal");
         entry.setField(StandardField.NUMBER, "2");
-        entry.setField(StandardField.PUBLISHER, "Brill");
+        entry.setField(StandardField.PUBLISHER, "Walter de Gruyter GmbH");
 
         assertEquals(Optional.of(entry), fetcher.performSearchById("10.1023/a:1003473214310"));
     }