Merge remote-tracking branch 'upstream/master'

* upstream/master: Remove "Merge Entries" from Quality Menu (#6021) Raise codecov threshold (#6027) Translation for SpecialField names in preferences (#6031) Fix dependency updates workflow (#6033) Add graal info to module file (#6010) Group remote database actions in menu Move journal abbreviations to quality
JabRef · Feb 28, 2020 · 070f3cc · 070f3cc
2 parents 30146a3 + 9424777
commit 070f3cc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -46,10 +46,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where changing entry type doesn't always work when biblatex source is shown. [#5905](https://github.com/JabRef/jabref/issues/5905)
 - We fixed an issue where the group and the link column were not updated after changing the entry in the main table. [#5985](https://github.com/JabRef/jabref/issues/5985)
 - We fixed an issue where reordering the groups was not possible after inserting an article. [#6008](https://github.com/JabRef/jabref/issues/6008)
+- We fixed an issue where citation styles except the default "Preview" could not be used. [#56220](https://github.com/JabRef/jabref/issues/5622)
 
 ### Removed
 
 - Ampersands are no longer escaped by default in the `bib` file. If you want to keep the current behaviour, you can use the new "Escape Ampersands" formatter as a save action. [#5869](https://github.com/JabRef/jabref/issues/5869)
+- The "Merge Entries" entry was removed from the Quality Menu. Users should use the right-click menu instead. [#6021](https://github.com/JabRef/jabref/pull/6021)
 
 
 ## [5.0-beta] – 2019-12-15

diff --git a/build.gradle b/build.gradle
@@ -181,7 +181,7 @@ dependencies {
     implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
 
-    implementation 'de.undercouch:citeproc-java:2.0.0'
+    implementation 'de.undercouch:citeproc-java:2.1.0-SNAPSHOT'
 
     implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
     implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
@@ -205,7 +205,7 @@ dependencies {
     testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.8'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:3.3.0'
+    testImplementation 'org.mockito:mockito-core:3.3.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.6.3'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.6.3'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.13.1'
@@ -238,14 +238,12 @@ dependencyUpdates.resolutionStrategy = {
             }
         }
         rules.withModule("org.python:jython-standalone") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.7.2b2/) {
+            if (selection.candidate.version ==~ /2.7.2b\d/) {
                 selection.reject('Release candidate')
             }
         }
         rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.0.26-9.1.2/
-                || selection.candidate.version ==~ /2.0.26-9.1.1/
-                || selection.candidate.version ==~ /2.0.26-9.1.0/) {
+            if (selection.candidate.version ==~ /2.0.26.*/) {
                 selection.reject('1.7.22-11 is actually newer (strange version system)')
             }
         }
@@ -546,7 +544,7 @@ task deleteInstallerTemp(type: Delete) {
 
 jpackage.dependsOn deleteInstallerTemp
 jlink {
-    options = ['--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages']
+    options = ['--strip-debug','--compress', '2', '--no-header-files', '--no-man-pages']
     launcher {
         name = 'JabRef'
     }

diff --git a/codecov.yml b/codecov.yml
@@ -3,4 +3,7 @@ coverage:
   - src/gen/.*
   status:
     patch: false
+  project:
+    default:
+      threshold: 0.005
 comment: off
diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
@@ -61,7 +61,11 @@
     requires jbibtex;
     requires citeproc.java;
     requires antlr.runtime;
-    requires org.graalvm.js;
+    requires org.graalvm.truffle;
+    requires org.graalvm.sdk;
+    requires transitive org.graalvm.js;
+    requires java.scripting;
+    requires jdk.internal.vm.compiler;
     requires org.apache.xmpbox;
     requires de.saxsys.mvvmfx.validation;
     requires com.google.gson;

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -89,7 +89,6 @@
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.libraryproperties.LibraryPropertiesAction;
 import org.jabref.gui.menus.FileHistoryMenu;
-import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.metadata.BibtexStringEditorAction;
 import org.jabref.gui.metadata.PreambleEditor;
 import org.jabref.gui.preferences.ShowPreferencesAction;
@@ -409,7 +408,7 @@ private void initLayout() {
 
         setId("frame");
 
-        VBox head = new VBox(createMenu(),createToolbar());
+        VBox head = new VBox(createMenu(), createToolbar());
         head.setSpacing(0d);
         setTop(head);
 
@@ -682,8 +681,12 @@ private MenuBar createMenu() {
                         factory.createMenuItem(StandardActions.EXPORT_SELECTED, new ExportCommand(this, true, Globals.prefs)),
                         factory.createMenuItem(StandardActions.SAVE_SELECTED_AS_PLAIN_BIBTEX, new OldDatabaseCommandWrapper(Actions.SAVE_SELECTED_AS_PLAIN, this, stateManager))),
 
-                factory.createMenuItem(StandardActions.CONNECT_TO_SHARED_DB, new ConnectToSharedDatabaseCommand(this)),
-                factory.createMenuItem(StandardActions.PULL_CHANGES_FROM_SHARED_DB, new OldDatabaseCommandWrapper(Actions.PULL_CHANGES_FROM_SHARED_DATABASE, this, stateManager)),
+                new SeparatorMenuItem(),
+
+                factory.createSubMenu(StandardActions.REMOTE_DB,
+                        factory.createMenuItem(StandardActions.CONNECT_TO_SHARED_DB, new ConnectToSharedDatabaseCommand(this)),
+                        factory.createMenuItem(StandardActions.PULL_CHANGES_FROM_SHARED_DB, new OldDatabaseCommandWrapper(Actions.PULL_CHANGES_FROM_SHARED_DATABASE, this, stateManager))
+                ),
 
                 new SeparatorMenuItem(),
 
@@ -756,19 +759,27 @@ private MenuBar createMenu() {
 
         quality.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService, stateManager)),
-                factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(this, stateManager)),
                 factory.createMenuItem(StandardActions.CHECK_INTEGRITY, new IntegrityCheckAction(this, stateManager, Globals.TASK_EXECUTOR)),
                 factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new OldDatabaseCommandWrapper(Actions.CLEANUP, this, stateManager)),
 
                 new SeparatorMenuItem(),
 
-                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs, stateManager, undoManager, Globals.TASK_EXECUTOR))
+                factory.createMenuItem(StandardActions.SET_FILE_LINKS, new AutoLinkFilesAction(this, prefs, stateManager, undoManager, Globals.TASK_EXECUTOR)),
+
+                new SeparatorMenuItem(),
+
+                factory.createSubMenu(StandardActions.ABBREVIATE,
+                        factory.createMenuItem(StandardActions.ABBREVIATE_DEFAULT, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_DEFAULT, this, stateManager)),
+                        factory.createMenuItem(StandardActions.ABBREVIATE_MEDLINE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_MEDLINE, this, stateManager)),
+                        factory.createMenuItem(StandardActions.ABBREVIATE_SHORTEST_UNIQUE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_SHORTEST_UNIQUE, this, stateManager))),
+
+                factory.createMenuItem(StandardActions.UNABBREVIATE, new OldDatabaseCommandWrapper(Actions.UNABBREVIATE, this, stateManager))
         );
 
         lookup.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(this, dialogService, stateManager))
         );
-        
+
         // PushToApplication
         final PushToApplicationAction pushToApplicationAction = pushToApplicationsManager.getPushToApplicationAction();
         final MenuItem pushToApplicationMenuItem = factory.createMenuItem(pushToApplicationAction.getActionInformation(), pushToApplicationAction);
@@ -792,14 +803,7 @@ private MenuBar createMenu() {
                 new SeparatorMenuItem(),
 
                 factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new OldDatabaseCommandWrapper(Actions.SEND_AS_EMAIL, this, stateManager)),
-                pushToApplicationMenuItem,
-
-                factory.createSubMenu(StandardActions.ABBREVIATE,
-                        factory.createMenuItem(StandardActions.ABBREVIATE_DEFAULT, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_DEFAULT, this, stateManager)),
-                        factory.createMenuItem(StandardActions.ABBREVIATE_MEDLINE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_MEDLINE, this, stateManager)),
-                        factory.createMenuItem(StandardActions.ABBREVIATE_SHORTEST_UNIQUE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_SHORTEST_UNIQUE, this, stateManager))),
-
-                factory.createMenuItem(StandardActions.UNABBREVIATE, new OldDatabaseCommandWrapper(Actions.UNABBREVIATE, this, stateManager))
+                pushToApplicationMenuItem
         );
 
         SidePaneComponent webSearch = sidePaneManager.getComponent(SidePaneType.WEB_SEARCH);

diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -71,6 +71,7 @@ public enum StandardActions implements Action {
     IMPORT_INTO_NEW_LIBRARY(Localization.lang("Import into new library"), KeyBinding.IMPORT_INTO_NEW_DATABASE),
     IMPORT_INTO_CURRENT_LIBRARY(Localization.lang("Import into current library"), KeyBinding.IMPORT_INTO_CURRENT_DATABASE),
     EXPORT_ALL(Localization.lang("Export all entries")),
+    REMOTE_DB(Localization.lang("Shared database"), IconTheme.JabRefIcons.REMOTE_DATABASE),
     EXPORT_SELECTED(Localization.lang("Export selected entries"), KeyBinding.EXPORT_SELECTED),
     CONNECT_TO_SHARED_DB(Localization.lang("Connect to shared database"), IconTheme.JabRefIcons.CONNECT_DB),
     PULL_CHANGES_FROM_SHARED_DB(Localization.lang("Pull changes from shared database"), KeyBinding.PULL_CHANGES_FROM_SHARED_DATABASE),

diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -300,6 +300,7 @@ public enum JabRefIcons implements JabRefIcon {
         ADD_ABBREVIATION(MaterialDesignIcon.PLAYLIST_PLUS),
         REMOVE_ABBREVIATION(MaterialDesignIcon.PLAYLIST_MINUS),
         NEW_ENTRY_FROM_PLAIN_TEXT(MaterialDesignIcon.PLUS_BOX),
+        REMOTE_DATABASE(MaterialDesignIcon.DATABASE),
         HOME(MaterialDesignIcon.HOME);
 
         private final JabRefIcon icon;

diff --git a/src/main/java/org/jabref/gui/util/FieldsUtil.java b/src/main/java/org/jabref/gui/util/FieldsUtil.java
@@ -2,6 +2,8 @@
 
 import javafx.util.StringConverter;
 
+import org.jabref.Globals;
+import org.jabref.gui.specialfields.SpecialFieldViewModel;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
@@ -30,7 +32,8 @@ public Field fromString(String string) {
 
     public static String getNameWithType(Field field) {
         if (field instanceof SpecialField) {
-            return field.getDisplayName() + " (" + Localization.lang("Special") + ")";
+            return new SpecialFieldViewModel((SpecialField) field, Globals.undoManager).getLocalization()
+                    + " (" + Localization.lang("Special") + ")";
         } else if (field instanceof IEEEField) {
             return field.getDisplayName() + " (" + Localization.lang("IEEE") + ")";
         } else if (field instanceof InternalField) {

diff --git a/src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java b/src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java
@@ -14,6 +14,7 @@
 import org.jabref.model.strings.LatexToUnicodeAdapter;
 
 import de.undercouch.citeproc.CSL;
+import de.undercouch.citeproc.DefaultAbbreviationProvider;
 import de.undercouch.citeproc.ItemDataProvider;
 import de.undercouch.citeproc.bibtex.BibTeXConverter;
 import de.undercouch.citeproc.csl.CSLItemData;
@@ -66,7 +67,8 @@ public synchronized List<String> makeBibliography(List<BibEntry> bibEntries, Str
     private void initialize(String newStyle, CitationStyleOutputFormat newFormat) throws IOException {
         if ((cslInstance == null) || !Objects.equals(newStyle, style)) {
             // lang and forceLang are set to the default values of other CSL constructors
-            cslInstance = new CSL(dataProvider, new JabRefLocaleProvider(), newStyle, "en-US", false);
+            cslInstance = new CSL(dataProvider, new JabRefLocaleProvider(),
+                  new DefaultAbbreviationProvider(), null, newStyle, "en-US", false, true);
             style = newStyle;
         }
 

diff --git a/src/main/java/org/jabref/logic/citationstyle/CitationStyle.java b/src/main/java/org/jabref/logic/citationstyle/CitationStyle.java
@@ -6,9 +6,6 @@
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
-import java.nio.file.FileSystem;
-import java.nio.file.FileSystemAlreadyExistsException;
-import java.nio.file.FileSystems;
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
@@ -25,6 +22,7 @@
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.jabref.JabRefMain;
 import org.jabref.logic.util.StandardFileType;
 
 import de.undercouch.citeproc.helper.CSLUtils;
@@ -138,28 +136,18 @@ public static List<CitationStyle> discoverCitationStyles() {
             return STYLES;
         }
 
-        URL url = CitationStyle.class.getResource(STYLES_ROOT);
-        if (url == null) {
-            return Collections.emptyList();
-        }
+        URL url = JabRefMain.class.getResource(STYLES_ROOT + "/acm-siggraph.csl");
+        Objects.requireNonNull(url);
+
         try {
             URI uri = url.toURI();
-            if ("jar".equals(uri.getScheme())) {
-                try (FileSystem fs = FileSystems.newFileSystem(uri, Collections.emptyMap())) {
-                    Path path = fs.getPath(STYLES_ROOT);
-                    STYLES.addAll(discoverCitationStylesInPath(path));
-                } catch (FileSystemAlreadyExistsException e) {
-                    try (FileSystem fs = FileSystems.getFileSystem(uri)) {
-                        Path path = fs.getPath(STYLES_ROOT);
-                        STYLES.addAll(discoverCitationStylesInPath(path));
-                    }
-                }
-            } else {
-                STYLES.addAll(discoverCitationStylesInPath(Paths.get(uri)));
-            }
+            Path path = Path.of(uri).getParent();
+
+            STYLES.addAll(discoverCitationStylesInPath(path));
+
             return STYLES;
         } catch (URISyntaxException | IOException e) {
-            LOGGER.error("something went wrong while searching available CitationStyles. Are you running directly from source code?", e);
+            LOGGER.error("something went wrong while searching available CitationStyles", e);
             return Collections.emptyList();
         }
     }

diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
@@ -2115,4 +2115,5 @@ Optional=Optional
 Required=Required
 Entry\ type\ cannot\ be\ empty.\ Please\ enter\ a\ name.=Entry type cannot be empty. Please enter a name.
 Field\ cannot\ be\ empty.\ Please\ enter\ a\ name.=Field cannot be empty. Please enter a name.
+Shared\ database=Shared database
 Lookup=Lookup