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

* upstream/master: (23 commits)
  Implement #2785: resort groups using drag & drop (#2864)
  Add Library of Congress as ID-fetcher (#2865)
  Fix export and import of MS office day/year/month acessed fields (#2862)
  Adsurl to url (#2861)
  Update LICENSE.md
  Update
  Update LICENSE.md
  Update license file so that github recognize it properly
  Improve Issue Template Using a Collapsible Log Area
  Fix #2852: Improve performance of group filtering.
  Rename GroupSelector to GroupSidePane
  Fix #2843: Show information correctly in entry editor
  Remove old entry editor code related to focus selection
  Implement feedback
  Menu Greek Translation (#2836)
  Relaxed the regex to also match negative timezone formats when parsing pdf annotation dates (#2841)
  Update localization
  Remove unnecessary group code (and move remaining settings to preferences)
  Add Local Maven repo as first lookup resource, to avoid having duplicate libs in gradle and maven
  Implement #2786: Allow selection of multiple groups
  ...

Author: Siedlerchr

.github/ISSUE_TEMPLATE.md

@@ -13,6 +13,10 @@ Steps to reproduce:
 
 <!-- If applicable, excerpt of the bibliography file, screenshot, and excerpt of log (available in the error console) -->
 
-```
-Put the excerpt of the log file here
-```
+<details>
+  <summary>Log File</summary>
+  
+  ```
+  Paste an excerpt of your log file here
+  ```
+</details>

.gitignore

@@ -269,3 +269,4 @@ gradle-app.setting
 
 # # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
 # gradle/wrapper/gradle-wrapper.properties
+scenicView.properties

CHANGELOG.md

@@ -11,15 +11,27 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
-- Continued to redesign the user interface: this time the editor got a fresh coat of paint:
+- We moved the `adsurl` field to `url` field when fetching with the ADS fetcher. 
+- We continued to improve the new groups interface:
+  - You can now again select multiple groups (and a few related settings were added to the preferences) [#2786](https://github.com/JabRef/jabref/issues/2786).
+  - We further improved performance of group operations, especially of the new filter feature [#2852](https://github.com/JabRef/jabref/issues/2852). 
+  - It is now possible to resort groups using drag & drop [#2785](https://github.com/JabRef/jabref/issues/2785).
+- The entry editor got a fresh coat of paint:
+  - Homogenize the size of text fields.
   - The buttons were changed to icons.
+  - Completely new interface to add or modify linked files.
   - Removed the hidden feature that a double click in the editor inserted the current date.
 - All authors and editors are separated using semicolons when exporting to csv. [#2762](https://github.com/JabRef/jabref/issues/2762)
-- Improved wording of "Show recommendationns: into "Show 'Related Articles' tab" in the preferences
+- Improved wording of "Show recommendations: into "Show 'Related Articles' tab" in the preferences
+- We added integration of the Library of Congress catalog as a fetcher based on the [LCCN identifier](https://en.wikipedia.org/wiki/Library_of_Congress_Control_Number). [Feature request 636 in the forum](http://discourse.jabref.org/t/loc-marc-mods-connection/636)
 
 ### Fixed
 - We fixed the IEEE Xplore web search functionality [#2789](https://github.com/JabRef/jabref/issues/2789)
 - We fixed an error in the CrossRef fetcher that occurred if one of the fetched entries had no title
+- We fixed an issue that prevented new entries to be automatically assigned to the currently selected group [#2783](https://github.com/JabRef/jabref/issues/2783).
+- We fixed a bug that only allowed parsing positive timezones from a FileAnnotation [#2839](https://github.com/JabRef/jabref/issues/22839)
+- We fixed a bug that did not allow the correct re-export of the MS-Office XML field `msbib-accessed` with a different date format [#2859](https://github.com/JabRef/jabref/issues/2859).
+
 ### Removed
 
 

LICENSE.md

@@ -1,26 +1,21 @@
-The MIT License (MIT)
-=====================
+MIT License
 
 Copyright © 2003-2016 [JabRef Authors](https://github.com/JabRef/jabref/blob/master/AUTHORS)
 
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation
-files (the “Software”), to deal in the Software without
-restriction, including without limitation the rights to use,
-copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the
-Software is furnished to do so, subject to the following
-conditions:
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS IN THE SOFTWARE.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

build.gradle

@@ -55,6 +55,7 @@ install4j {
 
 
 repositories {
+    mavenLocal()
     jcenter()
     maven { url "https://oss.sonatype.org/content/groups/public"  }
 	maven { url "https://repo.eclipse.org/content/repositories/paho-snapshots/"  }
@@ -113,6 +114,7 @@ dependencies {
     compile 'de.codecentric.centerdevice:javafxsvg:1.2.1'
     compile 'org.controlsfx:controlsfx:8.40.12'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
+    compile 'net.corda:jfx:0.11.0'
     compile 'org.fxmisc.flowless:flowless:0.5.2'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
 

external-libraries.txt

@@ -131,12 +131,17 @@ URL:     http://fxexperience.com/controlsfx/
 License: BSD-3-Clause
 
 Id:      org.fx.misc.easybin:easybind
-Projekt: EasyBind
+Project: EasyBind
 URL:     https://github.com/TomasMikula/EasyBind
 License: BSD-2-Clause
 
+Id:      net.corda:jfx
+Project: Corda
+URL:     https://github.com/corda/corda/tree/master/client/jfx
+License: Apache-2.0
+
 Id:      org.fxmisc.flowless:flowless
-Projekt: Flowless
+Project: Flowless
 URL:     https://github.com/TomasMikula/Flowless
 License: BSD-2-Clause
 
@@ -151,7 +156,7 @@ URL:     https://github.com/google/gson
 License: Apache-2.0
 
 Id:      de.jensd:fontawesomefx-materialdesignfont
-Projekt: FontAwesomeFX
+Project: FontAwesomeFX
 URL:     https://bitbucket.org/Jerady/fontawesomefx
 License: Apache-2.0
 

src/main/java/org/jabref/gui/BasePanel.java

@@ -26,7 +26,6 @@
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
-import java.util.TimerTask;
 import java.util.stream.Collectors;
 
 import javax.swing.AbstractAction;
@@ -37,7 +36,6 @@
 import javax.swing.JSplitPane;
 import javax.swing.JTextArea;
 import javax.swing.SwingUtilities;
-import javax.swing.tree.TreePath;
 import javax.swing.undo.CannotRedoException;
 import javax.swing.undo.CannotUndoException;
 
@@ -69,8 +67,6 @@
 import org.jabref.gui.filelist.FileListEntry;
 import org.jabref.gui.filelist.FileListTableModel;
 import org.jabref.gui.groups.GroupAddRemoveDialog;
-import org.jabref.gui.groups.GroupSelector;
-import org.jabref.gui.groups.GroupTreeNodeViewModel;
 import org.jabref.gui.importer.actions.AppendDatabaseAction;
 import org.jabref.gui.journals.AbbreviateAction;
 import org.jabref.gui.journals.UnabbreviateAction;
@@ -1313,9 +1309,6 @@ public void actionPerformed(ActionEvent e) {
             @Override
             public void keyPressed(KeyEvent e) {
                 final int keyCode = e.getKeyCode();
-                final TreePath path = frame.getGroupSelector().getSelectionPath();
-                final GroupTreeNodeViewModel node = path == null ? null : (GroupTreeNodeViewModel) path
-                        .getLastPathComponent();
 
                 if (e.isControlDown()) {
                     switch (keyCode) {
@@ -1479,7 +1472,6 @@ public void showEntry(final BibEntry be) {
         showEntryEditor(entryEditor);
 
         newEntryShowing(be);
-        setEntryEditorEnabled(true); // Make sure it is enabled.
     }
 
     /**
@@ -1905,10 +1897,6 @@ public BibDatabaseContext getBibDatabaseContext() {
         return this.bibDatabaseContext;
     }
 
-    public GroupSelector getGroupSelector() {
-        return frame.getGroupSelector();
-    }
-
     public boolean isUpdatedExternally() {
         return updatedExternally;
     }
@@ -2121,68 +2109,18 @@ public void searchAndOpen() {
     }
 
     private class GroupTreeListener {
-
-        private final Runnable task = new Runnable() {
-
-            @Override
-            public void run() {
-                // Update group display (for example to reflect that the number of contained entries has changed)
-                frame.getGroupSelector().revalidateGroups();
-            }
-        };
-
-        /**
-         * Only access when you have the lock of the task instance
-         *
-         * Guarded by "task"
-         */
-        private TimerTask timerTask = new TimerTask() {
-
-            @Override
-            public void run() {
-                task.run();
-            }
-        };
-
         @Subscribe
         public void listen(EntryAddedEvent addedEntryEvent) {
             // if the added entry is an undo don't add it to the current group
             if (addedEntryEvent.getEntryEventSource() == EntryEventSource.UNDO) {
-                scheduleUpdate();
                 return;
             }
 
             // Automatically add new entry to the selected group (or set of groups)
-            if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_ASSIGN_GROUP)
-                    && frame.getGroupSelector().getToggleAction().isSelected()) {
+            if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_ASSIGN_GROUP)) {
                 final List<BibEntry> entries = Collections.singletonList(addedEntryEvent.getBibEntry());
-                final TreePath[] selection = frame.getGroupSelector().getGroupsTree().getSelectionPaths();
-                if (selection != null) {
-                    // it is possible that the user selected nothing. Therefore, checked for "!= null"
-                    for (final TreePath tree : selection) {
-                        ((GroupTreeNodeViewModel) tree.getLastPathComponent()).addEntriesToGroup(entries);
-                    }
-                }
-                SwingUtilities.invokeLater(() -> BasePanel.this.getGroupSelector().valueChanged(null));
-            }
-
-            scheduleUpdate();
-        }
-
-        private void scheduleUpdate() {
-            // This is a quickfix/dirty hack.
-            // a better solution would be using RxJava or something reactive instead
-            // nevertheless it works correctly
-            synchronized (task) {
-                timerTask.cancel();
-                timerTask = new TimerTask() {
-
-                    @Override
-                    public void run() {
-                        task.run();
-                    }
-                };
-                JabRefExecutorService.INSTANCE.submit(timerTask, 200);
+                Globals.stateManager.getSelectedGroup(bibDatabaseContext).forEach(
+                        selectedGroup -> selectedGroup.addEntriesToGroup(entries));
             }
         }
     }

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -91,7 +91,7 @@
 import org.jabref.gui.exporter.SaveDatabaseAction;
 import org.jabref.gui.externalfiletype.ExternalFileTypeEditor;
 import org.jabref.gui.groups.EntryTableTransferHandler;
-import org.jabref.gui.groups.GroupSelector;
+import org.jabref.gui.groups.GroupSidePane;
 import org.jabref.gui.help.AboutAction;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.importer.ImportCustomizationDialog;
@@ -462,7 +462,7 @@ public void actionPerformed(ActionEvent e) {
     private PushToApplications pushApplications;
     private GeneralFetcher generalFetcher;
     private OpenOfficePanel openOfficePanel;
-    private GroupSelector groupSelector;
+    private GroupSidePane groupSidePane;
     private int previousTabCount = -1;
     private JMenu newSpec;
 
@@ -632,7 +632,7 @@ public void windowClosing(WindowEvent e) {
 
             currentBasePanel.getPreviewPanel().updateLayout();
 
-            groupSelector.getToggleAction().setSelected(sidePaneManager.isComponentVisible(GroupSelector.class));
+            groupSidePane.getToggleAction().setSelected(sidePaneManager.isComponentVisible(GroupSidePane.class));
             previewToggle.setSelected(Globals.prefs.getPreviewPreferences().isPreviewPanelEnabled());
             generalFetcher.getToggleAction().setSelected(sidePaneManager.isComponentVisible(GeneralFetcher.class));
             openOfficePanel.getToggleAction().setSelected(sidePaneManager.isComponentVisible(OpenOfficeSidePanel.class));
@@ -720,11 +720,11 @@ public void setWindowTitle() {
     private void initSidePane() {
         sidePaneManager = new SidePaneManager(this);
 
-        groupSelector = new GroupSelector(this, sidePaneManager);
+        groupSidePane = new GroupSidePane(this, sidePaneManager);
         openOfficePanel = new OpenOfficePanel(this, sidePaneManager);
         generalFetcher = new GeneralFetcher(this, sidePaneManager);
 
-        sidePaneManager.register(groupSelector);
+        sidePaneManager.register(groupSidePane);
     }
 
     /**
@@ -1153,10 +1153,10 @@ private void fillMenu() {
         }
         mb.add(search);
 
-        groups.add(new JCheckBoxMenuItem(groupSelector.getToggleAction()));
+        groups.add(new JCheckBoxMenuItem(groupSidePane.getToggleAction()));
         if (prefs.getBoolean(JabRefPreferences.GROUP_SIDEPANE_VISIBLE)) {
-            sidePaneManager.register(groupSelector);
-            sidePaneManager.show(GroupSelector.class);
+            sidePaneManager.register(groupSidePane);
+            sidePaneManager.show(GroupSidePane.class);
         }
 
         groups.addSeparator();
@@ -1178,7 +1178,7 @@ private void fillMenu() {
         view.addSeparator();
         view.add(new JCheckBoxMenuItem(toggleToolbar));
         view.add(new JCheckBoxMenuItem(enableToggle(generalFetcher.getToggleAction())));
-        view.add(new JCheckBoxMenuItem(groupSelector.getToggleAction()));
+        view.add(new JCheckBoxMenuItem(groupSidePane.getToggleAction()));
         view.add(new JCheckBoxMenuItem(togglePreview));
         view.add(showPdvViewer);
         view.add(getNextPreviewStyleAction());
@@ -1377,7 +1377,7 @@ private void createToolBar() {
         previewToggle = new JToggleButton(togglePreview);
         tlb.addJToggleButton(previewToggle);
 
-        tlb.addJToggleButton(new JToggleButton(groupSelector.getToggleAction()));
+        tlb.addJToggleButton(new JToggleButton(groupSidePane.getToggleAction()));
 
         tlb.addSeparator();
 
@@ -1404,7 +1404,7 @@ private void initActions() {
         openDatabaseOnlyActions.addAll(Arrays.asList(manageSelectors, mergeDatabaseAction, newSubDatabaseAction, save, copyPreview,
                 saveAs, saveSelectedAs, saveSelectedAsPlain, editModeAction, undo, redo, cut, deleteEntry, copy, paste, mark, markSpecific, unmark,
                 unmarkAll, rankSubMenu, editEntry, selectAll, copyKey, copyCiteKey, copyKeyAndTitle, copyKeyAndLink, editPreamble, editStrings,
-                groupSelector.getToggleAction(), makeKeyAction, normalSearch, generalFetcher.getToggleAction(), mergeEntries, cleanupEntries, exportToClipboard, replaceAll,
+                groupSidePane.getToggleAction(), makeKeyAction, normalSearch, generalFetcher.getToggleAction(), mergeEntries, cleanupEntries, exportToClipboard, replaceAll,
                 sendAsEmail, downloadFullText, lookupIdentifiers, writeXmpAction, openOfficePanel.getToggleAction(), findUnlinkedFiles, addToGroup, removeFromGroup,
                 moveToGroup, autoLinkFile, resolveDuplicateKeys, openUrl, openFolder, openFile, togglePreview,
                 dupliCheck, autoSetFile, newEntryAction, newSpec, customizeAction, plainTextImport, getMassSetField(), getManageKeywords(),
@@ -1918,10 +1918,6 @@ public SidePaneManager getSidePaneManager() {
         return sidePaneManager;
     }
 
-    public GroupSelector getGroupSelector() {
-        return groupSelector;
-    }
-
     public void setPreviewToggle(boolean enabled) {
         previewToggle.setSelected(enabled);
     }