Merge remote-tracking branch 'upstream/main' into feature/arXivId

* upstream/main: (29 commits) Bump org.glassfish.jersey.containers:jersey-container-grizzly2-http (JabRef#12384) Bump src/main/resources/csl-styles from `080516e` to `6bae16d` (JabRef#12387) Bump src/main/resources/csl-locales from `96d704d` to `9914965` (JabRef#12386) Bump buildres/abbrv.jabref.org from `93a2cad` to `e74e6eb` (JabRef#12385) Bump org.openrewrite.rewrite from 6.29.3 to 7.0.0 (JabRef#12383) Bump org.glassfish.jersey.core:jersey-server from 3.1.9 to 3.1.10 (JabRef#12381) Bump org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2 (JabRef#12380) fix linux build not updated Refactor the isUnwantedText (JabRef#12369) Searching for entries with empty field (JabRef#12376) Downgrade Ubuntu (JabRef#12375) Downgrade Ubuntu Fix main table sorting (JabRef#12371) fix bib and pdf name (JabRef#12366) use v4 instead of master Update abbrv.jabref.org (JabRef#12365) Bump buildres/abbrv.jabref.org from `78e1b08` to `c202741` (JabRef#12363) Bump org.beryx.jlink from 3.1.0-rc-1 to 3.1.1 (JabRef#12362) Bump tech.units:indriya from 2.2.1 to 2.2.2 (JabRef#12361) Bump com.dlsc.gemsfx:gemsfx from 2.80.0 to 2.81.0 (JabRef#12360) ... # Conflicts: # buildres/abbrv.jabref.org # src/main/resources/csl-styles
ar-rana · Jan 13, 2025 · 0308a0b · 0308a0b
2 parents 1512d7e + b701821
commit 0308a0b
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diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -245,7 +245,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Download from GitHub workflow artifacts store (macOS)
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v4
         with:
           name: JabRef-macOS-arm-tbn
           path: build/distribution/

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -37,10 +37,10 @@ jobs:
   build:
     strategy:
       fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-13]
+      matrix: # if you change the os version rename all other occurrences
+        os: [ubuntu-22.04, windows-latest, macos-13]
         include:
-          - os: ubuntu-latest
+          - os: ubuntu-22.04
             displayName: linux
             archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
           - os: windows-latest
@@ -75,7 +75,7 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install pigz and cache (linux)
-        if: (matrix.os == 'ubuntu-latest')
+        if: (matrix.os == 'ubuntu-22.04')
         uses: awalsh128/cache-apt-pkgs-action@latest
         with:
           packages: pigz
@@ -212,7 +212,7 @@ jobs:
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Repack deb file for Debian
-        if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        if: (matrix.os == 'ubuntu-22.04') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           cd build/distribution
@@ -247,7 +247,7 @@ jobs:
         # 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)))) }}
+        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-22.04') || ((matrix.os == 'macos-13') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)))) }}
         shell: bash
         run: |
           rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ 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 }}/ || true
@@ -268,7 +268,7 @@ jobs:
           compression-level: 0 # no compression
   announce:
     name: Comment on pull request
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     needs: [build]
     if: ${{ github.event_name == 'pull_request' }}
     steps:
@@ -314,7 +314,7 @@ jobs:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Download from GitHub workflow artifacts store (macOS)
         if: (steps.checksecrets.outputs.secretspresent == 'YES')
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v4
         with:
           name: JabRef-macOS-tbn
           path: build/distribution/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,10 +13,18 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
+- We improved the offline parsing of BibTeX data from PDF-documents. [#12278](/~https://github.com/JabRef/jabref/issues/12278)
+
 ### Fixed
 
+- We fixed an issue where a bib file with UFF-8 charset was wrongly loaded with a different charset [forum#5369](https://discourse.jabref.org/t/jabref-5-15-opens-bib-files-with-shift-jis-encoding-instead-of-utf-8/5369/)
+- We fixed an issue where new entries were inserted in the middle of the table instead of at the end. [#12371](/~https://github.com/JabRef/jabref/pull/12371)
+- We fixed an issue where removing the sort from the table did not restore the original order. [#12371](/~https://github.com/JabRef/jabref/pull/12371)
+
 ### Removed
 
+- "Web of Science" [journal abbreviation list](https://docs.jabref.org/advanced/journalabbreviations) was removed. [abbrv.jabref.org#176](/~https://github.com/JabRef/abbrv.jabref.org/issues/176)
+
 ## [6.0-alpha] – 2024-12-23
 
 ### Added

diff --git a/build.gradle b/build.gradle
@@ -15,7 +15,7 @@ plugins {
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
-    id 'org.beryx.jlink' version '3.1.0-rc-1'
+    id 'org.beryx.jlink' version '3.1.1'
 
     // nicer test outputs during running and completion
     // Homepage: /~https://github.com/radarsh/gradle-test-logger-plugin
@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.29.0'
+    id 'org.openrewrite.rewrite' version '7.0.0'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -211,7 +211,7 @@ dependencies {
 
     implementation 'com.fasterxml:aalto-xml:1.3.3'
 
-    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.9'
+    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.12'
 
     implementation 'org.postgresql:postgresql:42.7.4'
 
@@ -243,8 +243,8 @@ dependencies {
         exclude group: 'org.openjfx'
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
-    implementation 'org.fxmisc.richtext:richtextfx:0.11.3'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.80.0') {
+    implementation 'org.fxmisc.richtext:richtextfx:0.11.4'
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.81.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.apache.commons.validator'
@@ -256,7 +256,7 @@ dependencies {
         exclude group: 'tech.units'
     }
     // Required by gemsfx
-    implementation 'tech.units:indriya:2.2.1'
+    implementation 'tech.units:indriya:2.2.2'
     // Required by gemsfx and langchain4j
     implementation ('com.squareup.retrofit2:retrofit:2.11.0') {
         exclude group: 'com.squareup.okhttp3'
@@ -281,7 +281,7 @@ dependencies {
     // route all requests to log4j to SLF4J
     implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.3'
 
-    implementation('de.undercouch:citeproc-java:3.1.0') {
+    implementation('de.undercouch:citeproc-java:3.2.0') {
         exclude group: 'org.antlr'
     }
 
@@ -308,7 +308,7 @@ dependencies {
     // API
     implementation 'jakarta.ws.rs:jakarta.ws.rs-api:4.0.0'
     // Implementation of the API
-    implementation 'org.glassfish.jersey.core:jersey-server:3.1.9'
+    implementation 'org.glassfish.jersey.core:jersey-server:3.1.10'
     // injection framework
     implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.9'
     implementation 'org.glassfish.hk2:hk2-api:3.1.1'
@@ -317,8 +317,8 @@ dependencies {
     // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
     // HTTP server
     // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
-    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.9'
-    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.9'
+    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.10'
+    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.10'
     // Allow objects "magically" to be mapped to JSON using GSON
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
 
@@ -358,7 +358,7 @@ dependencies {
     }
 
     implementation 'org.apache.velocity:velocity-engine-core:2.4.1'
-    implementation platform('ai.djl:bom:0.30.0')
+    implementation platform('ai.djl:bom:0.31.1')
     implementation 'ai.djl:api'
     implementation 'ai.djl.huggingface:tokenizers'
     implementation 'ai.djl.pytorch:pytorch-model-zoo'
@@ -383,7 +383,7 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.11.4'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.11.4'
 
-    testImplementation 'org.mockito:mockito-core:5.14.2'
+    testImplementation 'org.mockito:mockito-core:5.15.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'
@@ -396,12 +396,12 @@ dependencies {
     // recommended by /~https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
     testImplementation 'org.wiremock:wiremock-standalone:3.10.0'
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.21.0'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.21.1'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.22.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.23.2"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

diff --git a/buildres/abbrv.jabref.org b/buildres/abbrv.jabref.org
diff --git a/src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternsPanel.java b/src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternsPanel.java
@@ -124,7 +124,7 @@ public void updateItem(CitationKeyPatternsPanelItemModel item, boolean empty) {
                 setStyle("");
             } else if (isSelected()) {
                 setStyle("-fx-background-color: -fx-selection-bar");
-            } else if (item.getEntryType().getName().equals(CitationKeyPatternsPanelViewModel.ENTRY_TYPE_DEFAULT_NAME)) {
+            } else if (CitationKeyPatternsPanelViewModel.ENTRY_TYPE_DEFAULT_NAME.equals(item.getEntryType().getName())) {
                 setStyle("-fx-background-color: -fx-default-button");
             } else {
                 setStyle("");

diff --git a/src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternsPanelViewModel.java b/src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternsPanelViewModel.java
@@ -26,9 +26,9 @@ public class CitationKeyPatternsPanelViewModel {
 
         if (itemOneName.equals(itemTwoName)) {
             return 0;
-        } else if (itemOneName.equals(ENTRY_TYPE_DEFAULT_NAME)) {
+        } else if (ENTRY_TYPE_DEFAULT_NAME.equals(itemOneName)) {
             return -1;
-        } else if (itemTwoName.equals(ENTRY_TYPE_DEFAULT_NAME)) {
+        } else if (ENTRY_TYPE_DEFAULT_NAME.equals(itemTwoName)) {
             return 1;
         }
 

diff --git a/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.java b/src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.java
@@ -205,7 +205,7 @@ public static Set<ExternalFileType> fromString(String storedFileTypes) {
         // Read the prefs information for file types:
         String[][] vals = StringUtil.decodeStringDoubleArray(storedFileTypes);
         for (String[] val : vals) {
-            if ((val.length == 2) && val[1].equals(FILE_TYPE_REMOVED_FLAG)) {
+            if ((val.length == 2) && FILE_TYPE_REMOVED_FLAG.equals(val[1])) {
                 // This entry indicates that a default entry type should be removed:
                 ExternalFileType toRemove = null;
                 for (ExternalFileType type : types) {

diff --git a/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java b/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java
@@ -403,7 +403,7 @@ public void setValues() {
             if (parentNode != null) {
                 parentNode.getGroup()
                           .getIconName()
-                          .filter(iconName -> !iconName.equals(DefaultGroupsFactory.ALL_ENTRIES_GROUP_DEFAULT_ICON))
+                          .filter(iconName -> !DefaultGroupsFactory.ALL_ENTRIES_GROUP_DEFAULT_ICON.equals(iconName))
                           .ifPresent(iconProperty::setValue);
                 parentNode.getGroup().getColor().ifPresent(color -> colorUseProperty.setValue(true));
             }

diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -185,7 +185,28 @@ public MainTable(MainTableDataModel model,
         this.setItems(model.getEntriesFilteredAndSorted());
 
         // Enable sorting
-        model.getEntriesFilteredAndSorted().comparatorProperty().bind(this.comparatorProperty());
+        // Workaround for a JavaFX bug: https://bugs.openjdk.org/browse/JDK-8301761 (The sorting of the SortedList can become invalid)
+        // The default comparator of the SortedList does not consider the insertion index of entries that are equal according to the comparator.
+        // When two entries are equal based on the comparator, the entry that was inserted first should be considered smaller.
+        this.setSortPolicy(_ -> true);
+        model.getEntriesFilteredAndSorted().comparatorProperty().bind(
+                this.comparatorProperty().map(comparator -> {
+                    if (comparator == null) {
+                        return null;
+                    }
+
+                    return (entry1, entry2) -> {
+                        int result = comparator.compare(entry1, entry2);
+                        if (result != 0) {
+                            return result;
+                        }
+                        // If the entries are equal according to the comparator, compare them by their index in the database.
+                        // The comparison should ideally be based on the database index, but retrieving the index takes log(n). See {@link BibDatabase#indexOf}.
+                        // Using the entry ID is also valid since IDs are monotonically increasing.
+                        return entry1.getEntry().getId().compareTo(entry2.getEntry().getId());
+                    };
+                })
+        );
 
         // Store visual state
         new PersistenceVisualStateTable(this, mainTablePreferences.getColumnPreferences()).addListeners();

diff --git a/src/main/java/org/jabref/gui/preferences/websearch/WebSearchTabViewModel.java b/src/main/java/org/jabref/gui/preferences/websearch/WebSearchTabViewModel.java
@@ -147,7 +147,7 @@ public void setValues() {
         catalogs.addAll(WebFetchers.getSearchBasedFetchers(importFormatPreferences, importerPreferences)
                                    .stream()
                                    .map(SearchBasedFetcher::getName)
-                                   .filter(name -> !name.equals(CompositeSearchBasedFetcher.FETCHER_NAME))
+                                   .filter(name -> !CompositeSearchBasedFetcher.FETCHER_NAME.equals(name))
                                    .map(name -> {
                                        boolean enabled = importerPreferences.getCatalogs().contains(name);
                                        return new StudyCatalogItem(name, enabled);

diff --git a/src/main/java/org/jabref/gui/slr/ManageStudyDefinitionViewModel.java b/src/main/java/org/jabref/gui/slr/ManageStudyDefinitionViewModel.java
@@ -75,7 +75,7 @@ public ManageStudyDefinitionViewModel(ImportFormatPreferences importFormatPrefer
                                     .map(SearchBasedFetcher::getName)
                                     // The user wants to select specific fetchers
                                     // The fetcher summarizing ALL fetchers can be emulated by selecting ALL fetchers (which happens rarely when doing an SLR)
-                                    .filter(name -> !name.equals(CompositeSearchBasedFetcher.FETCHER_NAME))
+                                    .filter(name -> !CompositeSearchBasedFetcher.FETCHER_NAME.equals(name))
                                     .map(name -> {
                                         boolean enabled = DEFAULT_SELECTION.contains(name);
                                         return new StudyCatalogItem(name, enabled);
@@ -108,7 +108,7 @@ public ManageStudyDefinitionViewModel(Study study,
                                     .map(SearchBasedFetcher::getName)
                                     // The user wants to select specific fetchers
                                     // The fetcher summarizing ALL fetchers can be emulated by selecting ALL fetchers (which happens rarely when doing an SLR)
-                                    .filter(name -> !name.equals(CompositeSearchBasedFetcher.FETCHER_NAME))
+                                    .filter(name -> !CompositeSearchBasedFetcher.FETCHER_NAME.equals(name))
                                     .map(name -> {
                                         boolean enabled = studyDatabases.contains(new StudyDatabase(name, true));
                                         return new StudyCatalogItem(name, enabled);

diff --git a/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java b/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
@@ -98,7 +98,7 @@ private static Map<String, String> serializeMetaData(Map<String, List<String>> s
                 continue;
             }
 
-            boolean isSaveActions = metaItem.getKey().equals(MetaData.SAVE_ACTIONS);
+            boolean isSaveActions = MetaData.SAVE_ACTIONS.equals(metaItem.getKey());
             // The last "MetaData.SEPARATOR_STRING" adds compatibility to JabRef v5.9 and earlier
             StringJoiner joiner = new StringJoiner(MetaData.SEPARATOR_STRING, "", MetaData.SEPARATOR_STRING);
             boolean lastWasSaveActionsEnablement = false;

diff --git a/src/main/java/org/jabref/logic/exporter/XmpExporter.java b/src/main/java/org/jabref/logic/exporter/XmpExporter.java
@@ -47,7 +47,7 @@ public void export(BibDatabaseContext databaseContext, Path file, List<BibEntry>
 
         // This is a distinction between writing all entries from the supplied list to a single .xmp file,
         // or write every entry to a separate file.
-        if (file.getFileName().toString().trim().equals(XMP_SPLIT_DIRECTORY_INDICATOR)) {
+        if (XMP_SPLIT_DIRECTORY_INDICATOR.equals(file.getFileName().toString().trim())) {
             for (BibEntry entry : entries) {
                 // Avoid situations, where two citation keys are null
                 Path entryFile;

diff --git a/src/main/java/org/jabref/logic/importer/Importer.java b/src/main/java/org/jabref/logic/importer/Importer.java
@@ -121,7 +121,8 @@ protected static Charset getCharset(BufferedInputStream bufferedInputStream) {
                 return defaultCharSet;
             }
 
-            if (Arrays.stream(matches).anyMatch(charset -> "ASCII".equals(charset.getName()))) {
+            // if we have utf8 with 100 confidence we assume that the file is in utf8, more likely
+            if (Arrays.stream(matches).anyMatch(charset -> "ASCII".equals(charset.getName()) || ("UTF-8".equals(charset.getName()) && charset.getConfidence() == 100))) {
                 return defaultCharSet;
             }
 

diff --git a/src/main/java/org/jabref/logic/importer/fetcher/DoiFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/DoiFetcher.java
@@ -244,6 +244,6 @@ private boolean isAPSJournal(BibEntry entry, String doiAsString) {
         }
         String suffix = doiAsString.substring(doiAsString.lastIndexOf('/') + 1);
         String organizationId = doiAsString.substring(doiAsString.indexOf('.') + 1, doiAsString.indexOf('/'));
-        return organizationId.equals(APS_JOURNAL_ORG_DOI_ID) && APS_SUFFIX_PATTERN.matcher(suffix).matches();
+        return APS_JOURNAL_ORG_DOI_ID.equals(organizationId) && APS_SUFFIX_PATTERN.matcher(suffix).matches();
     }
 }
+9 −0		journals/journal_abbreviations_mathematics.csv
+20 −1		journals/journal_abbreviations_ubc.csv