Merge branch 'master' into menu_select_push_app

CHANGELOG.md

@@ -117,8 +117,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 - We fixed an issue where an NullPointer exception was thrown when a referenced entry in an Open/Libre Office document was no longer present in the library. Now an error message with the reference marker of the missing entry is shown. [#4932](https://github.com/JabRef/jabref/issues/4932)
 - We fixed an issue where a database exception related to a missing timezone was too big. [#4827](https://github.com/JabRef/jabref/issues/4827)
+- We fixed an issue where the IEEE fetcher returned an error if no keywords were present in the result from the IEEE website [#4997](https://github.com/JabRef/jabref/issues/4997)
 - We fixed an issue where the command line help text had several errors, and arguments and descriptions have been rewritten to simplify and detail them better. [#4932](https://github.com/JabRef/jabref/issues/2016)
 - 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)
+
 
 
 ### Removed

README.md

@@ -9,6 +9,14 @@ JabRef is an open-source, cross-platform citation and reference management tool
 Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research.
 ![main table](https://www.jabref.org/img/JabRef-4-0-MainTable.png)
 
+## Table of Contents
+
+- [Features](#features)
+- [Installation](#installation)
+- [Bug Reports, Suggestions, Other Feedback](#bug-reports-suggestions-other-feedback)
+- [Contributing](#contributing)
+- [Acknowledgements](#acknowledgements) / [License](#license)
+
 ## Features
 
 JabRef is a cross-platform application that works on Windows, Linux and Mac OS X. It is available free of charge and is actively developed.

build.gradle

@@ -173,7 +173,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.20'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.21'
     xjc 'com.sun.xml.bind:jaxb-xjc:2.2.4-1'
     jython 'org.python:jython-standalone:2.7.1'
 }

jabref.install4j

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<install4j version="7.0.8" transformSequenceNumber="7">
+<install4j version="7.0.11" transformSequenceNumber="7">
   <directoryPresets config="./buildres/jabref.json" />
   <application name="JabRef" distributionSourceDir="" applicationId="0034-7691-1464-4754" mediaDir="build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="JabRef" publisher="JabRef Community" publisherWeb="https://www.jabref.org/" version="DEV" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="true" macSignature="????" macVolumeId="780dfea2d33a0244" javaMinVersion="1.8" javaMaxVersion="1.8" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
     <languages skipLanguageSelection="true" languageSelectionInPrincipalLanguage="false">

scripts/download-install4j-and-jres.sh

@@ -5,7 +5,7 @@ if [ ! -d ~/downloads ]; then
   mkdir ~/downloads
 fi
 cd ~/downloads
-wget --quiet -nc --show-progress http://download-keycdn.ej-technologies.com/install4j/install4j_unix_7_0_8.tar.gz
+wget --quiet -nc --show-progress http://download-keycdn.ej-technologies.com/install4j/install4j_unix_7_0_11.tar.gz
 
 # fetch JREs
 if [ ! -d ~/.install4j7/jres ]; then

scripts/extract-install4j.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
-tar -xf ~/downloads/install4j_unix_7_0_8.tar.gz
+tar -xf ~/downloads/install4j_unix_7_0_11.tar.gz
 # fix directory name (until install4j 6.1.5 it was install4j6
-mv install4j7.0.8 install4j7
+mv install4j7.0.11 install4j7

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

@@ -1032,3 +1032,7 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-font-size: 1.5em;
     -fx-padding: 1em 0em 1em 0em;
 }
+
+.dialog-pane {
+    -fx-background-color: -fx-control-inner-background;
+}

src/main/java/org/jabref/gui/actions/ActionFactory.java

@@ -4,7 +4,6 @@
 import java.lang.reflect.Method;
 import java.util.Objects;
 
-import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonBase;
 import javafx.scene.control.CheckMenuItem;
@@ -157,13 +156,9 @@ public ButtonBase configureIconButton(Action action, Command command, ButtonBase
         button.getStyleClass().add("icon-button");
 
         // For some reason the graphic is not set correctly, so let's fix this
+        // ToDO: Find a way to reuse JabRefIconView
         button.graphicProperty().unbind();
-        action.getIcon().ifPresent(icon -> {
-            // ToDO: Find a way to reuse JabRefIconView
-            Node graphicNode = icon.getGraphicNode();
-            graphicNode.setStyle(String.format("-fx-font-family: %s; -fx-font-size: %s;", icon.fontFamily(), "1em"));
-            button.setGraphic(graphicNode);
-        });
+        action.getIcon().ifPresent(icon -> button.setGraphic(icon.getGraphicNode()));
 
         return button;
     }

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

@@ -40,7 +40,14 @@
                     <Tooltip text="%Change entry type"/>
                 </tooltip>
             </Button>
-            <Button fx:id="generateCiteKeyButton" styleClass="narrow"/>
+            <Button styleClass="icon-button,narrow" onAction="#generateCiteKeyButton">
+                <graphic>
+                    <JabRefIconView glyph="MAKE_KEY"/>
+                </graphic>
+                <tooltip>
+                    <Tooltip text="%Generate BibTeX key"/>
+                </tooltip>
+            </Button>
             <Button fx:id="fetcherButton" styleClass="icon-button,narrow">
                 <graphic>
                     <JabRefIconView glyph="REFRESH"/>

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

@@ -27,8 +27,6 @@
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.GUIGlobals;
-import org.jabref.gui.actions.ActionFactory;
-import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.bibtexkeypattern.GenerateBibtexKeySingleAction;
 import org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTab;
 import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
@@ -87,7 +85,6 @@ public class EntryEditor extends BorderPane {
     @FXML private Button typeChangeButton;
     @FXML private Button fetcherButton;
     @FXML private Label typeLabel;
-    @FXML private Button generateCiteKeyButton;
 
     private final EntryEditorPreferences preferences;
     private final DialogService dialogService;
@@ -261,6 +258,12 @@ private void deleteEntry() {
         panel.delete(entry);
     }
 
+    @FXML
+    void generateCiteKeyButton() {
+        GenerateBibtexKeySingleAction action = new GenerateBibtexKeySingleAction(getEntry(), databaseContext, dialogService, preferences, undoManager);
+        action.execute();
+    }
+
     @FXML
     private void navigateToPreviousEntry() {
         panel.selectPreviousEntry();
@@ -387,13 +390,6 @@ private void setupToolBar() {
             fetcherMenu.getItems().add(fetcherMenuItem);
         }
         fetcherButton.setOnMouseClicked(event -> fetcherMenu.show(fetcherButton, Side.RIGHT, 0, 0));
-
-        // Configure cite key button
-        new ActionFactory(preferences.getKeyBindings())
-                .configureIconButton(
-                        StandardActions.GENERATE_CITE_KEY,
-                        new GenerateBibtexKeySingleAction(getEntry(), databaseContext, dialogService, preferences, undoManager),
-                        generateCiteKeyButton);
     }
 
     private void fetchAndMerge(EntryBasedFetcher fetcher) {

src/main/java/org/jabref/gui/filelist/AttachFileAction.java

@@ -1,5 +1,7 @@
 package org.jabref.gui.filelist;
 
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Optional;
 
 import org.jabref.Globals;
@@ -32,14 +34,21 @@ public void execute() {
             dialogService.notify(Localization.lang("This operation requires exactly one item to be selected."));
             return;
         }
+
         BibEntry entry = panel.getSelectedEntries().get(0);
+
+        Path workingDirectory = panel.getBibDatabaseContext()
+                                     .getFirstExistingFileDir(Globals.prefs.getFilePreferences())
+                                     .orElse(Paths.get(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)));
+
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                                                                                               .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY))
-                                                                                               .build();
+                .withInitialDirectory(workingDirectory)
+                .build();
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {
-
-            LinkedFile linkedFile = LinkedFilesEditorViewModel.fromFile(newFile, panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()), ExternalFileTypes.getInstance());
+            LinkedFile linkedFile = LinkedFilesEditorViewModel.fromFile(newFile,
+                    panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()),
+                    ExternalFileTypes.getInstance());
 
             LinkedFileEditDialogView dialog = new LinkedFileEditDialogView(linkedFile);
 

src/main/java/org/jabref/gui/help/AboutDialog.css

@@ -1,9 +1,10 @@
 .about-heading {
     -fx-font-size: 30;
+    -fx-text-fill: -jr-theme;
 }
 
 .about-heading:pressed {
-	-fx-text-fill: -fx-focus-color;
+    -fx-text-fill: -jr-selected;
 }
 
 .top-padding {
@@ -33,7 +34,7 @@
 }
 
 .info-sections {
-	-fx-padding: 5px;
+    -fx-padding: 5px;
 }
 
 .logo-pane {

src/main/java/org/jabref/gui/importer/fetcher/WebSearchPane.java

@@ -35,7 +35,7 @@ public class WebSearchPane extends SidePaneComponent {
     public WebSearchPane(SidePaneManager sidePaneManager, JabRefPreferences preferences, JabRefFrame frame) {
         super(sidePaneManager, IconTheme.JabRefIcons.WWW, Localization.lang("Web search"));
         this.preferences = preferences;
-        this.viewModel = new WebSearchPaneViewModel(preferences.getImportFormatPreferences(), frame, preferences);
+        this.viewModel = new WebSearchPaneViewModel(preferences.getImportFormatPreferences(), frame, preferences, frame.getDialogService());
     }
 
     @Override

src/main/java/org/jabref/gui/importer/fetcher/WebSearchPaneViewModel.java

@@ -12,6 +12,7 @@
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.importer.ImportEntriesDialog;
 import org.jabref.gui.util.BackgroundTask;
@@ -25,21 +26,19 @@
 import org.jabref.preferences.JabRefPreferences;
 
 import org.fxmisc.easybind.EasyBind;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 public class WebSearchPaneViewModel {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(WebSearchPaneViewModel.class);
-
     private final ObjectProperty<SearchBasedFetcher> selectedFetcher = new SimpleObjectProperty<>();
     private final ListProperty<SearchBasedFetcher> fetchers = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final StringProperty query = new SimpleStringProperty();
     private final JabRefFrame frame;
+    private final DialogService dialogService;
 
-    public WebSearchPaneViewModel(ImportFormatPreferences importPreferences, JabRefFrame frame, JabRefPreferences preferences) {
+    public WebSearchPaneViewModel(ImportFormatPreferences importPreferences, JabRefFrame frame, JabRefPreferences preferences, DialogService dialogService) {
         // TODO: Rework so that we don't rely on JabRefFrame and not the complete preferences
         this.frame = frame;
+        this.dialogService = dialogService;
 
         List<SearchBasedFetcher> allFetchers = WebFetchers.getSearchBasedFetchers(importPreferences);
         allFetchers.sort(Comparator.comparing(WebFetcher::getName));
@@ -84,12 +83,12 @@ public StringProperty queryProperty() {
 
     public void search() {
         if (StringUtil.isBlank(getQuery())) {
-            frame.getDialogService().notify(Localization.lang("Please enter a search string"));
+            dialogService.notify(Localization.lang("Please enter a search string"));
             return;
         }
 
         if (frame.getCurrentBasePanel() == null) {
-            frame.getDialogService().notify(Localization.lang("Please open or start a new library before searching"));
+            dialogService.notify(Localization.lang("Please open or start a new library before searching"));
             return;
         }
 
@@ -98,6 +97,8 @@ public void search() {
         BackgroundTask<List<BibEntry>> task = BackgroundTask.wrap(() -> activeFetcher.performSearch(getQuery().trim()))
                                                             .withInitialMessage(Localization.lang("Processing %0", getQuery()));
 
+        task.onFailure(ex -> dialogService.showErrorDialogAndWait(ex));
+
         ImportEntriesDialog dialog = new ImportEntriesDialog(frame.getCurrentBasePanel().getBibDatabaseContext(), task);
         dialog.setTitle(activeFetcher.getName());
         dialog.showAndWait();

src/main/java/org/jabref/gui/preferences/PreferencesDialog.css

@@ -1,12 +1,12 @@
 #sideMenu {
-    -fx-background-color: -jr-white;
+    -fx-background-color: -fx-control-inner-background;
     -fx-border-color: -fx-outer-border;
     -fx-border-width: 1;
 }
 
 #sideMenu > .virtual-flow > .clipped-container > .sheet > .list-cell {
     -fx-padding: 8 8 8 8;
-    -fx-background: -jr-white;
+    -fx-background: -fx-control-inner-background;
 }
 
 .preferencePaneContainer {

src/main/java/org/jabref/logic/importer/fetcher/IEEE.java

@@ -85,25 +85,28 @@ private static BibEntry parseJsonRespone(JSONObject jsonEntry, Character keyword
         final List<String> authors = new ArrayList<>();
         JSONObject authorsContainer = jsonEntry.optJSONObject("authors");
         authorsContainer.getJSONArray("authors").forEach(authorPure -> {
-                    JSONObject author = (JSONObject) authorPure;
-                    authors.add(author.optString("full_name"));
-                }
-        );
+            JSONObject author = (JSONObject) authorPure;
+            authors.add(author.optString("full_name"));
+        });
         entry.setField(FieldName.AUTHOR, authors.stream().collect(Collectors.joining(" and ")));
         entry.setField(FieldName.LOCATION, jsonEntry.optString("conference_location"));
         entry.setField(FieldName.DOI, jsonEntry.optString("doi"));
         entry.setField(FieldName.PAGES, jsonEntry.optString("start_page") + "--" + jsonEntry.optString("end_page"));
 
         JSONObject keywordsContainer = jsonEntry.optJSONObject("index_terms");
         if (keywordsContainer != null) {
-            keywordsContainer.getJSONObject("ieee_terms").getJSONArray("terms").forEach(data -> {
-                String keyword = (String) data;
-                entry.addKeyword(keyword, keywordSeparator);
-            });
-            keywordsContainer.getJSONObject("author_terms").getJSONArray("terms").forEach(data -> {
-                String keyword = (String) data;
-                entry.addKeyword(keyword, keywordSeparator);
-            });
+            if (keywordsContainer.has("ieee_terms")) {
+                keywordsContainer.getJSONObject("ieee_terms").getJSONArray("terms").forEach(data -> {
+                    String keyword = (String) data;
+                    entry.addKeyword(keyword, keywordSeparator);
+                });
+            }
+            if (keywordsContainer.has("author_terms")) {
+                keywordsContainer.getJSONObject("author_terms").getJSONArray("terms").forEach(data -> {
+                    String keyword = (String) data;
+                    entry.addKeyword(keyword, keywordSeparator);
+                });
+            }
         }
 
         entry.setField(FieldName.ISBN, jsonEntry.optString("isbn"));