Merge remote-tracking branch 'upstream/master' into change-upload-bac…

…k-to-script

* upstream/master:
  Bump mockito-core from 3.2.0 to 3.2.4 (#5760)
  Bump classgraph from 4.8.58 to 4.8.59 (#5761)
  Improve dependency update rules
  Update jpackage to build 27 (#5758)
  Persistent column sortorder (#5730)
  Fix medline fetcher/importer when using installer (#5752)
  New Crowdin translations (#5751)
  Bump byte-buddy-parent from 1.10.4 to 1.10.5 (#5750)
  Fix checkstyle
  Fix filename

.github/workflows/deployment.yml

@@ -11,17 +11,17 @@ jobs:
         include:
          - os: ubuntu-latest
            displayName: linux
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_linux-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_linux-x64_bin.tar.gz
            jdk14Path: /jdk-14
            archivePortable: tar -czf build/distribution/JabRef-portable_linux.tar.gz -C build/distribution JabRef && rm -R build/distribution/JabRef
          - os: windows-latest
            displayName: windows
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_windows-x64_bin.zip
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_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/jpackage/1/openjdk-14-jpackage+1-70_osx-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_osx-x64_bin.tar.gz
            jdk14Path: /jdk-14.jdk/Contents/Home
            archivePortable: tar -czf build/distribution/JabRef-portable_macos.tar.gz -C build/distribution JabRef.app && rm -R build/distribution/JabRef.app
 

CHANGELOG.md

@@ -15,6 +15,9 @@ 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)
+
+
 ### Removed
 
 
@@ -34,6 +37,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the save action buttons to be easier to understand. [#5565](https://github.com/JabRef/jabref/issues/5565)
 - We made the columns for groups, files and uri in the main table reorderable and merged the clickable icon columns for uri, url, doi and eprint. [#5544](https://github.com/JabRef/jabref/pull/5544)
 - We reduced the number of write actions performed when autosave is enabled [#5679](https://github.com/JabRef/jabref/issues/5679)
+- We made the column sort order in the main table persistent [#5730](https://github.com/JabRef/jabref/pull/5730)
 
 ### Fixed
 

build.gradle

@@ -206,15 +206,15 @@ dependencies {
     }
 
 
-    testCompile 'io.github.classgraph:classgraph:4.8.58'
+    testCompile 'io.github.classgraph:classgraph:4.8.59'
     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'
 
-    testCompile 'net.bytebuddy:byte-buddy-parent:1.10.4'
+    testCompile 'net.bytebuddy:byte-buddy-parent:1.10.5'
     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'
-    testCompile 'org.mockito:mockito-core:3.2.0'
+    testCompile 'org.mockito:mockito-core:3.2.4'
     //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
@@ -249,20 +249,29 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject('Release candidate')
             }
         }
-        rules.withModule("com.github.tomtung:latex2unicode_2.12") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /0.2.*/) {
-                // Reject version higher than 2.0.2. see https://github.com/JabRef/jabref/pull/3781
-                selection.reject("Cannot be updated to 0.2.4 until JabRef is prepared for it")
+        rules.withModule("org.python:jython-standalone") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.7.2b2/) {
+                selection.reject('Release candidate')
+            }
+        }
+        rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.0.26-9.1.2/) {
+                selection.reject('1.7.22-11 is actually newer (strange version system)')
+            }
+        }
+        rules.withModule("org.javamodularity.moduleplugin:org.javamodularity.moduleplugin.gradle.plugin") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /1.6.0/) {
+                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5270")
             }
         }
-        rules.withModule("com.github.johnrengelman.shadow:com.github.johnrengelman.shadow.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /4.*/) {
-                selection.reject("Version 4.X breaks the release process.")
+        rules.withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.5.1/) {
+                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
             }
         }
-        rules.withModule("com.google.errorprone:error_prone_core") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.3.3/) {
-                selection.reject("Does not work due to bug https://github.com/google/error-prone/issues/1240")
+        rules.withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.5.1/) {
+                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
             }
         }
     }
@@ -597,6 +606,7 @@ jlink {
         uses 'com.airhacks.afterburner.injection.PresenterFactory'
         uses 'org.controlsfx.glyphfont.GlyphFont'
         uses 'com.airhacks.afterburner.views.ResourceLocator'
+        uses 'javax.xml.bind.JAXBContextFactory'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'
         provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
         provides 'org.apache.commons.logging.LogFactory' with 'org.apache.logging.log4j.jcl.LogFactoryImpl'

src/main/java/org/jabref/gui/maintable/ColumnPreferences.java

@@ -1,32 +1,25 @@
 package org.jabref.gui.maintable;
 
 import java.util.List;
-import java.util.Map;
-
-import javafx.scene.control.TableColumn.SortType;
 
 public class ColumnPreferences {
 
-    public static final double DEFAULT_WIDTH = 100;
+    public static final double DEFAULT_COLUMN_WIDTH = 100;
     public static final double ICON_COLUMN_WIDTH = 16 + 12; // add some additional space to improve appearance
 
     private final List<MainTableColumnModel> columns;
-    private final boolean extraFileColumnsEnabled;
-    private final Map<String, SortType> columnSortType;
+    private final List<MainTableColumnModel> columnSortOrder;
 
-    public ColumnPreferences(List<MainTableColumnModel> columns, boolean extraFileColumnsEnabled, Map<String, SortType> columnSortType) {
+    public ColumnPreferences(List<MainTableColumnModel> columns, List<MainTableColumnModel> columnSortOrder) {
         this.columns = columns;
-        this.extraFileColumnsEnabled = extraFileColumnsEnabled;
-        this.columnSortType = columnSortType;
+        this.columnSortOrder = columnSortOrder;
     }
 
-    public boolean getExtraFileColumnsEnabled() { return extraFileColumnsEnabled; }
-
     public List<MainTableColumnModel> getColumns() {
         return columns;
     }
 
-    public Map<String, SortType> getSortTypesForColumns() {
-        return columnSortType;
+    public List<MainTableColumnModel> getColumnSortOrder() {
+        return columnSortOrder;
     }
 }

src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -97,15 +97,15 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
                 .setOnMouseDragEntered(this::handleOnDragEntered)
                 .install(this);
 
-        /*for (Entry<String, SortType> entries : preferences.getColumnPreferences().getSortTypesForColumns().entrySet()) {
-            Optional<TableColumn<BibEntryTableViewModel, ?>> column = this.getColumns().stream().filter(col -> entries.getKey().equals(col.getText())).findFirst();
-            column.ifPresent(col -> {
-                col.setSortType(entries.getValue());
-                this.getSortOrder().add(col);
-            });
-        }*/
-
-        if (preferences.resizeColumnsToFit()) {
+        this.getSortOrder().clear();
+        preferences.getColumnPreferences().getColumnSortOrder().forEach(columnModel ->
+                this.getColumns().stream()
+                        .map(column -> (MainTableColumn<?>) column)
+                        .filter(column -> column.getModel().equals(columnModel))
+                        .findFirst()
+                        .ifPresent(column -> this.getSortOrder().add(column)));
+
+        if (preferences.getResizeColumnsToFit()) {
             this.setColumnResizePolicy(new SmartConstrainedResizePolicy());
         }
         this.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);

src/main/java/org/jabref/gui/maintable/MainTableColumn.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.maintable;
 
+import javafx.beans.value.ObservableValue;
 import javafx.scene.control.TableColumn;
 
 import org.jabref.gui.util.BindingsHelper;
@@ -16,6 +17,12 @@ public MainTableColumn(MainTableColumnModel model) {
                 model.widthProperty(),
                 value -> this.setPrefWidth(model.widthProperty().getValue()),
                 value -> model.widthProperty().setValue(this.getWidth()));
+
+        BindingsHelper.bindBidirectional(
+                this.sortTypeProperty(),
+                (ObservableValue<SortType>) model.sortTypeProperty(),
+                value -> this.setSortType(model.sortTypeProperty().getValue()),
+                value -> model.sortTypeProperty().setValue(this.getSortType()));
     }
 
     public MainTableColumnModel getModel() { return model; }

src/main/java/org/jabref/gui/maintable/MainTableColumnModel.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.maintable;
 
+import java.util.EnumSet;
 import java.util.Objects;
 
 import javafx.beans.property.DoubleProperty;
@@ -9,6 +10,7 @@
 import javafx.beans.property.SimpleObjectProperty;
 import javafx.beans.property.SimpleStringProperty;
 import javafx.beans.property.StringProperty;
+import javafx.scene.control.TableColumn;
 
 import org.jabref.gui.util.FieldsUtil;
 import org.jabref.logic.l10n.Localization;
@@ -35,6 +37,8 @@ public enum Type {
         NORMALFIELD("field"),
         SPECIALFIELD("special", Localization.lang("Special"));
 
+        public static final EnumSet<Type> ICON_COLUMNS = EnumSet.of(EXTRAFILE,FILES,GROUPS,LINKED_IDENTIFIER);
+
         private String name;
         private String displayName;
 
@@ -67,35 +71,54 @@ public static Type fromString(String text) {
         }
     }
 
-    private final ObjectProperty<Type> typeProperty;
-    private final StringProperty qualifierProperty;
-    private final DoubleProperty widthProperty;
+    private final ObjectProperty<Type> typeProperty = new SimpleObjectProperty<>();
+    private final StringProperty qualifierProperty = new SimpleStringProperty();
+    private final DoubleProperty widthProperty = new SimpleDoubleProperty();
+    private final ObjectProperty<TableColumn.SortType> sortTypeProperty = new SimpleObjectProperty<>();
 
     /**
      * This is used by the preferences dialog, to initialize available columns the user can add to the table.
      *
-     * @param type the {@code MainTableColumnModel.Type} of the column, e.g. "NORMALFIELD" or "GROUPS"
+     * @param type the {@code MainTableColumnModel.Type} of the column, e.g. "NORMALFIELD" or "EXTRAFILE"
      * @param qualifier the stored qualifier of the column, e.g. "author/editor"
      */
-    public MainTableColumnModel(Type type, String qualifier, double width) {
+    public MainTableColumnModel(Type type, String qualifier) {
         Objects.requireNonNull(type);
-        typeProperty = new SimpleObjectProperty<>(type);
-        qualifierProperty = new SimpleStringProperty(qualifier);
-        widthProperty = new SimpleDoubleProperty(width);
-    }
+        Objects.requireNonNull(qualifier);
 
-    public MainTableColumnModel(Type type, String qualifier) {
-        this(type, qualifier, ColumnPreferences.DEFAULT_WIDTH);
-    }
+        this.typeProperty.setValue(type);
+        this.qualifierProperty.setValue(qualifier);
+        this.sortTypeProperty.setValue(TableColumn.SortType.ASCENDING);
 
-    public MainTableColumnModel(Type type, double width) {
-        this(type, "", width);
+        if (Type.ICON_COLUMNS.contains(type)) {
+            this.widthProperty.setValue(ColumnPreferences.ICON_COLUMN_WIDTH);
+        } else {
+            this.widthProperty.setValue(ColumnPreferences.DEFAULT_COLUMN_WIDTH);
+        }
     }
 
+    /**
+     * This is used by the preferences dialog, to initialize available basic icon columns, the user can add to the table.
+     *
+     * @param type the {@code MainTableColumnModel.Type} of the column, e.g. "GROUPS" or "LINKED_IDENTIFIER"
+     */
     public MainTableColumnModel(Type type) {
         this(type, "");
     }
 
+    /**
+     * This is used by the preference migrations.
+     *
+     * @param type the {@code MainTableColumnModel.Type} of the column, e.g. "NORMALFIELD" or "GROUPS"
+     * @param qualifier the stored qualifier of the column, e.g. "author/editor"
+     * @param width the stored width of the column
+     */
+    public MainTableColumnModel(Type type, String qualifier, double width) {
+        this(type, qualifier);
+
+        this.widthProperty.setValue(width);
+    }
+
     public Type getType() { return typeProperty.getValue(); }
 
     public String getQualifier() { return qualifierProperty.getValue(); }
@@ -109,10 +132,7 @@ public String getName() {
     }
 
     public String getDisplayName() {
-        if ((typeProperty.getValue() == Type.GROUPS
-                || typeProperty.getValue() == Type.FILES
-                || typeProperty.getValue() == Type.LINKED_IDENTIFIER)
-                && qualifierProperty.getValue().isBlank()) {
+        if (Type.ICON_COLUMNS.contains(typeProperty.getValue()) && qualifierProperty.getValue().isBlank()) {
             return typeProperty.getValue().getDisplayName();
         } else {
             return FieldsUtil.getNameWithType(FieldFactory.parseField(qualifierProperty.getValue()));
@@ -121,12 +141,14 @@ public String getDisplayName() {
 
     public StringProperty nameProperty() { return new ReadOnlyStringWrapper(getDisplayName()); }
 
-    public double getWidth() {
-        return widthProperty.get();
-    }
+    public double getWidth() { return widthProperty.getValue(); }
 
     public DoubleProperty widthProperty() { return widthProperty; }
 
+    public TableColumn.SortType getSortType() { return sortTypeProperty.getValue(); }
+
+    public ObjectProperty<TableColumn.SortType> sortTypeProperty() { return sortTypeProperty; }
+
     public boolean equals(Object o) {
         if (this == o) {
             return true;
@@ -149,23 +171,11 @@ public int hashCode() {
     }
 
     /**
-     * This is used by JabRefPreferences, to create a new ColumnModel out ouf the stored preferences.
+     * This creates a new {@code MainTableColumnModel} out of a given string
      *
-     * @param rawColumnName the stored name of the column, e.g. "field:author"
-     * @param width the stored width of the column
-     */
-    public static MainTableColumnModel parse(String rawColumnName, Double width) {
-        MainTableColumnModel columnModel = parse(rawColumnName);
-
-        Objects.requireNonNull(width);
-        columnModel.widthProperty().setValue(width);
-        return columnModel;
-    }
-
-    /**
-     * This is used by the preferences dialog, to allow the user to type in a field he wants to add to the table.
+     * @param rawColumnName the name of the column, e.g. "field:author", or "author"
      *
-     * @param rawColumnName the stored name of the column, e.g. "field:author", or "author"
+     * @return A new {@code MainTableColumnModel}
      */
     public static MainTableColumnModel parse(String rawColumnName) {
         Objects.requireNonNull(rawColumnName);
@@ -174,7 +184,9 @@ public static MainTableColumnModel parse(String rawColumnName) {
         Type type = Type.fromString(splittedName[0]);
         String qualifier = "";
 
-        if (type == Type.NORMALFIELD || type == Type.SPECIALFIELD || type == Type.EXTRAFILE) {
+        if (type == Type.NORMALFIELD
+                || type == Type.SPECIALFIELD
+                || type == Type.EXTRAFILE) {
             if (splittedName.length == 1) {
                 qualifier = splittedName[0]; // By default the rawColumnName is parsed as NORMALFIELD
             } else {

src/main/java/org/jabref/gui/maintable/MainTablePreferences.java

@@ -3,17 +3,21 @@
 public class MainTablePreferences {
     private final ColumnPreferences columnPreferences;
     private final boolean resizeColumnsToFit;
+    private final boolean extraFileColumnsEnabled;
 
-    public MainTablePreferences(ColumnPreferences columnPreferences, boolean resizeColumnsToFit) {
+    public MainTablePreferences(ColumnPreferences columnPreferences, boolean resizeColumnsToFit, boolean extraFileColumnsEnabled) {
         this.columnPreferences = columnPreferences;
         this.resizeColumnsToFit = resizeColumnsToFit;
+        this.extraFileColumnsEnabled = extraFileColumnsEnabled;
     }
 
     public ColumnPreferences getColumnPreferences() {
         return columnPreferences;
     }
 
-    public boolean resizeColumnsToFit() {
+    public boolean getResizeColumnsToFit() {
         return resizeColumnsToFit;
     }
+
+    public boolean getExtraFileColumnsEnabled() { return extraFileColumnsEnabled; }
 }