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; }
 }