Merge remote-tracking branch 'upstream/main'

* upstream/main:
  Add missing variables
  Reformat BibTex in Show BibTex Source (#13761)
  Auto publish before JBang tests (#13779)
  Hotfix: calling of publish.yml
  Support BibLaTeX datamodel validations (#13693)
  Auto add and remove of "status: changes-required" label (#13778)
  New Crowdin updates (#13777)
  Restore local-only Git behavior for SLR to fix repository initialization error (#13775)
  Use vanilla hashset (#13771)
  Fix Springer Fetcher names (#13770)
  Fix condition
  Publish SNAPSHOT on jablib change (#13774)
  Adapt as per new set of checks (#13772)
  Bump jablib/src/main/resources/csl-styles from `1194364` to `17cfa60` (#13750)

Author: Siedlerchr

.github/workflows/on-pr-changes-requested.yml

@@ -0,0 +1,18 @@
+name: Adapt PR status labels
+
+on:
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  label-changes-required:
+    if: github.event.review.state == 'changes_requested'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Adapt labels
+        run: |
+          gh issue --repo ${{ github.repository }} edit ${{ github.event.pull_request.number }} --remove-label "status: ready-for-review"
+          gh issue --repo ${{ github.repository }} edit ${{ github.event.pull_request.number }} --remove-label "status: awaiting-second-review"
+          gh issue --repo ${{ github.repository }} edit ${{ github.event.pull_request.number }} --add-label "status: changes-required"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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

@@ -160,6 +160,12 @@ jobs:
           echo "✅ No merge conflicts"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  remove_label:
+    if: github.repository == 'JabRef/jabref'
+    name: Remove label "status: changes-required"
+    runs-on: ubuntu-latest
+    steps:
+      - run: gh issue --repo ${{ github.repository }} edit ${{ github.event.pull_request.number }} --remove-label "status: changes-required"
   upload-pr-number:
     if: github.repository == 'JabRef/jabref'
     runs-on: ubuntu-latest

.github/workflows/publish.yml

@@ -1,17 +1,25 @@
 name: Publish to maven central
 
 on:
-  pull_request:
-    paths:
-     - .github/workflows/publish.yml
+  # On releases
   push:
-    paths:
-     - .github/workflows/publish.yml
     tags:
-      - '*'
-  schedule:
-    # run on each Monday
-    - cron: '2 3 * * 1'
+      - '**'
+
+  # Called by the JBang testing jobs to ensure that SNAPSHOT is uptodate
+  workflow_call:
+    secrets:
+      KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64:
+        required: true
+      KOPPOR_SIGNING_KEYID:
+        required: true
+      KOPPOR_SIGNING_PASSWORD:
+        required: true
+      KOPPOR_MAVENCENTRALUSERNAME:
+        required: true
+      KOPPOR_MAVENCENTRALPASSWORD:
+        required: true
+
   workflow_dispatch:
     inputs:
       tagbuild:
@@ -20,6 +28,11 @@ on:
         default: false
         type: boolean
 
+  # Additional run in addition to the other events, because some resources could have changes
+  schedule:
+    # Run on each Monday
+    - cron: '2 3 * * 1'
+
 permissions:
   actions: write
   contents: read
@@ -34,9 +47,33 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  detect_changes:
+    runs-on: ubuntu-latest
+    outputs:
+      changed: ${{ steps.changed.outputs.any_changed }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+      - name: Detect changed jablib classes or workflow
+        id: changed
+        uses: tj-actions/changed-files@v45
+        with:
+          files: |
+            jablib/src/main/java/**/*.java
+            .github/workflows/publish.yml
+
   publish:
     name: jablib
-    if: github.repository == 'JabRef/jabref'
+    needs: detect_changes
+    if: >
+      github.event_name == 'schedule' ||
+      github.event_name == 'workflow_dispatch' ||
+      (needs.detect_changes.outputs.changed == 'true' &&
+        ((github.event_name == 'workflow_call' && github.repository == 'JabRef/jabref') ||
+         (github.event_name == 'push' && github.repository == 'JabRef/jabref') ||
+         (github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == 'JabRef/jabref'))
+      )
     runs-on: ubuntu-latest
     steps:
       - name: Fetch all history for all tags and branches

.github/workflows/tests-code.yml

@@ -22,6 +22,9 @@ concurrency:
   cancel-in-progress: true
 
 permissions:
+  # required for publish.yml
+  actions: write
+  contents: read
   pull-requests: write
 
 jobs:
@@ -393,9 +396,20 @@ jobs:
           CI: "true"
           DBMS: "postgresql"
 
+  publish:
+    if: github.ref == 'refs/heads/main'
+    uses: ./.github/workflows/publish.yml
+    secrets:
+      KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64: ${{ secrets.KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64 }}
+      KOPPOR_SIGNING_KEYID: ${{ secrets.KOPPOR_SIGNING_KEYID }}
+      KOPPOR_SIGNING_PASSWORD: ${{ secrets.KOPPOR_SIGNING_PASSWORD }}
+      KOPPOR_MAVENCENTRALUSERNAME: ${{ secrets.KOPPOR_MAVENCENTRALUSERNAME }}
+      KOPPOR_MAVENCENTRALPASSWORD: ${{ secrets.KOPPOR_MAVENCENTRALPASSWORD }}
+
   jbang:
     name: JBang (main)
     runs-on: ubuntu-latest
+    needs: publish
     if: github.ref == 'refs/heads/main'
     steps:
       - name: Checkout source
@@ -431,6 +445,7 @@ jobs:
   jbang-pr:
     name: JBang (PR)
     runs-on: ubuntu-latest
+    # does not need publish, because the JBang scripts are modified
     if: github.ref != 'refs/heads/main'
     strategy:
       fail-fast: false

.github/workflows/tests-pr.yml

@@ -127,8 +127,8 @@ jobs:
 
           LINE_COUNT=$(echo "$BOXES" | wc -l)
 
-          if [ "$LINE_COUNT" -ne 7 ]; then
-            echo "❌ Found $LINE_COUNT lines instead of 7 required lines"
+          if [ "$LINE_COUNT" -ne 6 ]; then
+            echo "❌ Found $LINE_COUNT lines instead of 6 required lines"
             exit 1
           fi
 

CHANGELOG.md

@@ -32,6 +32,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When relativizing file names, symlinks are now taken into account. [#12995](https://github.com/JabRef/jabref/issues/12995)
 - We added a new button for shortening the DOI near the DOI field in the general tab when viewing an entry. [#13639](https://github.com/JabRef/jabref/issues/13639)
 - We added support for finding CSL-Styles based on their short title (e.g. apa instead of "american psychological association"). [#13728](https://github.com/JabRef/jabref/pull/13728)
+- We added BibLaTeX datamodel validation support in order to improve error message quality in entries' fields validation. [#13318](https://github.com/JabRef/jabref/issues/13318)
 
 ### Changed
 
@@ -72,6 +73,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We improved JabRef's internal document viewer. It now allows text section, searching and highlighting of search terms and page rotation [#13193](https://github.com/JabRef/jabref/pull/13193).
 - When importing a PDF, there is no empty entry column shown in the multi merge dialog. [#13132](https://github.com/JabRef/jabref/issues/13132)
 - We added a progress dialog to the "Check consistency" action and progress output to the corresponding cli command. [#12487](https://github.com/JabRef/jabref/issues/12487)
+- The BibTeX source is now formatted using the JabRef style at the import inspection dialog. [#13015](https://github.com/JabRef/jabref/issues/13015)
 - We made the `check-consistency` command of the toolkit always return an exit code; 0 means no issues found, a non-zero exit code reflects any issues, which allows CI to fail in these cases [#13328](https://github.com/JabRef/jabref/issues/13328).
 - We changed the validation error dialog for overriding the default file directories to a confirmation dialog for saving other preferences under the library properties. [#13488](https://github.com/JabRef/jabref/pull/13488)
 - We made the copy sub menu on the context menu consistent with the copy sub menu at "Edit". [#13280](https://github.com/JabRef/jabref/pull/13280)

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

@@ -125,9 +125,11 @@ public String getSourceString(BibEntry entry) {
         BibWriter bibWriter = new BibWriter(writer, OS.NEWLINE);
         FieldWriter fieldWriter = FieldWriter.buildIgnoreHashes(preferences.getFieldPreferences());
         try {
-            new BibEntryWriter(fieldWriter, entryTypesManager).write(entry, bibWriter, selectedDb.getValue().getMode());
+            // Force reformatting so the displayed BibTeX is consistently formatted
+            new BibEntryWriter(fieldWriter, entryTypesManager).write(entry, bibWriter, selectedDb.getValue().getMode(), true);
         } catch (IOException ioException) {
-            return "";
+            // In case of error, fall back to the original parsed serialization if available
+            return entry.getParsedSerialization();
         }
         return writer.toString();
     }

jabgui/src/main/java/org/jabref/gui/slr/ManageStudyDefinitionViewModel.java

@@ -28,7 +28,7 @@
 import org.jabref.logic.importer.fetcher.CompositeSearchBasedFetcher;
 import org.jabref.logic.importer.fetcher.DBLPFetcher;
 import org.jabref.logic.importer.fetcher.IEEE;
-import org.jabref.logic.importer.fetcher.SpringerFetcher;
+import org.jabref.logic.importer.fetcher.SpringerNatureWebFetcher;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.study.Study;
 import org.jabref.model.study.StudyDatabase;
@@ -48,7 +48,7 @@ public class ManageStudyDefinitionViewModel {
     private static final Set<String> DEFAULT_SELECTION = Set.of(
             ACMPortalFetcher.FETCHER_NAME,
             IEEE.FETCHER_NAME,
-            SpringerFetcher.FETCHER_NAME,
+            SpringerNatureWebFetcher.FETCHER_NAME,
             DBLPFetcher.FETCHER_NAME);
 
     private final StringProperty title = new SimpleStringProperty();

jabgui/src/main/java/org/jabref/gui/slr/StartNewStudyAction.java

@@ -64,7 +64,9 @@ protected void crawlPreparation(Path studyRepositoryRoot) throws IOException, Gi
         // The GitHandler is already called to initialize the repository with one single commit "Initial commit".
         // The "Initial commit" should also contain the created YAML.
         // Thus, we append to that commit.
-        new GitHandler(studyRepositoryRoot).createCommitOnCurrentBranch("Initial commit", true);
+        GitHandler gitHandler = new GitHandler(studyRepositoryRoot);
+        gitHandler.initIfNeeded();
+        gitHandler.createCommitOnCurrentBranch("Initial commit", true);
     }
 
     @Override

jablib/src/main/java/org/jabref/logic/biblog/BibtexLogParser.java

@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.regex.Matcher;
@@ -19,52 +18,88 @@
  * Parses the contents of a .blg (BibTeX log) file to extract warning messages.
  */
 public class BibtexLogParser {
-    private static final Pattern WARNING_PATTERN = Pattern.compile("^Warning--(?<message>[a-zA-Z ]+) in (?<entryKey>[^\\s]+)$");
+    private static final Pattern BIBTEX_WARNING_PATTERN = Pattern.compile("^Warning--(?<message>[a-zA-Z ]+) in (?<entryKey>[^\\s]+)$");
+    private static final Pattern BIBLATEX_WARNING_PATTERN = Pattern.compile(
+            "(?:(?:\\[\\d+\\] )?Biber\\.pm:\\d+> )?WARN - Datamodel: [a-z]+ entry '(?<entryKey>[^']+)' \\((?<fileName>[^)]+)\\): (?<message>.+)");
+
     private static final String EMPTY_FIELD_PREFIX = "empty";
+    private static final String INVALID_FIELD_PREFIX = "field '";
+    private static final String MULTI_INVALID_FIELD_PREFIX = "field - one of '";
 
     public List<BibWarning> parseBiblog(@NonNull Path blgFilePath) throws IOException {
-        List<BibWarning> warnings = new ArrayList<>();
-        List<String> lines = Files.readAllLines(blgFilePath);
-        for (String line : lines) {
-            Optional<BibWarning> potentialWarning = parseWarningLine(line);
-            potentialWarning.ifPresent(warnings::add);
-        }
-        return warnings;
+        return Files.lines(blgFilePath)
+                    .map(this::parseWarningLine)
+                    .flatMap(Optional::stream)
+                    .toList();
     }
 
-    /**
-     * Parses a single line from the .blg file to identify a warning.
-     * <p>
-     * Currently supports parsing warnings of the format:
-     * <pre>
-     * Warning--[message] in [entryKey]
-     * </pre>
-     * For example: {@code Warning--empty journal in Scholey_2013}
-     *
-     * @param line a single line from the .blg file
-     * @return an Optional containing a {@link BibWarning} if a match is found, or empty otherwise
-     */
-    private Optional<BibWarning> parseWarningLine(String line) {
-        // TODO: Support additional warning formats
-        Matcher matcher = WARNING_PATTERN.matcher(line);
-        if (!matcher.find()) {
-            return Optional.empty();
+    /// Parses a single line from a .blg file to identify a warning.
+    ///
+    /// This method supports two warning formats:
+    ///
+    /// 1.  **BibTeX Warnings:** Simple warnings from the legacy BibTeX backend.
+    ///     `Warning--[message] in [entryKey]`
+    ///     For example: `Warning--empty journal in Scholey_2013`
+    ///
+    /// 2.  **BibLaTeX Datamodel Warnings:** Detailed warnings from the Biber backend, including datamodel validation issues.
+    ///     `[Log line] > WARN - Datamodel: [entry type] entry '[entryKey]' ([fileName]): [message]`
+    ///     For example: `Biber.pm:123> WARN - Datamodel: article entry 'Scholey_2013' (file.bib): Invalid field 'journal'`
+    ///
+    /// @param line The single line from the .blg file to parse.
+    ///
+    /// @returns An `Optional` containing a `BibWarning` if a match is found, or an empty `Optional` otherwise.
+    Optional<BibWarning> parseWarningLine(String line) {
+        Matcher bibtexMatcher = BIBTEX_WARNING_PATTERN.matcher(line);
+        if (bibtexMatcher.find()) {
+            String message = bibtexMatcher.group("message").trim();
+            String entryKey = bibtexMatcher.group("entryKey");
+            // Extract field name for warnings related to empty fields  (e.g., "empty journal" -> fieldName = "journal")
+            String fieldName = null;
+            if (message.startsWith(EMPTY_FIELD_PREFIX)) {
+                fieldName = message.substring(EMPTY_FIELD_PREFIX.length()).trim();
+                fieldName = FieldFactory.parseField(fieldName).getName();
+            }
+
+            return Optional.of(new BibWarning(
+                    SeverityType.WARNING,
+                    message,
+                    fieldName,
+                    entryKey
+            ));
         }
 
-        String message = matcher.group("message").trim();
-        String entryKey = matcher.group("entryKey");
-        // Extract field name for warnings related to empty fields  (e.g., "empty journal" -> fieldName = "journal")
-        String fieldName = null;
-        if (message.startsWith(EMPTY_FIELD_PREFIX)) {
-            fieldName = message.substring(EMPTY_FIELD_PREFIX.length()).trim();
-            fieldName = FieldFactory.parseField(fieldName).getName();
+        Matcher biblatexMatcher = BIBLATEX_WARNING_PATTERN.matcher(line);
+        if (biblatexMatcher.find()) {
+            String message = biblatexMatcher.group("message").trim();
+            String entryKey = biblatexMatcher.group("entryKey");
+            String fieldName = null;
+
+            // Extract field name for warnings related to invalid fields (e.g., "Invalid field 'publisher' for entrytype 'article'" -> fieldName = "publisher")
+            String lowerCaseMessage = message.toLowerCase();
+            if (lowerCaseMessage.contains(INVALID_FIELD_PREFIX)) {
+                int startIndex = lowerCaseMessage.indexOf(INVALID_FIELD_PREFIX) + INVALID_FIELD_PREFIX.length();
+                int endIndex = lowerCaseMessage.indexOf('\'', startIndex);
+                if (endIndex != -1) {
+                    fieldName = lowerCaseMessage.substring(startIndex, endIndex).trim();
+                    fieldName = FieldFactory.parseField(fieldName).getName();
+                }
+            } else if (lowerCaseMessage.contains(MULTI_INVALID_FIELD_PREFIX)) {
+                int startIndex = lowerCaseMessage.indexOf(MULTI_INVALID_FIELD_PREFIX) + MULTI_INVALID_FIELD_PREFIX.length();
+                int endIndex = lowerCaseMessage.indexOf('\'', startIndex);
+                if (endIndex != -1) {
+                    fieldName = lowerCaseMessage.substring(startIndex, endIndex).trim().split(",")[0].trim();
+                    fieldName = FieldFactory.parseField(fieldName).getName();
+                }
+            }
+
+            return Optional.of(new BibWarning(
+                    SeverityType.WARNING,
+                    message,
+                    fieldName,
+                    entryKey
+            ));
         }
 
-        return Optional.of(new BibWarning(
-                SeverityType.WARNING,
-                message,
-                fieldName,
-                entryKey
-        ));
+        return Optional.empty();
     }
 }