Merge pull request #3684 from JabRef/javafxGlobalEverything

Make JavaFX a first-class citizen

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,4 +1,6 @@
-<!-- describe the changes you have made here: what, why, ... -->
+<!-- describe the changes you have made here: what, why, ... 
+     Link issues by using the following pattern: [#333](https://github.com/JabRef/jabref/issues/333) or [koppor#49](https://github.com/koppor/jabref/issues/47).
+     The title of the PR must not reference an issue, because GitHub does not support autolinking there. -->
 
 
 ----

.mailmap

@@ -5,8 +5,9 @@
 # duplicates that aren't also email duplicates): scan the output of:
 #   git log --format='%aE - %aN' | sort --unique --ignore-case
 #
-# One can find out the real name by using the GitHub API.
-# E.g., https://api.github.com/users/sauliusg/events/public
+# One can find out the real name by using the GitHub user page and API.
+# https://github.com/sauliusg
+# https://api.github.com/users/sauliusg/events/public
 #
 # For explanation on this file format: man git-shortlog
 Ruy Minoru Ito Takata <[email protected]>
@@ -137,3 +138,5 @@ Tobias Bouschen <[email protected]>
 József Pallagi <[email protected]>
 Mattia Bunel <[email protected]>
 Waida Fan <[email protected]>
+Johannes Manner <[email protected]>
+Dominik Traczyk <[email protected]>

AUTHORS

@@ -21,6 +21,7 @@ Anita Armbruster
 Antonio Ribeiro
 Arno Blouin
 Bartosz J. Kaczkowski
+Bartłomiej Dach
 Behrouz Javanmardi
 Benjamin Köhler
 Berk Gureken
@@ -46,6 +47,7 @@ David Gleich
 David Weitzman
 Dennis Tschechlov
 Domenico Cufalo
+Dominik Traczyk
 Dominik Waßenhoven
 Douglas Nassif Roma Junior
 Eduard Braun
@@ -87,6 +89,7 @@ Jeff Kerr
 Jeff Miller
 Jeffrey Kuhn
 Jens Döcke
+Johannes Manner
 John David
 John Relph
 John Zedlewski
@@ -159,6 +162,7 @@ Philip Johnson
 Predrag Milanovic
 Raik Nagel
 Renato Massao
+Richard Schneeman
 Robert Jäschke
 Rolf Starre
 Rudolf Seemann
@@ -171,6 +175,7 @@ Sascha Hunold
 Sascha Zeller
 Saulius Gražulis
 Saverio Mori
+Scott Pogatetz
 Scott Townsend
 Seb Wills
 Shitikanth

CHANGELOG.md

@@ -12,26 +12,44 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- Abbreviate journal names functionality is now running parallel, increasing performance significantly. [#2831] (https://github.com/JabRef/jabref/issues/2831)
+- Changed order of items in context menu [#298] (https://github.com/koppor/jabref/issues/298)
+- Changed ID-based entry generator to store the last used fetcher. [#2796] (https://github.com/JabRef/jabref/issues/2796)
+- Reorganised annotation information on the right side of the "File annotations" tab. [#3109](https://github.com/JabRef/jabref/issues/3109)
 - 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 a new type of group that shows all items referenced in a given LaTeX file (actually the generated AUX file). [#1664](https://github.com/JabRef/jabref/issues/1664)
+- We added an importer for the EndNote XML format. [Feature request in the forum](http://discourse.jabref.org/t/import-from-bookends-or-endnote/1048)
 - 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 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) 
+- 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.
+- Renamed the _Review_ Tab into _Comments_ Tab
 - We no longer print empty lines when exporting an entry in RIS format [#3634](https://github.com/JabRef/jabref/issues/3634)
 - We improved file saving so that hard links are now preserved when a save is performed [#2633](https://github.com/JabRef/jabref/issues/2633)
+- We changed the default dialog option when removing a [file link](http://help.jabref.org/en/FileLinks#adding-external-links-to-an-entry) from an entry.
+The new default removes the linked file from the entry instead of deleting the file from disk. [#3679](https://github.com/JabRef/jabref/issues/3679)
+- The group editing window can now also be called by double-clicking the group to be edited. [koppor#277](https://github.com/koppor/jabref/issues/277)
+- The magnifier icon at the search shows the [search mode](https://help.jabref.org/en/Search#search-modes) again. [#3535](https://github.com/JabRef/jabref/issues/3535)
+- We added a new cleanup operation that replaces ligatures with their expanded form. [#3613](https://github.com/JabRef/jabref/issues/3613)
+- Pressing <kbd>ESC</kbd> while searching will clear the search field and select the first entry, if available, in the table. [koppor#293](https://github.com/koppor/jabref/issues/293)
 
 ### Fixed
+- We fixed several performance problems with the management of journal abbreviations [#3323](https://github.com/JabRef/jabref/issues/3323)
+- We fixed an issue where changing the type of an entry did not update the label in the tool bar of the entry editor and the contents of the currently visible entry editor tab
+- We fixed an issue where pressing space caused the cursor to jump to the start of the text field. [#3471](https://github.com/JabRef/jabref/issues/3471)
 - 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 an issue where odd linked files could not be selected in the entry editor. [#3639](https://github.com/JabRef/jabref/issues/3639)
 - 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)
 - Chaining modifiers in BibTeX key pattern now works as described in the documentation. [#3648](https://github.com/JabRef/jabref/issues/3648)
 - We fixed an issue where not all bibtex/biblatex fields would be exported as latex-free to MS-Office XML [koppor#284](https://github.com/koppor/jabref/issues/284)
+- We fixed an issue where linked files would be deleted from bibliography entries despite choosing the "Cancel" option in the dialog menu.
+- We fixed the name of the group editing window to "Add group" instead of "Edit Group" when adding a new group. [koppor#277](https://github.com/koppor/jabref/issues/277)
 
 ### 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.

CONTRIBUTING.md

@@ -48,6 +48,8 @@ Your contribution is considered being made under [MIT license](https://tldrlegal
 
 ### Write a good commit message
 See [good commit message] or [commit guidelines section of Pro Git].
+The first line of your commit message is automatically taken as title for the pull-request.
+All other lines make up the body of the pull request. Add the words `fixes #xxx` to your PR to auto-close the corresponding issue.
 
 
 ### Test your code
@@ -66,7 +68,7 @@ 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.
+In case you add a library or do major code rewrites, we ask you to document your decision.
 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/>.

DEVELOPERS

@@ -1,9 +1,7 @@
 Oliver Kopp (since 2011)
-Simon Harrer (since 2014)
 Jörg Lenhard (since 2015)
 Stefan Kolb (since 2015)
 Matthias Geiger (since 2015)
-Oscar Gustafsson (since 2015)
 Tobias Diez (since 2015)
 Christoph Schwentker (since 2016)
 Linus Dietz (since 2017)

README.md

@@ -12,7 +12,7 @@ Stay on top of your literature: JabRef helps you to collect and organize sources
 ## 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.
+JabRef supports you in every step of your research work.
 
 #### Collect
 
@@ -21,7 +21,7 @@ JabRef supports you every step of your research work.
 - 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
+- [JabFox Firefox Add-on](https://addons.mozilla.org/en-US/firefox/addon/jabfox/) lets you import new references directly from the browser with one click
 
 #### Organize
 
@@ -32,21 +32,21 @@ JabRef supports you every step of your research work.
 - 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
+- Automatically rename and move 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
+- Support for Word and LibreOffice/OpenOffice for inserting and formatting 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
+- Library is saved as a simple text file and thus it is easy to share with others via Dropbox and is version-control friendly
+- Work in a team: sync the contents of your library via a SQL database
 
 ## Installation
 
@@ -70,16 +70,18 @@ Try to double click the `jar` file or execute the following command:
 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.
+You can use our [GitHub issue tracker](https://github.com/JabRef/jabref/issues) to file bug reports.
 
-Explanation of donation possibilities and usage of donations is available at our [donations page](https://donations.jabref.org).
+An explanation of donation possibilities and usage of donations is available at our [donations page](https://donations.jabref.org).
 
 ## 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)
 
+> Not a programmer? [Learn how to help.](http://contribute.jabref.org)
+
 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.

build.gradle

@@ -13,7 +13,7 @@ buildscript {
         }
     }
     dependencies {
-        classpath 'org.junit.platform:junit-platform-gradle-plugin:1.1.0-M1'
+        classpath 'org.junit.platform:junit-platform-gradle-plugin:1.1.0'
     }
 }
 
@@ -90,10 +90,9 @@ dependencies {
     compile 'com.jgoodies:jgoodies-common:1.8.1'
     compile 'com.jgoodies:jgoodies-forms:1.9.0'
 
-    // update to 2.0.x is not possible - see https://github.com/JabRef/jabref/pull/1096#issuecomment-208857517
-    compile 'org.apache.pdfbox:pdfbox:1.8.13'
-    compile 'org.apache.pdfbox:fontbox:1.8.13'
-    compile 'org.apache.pdfbox:jempbox:1.8.13'
+    compile 'org.apache.pdfbox:pdfbox:2.0.8'
+    compile 'org.apache.pdfbox:fontbox:2.0.8'
+    compile 'org.apache.pdfbox:xmpbox:2.0.8'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     compile 'org.bouncycastle:bcprov-jdk15on:1.59'
@@ -121,7 +120,7 @@ dependencies {
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:23.6-jre'
+    compile 'com.google.guava:guava:24.0-jre'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'
@@ -156,15 +155,15 @@ dependencies {
     compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '1.0.9'
     compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.9'
 
-    testCompile 'org.junit.jupiter:junit-jupiter-api:5.1.0-M2'
-    testCompile 'org.junit.jupiter:junit-jupiter-params:5.1.0-M2'
-    testRuntime 'org.junit.jupiter:junit-jupiter-engine:5.1.0-M2'
-    testRuntime 'org.junit.vintage:junit-vintage-engine:5.1.0-M2'
-    testCompile 'org.junit.platform:junit-platform-launcher:1.1.0-M2'
+    testCompile 'org.junit.jupiter:junit-jupiter-api:5.1.0'
+    testCompile 'org.junit.jupiter:junit-jupiter-params:5.1.0'
+    testRuntime 'org.junit.jupiter:junit-jupiter-engine:5.1.0'
+    testRuntime 'org.junit.vintage:junit-vintage-engine:5.1.0'
+    testCompile 'org.junit.platform:junit-platform-launcher:1.1.0'
     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:2.14.0'
+    testCompile 'org.mockito:mockito-core:2.15.0'
+    testCompile 'com.github.tomakehurst:wiremock:2.15.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.5.1'
@@ -176,6 +175,10 @@ dependencies {
     checkstyle 'com.puppycrawl.tools:checkstyle:8.8'
 }
 
+jacoco {
+    toolVersion = '0.8.0'
+}
+
 dependencyUpdates {
     outputFormatter = "json"
 }
@@ -213,22 +216,21 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("Cannot be upgraded to version 2")
             }
         }
-        withModule("org.apache.pdfbox:fontbox") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.*/) {
-                selection.reject("update to 2.0.x is not possible - see https://github.com/JabRef/jabref/pull/1096#issuecomment-208857517")
+        withModule("mysql:mysql-connector-java") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /[6-9].*/) {
+                selection.reject("http://dev.mysql.com/downloads/connector/j/ lists the version 5.* as last stable version.")
             }
         }
-        withModule("org.apache.pdfbox:pdfbox") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.*/) {
-                selection.reject("update to 2.0.x is not possible - see https://github.com/JabRef/jabref/pull/1096#issuecomment-208857517")
+        withModule("org.jacoco:org.jacoco.agent") { ComponentSelection selection ->
+            if (selection.candidate.version.equals("0.8.0")) {
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
             }
         }
-        withModule("mysql:mysql-connector-java") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /[6-9].*/) {
-                selection.reject("http://dev.mysql.com/downloads/connector/j/ lists the version 5.* as last stable version.")
+        withModule("org.jacoco:org.jacoco.ant") { ComponentSelection selection ->
+            if (selection.candidate.version.equals("0.8.0")) {
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
             }
         }
-
     }
 }
 
@@ -392,7 +394,6 @@ afterEvaluate {
     def junitPlatformTest = tasks.junitPlatformTest
 
     jacoco {
-        toolVersion = '0.8.0'
         applyTo(junitPlatformTest)
     }
 

config/IntelliJ Code Style.xml

@@ -31,6 +31,7 @@
     <option name="KEEP_BLANK_LINES_IN_DECLARATIONS" value="1" />
     <option name="KEEP_BLANK_LINES_IN_CODE" value="1" />
     <option name="KEEP_BLANK_LINES_BEFORE_RBRACE" value="0" />
+    <option name="ALIGN_MULTILINE_CHAINED_METHODS" value="true" />
     <arrangement>
       <rules>
         <section>