Merge remote-tracking branch 'upstream/main' into addRightlickToGroup

* upstream/main:
  Update abbrv.jabref.org (#12365)
  Bump buildres/abbrv.jabref.org from `78e1b08` to `c202741` (#12363)
  Bump org.beryx.jlink from 3.1.0-rc-1 to 3.1.1 (#12362)
  Bump tech.units:indriya from 2.2.1 to 2.2.2 (#12361)
  Bump com.dlsc.gemsfx:gemsfx from 2.80.0 to 2.81.0 (#12360)
  Bump org.mariadb.jdbc:mariadb-java-client from 2.7.9 to 2.7.12 (#12359)
  Bump org.mockito:mockito-core from 5.14.2 to 5.15.2 (#12358)
  Fix content not correctly parsed at pdf content importer (#12338)
  Bump de.undercouch:citeproc-java from 3.1.0 to 3.2.0 (#12347)
  Bump org.openrewrite.rewrite from 6.29.0 to 6.29.2 (#12345)
  Improve utf8 detection  (#12342)
  Bump org.fxmisc.richtext:richtextfx from 0.11.3 to 0.11.4 (#12346)
  Bump ai.djl:bom from 0.30.0 to 0.31.1 (#12344)
  Bump com.puppycrawl.tools:checkstyle from 10.21.0 to 10.21.1 (#12343)

Author: Siedlerchr

CHANGELOG.md

@@ -13,10 +13,16 @@ 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/)
+
 ### 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

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 '6.29.3'
 
     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'
     }
 
@@ -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")

buildres/abbrv.jabref.org

@@ -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("");

src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternsPanel.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;
         }
 

src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternsPanelViewModel.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) {

src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.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));
             }

src/main/java/org/jabref/gui/groups/GroupDialogViewModel.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);

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

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