Merge branch 'master' into master

.circleci/config.yml

@@ -5,13 +5,13 @@ jobs:
     docker:
       - image: circleci/openjdk:8-jdk
     steps:
+      - checkout
       - restore_cache:
           keys:
-            - install4j
-      - checkout
+            - install4j-{{ checksum "scripts/extract-install4j.sh" }}
       - run: scripts/download-install4j-and-jres.sh
       - save_cache:
-          key: install4j
+          key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
           paths:
             - "~/downloads"
             - "~/.install4j7"
@@ -25,9 +25,9 @@ jobs:
     steps:
       - restore_cache:
           key: dependency-cache
-      - restore_cache:
-          key: install4j
       - checkout
+      - restore_cache:
+          key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
       - run: scripts/extract-install4j.sh
       - run: install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY
       - run: ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
@@ -46,9 +46,9 @@ jobs:
     steps:
       - restore_cache:
           key: dependency-cache
-      - restore_cache:
-          key: install4j
       - checkout
+      - restore_cache:
+          key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
       - run: scripts/extract-install4j.sh
       - run: install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY
       - run: ./gradlew -Pinstall4jDir="install4j7" release --stacktrace

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "src/main/resources/csl-styles"]
+	path = src/main/resources/csl-styles
+	url = https://github.com/citation-style-language/styles.git
+[submodule "src/main/resources/csl-locales"]
+	path = src/main/resources/csl-locales
+	url = https://github.com/citation-style-language/locales.git

CHANGELOG.md

@@ -31,7 +31,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Files without a defined external file type are now directly opened with the default application of the operating system
 - We streamlined the process to rename and move files by removing the confirmation dialogs.
 - We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
-- We add auto url formatting when user paste link to URL field in entry editor. [#254](https://github.com/koppor/jabref/issues/254)
+- We add auto url formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
 - We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
 - We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl<kbd> + <kbd>E<kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
 - We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
@@ -44,6 +44,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 ### Fixed
+- We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
 - We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
 - Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
 - The entry editor no longer gets corrupted after using the source tab. https://github.com/JabRef/jabref/issues/3532 https://github.com/JabRef/jabref/issues/3608 https://github.com/JabRef/jabref/issues/3616
@@ -61,6 +62,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
 - We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
 - We fixed an issue where the "Open file dialog" may disappear behind other windows. https://github.com/JabRef/jabref/issues/3410
+- We fixed an issue where the number of entries matched was not updated correctly upon adding or removing an entry. [#3537](https://github.com/JabRef/jabref/issues/3537)
 - We fixed an issue where the default icon of a group was not colored correctly.
 - We fixed an issue where the first field in entry editor was not focused when adding a new entry. [#4024](https://github.com/JabRef/jabref/issues/4024)
 - We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files https://github.com/JabRef/jabref/issues/2970
@@ -73,8 +75,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where files added via the "Attach file" contextmenu of an entry were not made relative. [#4201](https://github.com/JabRef/jabref/issues/4201) and [#4241](https://github.com/JabRef/jabref/issues/4241)
 - We fixed an issue where author list parser can't generate bibtex for Chinese author. [#4169](https://github.com/JabRef/jabref/issues/4169)
 - We fixed an issue where the list of XMP Exclusion fields in the preferences was not be saved [#4072](https://github.com/JabRef/jabref/issues/4072)
-- We fixed an issue where the ArXiv Fetcher did not support HTTP URLs [#4367](https://github.com/JabRef/jabref/pull/4367)
-
+- We fixed an issue where the ArXiv Fetcher did not support HTTP URLs [koppor#328](https://github.com/koppor/jabref/issues/328)
+- We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
 
 
 

README.md

@@ -101,9 +101,7 @@ When you want to develop, it is necessary to generate additional sources using `
 and then generate the Eclipse `gradlew eclipse`.
 For IntelliJ IDEA, just import the project via a Gradle Import by pointing at the `build.gradle`.
 
-`gradlew test` executes the normal unit tests.
-If you want to test the UI, execute `gradlew integrationTest`.
-Sources for the integration test are kept in `src/integrationTest`.
+`gradlew test` executes all tests. We use [Travis CI](https://travis-ci.org/) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Travis will report any other failure.
 
 
 ## Acknowledgements

build.gradle

@@ -151,9 +151,6 @@ dependencies {
     compile 'org.apache.logging.log4j:log4j-api:2.11.1'
     compile 'org.apache.logging.log4j:log4j-core:2.11.1'
 
-    // need to use snapshots as the stable version is from 2013 and doesn't support v1.0.1 CitationStyles
-    compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
-    compile 'org.citationstyles:locales:1.0.1-SNAPSHOT'
     compile 'de.undercouch:citeproc-java:1.0.1'
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'

config/checkstyle/checkstyle.xml

@@ -49,6 +49,8 @@
         <module name="ConstantName">
             <property name="format" value="^log(ger)?|[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$"/>
         </module>
+
+        <module name="NeedBraces"/>
     </module>
 
     <module name="SuppressionFilter">

jabref.install4j

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<install4j version="7.0.4" transformSequenceNumber="7">
+<install4j version="7.0.8" 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">
@@ -42,7 +42,10 @@
       <variable name="version" value="3.1dev" description="" category="" />
     </variables>
     <mergedProjects />
-    <codeSigning macEnabled="false" macPkcs12File="" windowsEnabled="false" windowsKeySource="pkcs12" windowsPvkFile="" windowsSpcFile="" windowsPkcs12File="" />
+    <codeSigning macEnabled="false" macPkcs12File="" windowsEnabled="false" windowsKeySource="pkcs12" windowsPvkFile="" windowsSpcFile="" windowsPkcs12File="" windowsPkcs11Library="" windowsPkcs11Slot="">
+      <windowsKeystoreIdentifier issuer="" serial="" subject="" />
+      <windowsPkcs11Identifier issuer="" serial="" subject="" />
+    </codeSigning>
   </application>
   <files keepModificationTimes="false" missingFilesStrategy="warn" globalExcludeSuffixes="" defaultOverwriteMode="4" defaultUninstallMode="0" launcherOverwriteMode="3" defaultFileMode="644" defaultDirMode="755">
     <filesets />
@@ -105,7 +108,7 @@
       <customAttributes />
     </autoUpdate>
     <applications>
-      <application name="" id="installer" customizedId="" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" enabled="true" commentSet="false" comment="" actionElevationType="none" styleId="" fileset="" customIcnsFile="./src/main/resources/icons/jabref.icns" customIcoFile="./src/main/resources/icons/jabref.ico" macEntitlementsFile="" automaticLauncherIntegration="false" launchMode="startupFirstWindow" launchInNewProcess="false" launchSchedule="updateSchedule" allLaunchers="true">
+      <application name="" id="installer" customizedId="" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" enabled="true" commentSet="false" comment="" actionElevationType="none" styleId="326" fileset="" customIcnsFile="./src/main/resources/icons/jabref.icns" customIcoFile="./src/main/resources/icons/jabref.ico" macEntitlementsFile="" automaticLauncherIntegration="false" launchMode="startupFirstWindow" launchInNewProcess="false" launchSchedule="updateSchedule" allLaunchers="true">
         <serializedBean>
           <java class="java.beans.XMLDecoder">
             <object class="com.install4j.runtime.beans.applications.InstallerApplication">
@@ -116,6 +119,9 @@
           </java>
         </serializedBean>
         <styleOverrides />
+        <customScript mode="1" file="">
+          <content />
+        </customScript>
         <launcherIds />
         <variables />
         <startup>
@@ -144,7 +150,7 @@
           </screen>
         </startup>
         <screens>
-          <screen name="" id="2" customizedId="" beanClass="com.install4j.runtime.beans.screens.WelcomeScreen" enabled="true" commentSet="false" comment="" actionElevationType="inherit" styleId="332" rollbackBarrier="false" rollbackBarrierExitCode="1" backButton="2" finishScreen="false" wizardIndexChangeType="unchanged" wizardIndexKey="">
+          <screen name="" id="2" customizedId="" beanClass="com.install4j.runtime.beans.screens.WelcomeScreen" enabled="true" commentSet="false" comment="" actionElevationType="inherit" styleId="" rollbackBarrier="false" rollbackBarrierExitCode="1" backButton="2" finishScreen="false" wizardIndexChangeType="unchanged" wizardIndexKey="">
             <serializedBean>
               <java class="java.beans.XMLDecoder">
                 <object class="com.install4j.runtime.beans.screens.WelcomeScreen" />
@@ -766,6 +772,9 @@ return console.askOkCancel(message, true);
           </java>
         </serializedBean>
         <styleOverrides />
+        <customScript mode="1" file="">
+          <content />
+        </customScript>
         <launcherIds />
         <variables />
         <startup>
@@ -1054,7 +1063,7 @@ return console.askYesNo(message, true);
                         <boolean>false</boolean>
                       </void>
                       <void property="labelText">
-                        <string>install4j</string>
+                        <string>JabRef</string>
                       </void>
                     </object>
                   </java>
@@ -1262,7 +1271,7 @@ return console.askYesNo(message, true);
                       </void>
                       <void property="imageFile">
                         <object class="com.install4j.api.beans.ExternalFile">
-                          <string>icon:${installer:sys.installerApplicationMode}_header.png</string>
+                          <string>./src/main/resources/icons/JabRef-icon-64.png</string>
                         </object>
                       </void>
                       <void property="imageInsets">

scripts/download-install4j-and-jres.sh

@@ -5,7 +5,7 @@ if [ ! -d ~/downloads ]; then
   mkdir ~/downloads
 fi
 cd ~/downloads
-wget --quiet -nc http://download-keycdn.ej-technologies.com/install4j/install4j_unix_7_0_4.tar.gz
+wget --quiet -nc --show-progress http://download-keycdn.ej-technologies.com/install4j/install4j_unix_7_0_8.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_4.tar.gz
+tar -xf ~/downloads/install4j_unix_7_0_8.tar.gz
 # fix directory name (until install4j 6.1.5 it was install4j6
-mv install4j7.0.4 install4j7
+mv install4j7.0.8 install4j7

src/main/java/org/jabref/JabRefGUI.java

@@ -150,7 +150,7 @@ private void openWindow(Stage mainStage) {
         root.getChildren().add(JabRefGUI.mainFrame);
 
         Scene scene = new Scene(root, 800, 800);
-        Globals.getThemeLoader().installBaseCss(scene, Globals.prefs);
+        Globals.getThemeLoader().installCss(scene, Globals.prefs);
         mainStage.setTitle(JabRefFrame.FRAME_TITLE);
         mainStage.getIcons().addAll(IconTheme.getLogoSetFX());
         mainStage.setScene(scene);

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

@@ -242,6 +242,7 @@
 /*
  * The base css file defining the style that is valid for every pane and dialog.
  */
+
 .hyperlink {
     -fx-padding: 0;
     -fx-underline: false;
@@ -630,8 +631,10 @@
 }
 
 .text-input:focused {
+    -fx-highlight-fill: derive(-jr-accent, 20%);
     -fx-background-color: -jr-accent, -fx-control-inner-background;
     -fx-background-insets: 0, 2;
+    -fx-highlight-text-fill: -fx-text-inner-color;
 }
 
 .text-area {
@@ -941,3 +944,15 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-text-fill: -fx-light-text-color;
     -fx-padding: -1ex -0.5ex -1ex -0.5ex;
 }
+
+.progress-bar > .bar {
+    -fx-background-color: -jr-theme;
+}
+
+.progress-bar:indeterminate > .bar {
+    -fx-background-color: -jr-theme;
+}
+
+.progress-bar > .track {
+    -fx-background-color: -jr-accent;
+}

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

@@ -60,7 +60,7 @@
 import org.jabref.gui.journals.UnabbreviateAction;
 import org.jabref.gui.maintable.MainTable;
 import org.jabref.gui.maintable.MainTableDataModel;
-import org.jabref.gui.mergeentries.MergeEntriesDialog;
+import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.mergeentries.MergeWithFetchedEntryAction;
 import org.jabref.gui.specialfields.SpecialFieldDatabaseChangeListener;
 import org.jabref.gui.specialfields.SpecialFieldValueViewModel;
@@ -324,7 +324,7 @@ private void setupActions() {
         // The action for cleaning up entry.
         actions.put(Actions.CLEANUP, cleanUpAction);
 
-        actions.put(Actions.MERGE_ENTRIES, () -> new MergeEntriesDialog(BasePanel.this, dialogService));
+        actions.put(Actions.MERGE_ENTRIES, () -> new MergeEntriesAction(frame).execute());
 
         // The action for copying the selected entry's key.
         actions.put(Actions.COPY_KEY, this::copyKey);

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

@@ -8,6 +8,9 @@
 import javax.swing.JButton;
 import javax.swing.JPanel;
 
+import javafx.scene.Scene;
+
+import org.jabref.gui.customjfx.CustomJFXPanel;
 import org.jabref.gui.help.HelpAction;
 import org.jabref.gui.importer.ImportInspectionDialog;
 import org.jabref.gui.mergeentries.MergeEntries;
@@ -119,7 +122,7 @@ public void windowClosing(WindowEvent e) {
             }
         });
 
-        getContentPane().add(me.getMergeEntryPanel());
+        getContentPane().add(CustomJFXPanel.wrap(new Scene(me)));
         getContentPane().add(options, BorderLayout.SOUTH);
         pack();
 

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

@@ -69,7 +69,6 @@
 import org.jabref.gui.actions.ManageJournalsAction;
 import org.jabref.gui.actions.ManageKeywordsAction;
 import org.jabref.gui.actions.ManageProtectedTermsAction;
-import org.jabref.gui.actions.MergeEntriesAction;
 import org.jabref.gui.actions.NewDatabaseAction;
 import org.jabref.gui.actions.NewEntryAction;
 import org.jabref.gui.actions.NewEntryFromPlainTextAction;
@@ -97,6 +96,7 @@
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.menus.FileHistoryMenu;
+import org.jabref.gui.mergeentries.MergeEntriesAction;
 import org.jabref.gui.push.PushToApplicationButton;
 import org.jabref.gui.push.PushToApplications;
 import org.jabref.gui.search.GlobalSearchBar;