Merge remote-tracking branch 'origin/master' into maintable-beta

# Conflicts:
#	CHANGELOG.md

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,4 +8,3 @@
 - [ ] Screenshots added (for bigger UI changes)
 - [ ] Manually tested changed features in running JabRef
 - [ ] Check documentation status (Issue created for outdated help page at [help.jabref.org](https://github.com/JabRef/help.jabref.org/issues)?)
-- [ ] If you changed the localization: Did you run `gradle localizationUpdate`?

CHANGELOG.md

@@ -12,9 +12,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We now show a small notification icon in the entry editor when we detect data inconsistency or other problems. [#3145](https://github.com/JabRef/jabref/issues/3145)
 - We added [oaDOI](https://oadoi.org/) as a fulltext provider, so that JabRef is now able to provide fulltexts for more than 90 million open-access articles.
 - We completely reworked and redesigned the main table.
-
+- We changed one default of [Cleanup entries dialog](http://help.jabref.org/en/CleanupEntries): Per default, the PDF are not moved to the default file directory anymore. [#3619](https://github.com/JabRef/jabref/issues/3619)
+- We added the export of the the `translator` field to the according MS-Office XML field. [#1750, comment](https://github.com/JabRef/jabref/issues/1750#issuecomment-357350986)
+- We changed the import of the MS-Office XML fields `bookauthor` and `translator`. Both are now imported to their corresponding bibtex/biblatex fields.
+- We improved the export of the `address` and `location` field to the MS-Office XML fields. If the address field does not contain a comma, it is treated as single value and exported to the field `city`. [#1750, comment](https://github.com/JabRef/jabref/issues/1750#issuecomment-357539167) 
+For more details refer to the [field mapping help page](http://help.jabref.org/en/MsOfficeBibFieldMapping)
+- We added Facebook and Twitter icons in the toolbar to link to our [Facebook](https://www.facebook.com/JabRef/) and [Twitter](https://twitter.com/jabref_org) pages.
 
 ### Fixed
 - We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)

CONTRIBUTING.md

@@ -6,6 +6,7 @@ Take a look at GitHub's excellent [help documentation] for a detailed explanatio
 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).
 
 In case you have any question, do not hesitate to write one of our [JabRef developers](https://github.com/orgs/JabRef/teams/developers) an email.
+We should also be online at [gitter](https://gitter.im/JabRef/jabref).
 
 
 ## Formal requirements for a pull request
@@ -83,10 +84,24 @@ because <additional rationale>.
 ### When adding a new Localization.lang entry
 Add new `Localization.lang("KEY")` to Java file.
 Tests fail. In the test output a snippet is generated which must be added to the English translation file.
+
+Example:
+
+```
+java.lang.AssertionError: DETECTED LANGUAGE KEYS WHICH ARE NOT IN THE ENGLISH LANGUAGE FILE
+PASTE THESE INTO THE ENGLISH LANGUAGE FILE
+[
+Opens\ JabRef's\ Twitter\ page=Opens JabRef's Twitter page
+]
+Expected :[]
+Actual   :[Opens\ JabRef's\ Twitter\ page (src\main\java\org\jabref\gui\JabRefFrame.java LANG)]
+```
+
 Add snippet to English translation file located at `src/main/resources/l10n/JabRef_en.properties`.
 [Crowdin](http://translate.jabref.org/) will automatically pick up the new string and add it to the other translations.
 
-You can also directly run the specific test in your IDE. The test "LocalizationConsistencyTest" is placed under `src/test/java/net.sf.jabref.logic.l10n/LocalizationConsistencyTest.java`
+You can also directly run the specific test in your IDE.
+The test "LocalizationConsistencyTest" is placed under `src/test/java/net.sf.jabref.logic.l10n/LocalizationConsistencyTest.java`
 Find more information in the [JabRef Wiki](https://github.com/JabRef/jabref/wiki/Code-Howtos#using-localization-correctly).
 
 

README.md

@@ -1,85 +1,95 @@
-# JabRef Development Version
+# JabRef Bibliography Management
 
 [![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
 [![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%20to-jabref-orange.svg)](https://donations.jabref.org)
-[![Help Contribute to Open Source](https://www.codetriage.com/jabref/jabref/badges/users.svg)](https://www.codetriage.com/jabref/jabref)
-
-This version is a development version. Features may not work as expected.
-
-Development builds are available at [builds.jabref.org](https://builds.jabref.org/master/) whereas the [latest release is available via GitHub](https://github.com/JabRef/jabref/releases/latest).
-
-Explanation of donation possibilities and usage of donations is available at our [donations page](https://donations.jabref.org).
 
-We use [install4j], the multi-platform installer builder.
-
-### Background
-
-JabRef is a graphical Java application for editing [BibTeX] and [Biblatex] `.bib` databases.
-JabRef lets you organize your entries into overlapping logical groups, and with a single click limit your view to a single group or an intersection or union of several groups.
-You can customize the entry information shown in the main window, and sort by any of the standard BibTeX fields.
-JabRef can autogenerate BibTeX keys for your entries.
-JabRef also lets you easily link to PDF or web sources for your reference entries.
-
-JabRef can import from and export to several formats, and you can customize export filters.
-JabRef can be run as a command line application to convert from any import format to any export format.
+JabRef is an open-source, cross-platform citation and reference management tool licensed under the  [MIT license](https://tldrlegal.com/license/mit-license).
+
+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)
+
+## 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.
+JabRef supports you every step of your research work.
+
+#### Collect
+
+- Search across many online scientific catalogues like CiteSeer, CrossRef, Google Scholar, IEEEXplore, INSPIRE-HEP, Medline PubMed, MathSciNet, Springer, arXiv, and zbMATH
+- Import options for over 15 reference formats
+- Easily retrieve and link full-text articles
+- Fetch complete bibliographic information based on ISBN, DOI, PubMed-ID and arXiv-ID
+- Extract metadata from PDFs
+- [Firefox Add-on](https://addons.mozilla.org/en-US/firefox/addon/jabfox/) that lets you import new references directly from the browser with one click
+
+#### Organize
+
+- Group your research into hierarchical collections and organize research items based on keywords/tags, search terms or your own manual assignments
+- Advanced search and filter features
+- Complete and fix bibliographic data by comparing with curated online catalogues such as Google Scholar, Springer or MathSciNet
+- Customizable citation key generator
+- Customize and add new metadata fields or reference types
+- Find and merge duplicates
+- Attach related documents: 20 different kinds of documents supported out of the box, completely customizable and extendable
+- Automatically rename and moves associated documents according to customizable rules
+- Keep track of what you read: ranking, priority, printed, quality-assured 
+
+#### Cite
+
+- Native [BibTeX] and [Biblatex] support
+- Cite-as-you-write functionality for external applications such as Emacs, Kile, LyX, Texmaker, TeXstudio, Vim and WinEdt.
+- Format references in one of the many thousand built-in citation styles or create your own style
+- Support for Word and LibreOffice/OpenOffice to insert and format citations
+
+#### Share
+
+- Many built-in export options or create your own export format
+- Library is saved as a simple text file and thus easy to share with others via Dropbox and is version-control friendly
+- Work in a team: sync the contents of your library with a SQL database
+
+## Installation
+
+Fresh development builds are available at [builds.jabref.org](https://builds.jabref.org/master/).
+The [latest stable release is available at FossHub](https://www.fosshub.com/JabRef.html).
+
+JabRef runs on any system equipped with the Java Virtual Machine (1.8), which can be downloaded at no cost from [Oracle](http://www.oracle.com/technetwork/java/javase/downloads/index.html). Note that Java 9 is currently not supported.
+From JabRef 4.0 onwards, [JavaFX] support has to be installed.
+ - Windows: JabRef offers an installer, which also adds a shortcut to JabRef to your start menu. Please also see our [Windows FAQ](https://help.jabref.org/en/FAQwindows)
+ - Linux: Please see our [Installation Guide](http://help.jabref.org/en/Installation).
+ - Mac OS X: Please see our [Mac OS X FAQ](https://help.jabref.org/en/FAQosx).
+
+In addition, JabRef can be downloaded as an executable `.jar` file. 
+Try to double click the `jar` file or execute the following command:
+     `java -jar <path to jar>`
 
-* Homepage: <https://www.jabref.org>
-* Development page: <https://github.com/JabRef/jabref>
-* Open HUB page: <https://www.openhub.net/p/jabref>
+## Bug Reports, Suggestions, Other Feedback
 
-### Bug Reports, Suggestions, Other Feedback
+[![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
 
 We are thankful for any bug reports or other feedback.
+If you have ideas for new features you want to be included in JabRef, [tell us in our forum](http://discourse.jabref.org/c/features)!
+If you need support in using JabRef, please read [the documentation](https://help.jabref.org/) first and have a look at our [community forum](http://discourse.jabref.org/c/help).
+You can use our [GitHub issue tracker](https://github.com/JabRef/jabref/issues) to send in bug reports.
 
-If there are features you want included in JabRef, [tell us in our forum](http://discourse.jabref.org/c/features)!
-
-If you have questions regarding the usage, or you want to give general feedback the forum is also the right place for this: [discourse.jabref.org](http://discourse.jabref.org/c/features)
-
-You can use our [GitHub issue tracker](https://github.com/JabRef/jabref/issues) to send in bug reports and suggestions.
-
-To get your code added to JabRef, just fork JabRef and create a pull request.
-For details see [CONTRIBUTING](CONTRIBUTING.md).
-
-
-## Installing and Running
-
-### Requirements
-
-JabRef runs on any system equipped with the Java Virtual Machine (1.8 or newer), which can be downloaded at no cost from [Oracle](http://www.oracle.com/technetwork/java/javase/downloads/index.html).
-From JabRef 4.0 onwards, [JavaFX] support has to be available.
-
-### Installing and Running, Linux:
-
-Please see our [Installation Guide](http://help.jabref.org/en/Installation).
-
-### Installing and Running, Mac OS X:
-
-Please see our [Mac OS X FAQ](https://help.jabref.org/en/FAQosx).
-
-### Installing and Running, Windows:
-
-JabRef offers an installer, which also adds a shortcut to JabRef to your start menu.
-
-Please also see our [Windows FAQ](https://help.jabref.org/en/FAQwindows)
-
-### Installing and Running, General:
-
-JabRef can be downloaded as an executable .jar file.
-Try to double click the `jar` file or execute the following command:
-     `java -jar <path to jar>`
-
-
-## Documentation
+Explanation of donation possibilities and usage of donations is available at our [donations page](https://donations.jabref.org).
 
-JabRef comes with an [online help](https://help.jabref.org/), accessed by pressing `F1` or clicking on a question mark icon.
-The help is are probably not exhaustive enough to satisfy everyone yet, but it should help sort out the most important issues about using the program. 
-If you choose languages other than English, some or all help pages may appear in your chosen languages.
+## Contributing
 
+[![Help Contribute to Open Source](https://www.codetriage.com/jabref/jabref/badges/users.svg)](https://www.codetriage.com/jabref/jabref)
+[![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![OpenHub](https://www.openhub.net/p/jabref/widgets/project_thin_badge.gif)](https://www.openhub.net/p/jabref)
 
-## Building JabRef From Source
+Want to be part of a free and open-source project that tens of thousands scientist use every day?
+Check out our [issue tracker](https://github.com/JabRef/jabref/issues) to find something to work on.
+You are also welcome to contribute new features.
+To get your code included into JabRef, just fork JabRef and create a pull request.
+For details have a look at our [guidelines for contributing](CONTRIBUTING.md).
+We view pull requests as a collaborative process.
+Submit a pull request early to get feedback from the team on work in progress.
+We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/master/DEVELOPERS) approve.
 
-If you want a step-by-step tutorial, please check [this guideline](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace)
+If you want a step-by-step walk-through on how to set-up your workspace, please check [this guideline](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
 
 To compile JabRef from source, you need a Java compiler supporting Java 1.8 and `JAVA_HOME` pointing to this JDK.
 You have to set `GRADLE_OPTS` to `-Dfile.encoding=UTF-8` as [gradle uses the JVM's platform encoding](https://discuss.gradle.org/t/is-there-a-way-to-tell-gradle-to-read-gradle-build-scripts-using-a-specified-encoding/7535).
@@ -89,19 +99,14 @@ 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`.
 
-
-## Testing
-
 `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`.
 
 
-## Release Process
-
-Building a release requires [install4j]. We've got an [Open Source License](https://www.ej-technologies.com/buy/install4j/openSource).
-Releasing is done using [CircleCI](https://circleci.com/gh/JabRef/jabref). A full release howto is available [in our wiki](https://github.com/JabRef/jabref/wiki/Releasing-a-new-Version).
+## Acknowledgements
 
+We use [install4j], the multi-platform installer builder. We've got an [open-source license](https://www.ej-technologies.com/buy/install4j/openSource).
 
 ## License
 

build.gradle

@@ -133,7 +133,7 @@ dependencies {
     compile 'org.fxmisc.richtext:richtextfx:0.8.1'
 
     // Cannot be updated to 9.*.* until Jabref works with Java 9
-    compile 'org.controlsfx:controlsfx:8.40.14'
+    compile 'org.controlsfx:controlsfx:8.40.15-SNAPSHOT'
 
     compile 'org.jsoup:jsoup:1.11.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
@@ -161,7 +161,7 @@ dependencies {
     testRuntime 'org.apache.logging.log4j:log4j-core:2.10.0'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.10.0'
     testCompile 'org.mockito:mockito-core:2.13.0'
-    testCompile 'com.github.tomakehurst:wiremock:2.13.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.14.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.5.1'
@@ -504,7 +504,7 @@ task releaseJar(dependsOn: "shadowJar") {
             }
         }
         // set executable with read permissions (first true) and for all (false)
-        file("$buildDir/releases/JabRef-${project.version}.jar").setExecutable(true, false);
+        file("$buildDir/releases/JabRef-${project.version}.jar").setExecutable(true, false)
     }
 }
 

scripts/syncLang.py

@@ -314,7 +314,9 @@ def __update_properties(self, main_property_file, other_property_files):
             for line in main_lines:
                 key = main_keys.key_from_line(line)
                 if key is not None:
-                    other_lines_to_write.append(u"{key}={value}\n".format(key=key, value=keys[key]))
+                    # Do not write empty keys
+                    if keys[key] !=  "":
+                        other_lines_to_write.append(u"{key}={value}\n".format(key=key, value=keys[key]))
                 else:
                     other_lines_to_write.append(line)
 

src/main/java/org/jabref/JabRefMain.java

@@ -80,6 +80,10 @@ private static void ensureCorrectJavaVersion() {
                             buildInfo.getMinRequiredJavaVersion()
                     )
             );
+
+            versionError.append("\n");
+            versionError.append(Localization.lang("Your Java Runtime Environment is located at %0.", checker.getJavaInstallationDirectory()));
+
             if (!buildInfo.isAllowJava9()) {
                 versionError.append("\n");
                 versionError.append(Localization.lang("Note that currently, JabRef does not run with Java 9."));

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

@@ -2012,18 +2012,19 @@ public void searchAndOpen() {
 
             // Run the search operation:
             FileFinder fileFinder = FileFinders.constructFromConfiguration(Globals.prefs.getAutoLinkPreferences());
+            try {
             List<Path> files = fileFinder.findAssociatedFiles(entry, dirs, extensions);
-            if (!files.isEmpty()) {
-                Path file = files.get(0);
-                Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByFile(file);
-                if (type.isPresent()) {
-                    try {
+                if (!files.isEmpty()) {
+                    Path file = files.get(0);
+                    Optional<ExternalFileType> type = ExternalFileTypes.getInstance().getExternalFileTypeByFile(file);
+                    if (type.isPresent()) {
                         JabRefDesktop.openExternalFileAnyFormat(file, basePanel.getBibDatabaseContext(), type);
                         basePanel.output(Localization.lang("External viewer called") + '.');
-                    } catch (IOException ex) {
-                        basePanel.output(Localization.lang("Error") + ": " + ex.getMessage());
                     }
                 }
+            } catch (IOException ex) {
+                LOGGER.error("Problems with finding/or opening files ", ex);
+                basePanel.output(Localization.lang("Error") + ": " + ex.getMessage());
             }
         }
     }

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

@@ -166,7 +166,7 @@ public static List<java.awt.Image> getLogoSet() {
 
         return jabrefLogos;
     }
-	
+
     public enum JabRefIcon {
 
         ADD(MaterialDesignIcon.PLUS_BOX),
@@ -260,12 +260,16 @@ public enum JabRefIcon {
         KEY_BINDINGS(MaterialDesignIcon.KEYBOARD), /*css: keyboard */
         FIND_DUPLICATES(MaterialDesignIcon.CODE_EQUAL), /*css: code-equal */
         PULL(MaterialDesignIcon.SOURCE_PULL), /*source-pull*/
+        SUCCESS(MaterialDesignIcon.CHECK_CIRCLE),
+        WARNING(MaterialDesignIcon.ALERT),
+        ERROR(MaterialDesignIcon.ALERT_CIRCLE),
         OPEN_IN_NEW_WINDOW(MaterialDesignIcon.OPEN_IN_NEW), /*css: open-in-new */
         CASE_SENSITIVE(MaterialDesignIcon.ALPHABETICAL), /* css: mdi-alphabetical */
         REG_EX(MaterialDesignIcon.REGEX), /*css: mdi-regex */
         CONSOLE(MaterialDesignIcon.CONSOLE), /*css: console */
         FORUM(MaterialDesignIcon.FORUM), /* css: forum */
         FACEBOOK(MaterialDesignIcon.FACEBOOK), /* css: facebook */
+        TWITTER(MaterialDesignIcon.TWITTER), /* css: twitter */
         BLOG(MaterialDesignIcon.RSS), /* css: rss */
         GLOBAL_SEARCH(MaterialDesignIcon.EARTH), /* css: earth */
         DATE_PICKER(MaterialDesignIcon.CALENDAR), /* css: calendar */