Merge remote-tracking branch 'upstream/maintable-beta' into selectFil…

…esDlg * upstream/maintable-beta: (346 commits) add missing localization fix keybinding of entry editor add missing keybinding of search Update java-string-similarity from 1.0.1 -> 1.1.0 Update log4j from 2.10.0 -> 2.11.0 Update guava from 24.0 -> 24.1 New Crowdin translations (#3853) Fetcher refactorings Fix ScienceDirect fetcher #3854 Fix Google Scholar fetcher test Fix DBLP fetcher tests Move migration to top level package New Crowdin translations (#3851) Update Eclipse style to intellij style (#3827) fix some not on fx thread dialogs in preferences fix inital save error Convert last dialog to javafx refactor exception Update mysql-connector from 5.1.45 -> 5.1.46 Update mockito-core from 2.15.0 -> 2.16.0 New translations JabRef_en.properties (Spanish) New translations Menu_en.properties (Spanish) Merge changes for renamed actions ...
JabRef · Mar 17, 2018 · 5305d43 · 5305d43
2 parents 514cd49 + 2c2a302
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,10 +1,13 @@
-<!-- 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. -->
 
 
 ----
 
 - [ ] Change in CHANGELOG.md described
 - [ ] Tests created for changes
-- [ ] Screenshots added (for bigger UI changes)
 - [ ] Manually tested changed features in running JabRef
+- [ ] Screenshots added in PR description (for bigger UI changes)
+- [ ] Ensured that [the git commit message is a good one](https://github.com/joelparkerhenderson/git_commit_message)
 - [ ] Check documentation status (Issue created for outdated help page at [help.jabref.org](https://github.com/JabRef/help.jabref.org/issues)?)
diff --git a/.mailmap b/.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 <ruy.takata@gmail.com>
@@ -137,3 +138,5 @@ Tobias Bouschen <tobias.bouschen@googlemail.com>
 József Pallagi <pallagijoe@gmail.com>
 Mattia Bunel <MBunel@users.noreply.github.com>
 Waida Fan <31742543+weidafan@users.noreply.github.com>
+Johannes Manner <johannes.manner@web.de>
+Dominik Traczyk <dominik646@gmail.com>
diff --git a/.travis.yml b/.travis.yml
@@ -17,11 +17,11 @@ env:
   global:
     - GRADLE_OPTS=-Dorg.gradle.daemon=false
   matrix:
+    - TEST_SUITE=checkstyle
     - TEST_SUITE=check OPTIONS=modernizer
     - TEST_SUITE=fetcherTest
     - TEST_SUITE=databaseTest
     - TEST_SUITE=guiTest
-    - TEST_SUITE=checkstyle
     - TEST_SUITE=codecov
     - DEPENDENCY_UPDATES=check
 
@@ -60,6 +60,7 @@ after_failure:
 branches:
   only:
     - master
+    - maintable-beta
 
 # cache gradle dependencies
 # https://docs.travis-ci.com/user/languages/java#Caching

diff --git a/AUTHORS b/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

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,28 +12,48 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- Added "*.*" (any file type) to the Import File Filter Dialog. [#3757] (https://github.com/JabRef/jabref/issues/3757)
+- 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)
 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 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)
+- We added the function to parse German month names. [#3536](https://github.com/JabRef/jabref/pull/3536)
+- 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)
+- We changed the metadata reading and writing. DublinCore is now the only metadata format, JabRef supports. (https://github.com/JabRef/jabref/pull/3710)
+- We added another CLI functionality for reading and writing metadata to pdfs. (see https://github.com/JabRef/jabref/pull/3756 and see http://help.jabref.org/en/CommandLine)
 
 ### 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)
+- We fixed an issue where the "Copy linked files" dialog produced an error when the entry had no file [#3818](https://github.com/JabRef/jabref/issues/3818)
 
 ### 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.

diff --git a/CONTRIBUTING.md b/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

diff --git a/README.md b/README.md
@@ -80,6 +80,8 @@ An explanation of donation possibilities and usage of donations is available at
 [![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.

diff --git a/build.gradle b/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'
@@ -106,7 +105,7 @@ dependencies {
     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'
+    compile 'info.debatty:java-string-similarity:1.1.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
     compile 'org.antlr:antlr-runtime:3.5.2'
@@ -115,22 +114,25 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.7.1'
 
     // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
-    compile 'mysql:mysql-connector-java:5.1.45'
+    compile 'mysql:mysql-connector-java:5.1.46'
 
     compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:24.0-jre'
+    compile 'com.google.guava:guava:24.1-jre'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'
-    compile 'de.codecentric.centerdevice:javafxsvg:1.2.1'
+    compile 'de.codecentric.centerdevice:javafxsvg:1.3.0'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
     compile 'de.saxsys:mvvmfx-validation:1.7.0'
+    compile 'de.saxsys:mvvmfx:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6'
     compile 'org.fxmisc.richtext:richtextfx:0.8.2'
+    compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
+
 
     // Cannot be updated to 9.*.* until Jabref works with Java 9
     compile 'org.controlsfx:controlsfx:8.40.15-SNAPSHOT'
@@ -140,10 +142,10 @@ dependencies {
 
     // >1.8.0-beta is required for java 9 compatibility
     compile 'org.slf4j:slf4j-api:1.8.0-beta1'
-    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'
+    compile 'org.apache.logging.log4j:log4j-slf4j-impl:2.11.0'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.11.0'
+    compile 'org.apache.logging.log4j:log4j-api:2.11.0'
+    compile 'org.apache.logging.log4j:log4j-core:2.11.0'
 
     // 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'
@@ -152,25 +154,25 @@ dependencies {
 
     compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    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'
-    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'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.0.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.0.1'
+
+    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:2.11.0'
+    testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.0'
+    testCompile 'org.mockito:mockito-core:2.16.0'
+    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'
     testCompile 'org.xmlunit:xmlunit-matchers:2.5.1'
     testCompile 'com.tngtech.archunit:archunit-junit:0.5.0'
     testCompile "org.testfx:testfx-core:4.0.+"
-    testCompile "org.testfx:testfx-junit:4.0.+"
+    testCompile "org.testfx:testfx-junit5:4.0.+"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:8.8'
 }
@@ -191,52 +193,22 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("Cannot be updated to 9.*.* until Jabref works with Java 9")
             }
         }
-        withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("1.0.10")) {
-                selection.reject("Version 1.0.10 is broken... waiting for 1.0.11")
-            }
-        }
-        withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("1.0.10")) {
-                selection.reject("Version 1.0.10 is broken... waiting for 1.0.11")
-            }
-        }
-        withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("2.0.0-BETA")) {
-                selection.reject("Version 2.0.0-BETA is broken... waiting for a working version... see #3561")
-            }
-        }
-        withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
-            if (selection.candidate.version.equals("2.0.0-BETA")) {
-                selection.reject("Version 2.0.0-BETA is broken... waiting for a working version... see #3561")
-            }
-        }
         withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
             if (selection.candidate.version ==~ /2.*/) {
                 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("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("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.agent") { ComponentSelection selection ->
+        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("org.jacoco.ant") { ComponentSelection selection ->
+        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.")
             }