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

* upstream/master: (102 commits)
  Removed unused test code (#2140)
  Fix main table bug when creating a duplicate (#2135)
  Remove explicit author and add SPDX-License-Identifier
  Remove GPL from README.md and CONTRIBUTING.md
  fix preview update (#2125)
  Remove some UnicodeToLatex uses (#2132)
  Fix mixup in french/farsi localization
  FetcherException should extend JabRefException
  Fix exception when opening preference dialog (#2127)
  Unify ParserException and ParseException (#2124)
  Small refactoring in Importer package (#2053)
  Implement Datepicker "none"-button (#2122)
  revert change from 816d30c
  Change title/tooltip of source panel in biblatex mode (#2120)
  Refactoring: completey typed metadata and add detailed travis output (#2112)
  RTFchars fix (#2097)
  Fix NPE in Medline fetcher on missing ISSN (#2113)
  Ctrl-s parsing error message (#2114)
  Fix bad web search error messages (#2034)
  parse error freeze (#2106)
  ...

# Conflicts:
#	src/main/java/net/sf/jabref/collab/FileUpdateMonitor.java
#	src/main/java/net/sf/jabref/gui/externalfiles/DownloadExternalFile.java
#	src/main/java/net/sf/jabref/gui/externalfiles/DroppedFileHandler.java
#	src/main/java/net/sf/jabref/gui/externalfiles/MoveFileAction.java
#	src/main/java/net/sf/jabref/logic/cleanup/RenamePdfCleanup.java
#	src/main/java/net/sf/jabref/logic/exporter/FileSaveSession.java
#	src/main/java/net/sf/jabref/logic/util/io/FileUtil.java
#	src/main/java/net/sf/jabref/preferences/JabRefPreferences.java

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,3 +5,4 @@
 - [ ] 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 - [ ] Check documentation status (Issue created for outdated help page at [help.jabref.org](https://github.com/JabRef/help.jabref.org/issues)?)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`?

.gitignore

@@ -49,3 +49,6 @@ bin/
 jabref.xml
 install4j6/
 *.sonargraph
+
+# ignore the generated markdown file if the user forgets to delete it
+status.md

.mailmap

@@ -84,11 +84,10 @@ Robert Jäschke <rjoberon@users.sf.net>
 Ulrik Stervbo <ulriks@users.sourceforge.net>
 Stefano Gariazzo <steog88@gmail.com>
 Lee Patton <lpatton@users.sourceforge.net>
-Jörg Lenhard <joerg.lenhard@uni-bamberg.de>
 Jörg Lenhard <joerg.lenhard@kau.se>
-<joerg.lenhard@uni-bamberg.de> <joerg@lenhard.info>
-<joerg.lenhard@uni-bamberg.de> <lenhard@users.noreply.github.com>
-<joerg.lenhard@uni-bamberg.de> <joerg.lenhard@kau.se>
+<joerg.lenhard@kau.se> <joerg@lenhard.info>
+<joerg.lenhard@kau.se> <lenhard@users.noreply.github.com>
+Jörg Lenhard <joerg.lenhard@kau.se> <joerg.lenhard@uni-bamberg.de>
 Matthias Geiger <matthias.geiger@uni-bamberg.de>
 Christoph Braun <braunch.dev@gmail.com>
 Felix Wilke <horstilaemmer@yahoo.com>
@@ -103,3 +102,4 @@ Christoph Schwentker <cschwentker@gmail.com>
 Christoph Schwentker <cschwentker@gmail.com> <siedlerkiller@gmail.com>
 Jens Döcke <jens.doecke@gmail.com>
 Jürgen Lange <juergen.lange@unitybox.de>
+Sascha Zeller <zeller.dev@gmail.com>

.travis.yml

@@ -59,6 +59,10 @@ after_script:
   - ./gradlew jacocoTestReport
   - bash <(curl -s https://codecov.io/bash)
 
+after_failure:
+  # show test results if build fails
+  - $TRAVIS_BUILD_DIR/scripts/after-failure.sh
+
 # cache gradle dependencies
 # https://docs.travis-ci.com/user/languages/java#Caching
 before_cache:

AUTHORS

@@ -12,6 +12,7 @@ Ambrogio Oliva
 Andreas Amann
 Andreas Rudert
 Anh Nghia Tran
+Antonio Ribeiro
 Behrouz Javanmardi
 Bernd Kalbfuss
 Bernhard Tempel
@@ -47,6 +48,7 @@ Fedor Bezrukov
 Felix Berger
 Felix Langner
 Felix Wilke
+Fernando Santagata
 Florian Straßer
 Francois Charette
 Frank Steimle

CHANGELOG.md

@@ -12,17 +12,28 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- Source tab in the entry editor displays "BibLaTeX Source" when using biblatex mode
+- Add session restoring functionality for shared database. Related to [#1703](https://github.com/JabRef/jabref/issues/1703)
+- Implementation of LiveUpdate for PostgreSQL & Oracle systems. Related to [#970](https://github.com/JabRef/jabref/issues/970).
+- [koppor#31](https://github.com/koppor/jabref/issues/31): Number column in the main table is always Left aligned
+- Added support for [1.0.1 CitationStyles](http://citationstyles.org/)
+- You can set and cycle between different preview styles (including CitationStyles)
 - Added fetcher for [MathSciNet](http://www.ams.org/mathscinet), [zbMATH](https://www.zbmath.org/) and [Astrophysics Data System](http://www.adsabs.harvard.edu/)
-- Implemented [#825](https://github.com/JabRef/jabref/issues/825): Search Bar across all bib files instead each having its own
-- Implemented [#573](https://github.com/JabRef/jabref/issues/573): Add key shortcut for global search (`ctrl+shift+f`, if the searchfield is empty it will be focused instead)
-- The search result Window will now show which entry belongs to which bib file
-- The search result Window will now remember its location
-- The search result Window won't stay on top anymore if the main Window is focused and will be present in the taskbar
-- The user can jump from the searchbar to the maintable  with `ctrl+enter`
-- Implemented [#573 (comment)](https://github.com/JabRef/jabref/issues/573#issuecomment-232284156): Added shortcut: closing the search result window with `ctrl+w`
+- Improved search:
+  - Search queries consisting of a normal query and a field-based query are now supported (for example, `JabRef AND author == you`)
+  - Implemented [#825](https://github.com/JabRef/jabref/issues/825): Search Bar across all bib files instead each having its own
+  - Implemented [#573](https://github.com/JabRef/jabref/issues/573): Add key shortcut for global search (`ctrl+shift+f`, if the searchfield is empty it will be focused instead)
+  - The search result Window will now show which entry belongs to which bib file
+  - The search result Window will now remember its location
+  - The search result Window won't stay on top anymore if the main Window is focused and will be present in the taskbar
+  - The user can jump from the searchbar to the maintable  with `ctrl+enter`
+  - Implemented [#573 (comment)](https://github.com/JabRef/jabref/issues/573#issuecomment-232284156): Added shortcut: closing the search result window with `ctrl+w`
 - Added integrity check for fields with BibTeX keys, e.g., `crossref` and `related`, to check that the key exists
+- Fields linking to other entries (e.g., `crossref` and `related`) have now specialized editors in the entry editor. Check the tabs "Other fields" and "General".
 - [#1496](https://github.com/JabRef/jabref/issues/1496) Keep track of which entry a downloaded file belongs to
 - Made it possible to download multiple entries in one action
+- [#1506](https://github.com/JabRef/jabref/issues/1506) It is possible to apply two new key modifier `title_case` for Title Case, `capitalize` for Capitalized first character of each word (difference is that title case will leave prepositions etc in lower case), and `sentence_case` for normal sentence case (first word capitalized). In addition `lower_case` and `upper_case` can be used instead of `lower` and `upper`. 
+- Added two new pseudo-fields for search: `anykeyword` to search for a specific keyword and `anyfield` to search in all fields (useful in combination with search in specific fields)
 - [#1813](https://github.com/JabRef/jabref/issues/1813) Import/Export preferences dialog default directory set to working directory
 - [#1897](https://github.com/JabRef/jabref/issues/1897) Implemented integrity check for `year` field: Last four nonpunctuation characters should be numerals
 - Address in MS-Office 2007 xml format is now imported as `location`
@@ -35,8 +46,26 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Implemented integrity check for `note` and `howpublished` field: Should have the first letter capitalized (BibTeX)
 - <kbd>Pos1</kbd> / <kbd>HOME</kbd> now select the first/last entry in the main table and the search result frame.
 - <kbd>UP</kbd> / <kbd>Down</kbd> / <kbd>Tab</kbd> / <kbd>shift+Tab</kbd> in the search result frame have now the same functionality as in the main  table.
+- Importer for MODS format added
+- [#2012](https://github.com/JabRef/jabref/issues/2012) Implemented integrity check for `month` field: Should be an integer or normalized (BibLaTeX), Should be normalized (BibTeX)
+- [#1779](https://github.com/JabRef/jabref/issues/1779) Implemented integrity check for `bibtexkey` field: Empty BibTeX key
+- Prohibit more than one connections to the same shared database.
+- Implemented integrity check for `journaltitle` field: BibLaTeX field only (BibTeX)
+- [#463](https://github.com/JabRef/jabref/issues/463): Disable certain menu items, toolbar buttons and context menu items while multiple entries are selected
+- [#490](https://github.com/JabRef/jabref/issues/490) Added right click menu to main table and entry editor to allow copying doi url
+- [#549](https://github.com/JabRef/jabref/issues/549) Added new shortcut to copy the BibTeX key as a hyperlink to its url to the clipboard
+- Complete vietnam language translation in menu
+- Generalize German translation of database into "Datenbank"
+- Improve language quality of the German translation of shared database
+- Change "Recent files" to "Recent databases" to keep the file menu consistent
+- Customized importer files need to be slightly changed since the class `ImportFormat` was renamed to `Importer`
 
 ### Fixed
+- Fixed [#2092](https://github.com/JabRef/jabref/issues/2092): "None"-button in date picker clears the date field
+- Fixed [#1993](https://github.com/JabRef/jabref/issues/1993): Various optimizations regarding search performance
+- Fixed [koppor#160](https://github.com/koppor/jabref/issues/160): Tooltips now working in the main table
+- Fixed [#2054](https://github.com/JabRef/jabref/issues/2054): Ignoring a new version now works as expected
+- Fixed [#1542](https://github.com/JabRef/jabref/issues/1542): Improved error messages when using fetcher
 - Fixed selecting an entry out of multiple duplicates
 - Fixed [#617](https://github.com/JabRef/jabref/issues/617): `Enter` in global search opens the selected entry & `Enter` in search dialog window opens the selected entry
 - Entries in the SearchResultPanel will be shown correctly (Latex to Unicode)
@@ -45,12 +74,13 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Selecting an entry in the search result Window will now select the correct entry in the bib file
 - Entries in the SearchResultDialog are now converted to Unicode
 - Suggestions in the autocomplete (search) are now in Unicode
-- Fixed NullPointerException when opening search result window for an untitled database 
+- Fixed NullPointerException when opening search result window for an untitled database
 - Fixed entry table traversal with Tab (no column traversal thus no double jump)
 - Fixed [#1757](https://github.com/JabRef/jabref/issues/1757): Crash after saving illegal argument in entry editor
 - Fixed [#1663](https://github.com/JabRef/jabref/issues/1663): Better multi-monitor support
 - Fixed [#1882](https://github.com/JabRef/jabref/issues/1882): Crash after saving illegal bibtexkey in entry editor
 - Fixed field `location` containing only city is not exported correctly to MS-Office 2007 xml format
+- Fixed [#1235](https://github.com/JabRef/jabref/issues/1235): Modified Key bindings do not work correctly
 - Fixed field `key` field is not exported to MS-Office 2008 xml format
 - Fixed [#1181](https://github.com/JabRef/jabref/issues/1181) and [#1504](https://github.com/JabRef/jabref/issues/1504): Improved "Normalize to BibTeX name format": Support separated names with commas and colons. Considered name affixes such as "Jr".
 - Fixed download files failed silently when an invalid directory is selected
@@ -59,11 +89,20 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Fixed loop when pulling changes (shared database) when current selected field has changed
 - Fixed [#1958](https://github.com/JabRef/jabref/issues/1958): Verbatim fields are no longer checked for HTML encoded characters by integrity checks
 - Fixed [#1937](https://github.com/JabRef/jabref/issues/1937): If no help page for the current chosen language exists, the english help page will be shown
+- Fixed [#2060](https://github.com/JabRef/jabref/issues/2060): Medline fetcher now imports data in UTF-8 encoding
+- Fixed file menu displays wrong hotkey in the German translation
+- Fixed [#2090](https://github.com/JabRef/jabref/issues/#2090): If special fields were not selected, two menu item separator were shown
+- Fixed [#2064](https://github.com/JabRef/jabref/issues/2064): Not all `other fields` are shown on entry change of same type
+- Fixed [#2104](https://github.com/JabRef/jabref/issues/#2104): Crash after saving BibTeX source with parsing error
+- Fixed [#2109](https://github.com/JabRef/jabref/issues/#2109): <kbd>Ctrl-s</kbd> doesn't trigger parsing error message
+- Fixed RTFChars would only use "?" for characters with unicode over the value of 127, now it uses the base character (é -> e instead of ?)
 
 ### Removed
-- The non-supported feature of being able to define file directories for any extension is removed. Still, it should work for older databases using the legacy `ps` and `pdf` fields, although we strongly encourage using the `file` field. 
+- Removed 2nd preview style
+- The non-supported feature of being able to define file directories for any extension is removed. Still, it should work for older databases using the legacy `ps` and `pdf` fields, although we strongly encourage using the `file` field.
 - Automatic migration for the `evastar_pdf` field is removed.
-
+- We removed the customizable "content selectors" since they are replaced by the auto-completion feature
+- Removed optional fields from `other fields` (BibTeX), Removed deprecated fields from `other fields` (BibLaTeX)
 
 
 

CONTRIBUTING.md

@@ -42,8 +42,7 @@ More information on this can be found via `man git-shortlog`.
 Please, **do not add yourself at `@authors`**.
 The contribution information is tracked via the version control system.
 
-We are currently in transition from [GPL](https://tldrlegal.com/license/gnu-general-public-license-v2) to the [MIT license](https://tldrlegal.com/license/mit-license).
-Thus, all your contributions are considered being made under MIT license.
+Your contribution is considered being made under [MIT license](https://tldrlegal.com/license/mit-license).
 
 
 ### Write a good commit message
@@ -85,7 +84,7 @@ because <additional rationale>.
 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. There is also a snippet generated for the non-English files, but this is irrelevant.
 Add snippet to English translation file located at `src/main/resources/l10n/JabRef_en.properties`
-With `gradlew generateMissingTranslationKeys` the "KEY" is added to the other translation files as well.
+With `gradlew localizationUpdate` the "KEY" is added to the other translation files as well.
 Tests are green again.
 
 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`

README.md

@@ -104,9 +104,7 @@ Releasing is done using [CircleCI](https://circleci.com/gh/JabRef/jabref). A ful
 
 ## License
 
-We are currently in transition from [GPL](https://tldrlegal.com/license/gnu-general-public-license-v2) to the [MIT license](https://tldrlegal.com/license/mit-license).
-Thus, all new contributions are considered being made under MIT license.
-
+Since version 3.6, JabRef is licensed under the [MIT license](https://tldrlegal.com/license/mit-license).
 See the [LICENSE.md](LICENSE.md) for the full MIT license.
 
 JabRef also uses libraries distributed by other parties.

build.gradle

@@ -51,6 +51,9 @@ install4j {
 
 repositories {
     jcenter()
+    maven {
+        url 'https://oss.sonatype.org/content/groups/public'
+    }
 }
 
 configurations {
@@ -97,7 +100,7 @@ dependencies {
     // VersionEye states that 6.0.4 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
     compile 'mysql:mysql-connector-java:5.1.39'
 
-    compile 'org.postgresql:postgresql:9.4.1210'
+    compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.6'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
     compile fileTree(dir: 'lib', includes: ['*.jar'])
@@ -118,6 +121,13 @@ dependencies {
     compile 'org.xmlunit:xmlunit-core:2.2.1'
     compile 'org.xmlunit:xmlunit-matchers:2.2.1'
 
+    // 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:0.6'
+    // in Java 8 Rhino was replaced by Nashorn, but 'de.undercouch:citeproc-java:0.6' depends on Rhino
+    compile 'org.mozilla:rhino:1.7.7.1'
+
     testCompile 'junit:junit:4.12'
     testCompile 'org.mockito:mockito-core:1.10.19'
     testCompile 'com.github.tomakehurst:wiremock:2.1.12'
@@ -127,7 +137,8 @@ dependencies {
 sourceSets {
     main {
         java {
-            srcDirs = ["src/main/java", "src/main/gen"]
+            // remove "src/oracleMock" if ojdbc.jar is available
+            srcDirs = ["src/main/java", "src/main/gen", "src/oracleMock"]
         }
     }
     databaseTest {

external-libraries.txt

@@ -52,6 +52,11 @@ Project: java-diff-utils
 URL:     http://code.google.com/p/java-diff-utils/
 License: Apache 2.0
 
+Id:      com.impossibl.pgjdbc-ng:pgjdbc-ng
+Project: pgjdbc-ng
+URL:     http://impossibl.github.io/pgjdbc-ng
+License: BSD
+
 Id:      com.jgoodies:jgoodies-common
 Project: JGoodies Common
 URL:     http://www.jgoodies.com/downloads/libraries/
@@ -142,11 +147,6 @@ Project: SwingX
 URL:     https://swingx.java.net/
 License: LGPL 3.0
 
-Id:      org.postgresql:postgresql
-Project: PostgreSQL JDBC Driver
-URL:     http://jdbc.postgresql.org/download.html
-License: BSD
-
 Id:      microba
 Path:    lib/microba.jar
 Project: Microba
@@ -159,4 +159,24 @@ Project: Spin
 URL:     http://spin.sourceforge.net/
 License: LGPL 2.1+
 
+Id:      org.citationstyles.styles
+Project: CSL Styles
+URL:     citationStyles.org
+Licence: Creative Commons Attribution-ShareAlike 3.0 Unported license
+
+Id:      org.citationstyles.locales
+Project: CSL Locales
+URL:     citationStyles.org
+Licence: Creative Commons Attribution-ShareAlike 3.0 Unported license
+
+Id:      de.undercouch.citeproc-java
+Project: Citeproc-Java
+URL:     http://michel-kraemer.github.io/citeproc-java/
+Licence: Apache License, Version 2.0
+
+Id:      org.mozilla.rhino
+Project: Rhino
+URL:     https://developer.mozilla.org/de/docs/Rhino
+Licence: Mozilla Public License Version 2.0
+
 The last entry has to end with an empty line. Otherwise the entry is not present in About.html.

jabref.install4j

@@ -750,4 +750,9 @@ return true;</string>
   </mediaSets>
   <buildIds buildAll="true" />
   <buildOptions verbose="false" faster="false" disableSigning="false" disableJreBundling="false" debug="false" />
+  <jvmArguments>
+      <arg>-XX:+UseG1GC</arg>
+      <arg>-XX:+UseStringDeduplication</arg>
+      <arg>-XX:StringTableSize=1000003</arg>
+  </jvmArguments>
 </install4j>