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

* upstream/master: (46 commits)
  Replace openoffice jars with libreoffice  jars (#3662)
  Export no empty lines in RIS format (#3661)
  Remove apache commons logging in favor of slf4j + log4j for JAVA 9 (#3653)
  fix isbn fetcher test as Joshua Bloch has published a new revivsion of Effetive Java convert to junit5 jupiter
  Extend RIS import with multiple fields (#3642)
  Fix ICAR fetcher test which resulted in build failure (#3654)
  New translations JabRef_en.properties (French) (#3650)
  Add link to MADR and fix typo
  [WIP] Add "Convert to BibTeX format" cleanup (#3541)
  Fix typo
  Fix typo
  Quickfix to get build running on all platforms (#3638)
  New translations JabRef_en.properties (French)
  New translations JabRef_en.properties (Vietnamese)
  New translations JabRef_en.properties (Chinese Simplified)
  New translations JabRef_en.properties (Dutch)
  New translations JabRef_en.properties (French)
  New translations JabRef_en.properties (German)
  New translations JabRef_en.properties (Greek)
  New translations JabRef_en.properties (Indonesian)
  ...

.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 - [ ] Check documentation status (Issue created for outdated help page at [help.jabref.org](https://github.com/JabRef/help.jabref.org/issues)?)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

@@ -15,10 +15,17 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - 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 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 `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.
+- We no longer print empty lines when exporting an entry in RIS format [#3634](https://github.com/JabRef/jabref/issues/3634)
 
 ### Fixed
 - We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
 - Autocompletion in the search bar can now be disabled via the preferences. [#3598](https://github.com/JabRef/jabref/issues/3598)
+- We fixed and extended the RIS import functionality to cover more fields. [#3634](https://github.com/JabRef/jabref/issues/3634) [#2607](https://github.com/JabRef/jabref/issues/2607)
 
 ### Removed
 - We removed the [Look and Feels from JGoodies](http://www.jgoodies.com/freeware/libraries/looks/), because the open source version is not compatible with Java 9.
@@ -74,7 +81,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [4.1] - 2017-12-23
 
 ### Changed
-- We added bracketed expresion support for file search patterns, import file name patterns and file directory patters, in addition to bibtexkey patterns.
+- We added bracketed expression support for file search patterns, import file name patterns and file directory patters, in addition to bibtexkey patterns.
 - We added support for `[entrytype]` bracketed expression.
 - Updated French translation
 - We improved the handling of abstracts in the "Astrophysics Data System" fetcher. [#2471](https://github.com/JabRef/jabref/issues/2471)
@@ -83,6 +90,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We increased the relative size of the "abstract" field in the entry editor. [Feature request in the forum](http://discourse.jabref.org/t/entry-preview-in-version-4/827)
 - Crossreferenced entries are now used when a BibTex key is generated for an entry with empty fields. [#2811](https://github.com/JabRef/jabref/issues/2811)
 - We now set the `WM_CLASS` of the UI to org-jabref-JabRefMain to allow certain Un*x window managers to properly identify its windows
+- We added an option to convert entries in the biblatex format to BibTeX so that you can again collaborate with these nostalgic diehards. [Feature request in the forum](http://discourse.jabref.org/t/convert-back-from-biblatex-to-bib/)
 - We changed the default paths for the OpenOffice/LibreOffice binaries to the default path for LibreOffice
 - File annotation tab now removes newlines and hyphens before newlines from content and displays an empty String instead of N/A if no contents are found. [#3280](https://github.com/JabRef/jabref/issues/3280)
 - We moved the groups field from the "Other fields" tab to "General" (you may have to reset your editor preferences under Options > Set up general fields)

CONTRIBUTING.md

@@ -67,27 +67,44 @@ You can see the result in `build\resources\main\help\en\About.html` or when clic
 
 ### When making an architectural decision
 In case you add a library or do mayor code rewrites, we ask you to document your decision.
-Recommended reading: http://www.infoq.com/articles/sustainable-architectural-design-decisions
+Recommended reading: <https://adr.github.io/>.
+
+We simply ask to create a new markdown file in `docs/adr` following the template presented at <https://adr.github.io/madr/>.
+
+In case you want to directly add a comment to a class, simply use following template (based on [sustainable architectural decisions](https://www.infoq.com/articles/sustainable-architectural-design-decisions)):
 
-Template:
 ```
 In the context of <use case/user story u>,
 facing <concern c>
 we decided for <option o>
 and neglected <other options>,
 to achieve <system qualities/desired consequences>,
-accepting <downside d/undesired consequences>,
+accepting <downside / undesired consequences>,
 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

@@ -1,86 +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)
-[![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)
-
-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).
@@ -90,19 +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

@@ -100,10 +100,10 @@ dependencies {
 
     compile 'commons-cli:commons-cli:1.4'
 
-    compile 'org.openoffice:juh:4.1.2'
-    compile 'org.openoffice:jurt:4.1.2'
-    compile 'org.openoffice:ridl:4.1.2'
-    compile 'org.openoffice:unoil:4.1.2'
+    compile "org.libreoffice:juh:5.4.2"
+    compile "org.libreoffice:jurt:5.4.2"
+    compile "org.libreoffice:ridl:5.4.2"
+    compile "org.libreoffice:unoil:5.4.2"
 
     compile 'com.github.bkromhout:java-diff-utils:2.1.1'
     compile 'info.debatty:java-string-similarity:1.0.1'
@@ -138,7 +138,9 @@ dependencies {
     compile 'org.jsoup:jsoup:1.11.2'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
-    compile 'commons-logging:commons-logging:1.2'
+    // >1.8.0-beta is required for java 9 compatibility
+    compile 'org.slf4j:slf4j-api:1.8.0-beta0'
+    compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.10.0'
     compile 'org.apache.logging.log4j:log4j-jcl:2.10.0'
     compile 'org.apache.logging.log4j:log4j-api:2.10.0'
     compile 'org.apache.logging.log4j:log4j-core:2.10.0'
@@ -161,13 +163,12 @@ 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'
     testCompile 'org.xmlunit:xmlunit-matchers:2.5.1'
     testCompile 'com.tngtech.archunit:archunit-junit:0.5.0'
-    testCompile 'org.slf4j:slf4j-jcl:1.7.25' // required by ArchUnit to enable logging over jcl
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit:4.0.+"