Merge remote-tracking branch 'upstream/master' into customizeEntrydlg

# By Oliver Kopp (4) and others
# Via github actions (3) and Christoph (1)
* upstream/master:
  Fix missing file extension for downloaded files. Fixes #5816 by falling back to PDF as default file type. (#5841)
  The PDF has a title - try another publication without an available PDF (#5840)
  Fix BibTeX VM for IEEE (and some micro other fixes) (#5839)
  Squashed 'src/main/resources/csl-styles/' changes from 19c89f5..9c0f5c6
  Improve serialization to fix #4877 (#5838)
  Build on all branches
  update unirest (#5836)
  Squashed 'src/main/resources/csl-locales/' changes from a3e8843f75..41da445acc
  Squashed 'src/main/resources/csl-styles/' changes from bb01625..19c89f5
  Build binaries only when src/main changes (#5806)
  Bump archunit-junit5-api from 0.12.0 to 0.13.0 (#5827)
  Bump classgraph from 4.8.59 to 4.8.60 (#5828)
  Bump mariadb-java-client from 2.5.2 to 2.5.3 (#5829)
  Update jdk to build 30
  Improve change detection (#5824)

# Conflicts:
#	src/main/resources/l10n/JabRef_en.properties

.github/workflows/deployment.yml

@@ -1,6 +1,18 @@
 name: Deployment
 
-on: [push]
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+      - 'src/test/**'
+      - 'README.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'src/test/**'
+      - 'README.md'
 
 jobs:
   build:
@@ -11,17 +23,17 @@ jobs:
         include:
          - os: ubuntu-latest
            displayName: linux
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_linux-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/30/GPL/openjdk-14-ea+30_linux-x64_bin.tar.gz
            jdk14Path: /jdk-14
            archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
          - os: windows-latest
            displayName: windows
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_windows-x64_bin.zip
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/30/GPL/openjdk-14-ea+30_windows-x64_bin.zip
            jdk14Path: /jdk-14
            archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
          - os: macOS-latest
            displayName: macOS
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_osx-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/30/GPL/openjdk-14-ea+30_osx-x64_bin.tar.gz
            jdk14Path: /jdk-14.jdk/Contents/Home
            archivePortable: brew install pigz && tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos.tar.gz && rm -R build/distribution/JabRef.app
 

.github/workflows/tests-oracle.yml

@@ -2,8 +2,7 @@ name: Oracle Tests
 
 on:
   push:
-    branches:
-      - master
+    # we need to trigger on all branches, because sometimes need copy of branches, because secrets are only available on "internal" pull requests
     paths:
       - 'src/test/java/org/jabref/model/database/**'
       - 'src/test/java/org/jabref/logic/shared/**'

.gitignore

@@ -1,5 +1,6 @@
 # no generated files in version control
 src/main/gen/
+src/main/generated/
 
 # private data
 /buildres/jabref-cert-2016.p12

CHANGELOG.md

@@ -15,11 +15,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Fixed
 
-- We fixed an issue where the Medline fetcher was only working when JabRef was running from source [#5645](https://github.com/JabRef/jabref/issues/5645)
-- We fixed some visual issues in the dark theme [#5764](https://github.com/JabRef/jabref/pull/5764) [#5753](https://github.com/JabRef/jabref/issues/5753)
+- We fixed an issue where the Medline fetcher was only working when JabRef was running from source. [#5645](https://github.com/JabRef/jabref/issues/5645)
+- We fixed some visual issues in the dark theme. [#5764](https://github.com/JabRef/jabref/pull/5764) [#5753](https://github.com/JabRef/jabref/issues/5753)
 - We fixed an issue where non-default previews didn't handle unicode characters. [#5779](https://github.com/JabRef/jabref/issues/5779)
-- We fixed an issue where the ampersand character wasn't rendering correctly on previews.[#3840](https://github.com/JabRef/jabref/issues/3840)
-
+- We fixed an issue where the ampersand character wasn't rendering correctly on previews. [#3840](https://github.com/JabRef/jabref/issues/3840)
+- We fixed an issue where an erroneous "The library has been modified by another program" message was shown when saving. [#4877](https://github.com/JabRef/jabref/issues/4877)
+- We fixed an issue where the file extension was missing after downloading a file (we now fall-back to pdf). [#5816](https://github.com/JabRef/jabref/issues/5816)
 
 ### Removed
 

build.gradle

@@ -140,7 +140,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.2'
     compile 'org.antlr:antlr4-runtime:4.7.2'
 
-    compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.5.2'
+    compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.5.3'
 
     compile 'org.postgresql:postgresql:42.2.9'
 
@@ -169,7 +169,7 @@ dependencies {
     compile 'org.controlsfx:controlsfx:11.0.1'
 
     compile 'org.jsoup:jsoup:1.12.1'
-    compile 'com.konghq:unirest-java:3.3.00'
+    compile 'com.konghq:unirest-java:3.4.00'
 
     compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
     compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -206,7 +206,7 @@ dependencies {
     }
 
 
-    testCompile 'io.github.classgraph:classgraph:4.8.59'
+    testCompile 'io.github.classgraph:classgraph:4.8.60'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.5.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.5.2'
     testCompile 'org.junit.platform:junit-platform-launcher:1.5.2'
@@ -218,9 +218,8 @@ dependencies {
     //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.12.0'
-    //testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.11.0'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.12.0'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.13.0'
+    //testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.13.0'
     testCompile "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testCompile "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testCompile "org.hamcrest:hamcrest-library:2.2"

external-libraries.txt

@@ -13,6 +13,12 @@ In case you add a library, please use these identifiers.
 For instance, "BSD" is not exact enough, there are numerous variants out there: BSD-2-Clause, BSD-3-Clause-No-Nuclear-Warranty, ...
 Note that the SPDX license identifiers are different from the ones used by debian. See https://wiki.debian.org/Proposals/CopyrightFormat for more information.
 
+# bst files
+
+Project: IEEEtran
+Path:    src/main/resources/bst/IEEEtran.bst
+URL:     https://www.ctan.org/tex-archive/macros/latex/contrib/IEEEtran/bibtex
+License: LPPL-1.3
 
 # Fonts and Icons
 

src/jmh/java/org/jabref/benchmarks/Benchmarks.java

@@ -16,7 +16,6 @@
 import org.jabref.logic.layout.format.HTMLChars;
 import org.jabref.logic.layout.format.LatexToUnicodeFormatter;
 import org.jabref.logic.search.SearchQuery;
-import org.jabref.model.Defaults;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -76,8 +75,7 @@ public void init() throws Exception {
     private StringWriter getOutputWriter() throws IOException {
         StringWriter outputWriter = new StringWriter();
         BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class), new BibEntryTypesManager());
-        databaseWriter.savePartOfDatabase(
-                new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
+        databaseWriter.savePartOfDatabase(new BibDatabaseContext(database, new MetaData()), database.getEntries());
         return outputWriter;
     }
 

src/main/antlr3/org/jabref/bst/Bst.g

@@ -73,7 +73,7 @@ QUOTED
 	: '\'' IDENTIFIER;
 
 IDENTIFIER
-	: LETTER (LETTER|NUMERAL)* ;
+	: LETTER (LETTER|NUMERAL|'_')* ;
 
 fragment LETTER
 	: ('a'..'z'|'A'..'Z'|'.'|'$');

src/main/java/module-info.java

@@ -68,5 +68,11 @@
     requires org.jsoup;
     requires commons.csv;
     requires io.github.javadiffutils;
+    requires java.string.similarity;
+    requires ojdbc10;
+    requires org.postgresql.jdbc;
+    requires org.apache.commons.lang3;
+    requires org.antlr.antlr4.runtime;
     requires flowless;
+    requires org.apache.tika.core;
 }

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -44,7 +44,6 @@
 import org.jabref.logic.shared.prefs.SharedDatabasePreferences;
 import org.jabref.logic.util.OS;
 import org.jabref.logic.xmp.XmpPreferences;
-import org.jabref.model.Defaults;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -392,8 +391,7 @@ private void saveDatabase(BibDatabase newBase, String subName) {
             SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
             AtomicFileWriter fileWriter = new AtomicFileWriter(Paths.get(subName), prefs.getEncoding());
             BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs, Globals.entryTypesManager);
-            Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
-            databaseWriter.saveDatabase(new BibDatabaseContext(newBase, defaults));
+            databaseWriter.saveDatabase(new BibDatabaseContext(newBase));
 
             // Show just a warning message if encoding did not work for all characters:
             if (fileWriter.hasEncodingProblems()) {

src/main/java/org/jabref/gui/ClipBoardManager.java

@@ -21,7 +21,7 @@
 
 import org.jabref.Globals;
 import org.jabref.logic.bibtex.BibEntryWriter;
-import org.jabref.logic.bibtex.LatexFieldFormatter;
+import org.jabref.logic.bibtex.FieldWriter;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportException;
 import org.jabref.logic.importer.ImportFormatReader;
@@ -152,7 +152,7 @@ public void setContent(String string) {
 
     public void setContent(List<BibEntry> entries) throws IOException {
         final ClipboardContent content = new ClipboardContent();
-        BibEntryWriter writer = new BibEntryWriter(new LatexFieldFormatter(Globals.prefs.getLatexFieldFormatterPreferences()), Globals.entryTypesManager);
+        BibEntryWriter writer = new BibEntryWriter(new FieldWriter(Globals.prefs.getFieldWriterPreferences()), Globals.entryTypesManager);
         String serializedEntries = writer.serializeAll(entries, BibDatabaseMode.BIBTEX);
         content.put(DragAndDropDataFormats.ENTRIES, serializedEntries);
         content.putString(serializedEntries);

src/main/java/org/jabref/gui/auximport/FromAuxDialog.java

@@ -20,7 +20,6 @@
 import org.jabref.logic.auxparser.DefaultAuxParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.StandardFileType;
-import org.jabref.model.Defaults;
 import org.jabref.model.auxparser.AuxParser;
 import org.jabref.model.auxparser.AuxParserResult;
 import org.jabref.model.database.BibDatabase;
@@ -59,8 +58,7 @@ public FromAuxDialog(JabRefFrame frame) {
         generateButton.defaultButtonProperty().bind(generateButton.disableProperty().not());
         setResultConverter(button -> {
             if (button == generateButtonType) {
-                Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
-                BasePanel bp = new BasePanel(frame, BasePanelPreferences.from(Globals.prefs), new BibDatabaseContext(auxParserResult.getGeneratedBibDatabase(), defaults), ExternalFileTypes.getInstance());
+                BasePanel bp = new BasePanel(frame, BasePanelPreferences.from(Globals.prefs), new BibDatabaseContext(auxParserResult.getGeneratedBibDatabase()), ExternalFileTypes.getInstance());
                 frame.addTab(bp, true);
             }
             return null;

src/main/java/org/jabref/gui/collab/ChangeScanner.java

@@ -44,7 +44,7 @@ public List<DatabaseChangeViewModel> scanForChanges() {
             // Start looking at changes.
             BibDatabaseDiff differences = BibDatabaseDiff.compare(database, databaseOnDisk);
             differences.getMetaDataDifferences().ifPresent(diff -> {
-                changes.add(new MetaDataChangeViewModel(diff));
+                changes.add(new MetaDataChangeViewModel(diff, Globals.prefs));
                 diff.getGroupDifferences().ifPresent(groupDiff -> changes.add(new GroupChangeViewModel(groupDiff)));
             });
             differences.getPreambleDifferences().ifPresent(diff -> changes.add(new PreambleChangeViewModel(diff)));
@@ -82,6 +82,6 @@ private DatabaseChangeViewModel createBibEntryDiff(BibEntryDiff diff) {
             return new EntryDeleteChangeViewModel(diff.getOriginalEntry());
         }
 
-        return new EntryChangeViewModel(diff.getOriginalEntry(), diff.getNewEntry(), database);
+        return new EntryChangeViewModel(diff.getOriginalEntry(), diff.getNewEntry());
     }
 }

src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java

@@ -13,30 +13,21 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 class EntryChangeViewModel extends DatabaseChangeViewModel {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(EntryChangeViewModel.class);
-
     private final BibEntry oldEntry;
     private final BibEntry newEntry;
     private MergeEntries mergePanel;
 
-    private final BibDatabaseContext database;
-
-    public EntryChangeViewModel(BibEntry entry, BibEntry newEntry, BibDatabaseContext database) {
+    public EntryChangeViewModel(BibEntry entry, BibEntry newEntry) {
         super();
 
         this.oldEntry = entry;
         this.newEntry = newEntry;
-        this.database = database;
 
         name = entry.getCiteKeyOptional()
                     .map(key -> Localization.lang("Modified entry") + ": '" + key + '\'')
                     .orElse(Localization.lang("Modified entry"));
-
     }
 
     /**
@@ -55,9 +46,11 @@ public void setAccepted(boolean accepted) {
     @Override
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         database.getDatabase().removeEntry(oldEntry);
-        database.getDatabase().insertEntry(mergePanel.getMergeEntry());
+        BibEntry mergedEntry = mergePanel.getMergeEntry();
+        mergedEntry.setId(oldEntry.getId()); // Keep ID
+        database.getDatabase().insertEntry(mergedEntry);
         undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), oldEntry));
-        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), mergePanel.getMergeEntry()));
+        undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), mergedEntry));
     }
 
     @Override
@@ -68,7 +61,7 @@ public Node description() {
         header.getStyleClass().add("sectionHeader");
         container.getChildren().add(header);
         container.getChildren().add(mergePanel);
-        container.setMargin(mergePanel, new Insets(5, 5, 5, 5));
+        VBox.setMargin(mergePanel, new Insets(5, 5, 5, 5));
         return container;
     }
 }

src/main/java/org/jabref/gui/collab/MetaDataChangeViewModel.java

@@ -2,39 +2,42 @@
 
 import javafx.scene.Node;
 import javafx.scene.control.Label;
+import javafx.scene.layout.VBox;
 
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.logic.bibtex.comparator.MetaDataDiff;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.metadata.MetaData;
+import org.jabref.preferences.JabRefPreferences;
 
 class MetaDataChangeViewModel extends DatabaseChangeViewModel {
 
-    private final MetaData newMetaData;
+    private final MetaDataDiff metaDataDiff;
+    private final JabRefPreferences preferences;
 
-    public MetaDataChangeViewModel(MetaDataDiff metaDataDiff) {
+    public MetaDataChangeViewModel(MetaDataDiff metaDataDiff, JabRefPreferences preferences) {
         super(Localization.lang("Metadata change"));
-        this.newMetaData = metaDataDiff.getNewMetaData();
+        this.metaDataDiff = metaDataDiff;
+        this.preferences = preferences;
     }
 
     @Override
     public Node description() {
+        VBox container = new VBox(15);
 
-        /*
-        // TODO: Show detailed description of the changes
-        StringBuilder sb = new StringBuilder(
-                "<html>" + Localization.lang("Changes have been made to the following metadata elements")
-                        + ":<p><br>&nbsp;&nbsp;");
-        sb.append(changes.stream().map(unit -> unit.key).collect(Collectors.joining("<br>&nbsp;&nbsp;")));
-        sb.append("</html>");
-        infoPane.setText(sb.toString());
-        */
-        return new Label(Localization.lang("Metadata change"));
+        Label header = new Label(Localization.lang("The following metadata changed:"));
+        header.getStyleClass().add("sectionHeader");
+        container.getChildren().add(header);
+
+        for (String change : metaDataDiff.getDifferences(preferences)) {
+            container.getChildren().add(new Label(change));
+        }
+
+        return container;
     }
 
     @Override
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
-        database.setMetaData(newMetaData);
+        database.setMetaData(metaDataDiff.getNewMetaData());
     }
 }

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -252,7 +252,7 @@ private List<EntryEditorTab> createTabs() {
 
         // Source tab
         sourceTab = new SourceTab(databaseContext, undoManager,
-                entryEditorPreferences.getLatexFieldFormatterPreferences(),
+                entryEditorPreferences.getFieldWriterPreferences(),
                 entryEditorPreferences.getImportFormatPreferences(), fileMonitor, dialogService, stateManager, Globals.getKeyPrefs());
         entryEditorTabs.add(sourceTab);
 

src/main/java/org/jabref/gui/entryeditor/EntryEditorPreferences.java

@@ -5,15 +5,15 @@
 import java.util.Set;
 
 import org.jabref.gui.keyboard.KeyBindingRepository;
-import org.jabref.logic.bibtex.LatexFieldFormatterPreferences;
+import org.jabref.logic.bibtex.FieldWriterPreferences;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternPreferences;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.model.entry.field.Field;
 
 public class EntryEditorPreferences {
 
     private final Map<String, Set<Field>> entryEditorTabList;
-    private final LatexFieldFormatterPreferences latexFieldFormatterPreferences;
+    private final FieldWriterPreferences fieldWriterPreferences;
     private final ImportFormatPreferences importFormatPreferences;
     private final BibtexKeyPatternPreferences bibtexKeyPatternPreferences;
     private final List<Field> customTabFieldNames;
@@ -24,9 +24,9 @@ public class EntryEditorPreferences {
     private boolean avoidOverwritingCiteKey;
     private final boolean shouldShowLatexCitationsTab;
 
-    public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList, LatexFieldFormatterPreferences latexFieldFormatterPreferences, ImportFormatPreferences importFormatPreferences, List<Field> customTabFieldNames, boolean shouldShowRecommendationsTab, boolean isMrdlibAccepted, boolean shouldShowLatexCitationsTab, boolean showSourceTabByDefault, BibtexKeyPatternPreferences bibtexKeyPatternPreferences, KeyBindingRepository keyBindings, boolean avoidOverwritingCiteKey) {
+    public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList, FieldWriterPreferences fieldWriterPreferences, ImportFormatPreferences importFormatPreferences, List<Field> customTabFieldNames, boolean shouldShowRecommendationsTab, boolean isMrdlibAccepted, boolean shouldShowLatexCitationsTab, boolean showSourceTabByDefault, BibtexKeyPatternPreferences bibtexKeyPatternPreferences, KeyBindingRepository keyBindings, boolean avoidOverwritingCiteKey) {
         this.entryEditorTabList = entryEditorTabList;
-        this.latexFieldFormatterPreferences = latexFieldFormatterPreferences;
+        this.fieldWriterPreferences = fieldWriterPreferences;
         this.importFormatPreferences = importFormatPreferences;
         this.customTabFieldNames = customTabFieldNames;
         this.shouldShowRecommendationsTab = shouldShowRecommendationsTab;
@@ -42,8 +42,8 @@ public Map<String, Set<Field>> getEntryEditorTabList() {
         return entryEditorTabList;
     }
 
-    public LatexFieldFormatterPreferences getLatexFieldFormatterPreferences() {
-        return latexFieldFormatterPreferences;
+    public FieldWriterPreferences getFieldWriterPreferences() {
+        return fieldWriterPreferences;
     }
 
     public ImportFormatPreferences getImportFormatPreferences() {