Merge remote-tracking branch 'upstream/master' into groupDragDrop

* upstream/master: Donate to JabRef! Issuestats.com is down Add link to logo creator Improve perfomance of opening a database that still used the old groups format (#2636) Set POSIX filepermissions to 644 (#2637) Fix #2629: Removing entry from group updates view properly Remove empty tooltip in group panel Refactored around the PDF Annotation Importer (#2624) Fix last import issue Fix imports and some reformatting Fix wrong import order Add missing svg icon RIP old icon Add new logo files (#2164) # Conflicts: # src/main/java/org/jabref/gui/groups/GroupSelector.java
JabRef · Mar 14, 2017 · 6b56eff · 6b56eff
2 parents 875678b + ef6cda5
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- JabRef has a new logo! The logo was designed by "[AikTheOne](https://99designs.de/profiles/theonestudio)" - who was the winner of a design contest at 99designs.com
 - Add tab which shows the MathSciNet review website if the `MRNumber` field is present.
 - Partly switched to a new UI technology (JavaFX).
     - Redesigned group panel.
@@ -61,9 +62,10 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - We fixed an issue where the `Move linked files to default file directory`- cleanup operation did not move the files to the location of the bib-file. [#2454](https://github.com/JabRef/jabref/issues/2454)
  - We fixed an issue where executing `Move file` on a selected file in the `general`-tab could overwrite an existing file. [#2385](https://github.com/JabRef/jabref/issues/2358)
  - We fixed an issue with importing groups and subgroups [#2600](https://github.com/JabRef/jabref/issues/2600)
- - Fixed an issue where title-related key patterns did not correspond to the documentation [#2604](https://github.com/JabRef/jabref/issues/2604) [#2589](https://github.com/JabRef/jabref/issues/2589)
- - We fixed an issue which prohibited the citation export to external programms on MacOS  [#2613](https://github.com/JabRef/jabref/issues/2613)
- - We fixed an issue where the file folder could not be changed when running `Get fulltext` in the `general`-tab [#2572](https://github.com/JabRef/jabref/issues/2572)
+ - Fixed an issue where title-related key patterns did not correspond to the documentation. [#2604](https://github.com/JabRef/jabref/issues/2604) [#2589](https://github.com/JabRef/jabref/issues/2589)
+ - We fixed an issue which prohibited the citation export to external programms on MacOS.  [#2613](https://github.com/JabRef/jabref/issues/2613)
+ - We fixed an issue where the file folder could not be changed when running `Get fulltext` in the `general`-tab. [#2572](https://github.com/JabRef/jabref/issues/2572)
+ - Newly created libraries no longer have the executable bit set under POSIX/Linux systems. The file permissions are now set to `664 (-rw-rw-r--)`. [#2635](https://github.com/JabRef/jabref/issues/#2635)
 ### Removed
 
 

diff --git a/README.md b/README.md
@@ -3,9 +3,7 @@
 [![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
 [![Dependency Status](https://www.versioneye.com/user/projects/557f2723386664002000009c/badge.svg?style=flat)](https://www.versioneye.com/user/projects/557f2723386664002000009c)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
-[![Donation](https://img.shields.io/badge/donate-something-orange.svg)](https://donations.jabref.org)
-[![Issue Stats](http://www.issuestats.com/github/jabref/jabref/badge/pr)](http://www.issuestats.com/github/jabref/jabref)
-[![Issue Stats](http://www.issuestats.com/github/jabref/jabref/badge/issue)](http://www.issuestats.com/github/jabref/jabref)
+[![Donation](https://img.shields.io/badge/donate-to%20jabref-orange.svg)](https://donations.jabref.org)
 
 This version is a development version. Features may not work as expected.
 

diff --git a/buildres/JabRef.VisualElementsManifest.xml b/buildres/JabRef.VisualElementsManifest.xml
@@ -1,4 +1,4 @@
 <?xml version="1.0" encoding="utf-8"?>
 <Application xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-  <VisualElements ForegroundText="light" BackgroundColor="#4F5F8F" ShowNameOnSquare150x150Logo="on"></VisualElements>
+  <VisualElements ForegroundText="dark" BackgroundColor="#a2aed1" ShowNameOnSquare150x150Logo="on"></VisualElements>
 </Application>
diff --git a/src/main/java/org/jabref/JabRefGUI.java b/src/main/java/org/jabref/JabRefGUI.java
@@ -179,7 +179,7 @@ private void openWindow() {
         for (int i = 0; (i < bibDatabases.size()) && (i < JabRefGUI.getMainFrame().getBasePanelCount()); i++) {
             ParserResult pr = bibDatabases.get(i);
             BasePanel panel = JabRefGUI.getMainFrame().getBasePanelAt(i);
-            OpenDatabaseAction.performPostOpenActions(panel, pr, true);
+            OpenDatabaseAction.performPostOpenActions(panel, pr);
         }
 
         LOGGER.debug("Finished adding panels");

diff --git a/src/main/java/org/jabref/cli/CrossrefFetcherEvaluator.java b/src/main/java/org/jabref/cli/CrossrefFetcherEvaluator.java
@@ -10,10 +10,10 @@
 import java.util.concurrent.atomic.AtomicInteger;
 
 import org.jabref.Globals;
+import org.jabref.logic.identifier.DOI;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fetcher.CrossRef;
 import org.jabref.logic.importer.fileformat.BibtexParser;
-import org.jabref.logic.identifier.DOI;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;

diff --git a/src/main/java/org/jabref/gui/ClipBoardManager.java b/src/main/java/org/jabref/gui/ClipBoardManager.java
@@ -14,10 +14,10 @@
 import java.util.Optional;
 
 import org.jabref.Globals;
+import org.jabref.logic.identifier.DOI;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.fetcher.DoiFetcher;
 import org.jabref.logic.importer.fileformat.BibtexParser;
-import org.jabref.logic.identifier.DOI;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
 

diff --git a/src/main/java/org/jabref/gui/IconTheme.java b/src/main/java/org/jabref/gui/IconTheme.java
@@ -14,7 +14,9 @@
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 
@@ -341,6 +343,18 @@ public FontBasedIcon createSmallIcon() {
         public FontBasedIcon createWithNewColor(Color newColor) {
             return new FontBasedIcon(this.iconCode, newColor, this.size);
         }
+    }
 
+    public static List<java.awt.Image> getLogoSet() {
+        List<java.awt.Image> jabrefLogos = new ArrayList<>();
+        jabrefLogos.add(new ImageIcon(getIconUrl("jabrefIcon16")).getImage());
+        jabrefLogos.add(new ImageIcon(getIconUrl("jabrefIcon20")).getImage());
+        jabrefLogos.add(new ImageIcon(getIconUrl("jabrefIcon32")).getImage());
+        jabrefLogos.add(new ImageIcon(getIconUrl("jabrefIcon40")).getImage());
+        jabrefLogos.add(new ImageIcon(getIconUrl("jabrefIcon48")).getImage());
+        jabrefLogos.add(new ImageIcon(getIconUrl("jabrefIcon64")).getImage());
+        jabrefLogos.add(new ImageIcon(getIconUrl("jabrefIcon128")).getImage());
+
+        return jabrefLogos;
     }
 }
diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -30,7 +30,6 @@
 import javax.swing.AbstractAction;
 import javax.swing.Action;
 import javax.swing.Icon;
-import javax.swing.ImageIcon;
 import javax.swing.JButton;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JComponent;
@@ -551,7 +550,7 @@ private void init() {
         setGlassPane(glassPane);
 
         setTitle(FRAME_TITLE);
-        setIconImage(new ImageIcon(IconTheme.getIconUrl("jabrefIcon48")).getImage());
+        setIconImages(IconTheme.getLogoSet());
         setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
         addWindowListener(new WindowAdapter() {
 

diff --git a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
@@ -8,8 +8,8 @@
 
 import org.jabref.JabRefGUI;
 import org.jabref.gui.ClipBoardManager;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.identifier.DOI;
+import org.jabref.logic.l10n.Localization;
 
 /**
  * Copies the doi url to the clipboard

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -29,9 +29,9 @@
 import org.jabref.gui.filelist.FileListEntryEditor;
 import org.jabref.gui.filelist.FileListTableModel;
 import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.identifier.DOI;
 import org.jabref.logic.identifier.Eprint;
+import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;

diff --git a/src/main/java/org/jabref/gui/entryeditor/FieldExtraComponents.java b/src/main/java/org/jabref/gui/entryeditor/FieldExtraComponents.java
@@ -31,11 +31,11 @@
 import org.jabref.gui.fieldeditors.FieldEditor;
 import org.jabref.gui.mergeentries.FetchAndMergeEntry;
 import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.logic.identifier.DOI;
+import org.jabref.logic.identifier.ISBN;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLUtil;
-import org.jabref.logic.identifier.DOI;
-import org.jabref.logic.identifier.ISBN;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;

diff --git a/src/main/java/org/jabref/gui/entryeditor/FileAnnotationTab.java b/src/main/java/org/jabref/gui/entryeditor/FileAnnotationTab.java
@@ -3,11 +3,14 @@
 import java.awt.Component;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Optional;
 import java.util.StringJoiner;
 
 import javax.swing.BoxLayout;
@@ -40,7 +43,7 @@ class FileAnnotationTab extends JPanel {
 
     private final JList<FileAnnotation> annotationList = new JList<>();
     private final JScrollPane annotationScrollPane = new JScrollPane();
-    private final JLabel fileNameLabel = new JLabel(Localization.lang("Filename"),JLabel.CENTER);
+    private final JLabel fileNameLabel = new JLabel(Localization.lang("Filename"), JLabel.CENTER);
     private final JComboBox<String> fileNameComboBox = new JComboBox<>();
     private final JScrollPane fileNameScrollPane = new JScrollPane();
     private final JLabel authorLabel = new JLabel(Localization.lang("Author"), JLabel.CENTER);
@@ -71,9 +74,8 @@ class FileAnnotationTab extends JPanel {
     FileAnnotationTab(EntryEditor parent) {
         this.parent = parent;
         setLayout(new BoxLayout(this, BoxLayout.X_AXIS));
-        listModel  = new DefaultListModel<>();
+        listModel = new DefaultListModel<>();
         this.isInitialized = false;
-
     }
 
     public FileAnnotationTab initializeTab(FileAnnotationTab tab) {
@@ -99,7 +101,6 @@ public FileAnnotationTab initializeTab(FileAnnotationTab tab, Map<String, List<F
         tab.isInitialized = true;
         tab.parent.repaint();
         return tab;
-
     }
 
     /**
@@ -130,32 +131,34 @@ private void addAnnotations() {
 
     /**
      * Updates the list model to show the given notes without those with no content
+     *
      * @param annotations value is the annotation name and the value is a pdfAnnotation object to add to the list model
      */
     private void updateShownAnnotations(List<FileAnnotation> annotations) {
         listModel.clear();
         if (annotations.isEmpty()) {
-            listModel.addElement(new FileAnnotation("", "", "", 0, Localization.lang("File has no attached annotations"), ""));
+            listModel.addElement(new FileAnnotation("", LocalDateTime.now(), 0, Localization.lang("File has no attached annotations"), "", Optional.empty()));
         } else {
             Comparator<FileAnnotation> byPage = Comparator.comparingInt(FileAnnotation::getPage);
             annotations.stream()
-                    .filter(annotation -> !(null == annotation.getContent()))
+                    .filter(annotation -> (null != annotation.getContent()))
                     .filter(annotation -> annotation.getAnnotationType().equals(FDFAnnotationHighlight.SUBTYPE)
-                            || (null == annotation.getLinkedFileAnnotation()))
+                            || !annotation.hasLinkedAnnotation())
                     .sorted(byPage)
                     .forEach(listModel::addElement);
         }
     }
 
     /**
      * Updates the text fields showing meta data and the content from the selected annotation
+     *
      * @param annotation pdf annotation which data should be shown in the text fields
      */
     private void updateTextFields(FileAnnotation annotation) {
         authorArea.setText(annotation.getAuthor());
-        dateArea.setText(annotation.getDate());
+        dateArea.setText(annotation.getTimeModified().format(DateTimeFormatter.ISO_LOCAL_DATE_TIME));
         pageArea.setText(String.valueOf(annotation.getPage()));
-        updateContentAndHighlightTextfields(annotation);
+        updateContentAndHighlightTextAreas(annotation);
     }
 
     /**
@@ -180,22 +183,22 @@ private void setUpGui() {
                 .columns("pref, $lcgap, pref:grow")
                 .rows("pref, $lg, fill:pref:grow, $lg, pref")
                 .padding(Paddings.DIALOG)
-                .add(fileNameLabel).xy(1,1, "left, top")
+                .add(fileNameLabel).xy(1, 1, "left, top")
                 .add(fileNameScrollPane).xyw(2, 1, 2)
                 .add(annotationScrollPane).xyw(1, 3, 3)
                 .build();
         annotationScrollPane.setViewportView(annotationList);
 
-        JPanel informationPanel  = FormBuilder.create()
+        JPanel informationPanel = FormBuilder.create()
                 .columns("pref, $lcgap, pref:grow")
                 .rows("pref, $lg, pref, $lg, pref, $lg, pref, $lg, pref:grow, $lg, pref:grow, $lg, fill:pref")
                 .padding(Paddings.DIALOG)
-                .add(authorLabel).xy(1,3, "left, top")
-                .add(authorScrollPane).xy(3,3)
-                .add(dateLabel).xy(1,5, "left, top")
-                .add(dateScrollPane).xy(3,5)
-                .add(pageLabel).xy(1,7, "left, top")
-                .add(pageScrollPane).xy(3,7)
+                .add(authorLabel).xy(1, 3, "left, top")
+                .add(authorScrollPane).xy(3, 3)
+                .add(dateLabel).xy(1, 5, "left, top")
+                .add(dateScrollPane).xy(3, 5)
+                .add(pageLabel).xy(1, 7, "left, top")
+                .add(pageScrollPane).xy(3, 7)
                 .add(annotationTextLabel).xy(1, 9, "left, top")
                 .add(annotationTextScrollPane).xywh(3, 9, 1, 2)
                 .add(highlightTxtLabel).xy(1, 11, "left, top")
@@ -237,7 +240,7 @@ private void setUpGui() {
                 .build());
     }
 
-    private JPanel setUpButtons(){
+    private JPanel setUpButtons() {
         JPanel buttonPanel = new JPanel(new GridBagLayout());
         GridBagConstraints buttonConstraints = new GridBagConstraints();
 
@@ -262,7 +265,7 @@ private JPanel setUpButtons(){
     /**
      * Copies the meta and content information of the pdf annotation to the clipboard
      */
-    private void copyToClipboard(){
+    private void copyToClipboard() {
         StringJoiner sj = new StringJoiner(System.getProperty("line.separator"));
         sj.add("Author: " + authorArea.getText());
         sj.add("Date: " + dateArea.getText());
@@ -286,22 +289,25 @@ private void reloadAnnotations() {
      *
      * @param annotation either a text annotation or a highlighting from a pdf
      */
-    private void updateContentAndHighlightTextfields(final FileAnnotation annotation) {
+    private void updateContentAndHighlightTextAreas(final FileAnnotation annotation) {
 
         if (annotation.hasLinkedAnnotation()) {
-            String annotationText;
-            String highlightedText;
+            // isPresent() of the optional is already checked in annotation.hasLinkedAnnotation()
+            if (!annotation.getLinkedFileAnnotation().getContent().isEmpty()) {
+                contentTxtArea.setText(annotation.getLinkedFileAnnotation().getContent());
+                contentTxtArea.setEnabled(true);
+            } else {
+                contentTxtArea.setText("N/A");
+                contentTxtArea.setEnabled(false);
+            }
 
-            if (annotation.getAnnotationType().equals(FDFAnnotationHighlight.SUBTYPE)) {
-                highlightedText = annotation.getContent();
-                annotationText = annotation.getLinkedFileAnnotation().getContent();
+            if (annotation.getContent().isEmpty()) {
+                highlightTxtArea.setEnabled(false);
+                highlightTxtArea.setText("JabRef: The highlighted area does not contain any legible text!");
             } else {
-                highlightedText = annotation.getLinkedFileAnnotation().getContent();
-                annotationText = annotation.getContent();
+                highlightTxtArea.setEnabled(true);
+                highlightTxtArea.setText(annotation.getContent());
             }
-            highlightTxtArea.setEnabled(true);
-            contentTxtArea.setText(annotationText);
-            highlightTxtArea.setText(highlightedText);
 
         } else {
             contentTxtArea.setText(annotation.getContent());
@@ -345,7 +351,7 @@ public Component getListCellRendererComponent(JList<?> list, Object value, int i
             FileAnnotation annotation = (FileAnnotation) value;
 
             //call the super method so that the cell selection is done as usual
-            label = (JLabel)super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+            label = (JLabel) super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
 
             //If more different annotation types should be reflected by icons in the list, add them here
             switch (annotation.getAnnotationType()) {

diff --git a/src/main/java/org/jabref/gui/groups/GroupSelector.java b/src/main/java/org/jabref/gui/groups/GroupSelector.java
@@ -68,9 +68,6 @@
 import org.jabref.model.groups.event.GroupUpdatedEvent;
 import org.jabref.model.metadata.MetaData;
 import org.jabref.model.search.SearchMatcher;
-import org.jabref.model.search.matchers.MatcherSet;
-import org.jabref.model.search.matchers.MatcherSets;
-import org.jabref.model.search.matchers.NotMatcher;
 import org.jabref.preferences.JabRefPreferences;
 
 import com.google.common.eventbus.Subscribe;
@@ -470,6 +467,7 @@ public void valueChanged(TreeSelectionEvent e) {
         if (panel == null) {
             return; // ignore this event (happens for example if the file was closed)
         }
+        /*
         if (getLeafsOfSelection().stream().allMatch(GroupTreeNodeViewModel::isAllEntriesGroup)) {
             panel.getMainTable().getTableModel().updateGroupingState(MainTableDataModel.DisplayOption.DISABLED);
             if (showOverlappingGroups.isSelected()) {
@@ -478,12 +476,13 @@ public void valueChanged(TreeSelectionEvent e) {
             frame.output(Localization.lang("Displaying no groups") + ".");
             return;
         }
-
+        */
         updateShownEntriesAccordingToSelectedGroups();
     }
 
     private void updateShownEntriesAccordingToSelectedGroups() {
-        final MatcherSet searchRules = MatcherSets
+        updateShownEntriesAccordingToSelectedGroups(Globals.stateManager.activeGroupProperty().get());
+        /*final MatcherSet searchRules = MatcherSets
                 .build(andCb.isSelected() ? MatcherSets.MatcherType.AND : MatcherSets.MatcherType.OR);
 
         for (GroupTreeNodeViewModel node : getLeafsOfSelection()) {
@@ -492,8 +491,9 @@ private void updateShownEntriesAccordingToSelectedGroups() {
         }
         SearchMatcher searchRule = invCb.isSelected() ? new NotMatcher(searchRules) : searchRules;
         GroupingWorker worker = new GroupingWorker(searchRule);
-        worker.run();
-        worker.update();
+        worker.getWorker().run();
+        worker.getCallBack().update();
+        */
     }
 
     private void updateShownEntriesAccordingToSelectedGroups(Optional<GroupTreeNode> selectedGroup) {

diff --git a/src/main/java/org/jabref/gui/help/AboutDialogController.java b/src/main/java/org/jabref/gui/help/AboutDialogController.java
@@ -25,7 +25,7 @@ private void initialize() {
         viewModel = new AboutDialogViewModel(dialogService, clipBoardManager, buildInfo);
 
         SvgImageLoaderFactory.install();
-        Image icon = new Image(this.getClass().getResourceAsStream("/images/icons/JabRef-icon.svg"));
+        Image icon = new Image(this.getClass().getResourceAsStream("/icons/jabref.svg"));
         iconImage.setImage(icon);
     }