Merge remote-tracking branch 'origin/main'

.github/workflows/deployment-arm64.yml

@@ -205,7 +205,7 @@ jobs:
         if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-latest') || ((matrix.os == 'macos-14') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
         shell: bash
         run: |
-          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload to GitHub workflow artifacts store (macOS)
         if: (matrix.os == 'macos-14') && (steps.checksecrets.outputs.secretspresent == 'YES') && (startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)
         uses: actions/upload-artifact@v4

.github/workflows/deployment-jdk-ea.yml

@@ -266,7 +266,7 @@ jobs:
         shell: cmd
         # for rsync installed by chocolatey, we need the ssh.exe delivered with that installation
         run: |
-          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/jdk-ea && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/jdk-ea/
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/jdk-ea && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/jdk-ea/ || true
       - name: Upload to builds.jabref.org (linux, macOS)
         if: (matrix.os != 'windows-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (github.ref == 'refs/heads/main')
         shell: bash

.github/workflows/deployment.yml

@@ -242,15 +242,15 @@ jobs:
         shell: cmd
         # for rsync installed by chocolatey, we need the ssh.exe delivered with that installation
         run: |
-          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload to builds.jabref.org (linux, macOS)
         # macOS: Negated condition of "Upload to GitHub workflow artifacts store (macOS)"
         #        Reason: We either upload the non-notarized files - or notarize the files later (and upload these later)
         # needs to be on one line; multi line does not work
         if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-latest') || ((matrix.os == 'macos-13') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
         shell: bash
         run: |
-          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
       - name: Upload to GitHub workflow artifacts store (macOS)
         if: (matrix.os == 'macos-13') && (steps.checksecrets.outputs.secretspresent == 'YES') && (startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)
         uses: actions/upload-artifact@v4

.github/workflows/tests.yml

@@ -347,6 +347,8 @@ jobs:
       - name: Setup Gradle
         uses: gradle/actions/setup-gradle@v4
       - run: ./gradlew traceRequirements
+      - if: failure()
+        run: cat build/reports/tracing.txt
 
   # This is https://github.com/marketplace/actions/gradle-wrapper-validation
   # It ensures that the jar file is from gradle and not by a strange third party.

.vscode/ltex.dictionary.en-US.txt

@@ -2,4 +2,5 @@ Checkstyle
 CouchDB
 JabDrive
 JabRef
+OpenFastTrace
 OpenRewrite

CHANGELOG.md

@@ -37,7 +37,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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)
+- By double clicking on a local citation in the Citation Relations Tab you can now jump the linked entry. [#11955](https://github.com/JabRef/jabref/pull/11955)
 
 ### Changed
 
@@ -54,6 +54,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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)
+- When importing BibTeX data starging from on a PDF, the XMP metadata takes precedence over Grobid data. [#11992](https://github.com/JabRef/jabref/pull/11992)
 - 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)
@@ -96,6 +97,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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)
 - We fixed an issue where <kbd>Tab</kbd> cannot be used to jump to next field in some single-line fields. [#11785](https://github.com/JabRef/jabref/issues/11785)
+- We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)
 
 ### Removed
 

CONTRIBUTING.md

@@ -14,6 +14,7 @@ Detailed instructions about this step can be found in our [guidelines for settin
 * [Getting a task assigned](#getting-a-task-assigned)
 * [Pull Request Process](#pull-request-process)
   * [Requirements on the pull request and code](#requirements-on-the-pull-request-and-code)
+  * [After submission of a pull request](#after-submission-of-a-pull-request)
   * [Development hints](#development-hints)
 
 ## Choosing a task [![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref)
@@ -126,6 +127,22 @@ More reading on that is available at <https://roe.dev/blog/using-ai-in-open-sour
 
 We reserve the right to reject pull requests that contain little or no genuine and original contribution from the contributor.
 
+### After submission of a pull request
+
+After you submitted a pull request, automated checks will run.
+You will maybe see "Some checks were not successful".
+Then, please look into them and handle accordingly.
+
+Afterwards, you will receive comments on it.
+Maybe, the pull request is approved immediatly, maybe changes are requested.
+In case changes are requested, please implement them.
+
+After changing your code, commit on the branch and push.
+The pull request will update automatically.
+
+Never ever close the pull request and open a new one.
+This causes much load on our side and is not the style of the GitHub open source community.
+
 ### Development hints
 
 #### When adding an external dependency
@@ -162,7 +179,7 @@ Add the above snippet to the English translation file located at `src/main/resou
 
 You can also directly run the specific test in your IDE.
 The test "`LocalizationConsistencyTest`" is placed under `src/test/java/org.jabref.logic.l10n/LocalizationConsistencyTest.java`.
-Find more information in the [JabRef developer docs](code-howtos/localization.md).
+Find more information in the [JabRef developer docs](https://devdocs.jabref.org/code-howtos/localization.html).
 
 #### **Format of keyboard shortcuts**
 

build.gradle

@@ -142,7 +142,7 @@ dependencyLocking {
 }
 
 javafx {
-    version = "23"
+    version = "23.0.1"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 

docs/code-howtos/ui-recommendations.md

@@ -23,6 +23,8 @@ More information:
 ### Name your buttons for the actions
 `req~ui.dialogs.confirmation.naming~1`
 
+Needs: impl
+
 ## Form validation
 
 * Only validate input after leaving the field (or after the user stopped typing for some time)

docs/decisions/0011-test-external-links-in-documentation.md

@@ -22,15 +22,16 @@ For high-quality documentation, external links should be working.
 
 ## Decision Outcome
 
-Chosen option: "\[option 1\]", because \[justification. e.g., only option, which meets k.o. criterion decision driver \| which resolves force force \| … \| comes out best \(see below\)\].
+Chosen option: "Check external links once a month", because it provides a basic quality baseline.
 
 ### Positive Consequences
 
 * Automatic notification of broken external links
 
 ### Negative Consequences
 
-* Some external sites need to [be disabled](https://github.com/JabRef/jabref/pull/6542/files). For instance, GitHub.com always returns "forbidden". A [filter for status is future work of the used tool](https://github.com/tcort/markdown-link-check/issues/94#issuecomment-634947466).
+* Some external sites need to [be disabled](https://github.com/JabRef/jabref/pull/6542/files). For instance, GitHub.com always returns "forbidden".
+* Contributors find it strange if external links are broken (example: [user-documentation#526](https://github.com/JabRef/user-documentation/pull/526#issuecomment-2416462977))
 
 ## Pros and Cons of the Options
 

docs/requirements/index.md

@@ -20,7 +20,7 @@ Example:
 It is important that there is no empty line directly after the heading.
 
 {: note}
-One needs to add `<!-- markdownlint-disable-file MD022 -->` to the end of the file, because the id of the requirement needs to follow the heading directly.
+One needs to add `<!-- markdownlint-disable-file MD022 -->` to the end of the file, because the ID of the requirement needs to follow the heading directly.
 
 ## Linking implementations
 

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

@@ -68,11 +68,9 @@ public void execute() {
             boolean confirmDownload = dialogService.showConfirmationDialogAndWait(
                     Localization.lang("Download full text documents"),
                     Localization.lang(
-                            "You are about to download full text documents for %0 entries.",
-                            String.valueOf(stateManager.getSelectedEntries().size())) + "\n"
-                            + Localization.lang("JabRef will send at least one request per entry to a publisher.")
-                            + "\n"
-                            + Localization.lang("Do you still want to continue?"),
+                            "You are attempting to download full text documents for %0 entries.\nJabRef will send at least one request per entry to a publisher.",
+                            String.valueOf(stateManager.getSelectedEntries().size())),
+                    // [impl->req~ui.dialogs.confirmation.naming~1]
                     Localization.lang("Download full text documents"),
                     Localization.lang("Cancel"));
 

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

@@ -25,6 +25,7 @@
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.database.DuplicateCheck;
 import org.jabref.logic.externalfiles.ExternalFilesContentImporter;
+import org.jabref.logic.importer.CompositeIdFetcher;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportCleanup;
 import org.jabref.logic.importer.ImportException;
@@ -359,22 +360,13 @@ public List<BibEntry> handleStringData(String data) throws FetcherException {
             return Collections.emptyList();
         }
 
-        Optional<DOI> doi = DOI.findInText(data);
-        if (doi.isPresent()) {
-            return fetchByDOI(doi.get());
+        if (!CompositeIdFetcher.containsValidId(data)) {
+            return tryImportFormats(data);
         }
 
-        Optional<ArXivIdentifier> arXiv = ArXivIdentifier.parse(data);
-        if (arXiv.isPresent()) {
-            return fetchByArXiv(arXiv.get());
-        }
-
-        Optional<ISBN> isbn = ISBN.parse(data);
-        if (isbn.isPresent()) {
-            return fetchByISBN(isbn.get());
-        }
-
-        return tryImportFormats(data);
+        CompositeIdFetcher compositeIdFetcher = new CompositeIdFetcher(preferences.getImportFormatPreferences());
+        Optional<BibEntry> optional = compositeIdFetcher.performSearchById(data);
+        return OptionalUtil.toList(optional);
     }
 
     private List<BibEntry> tryImportFormats(String data) {

src/main/java/org/jabref/gui/preferences/websearch/WebSearchTabViewModel.java

@@ -56,7 +56,7 @@ public class WebSearchTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty grobidEnabledProperty = new SimpleBooleanProperty();
     private final StringProperty grobidURLProperty = new SimpleStringProperty("");
 
-    private final ListProperty<FetcherApiKey> apiKeys = new SimpleListProperty<>();
+    private final ObservableList<FetcherApiKey> apiKeys = FXCollections.observableArrayList();
     private final ObjectProperty<FetcherApiKey> selectedApiKeyProperty = new SimpleObjectProperty<>();
     private final BooleanProperty apikeyPersistProperty = new SimpleBooleanProperty();
     private final BooleanProperty apikeyPersistAvailableProperty = new SimpleBooleanProperty();
@@ -138,7 +138,10 @@ public void setValues() {
         grobidEnabledProperty.setValue(grobidPreferences.isGrobidEnabled());
         grobidURLProperty.setValue(grobidPreferences.getGrobidURL());
 
-        apiKeys.setValue(FXCollections.observableArrayList(preferences.getImporterPreferences().getApiKeys()));
+        apiKeys.setAll(preferences.getImporterPreferences().getApiKeys().stream()
+                                  .map(apiKey -> new FetcherApiKey(apiKey.getName(), apiKey.shouldUse(), apiKey.getKey()))
+                                  .toList());
+
         apikeyPersistAvailableProperty.setValue(OS.isKeyringAvailable());
         apikeyPersistProperty.setValue(preferences.getImporterPreferences().shouldPersistCustomKeys());
         catalogs.addAll(WebFetchers.getSearchBasedFetchers(importFormatPreferences, importerPreferences)
@@ -213,7 +216,7 @@ public StringProperty grobidURLProperty() {
         return grobidURLProperty;
     }
 
-    public ListProperty<FetcherApiKey> fetcherApiKeys() {
+    public ObservableList<FetcherApiKey> fetcherApiKeys() {
         return apiKeys;
     }
 

src/main/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporter.java

@@ -49,10 +49,10 @@ public PdfMergeMetadataImporter(ImportFormatPreferences importFormatPreferences)
         this.metadataImporters = new ArrayList<>(5);
         this.metadataImporters.add(new PdfVerbatimBibtexImporter(importFormatPreferences));
         this.metadataImporters.add(new PdfEmbeddedBibFileImporter(importFormatPreferences));
+        this.metadataImporters.add(new PdfXmpImporter(importFormatPreferences.xmpPreferences()));
         if (importFormatPreferences.grobidPreferences().isGrobidEnabled()) {
             this.metadataImporters.add(new PdfGrobidImporter(importFormatPreferences));
         }
-        this.metadataImporters.add(new PdfXmpImporter(importFormatPreferences.xmpPreferences()));
         this.metadataImporters.add(new PdfContentImporter());
     }