Merge pull request #5 from JabRef/master

Merging from master

CHANGELOG.md

@@ -131,6 +131,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the same menu for changing entry type had two different sizes and weights. [#4977](https://github.com/JabRef/jabref/issues/4977)
 - We fixed an issue where the "Attach file" dialog, in the right-click menu for an entry, started on the working directory instead of the user's main directory. [#4995](https://github.com/JabRef/jabref/issues/4995)
 - We fixed an issue where the JabRef Icon in the macOS launchpad was not displayed correctly [#5003](https://github.com/JabRef/jabref/issues/5003)
+- We fixed an issue where the "Search for unlinked local files" would throw an exception when parsing the content of a PDF-file with missing "series" information [#5128](https://github.com/JabRef/jabref/issues/5128)
 
 
 ### Removed

build.gradle

@@ -16,13 +16,13 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '2.3'
+    id 'com.gradle.build-scan' version '2.4'
     id 'com.install4j.gradle' version '7.0.12'
     id 'com.github.johnrengelman.shadow' version '5.1.0'
     id "com.simonharrer.modernizer" version '1.8.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
     id 'net.ltgt.errorprone' version '0.8.1'
-    id 'com.github.ben-manes.versions' version '0.21.0'
+    id 'com.github.ben-manes.versions' version '0.22.0'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -143,10 +143,10 @@ dependencies {
 
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:2.0.0-alpha0'
-    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.12.0'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.12.0'
-    compile 'org.apache.logging.log4j:log4j-api:2.12.0'
-    compile 'org.apache.logging.log4j:log4j-core:2.12.0'
+    compile 'org.apache.logging.log4j:log4j-slf4j18-impl:2.12.1'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.12.1'
+    compile 'org.apache.logging.log4j:log4j-api:2.12.1'
+    compile 'org.apache.logging.log4j:log4j-core:2.12.1'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
@@ -162,9 +162,9 @@ dependencies {
     testCompile 'org.junit.platform:junit-platform-launcher:1.5.1'
 
     testRuntime 'org.apache.logging.log4j:log4j-core:2.12.0'
-    testRuntime 'org.apache.logging.log4j:log4j-jul:2.12.0'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.12.1'
     testCompile 'org.mockito:mockito-core:3.0.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.24.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'

src/main/java/org/jabref/gui/Base.css

@@ -1015,6 +1015,11 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-fill: -jr-warn;
 }
 
+.warning-message {
+    -fx-fill: -jr-error;
+    -fx-text-fill: -jr-error;
+}
+
 .error-icon {
     -fx-text-fill: -jr-error;
     -fx-fill: -jr-error;

src/main/java/org/jabref/gui/cleanup/FieldFormatterCleanupsPanel.java

@@ -105,7 +105,7 @@ private void buildLayout() {
         actionsList.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
         new ViewModelListCellFactory<FieldFormatterCleanup>()
                 .withText(action -> action.getField() + ": " + action.getFormatter().getName())
-                .withTooltip(action -> action.getFormatter().getDescription())
+                .withStringTooltip(action -> action.getFormatter().getDescription())
                 .install(actionsList);
         add(actionsList, 1, 1, 3, 1);
 
@@ -171,7 +171,7 @@ private GridPane getSelectorPanel() {
         formattersCombobox = new ComboBox<>(FXCollections.observableArrayList(availableFormatters));
         new ViewModelListCellFactory<Formatter>()
                 .withText(Formatter::getName)
-                .withTooltip(Formatter::getDescription)
+                .withStringTooltip(Formatter::getDescription)
                 .install(formattersCombobox);
         EasyBind.subscribe(formattersCombobox.valueProperty(), e -> updateDescription());
         builder.add(formattersCombobox, 3, 1);

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

@@ -1,6 +1,7 @@
 package org.jabref.gui.collab;
 
 import java.util.ArrayList;
+import java.util.Comparator;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
@@ -44,7 +45,7 @@ public EntryChangeViewModel(BibEntry memEntry, BibEntry tmpEntry, BibEntry diskE
         LOGGER.debug("Modified entry: " + memEntry.getCiteKeyOptional().orElse("<no BibTeX key set>")
                 + "\n Modified locally: " + isModifiedLocally + " Modifications agree: " + modificationsAgree);
 
-        Set<Field> allFields = new TreeSet<>();
+        Set<Field> allFields = new TreeSet<>(Comparator.comparing(Field::getName));
         allFields.addAll(memEntry.getFields());
         allFields.addAll(tmpEntry.getFields());
         allFields.addAll(diskEntry.getFields());

src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryAction.java

@@ -1,4 +1,4 @@
-package org.jabref.gui.BibEntryTypes;
+package org.jabref.gui.customentrytypes;
 
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.actions.SimpleCommand;

src/main/java/org/jabref/gui/customentrytypes/EntryTypeCustomizationDialog.java

@@ -1,4 +1,4 @@
-package org.jabref.gui.BibEntryTypes;
+package org.jabref.gui.customentrytypes;
 
 import org.jabref.gui.util.BaseDialog;
 

src/main/java/org/jabref/gui/customentrytypes/FieldSetComponent.java

@@ -1,4 +1,4 @@
-package org.jabref.gui.BibEntryTypes;
+package org.jabref.gui.customentrytypes;
 
 import java.awt.Component;
 import java.awt.GridBagConstraints;

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java

@@ -65,7 +65,7 @@ public LinkedFilesEditor(Field field, DialogService dialogService, BibDatabaseCo
                   .load();
 
         ViewModelListCellFactory<LinkedFileViewModel> cellFactory = new ViewModelListCellFactory<LinkedFileViewModel>()
-                   .withTooltip(LinkedFileViewModel::getDescription)
+                   .withStringTooltip(LinkedFileViewModel::getDescription)
                    .withGraphic(LinkedFilesEditor::createFileDisplay)
                    .withContextMenu(this::createContextMenuForFile)
                    .withOnMouseClickedEvent(this::handleItemMouseClick)

src/main/java/org/jabref/gui/icon/IconTheme.java

@@ -321,7 +321,8 @@ public enum JabRefIcons implements JabRefIcon {
         LATEX_FILE_DIRECTORY(MaterialDesignIcon.FOLDER_OUTLINE),
         LATEX_FILE(MaterialDesignIcon.FILE_OUTLINE),
         LATEX_COMMENT(MaterialDesignIcon.COMMENT_TEXT_OUTLINE),
-        LATEX_LINE(MaterialDesignIcon.FORMAT_LINE_SPACING);
+        LATEX_LINE(MaterialDesignIcon.FORMAT_LINE_SPACING),
+        PASSWORD_REVEALED(MaterialDesignIcon.EYE);
 
         private final JabRefIcon icon;
 

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

@@ -9,14 +9,16 @@
 
 import javax.swing.undo.UndoManager;
 
+import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.ContextMenu;
 import javafx.scene.control.MenuItem;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.Tooltip;
 import javafx.scene.input.MouseButton;
 import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.Pane;
+import javafx.scene.layout.StackPane;
 import javafx.scene.paint.Color;
 import javafx.scene.shape.Rectangle;
 
@@ -65,7 +67,7 @@ class MainTableColumnFactory {
     private final CellFactory cellFactory;
     private final UndoManager undoManager;
     private final DialogService dialogService;
-   
+
 
     public MainTableColumnFactory(BibDatabaseContext database, ColumnPreferences preferences, ExternalFileTypes externalFileTypes, UndoManager undoManager, DialogService dialogService) {
         this.database = Objects.requireNonNull(database);
@@ -78,9 +80,7 @@ public MainTableColumnFactory(BibDatabaseContext database, ColumnPreferences pre
 
     public List<TableColumn<BibEntryTableViewModel, ?>> createColumns() {
         List<TableColumn<BibEntryTableViewModel, ?>> columns = new ArrayList<>();
-
         columns.add(createGroupColumn());
-
         // Add column for linked files
         if (preferences.showFileColumn()) {
             columns.add(createFileColumn());
@@ -116,35 +116,51 @@ public MainTableColumnFactory(BibDatabaseContext database, ColumnPreferences pre
 
     private TableColumn<BibEntryTableViewModel, ?> createGroupColumn() {
         TableColumn<BibEntryTableViewModel, List<AbstractGroup>> column = new TableColumn<>();
-        column.getStyleClass().add(GROUP_COLUMN);
-        setExactWidth(column, 20);
+        Node headerGraphic = IconTheme.JabRefIcons.DEFAULT_GROUP_ICON.getGraphicNode();
+        Tooltip.install(headerGraphic, new Tooltip(Localization.lang("Group color")));
+        column.setGraphic(headerGraphic);
+        column.getStyleClass().add(ICON_COLUMN);
+        setExactWidth(column, GUIGlobals.WIDTH_ICON_COL);
         column.setCellValueFactory(cellData -> cellData.getValue().getMatchedGroups(database));
         new ValueTableCellFactory<BibEntryTableViewModel, List<AbstractGroup>>()
                 .withGraphic(this::createGroupColorRegion)
                 .install(column);
+        column.setStyle("-fx-padding: 0 0 0 0;");
         column.setSortable(true);
         return column;
     }
 
     private Node createGroupColorRegion(BibEntryTableViewModel entry, List<AbstractGroup> matchedGroups) {
-        Rectangle rectangle = new Rectangle();
-        rectangle.setWidth(3);
-        rectangle.setHeight(20);
-        Color color = matchedGroups.stream()
-                                   .flatMap(group -> OptionalUtil.toStream(group.getColor()))
-                                   .findFirst()
-                                   .orElse(Color.TRANSPARENT);
-        rectangle.setFill(color);
-
-        String matchedGroupsString = matchedGroups.stream()
-                                                  .map(AbstractGroup::getName)
-                                                  .collect(Collectors.joining(", "));
-        Tooltip tooltip = new Tooltip(Localization.lang("Entry is contained in the following groups:") + "\n" + matchedGroupsString);
-        Tooltip.install(rectangle, tooltip);
-
-        BorderPane container = new BorderPane();
-        container.setLeft(rectangle);
-        return container;
+        Color groupColor = matchedGroups.stream()
+                .flatMap(group -> OptionalUtil.toStream(group.getColor()))
+                .findFirst()
+                .orElse(Color.TRANSPARENT);
+
+        if (groupColor != Color.TRANSPARENT) {
+            Rectangle border = new Rectangle();
+            border.setWidth(5);
+            border.setHeight(20);
+            border.setFill(Color.DARKGRAY);
+
+            Rectangle groupRectangle = new Rectangle();
+            groupRectangle.setWidth(3);
+            groupRectangle.setHeight(18);
+            groupRectangle.setFill(groupColor);
+
+            StackPane container = new StackPane();
+            container.setMinWidth(10);
+            container.setAlignment(Pos.CENTER);
+
+            container.getChildren().addAll(border,groupRectangle);
+
+            String matchedGroupsString = matchedGroups.stream()
+                    .map(AbstractGroup::getName)
+                    .collect(Collectors.joining(", "));
+            Tooltip tooltip = new Tooltip(Localization.lang("Entry is contained in the following groups:") + "\n" + matchedGroupsString);
+            Tooltip.install(container, tooltip);
+            return container;
+        }
+        return new Pane();
     }
 
     private List<TableColumn<BibEntryTableViewModel, ?>> createNormalColumns() {

src/main/java/org/jabref/gui/mergeentries/FetchAndMergeEntry.java

@@ -2,6 +2,7 @@
 
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
@@ -92,8 +93,10 @@ private void showMergeDialog(BibEntry originalEntry, BibEntry fetchedEntry, WebF
             NamedCompound ce = new NamedCompound(Localization.lang("Merge entry with %0 information", fetcher.getName()));
 
             // Updated the original entry with the new fields
-            Set<Field> jointFields = new TreeSet<>(mergedEntry.get().getFields());
-            Set<Field> originalFields = new TreeSet<>(originalEntry.getFields());
+            Set<Field> jointFields = new TreeSet<>(Comparator.comparing(Field::getName));
+            jointFields.addAll(mergedEntry.get().getFields());
+            Set<Field> originalFields = new TreeSet<>(Comparator.comparing(Field::getName));
+            originalFields.addAll(originalEntry.getFields());
             boolean edited = false;
 
             // entry type

src/main/java/org/jabref/gui/mergeentries/MergeEntries.java

@@ -4,6 +4,7 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -46,18 +47,18 @@ public class MergeEntries extends BorderPane {
 
     // Headings
     private final List<String> columnHeadings = Arrays.asList(Localization.lang("Field"),
-            Localization.lang("Left entry"),
-            Localization.lang("Left"),
-            Localization.lang("None"),
-            Localization.lang("Right"),
-            Localization.lang("Right entry"));
+                                                              Localization.lang("Left entry"),
+                                                              Localization.lang("Left"),
+                                                              Localization.lang("None"),
+                                                              Localization.lang("Right"),
+                                                              Localization.lang("Right entry"));
     private final Set<Field> identicalFields = new HashSet<>();
     private final Set<Field> differentFields = new HashSet<>();
     private final BibEntry mergedEntry = new BibEntry();
     private final BibEntry leftEntry;
     private final BibEntry rightEntry;
     private final Map<Field, TextFlow> leftTextPanes = new HashMap<>();
-    private final Set<Field> allFields = new TreeSet<>();
+    private final Set<Field> allFields = new TreeSet<>(Comparator.comparing(Field::getName));
     private final Map<Field, TextFlow> rightTextPanes = new HashMap<>();
     private final Map<Field, List<RadioButton>> radioButtons = new HashMap<>();
     private Boolean identicalTypes;
@@ -81,7 +82,6 @@ public MergeEntries(BibEntry entryLeft, BibEntry entryRight, String headingLeft,
         setRightHeaderText(headingRight);
     }
 
-
     /**
      * Constructor taking two entries
      *
@@ -240,8 +240,8 @@ private void setupHeadingRows(GridPane mergePanel) {
     private void fillDiffModes() {
         diffMode.setItems(FXCollections.observableList(Arrays.asList(DiffMode.values())));
         new ViewModelListCellFactory<DiffMode>()
-                .withText(MergeEntries::getDisplayText)
-                .install(diffMode);
+                                                .withText(MergeEntries::getDisplayText)
+                                                .install(diffMode);
         DiffMode diffModePref = Globals.prefs.getAsOptional(JabRefPreferences.MERGE_ENTRIES_DIFF_MODE)
                                              .flatMap(DiffMode::parse)
                                              .orElse(DiffMode.WORD);

src/main/java/org/jabref/gui/preferences/AbstractPreferenceTabView.java

@@ -0,0 +1,37 @@
+package org.jabref.gui.preferences;
+
+import java.util.List;
+
+import javax.inject.Inject;
+
+import javafx.scene.Node;
+import javafx.scene.layout.VBox;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.util.TaskExecutor;
+import org.jabref.preferences.JabRefPreferences;
+
+public abstract class AbstractPreferenceTabView extends VBox implements PreferencesTab {
+
+    @Inject protected TaskExecutor taskExecutor;
+    @Inject protected DialogService dialogService;
+
+    protected PreferenceTabViewModel viewModel;
+
+    protected JabRefPreferences preferences;
+
+    @Override
+    public Node getBuilder() { return this; }
+
+    @Override
+    public void setValues() { viewModel.setValues(); }
+
+    @Override
+    public void storeSettings() { viewModel.storeSettings(); }
+
+    @Override
+    public boolean validateSettings() { return viewModel.validateSettings(); }
+
+    @Override
+    public List<String> getRestartWarnings() { return viewModel.getRestartWarnings(); }
+}