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

* upstream/master: (38 commits)
  Add link to "feature branch workflow"
  Support Annotations Created by Foxit (#2878)
  Fixes jacoco by excluding the fetcher tests from analysis (#2877)
  Fix entry editor (#2875)
  update bcprov-jdk15on from 1.56 -> 1.57
  update assertj-swing-junit from 3.5.0 -> 3.6.0
  update mockito-core from 2.7.22 -> 2.8.9
  update jfx from 0.11.0 -> 0.11.1
  update google guava from 21.0 -> 22.0
  Fix Divide by zero exception if rows is zero in Entry Editor Tab (#2873)
  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.
  ...

.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/2839)
+- 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).
+- We fixed some bugs that prevented the display of FileAnnotations that were created using the Foxit Reader. [#2839, comment](https://github.com/JabRef/jabref/issues/2839#issuecomment-302058227).
 ### Removed
 
 

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 ## Understanding the basics
 We welcome contributions to JabRef and encourage to create a fork, clone, **create a new branch** (such as `fix-for-issue-121`), **work on the new branch — not master**, and create a pull request.
 Be sure to create a **separate branch** for each improvement you implement.
-Take a look at GitHub's excellent [help documentation] for a detailed explanation.
+Take a look at GitHub's excellent [help documentation] for a detailed explanation and the explanation of [Feature Branch Workflow](https://de.atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
 
 We also have [code howtos](https://github.com/JabRef/jabref/wiki/Code-Howtos) and [guidelines for setting up a local workspace](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
 

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'
@@ -81,7 +82,7 @@ dependencies {
     compile 'org.apache.pdfbox:jempbox:1.8.13'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    compile 'org.bouncycastle:bcprov-jdk15on:1.56'
+    compile 'org.bouncycastle:bcprov-jdk15on:1.57'
 
     compile 'commons-cli:commons-cli:1.4'
 
@@ -106,13 +107,14 @@ dependencies {
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'com.google.guava:guava:21.0'
+    compile 'com.google.guava:guava:22.0'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'
     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:0.11.1'
     compile 'org.fxmisc.flowless:flowless:0.5.2'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
 
@@ -142,9 +144,9 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.+'
 
     testCompile 'junit:junit:4.12'
-    testCompile 'org.mockito:mockito-core:2.7.22'
+    testCompile 'org.mockito:mockito-core:2.8.9'
     testCompile 'com.github.tomakehurst:wiremock:2.6.0'
-    testCompile 'org.assertj:assertj-swing-junit:3.5.0'
+    testCompile 'org.assertj:assertj-swing-junit:3.6.0'
     testCompile 'org.reflections:reflections:0.9.11'
 }
 
@@ -288,7 +290,7 @@ tasks.withType(Test) {
 }
 
 task jacocoMerge(type: JacocoMerge) {
-    executionData test, fetcherTest, databaseTest
+    executionData test, databaseTest
 }
 
 jacocoTestReport {
@@ -308,26 +310,26 @@ shadowJar {
 
         // this is an adapter required for generating a fat jar with correct log4j2 output
 
-        com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer target = new com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer();
+        com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer target = new com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer()
 
         @Override
         boolean canTransformResource(FileTreeElement element) {
-            return target.canTransformResource(element.getPath());
+            return target.canTransformResource(element.getPath())
         }
 
         @Override
         void transform(String path, InputStream is, List<com.github.jengelman.gradle.plugins.shadow.relocation.Relocator> relocators) {
-            target.processResource(path, is, relocators);
+            target.processResource(path, is, relocators)
         }
 
         @Override
         boolean hasTransformedResource() {
-            return target.hasTransformedResource();
+            return target.hasTransformedResource()
         }
 
         @Override
         void modifyOutputStream(org.apache.tools.zip.ZipOutputStream jos) {
-            target.modifyOutputStream(jos);
+            target.modifyOutputStream(jos)
         }
     })
 }
@@ -356,7 +358,7 @@ if (hasProperty('dev')) {
     // In the context of github, the branch name could be something like "pull/277"
     // "/" is an illegal character. To be safe, all illegal filename characters are replaced by "_"
     // http://stackoverflow.com/a/15075907/873282 describes the used pattern.
-    branchName = branchName.trim().replaceAll("[^a-zA-Z0-9.-]", "_");
+    branchName = branchName.trim().replaceAll("[^a-zA-Z0-9.-]", "_")
 
     // hack string
     // first the date (%cd), then the branch name, and finally the commit id (%h)

config/checkstyle/checkstyle.xml

@@ -27,13 +27,26 @@
         </module>
 
         <module name="EmptyLineSeparator">
-            <property name="tokens" value="IMPORT, CLASS_DEF, INTERFACE_DEF, ENUM_DEF, STATIC_INIT, INSTANCE_INIT, METHOD_DEF"/>
+            <property name="tokens"
+                      value="IMPORT, CLASS_DEF, INTERFACE_DEF, ENUM_DEF, STATIC_INIT, INSTANCE_INIT, METHOD_DEF"/>
             <property name="allowMultipleEmptyLines" value="false"/>
             <property name="allowMultipleEmptyLinesInsideClassMembers" value="false"/>
         </module>
+
         <module name="DeclarationOrder"/>
 
+        <!-- RCULRY causes issues if classes are nested within arrays, therefore not activated -->
+        <module name="WhitespaceAround">
+            <property name="tokens"
+                      value="ASSIGN, BAND, BAND_ASSIGN, BOR, BOR_ASSIGN, BSR, BSR_ASSIGN, BXOR, BXOR_ASSIGN, COLON, DIV,
+                      DIV_ASSIGN, DO_WHILE, EQUAL, GE, GT, LAND, LCURLY, LE, LITERAL_CATCH, LITERAL_DO, LITERAL_ELSE,
+                      LITERAL_FINALLY, LITERAL_FOR, LITERAL_IF, LITERAL_RETURN, LITERAL_SWITCH, LITERAL_SYNCHRONIZED,
+                      LITERAL_TRY, LITERAL_WHILE, LOR, LT, MINUS, MINUS_ASSIGN, MOD, MOD_ASSIGN, NOT_EQUAL,
+                      PLUS, PLUS_ASSIGN, QUESTION,
+                      SL, SLIST, SL_ASSIGN, SR, SR_ASSIGN, STAR, STAR_ASSIGN, LITERAL_ASSERT, TYPE_EXTENSION_AND"/>
+        </module>
     </module>
+
     <module name="SuppressionFilter">
         <property name="file" value="config/checkstyle/suppressions.xml"/>
     </module>

external-libraries.txt

@@ -131,17 +131,22 @@ 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
 
 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));
             }
         }
     }