Merge branch 'master' into fileChooserRefactor

* master: (268 commits)
  Added DateFormatter to LayoutEntry so that it actually works... (JabRef#1619)
  Implemented JabRef#1345 - cleanup ISSN (JabRef#1590)
  Always use https for help files (JabRef#1615)
  Resolves JabRef#1613 Use Jabref default icon for uninstaller for now (JabRef#1616)
  Added more fields and fixed some issues (JabRef#1617)
  Added LayoutFormatterPreferences (and related files) (JabRef#1608)
  [WIP] Create new fetcher infrastructure (JabRef#1594)
  Set user agent to fix 403 status error
  More fields added to FieldName (JabRef#1614)
  Added model.entry.FieldName that contains field name constants (JabRef#1602)
  Fixes imports
  Test CustomImporter (JabRef#1501)
  The field list gets the focus as soon as it is focused (JabRef#1541)
  When clicking on a tab, the first field now has the focus (JabRef#988)
  Add test in BibEntryWriterTest for type change
  Rewrite MedlineImporter with JAXB and add nbib fields (JabRef#1479)
  Some Globals.prefs injection in logic and model (JabRef#1593)
  Added filter to not show selected integrity checks (JabRef#1588)
  Replace getField with getFieldOptional in all of the tests and in som… (JabRef#1591)
  Move preferences (JabRef#1604)
  ...

# Conflicts:
#	src/main/java/net/sf/jabref/importer/ImportMenuItem.java
#	src/main/java/net/sf/jabref/importer/OpenDatabaseAction.java

.gitattributes

@@ -5,6 +5,3 @@ gradlew eol=lf
 # ensure that line endings of *.java and *.properties are normalized
 *.properties text
 *.java text
-
-# ensure that CHANGELOG entries are merged instead of causing conflicts
-CHANGELOG.md merge=union

.github/ISSUE_TEMPLATE.md

@@ -1,10 +1,14 @@
-JabRef version <version as shown in the about box> on <Windows 10|Ubuntu 14.04|Mac OS X 10.8|...>
-Hint: If you use a [development version](http://builds.jabref.org/master/), ensure that you use the latest one.
+<!-- Note: Please use the GitHub Issue tracker only for BugReports. 
+Feature requests,  questions and general feedback is now handled at http://discourse.jabref.org 
+Thanks! --> 
+
+JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubuntu 14.04|Mac OS X 10.8|... -->
+<!-- Hint: If you use a development version (available at http://builds.jabref.org/master/), ensure that you use the latest one. -->
 
 Steps to reproduce:
 
 1. ...
 2. ...
 3. ...
 
-If applicable, excerpt of the bibliography file, screenshot, and excerpt of log (available in the error console)
+<!-- If applicable, excerpt of the bibliography file, screenshot, and excerpt of log (available in the error console) -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,4 +1,4 @@
-<describe the changes you have made here: what, why, ...>
+<!-- describe the changes you have made here: what, why, ... -->
 
 - [ ] Change in CHANGELOG.md described
 - [ ] Tests created for changes

.gitignore

@@ -45,3 +45,4 @@ bin/
 # UNKNWON
 jabref.xml
 install4j6/
+*.sonargraph

.mailmap

@@ -14,6 +14,7 @@ Nicolas Pavillon <[email protected]>
 Koji Yokota <[email protected]> kojiyokota <[email protected]>
 Koji Yokota <[email protected]> <[email protected]>
 Koji Yokota <[email protected]> <[email protected]>
+Koji Yokota <[email protected]>
 Dominik Waßenhoven <[email protected]> <[email protected]>
 <[email protected]> <[email protected]>
 Thomas Arildsen <[email protected]> ThomasArildsen <[email protected]>
@@ -33,6 +34,7 @@ Michael Falkenthal <[email protected]>
 Michael Falkenthal <[email protected]> <[email protected]>
 <[email protected]> <[email protected]>
 Eduardo Greco <[email protected]>
+Daniel Bruehl <[email protected]>
 Egon Willighagen <[email protected]> <[email protected]>
 Frédéric Darboux <[email protected]>
 Frédéric Darboux <[email protected]> <[email protected]>
@@ -82,8 +84,10 @@ Ulrik Stervbo <[email protected]>
 Stefano Gariazzo <[email protected]>
 Lee Patton <[email protected]>
 Jörg Lenhard <[email protected]>
+Jörg Lenhard <[email protected]>
 <[email protected]> <[email protected]>
 <[email protected]> <[email protected]>
+<[email protected]> <[email protected]>
 Matthias Geiger <[email protected]>
 Christoph Braun <[email protected]>
 Felix Wilke <[email protected]>

.travis.yml

@@ -1,7 +1,20 @@
 language: java
-jdk:
-  - oraclejdk8
-sudo: false
+
+# we test at Ubuntu Trusty (Ubuntu 14.04 LTS)
+# see https://docs.travis-ci.com/user/trusty-ci-environment/
+sudo: required
+dist: trusty
+
+# update to latest Java8 as described at https://github.com/travis-ci/travis-ci/issues/4042#issuecomment-109756980
+addons:
+  apt:
+    packages:
+      # most recent Java8 - this makes the DK switcher obsolete - see https://github.com/travis-ci/travis-ci/issues/5897#issuecomment-218354129
+      - oracle-java8-installer
+      # MySQL 5.6 as desccribed at https://docs.travis-ci.com/user/database-setup/#MySQL-5.6
+      - mysql-server-5.6
+      - mysql-client-core-5.6
+      - mysql-client-5.6
 
 services:
   - postgresql
@@ -12,21 +25,46 @@ install: true
 
 # allow gui testing on travis
 before_script:
-  - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
-  - sleep 3 # give xvfb some time to start
   - psql -c 'create database jabref;' -U postgres
 
 script:
-  - ./gradlew check integrationTest
+  - ./gradlew check
+  # Integration tests currently often fail with "Process 'Gradle Test Executor 1' finished with non-zero exit value 137"
+  # They should run, but the result is ignored
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - sleep 3 # give xvfb some time to start
+  # no need for databases for the integrationTest -> save memory
+  - sudo service mysql stop
+  - sudo service postgresql stop
+  # following services identified by "sudo service --status-all" do not need to run, too
+  # excluded: rsyslog (feels wrong), udev (feels wrong), friendly-recovery ("Unkonwn instance" error)
+  - sudo service acpid stop
+  - sudo service atd stop
+  - sudo service cron stop
+  - sudo service memcached stop
+  - sudo service ntp stop
+  - sudo service rabbitmq-server stop
+  - sudo service resolvconf stop
+  - sudo service sshguard stop
+  - sudo service ssh stop
+  - ./gradlew integrationTest --info || true
 
 after_script:
   # enable codecov report
   - ./gradlew jacocoTestReport
   - bash <(curl -s https://codecov.io/bash)
 
 # cache gradle dependencies
+# https://docs.travis-ci.com/user/languages/java#Caching
+before_cache:
+  - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
 cache:
   directories:
   - $HOME/.gradle/caches/
   - $HOME/.gradle/wrapper/
+
+# enable slack notifications
+notifications:
+  slack:
+    secure: B5LGefXS1Jt+d7tUzzmakoz+/ZnFUzmmmYuBXaikTUPDuxXacIrVTv4Vx+tcagxDrPQ3A20oi3+0t6p8xagytjLI9u3abACyWwO3+CbywuJDLBzxADVhg/+mKssfTmemRlZoBUrBlHZVk69LIJvqXFR5l5zAiBtDL1dWPeMEEvI=

AUTHORS

@@ -29,6 +29,7 @@ Christopher Oezbek
 Christopher S. Lester
 Cyrille d'Haese
 Dale Visser
+Daniel Bruehl
 Daniel Mair
 Daniel Svärd
 David Gleich
@@ -136,6 +137,7 @@ Samin Muhammad Ridwanul Karim
 Sascha Hunold
 Sascha Zeller
 Saverio Mori
+Scott Townsend
 Seb Wills
 Siedlerchr
 Simon Harrer

CHANGELOG.md

@@ -6,13 +6,115 @@ Here, the categories "Changed" for added and changed functionality,
 "Fixed" for fixed functionality, and
 "Removed" for removed functionality is used.
 
-We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`,
-to [sourceforge bugs](https://sourceforge.net/p/jabref/bugs/) by using `bug NUM`, and
-to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by using `feature request NUM`.
+We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`.
 
 
 ## [Unreleased]
 
+### Changed
+- [#462](https://github.com/JabRef/jabref/issues/462) Extend the OpenConsoleFeature by offering a selection between default terminal emulator and configurable command execution.
+- [#1516](https://github.com/JabRef/jabref/issues/1516) Selected field names are written in uppercase in the entry editor
+- For developers: Moved the bst package into logic. This requires the regeneration of antlr sources, execute: gradlew generateSource
+- [#1026](https://github.com/JabRef/jabref/issues/1026) JabRef does no longer delete user comments outside of BibTeX entries and strings
+- [#1249](https://github.com/JabRef/jabref/issues/1249) Date layout formatter added
+- Added ISBN integrity checker
+- Added filter to not show selected integrity checks
+- Enhance the entry customization dialog to give better visual feedback
+- The arXiv fetcher now also supports free-text search queries
+- [#1345](https://github.com/JabRef/jabref/issues/1345) Cleanup ISSN
+
+### Fixed
+- Fixed [#1264](https://github.com/JabRef/jabref/issues/1264): S with caron does not render correctly
+- LaTeX to Unicode converter now handles combining accents
+- Fixed [#1527](https://github.com/JabRef/jabref/issues/1527): 'Get BibTeX data from DOI' Removes Marking
+- Fixed [#1592](https://github.com/JabRef/jabref/issues/1592): LibreOffice: wrong numbers in citation labels
+
+### Removed
+- It is not longer possible to choose to convert HTML sub- and superscripts to equations
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+## [3.5] - 2016-07-13
+
+### Changed
+- Implemented [#1356](https://github.com/JabRef/jabref/issues/1356): Added a formatter for converting HTML to Unicode
+- Implemented [#661](https://github.com/JabRef/jabref/issues/661): Introducing a "check for updates" mechnism (manually/automatic at startup)
+- Implemented [#1338](https://github.com/JabRef/jabref/issues/1338): clicking on a crossref in the main table selects the parent entry and added a button in the entry editor to select the parent entry.
+- Implemented [#1485](https://github.com/JabRef/jabref/issues/1485): Biblatex field shorttitle is now exported/imported as standard field ShortTitle to Word bibliography
+- Implemented [#1431](https://github.com/JabRef/jabref/issues/1431): Import dialog shows file extensions and filters the view
+- When resolving duplicate BibTeX-keys there is now an "Ignore" button. "Cancel" and close key now quits the resolving.
+- The [online forum](http://discourse.jabref.org/) is now directly accessible via the "Help" menu
+- Updated German translation
+
+### Fixed
+- Fixed [#1530](https://github.com/JabRef/jabref/issues/1530): Unescaped hashes in the url field are ignored by the integrity checker
+- Fixed [#405](https://github.com/JabRef/jabref/issues/405): Added more {} around capital letters in Unicode/HTML to LaTeX conversion to preserve them
+- Fixed [#1476](https://github.com/JabRef/jabref/issues/1476): NPE when importing from SQL DB because of missing DatabaseMode
+- Fixed [#1481](https://github.com/JabRef/jabref/issues/1481): Mac OS X binary seems broken for JabRef 3.4 release
+- Fixed [#1430](https://github.com/JabRef/jabref/issues/1430): "review changes" did misinterpret changes
+- Fixed [#1434](https://github.com/JabRef/jabref/issues/1434): Static groups are now longer displayed as dynamic ones
+- Fixed [#1482](https://github.com/JabRef/jabref/issues/1482): Correct number of matched entries is displayed for refining subgroups
+- Fixed [#1444](https://github.com/JabRef/jabref/issues/1444): Implement getExtension and getDescription for importers.
+- Fixed [#1507](https://github.com/JabRef/jabref/issues/1507): Keywords are now separated by the delimiter specified in the preferences
+- Fixed [#1484](https://github.com/JabRef/jabref/issues/1484): HTML export handles some UTF characters wrong
+- Fixed [#1534](https://github.com/JabRef/jabref/issues/1534): "Mark entries imported into database" does not work correctly
+- Fixed [#1500](https://github.com/JabRef/jabref/issues/1500): Renaming of explicit groups now changes entries accordingly
+- Fixed issue where field changes were not undoable if the time stamp was updated on editing
+- Springer fetcher now fetches the requested number of entries (not one less as before)
+- Alleviate multiuser concurrency issue when near simultaneous saves occur to a shared database file
+
+
+## [3.4] - 2016-06-02
+
 ### Changed
 - Implemented [#629](https://github.com/JabRef/jabref/issues/629): Explicit groups are now written in the "groups" field of the entry instead of at the end of the bib file
 - Main table now accepts pasted DOIs and tries to retrieve the entry
@@ -25,6 +127,13 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 - Implemented [feature request #1294](https://github.com/JabRef/jabref/issues/1294): Added possibility to filter for `*.jstyle` files in OpenOffice/LibreOffice style selection dialog. Open style selection dialog in directory of last selected file
 - Added integrity check for ISSN
 - Add LaTeX to Unicode converter as cleanup operation
+- Added an option in the about dialog to easily copy the version information of JabRef
+- Integrity check table can be sorted by clicking on column headings
+- Added \SOFTWARE\Jabref 'Path' registry entry for installation path inside the installer
+- Added an additional icon to distinguish DOI and URL links ([feature request #696](https://github.com/JabRef/jabref/issues/696))
+- Added nbib fields to Medlineplain importer and to MedlineImporter
+- Implemented [#1342](https://github.com/JabRef/jabref/issues/1342): show description of case converters as tooltip 
+- Updated German translation
 
 ### Fixed
 - Fixed [#473](https://github.com/JabRef/jabref/issues/473): Values in an entry containing symbols like ' are now properly escaped for exporting to the database
@@ -36,25 +145,37 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 - Fixed [#1271](https://github.com/JabRef/jabref/issues/1271): Authors with compound first names are displayed properly 
 - Fixed: Selecting invalid jstyle causes NPE and prevents opening of style selection dialog
 - Fixed: Move linked files to default directory works again
+- Fixed [#1327](https://github.com/JabRef/jabref/issues/1327): PDF cleanup changes order of linked pdfs
+- Fixed [#1313](https://github.com/JabRef/jabref/issues/1313): Remove UI for a configuration option which was no longer available
+- Fixed [#1340](https://github.com/JabRef/jabref/issues/1340): Edit -> Mark Specific Color Dysfunctional on OSX
+- Fixed [#1245](https://github.com/JabRef/jabref/issues/1245): Empty jstyle properties can now be specified as ""
+- Fixed [#1364](https://github.com/JabRef/jabref/issues/1364): Windows: install to LOCALAPPDATA directory for non-admin users
+- Fixed [#1365](https://github.com/JabRef/jabref/issues/1365): Default label pattern back to `[auth][year]`
+- Fixed [#796](https://github.com/JabRef/jabref/issues/796): Undoing more than one entry at the same time is now working
+- Fixed [#1122](https://github.com/JabRef/jabref/issues/1122): Group view is immediately updated after adding an entry to a group
+- Fixed [#171](https://github.com/JabRef/jabref/issues/171): Dragging an entry to a group preserves scrolling
+- Fixed [#1353](https://github.com/JabRef/jabref/issues/1353): Fetch-Preview did not display updated BibTeX-Key after clicking on `Generate Now`
+- Fixed [#1381](https://github.com/JabRef/jabref/issues/1381): File links containing blanks are broken if non-default viewer is set
+- Fixed sourceforge bug 1000: shorttitleINI can generate the initials of the shorttitle
+- Fixed [#1394](https://github.com/JabRef/jabref/issues/1394): Personal journal abbrevations could not be saved
+- Fixed [#1400](https://github.com/JabRef/jabref/issues/1400): Detect path constructs wrong path for Windows
+- Fixed [#973](https://github.com/JabRef/jabref/issues/973): Add additional DOI field for English version of MS Office 2007 XML
+- Fixed [#1412](https://github.com/JabRef/jabref/issues/1412): Save action *protect terms* protects terms within words unecessarily
+- Fixed [#1420](https://github.com/JabRef/jabref/issues/1420): Auto downloader should respect file pattern and propose correct filename
+- Fixed [#651](https://github.com/JabRef/jabref/issues/651): Improve parsing of author names containing braces
+- Fixed [#1421](https://github.com/JabRef/jabref/issues/1421): Auto downloader should try to retrieve DOI if not present and fetch afterwards
+- Fixed [#1457](https://github.com/JabRef/jabref/issues/1457): Support multiple words inside LaTeX commands to RTF export
+- Entries retain their groupmembership when undoing their cut/deletion
+- Fixed [#1450](https://github.com/JabRef/jabref/issues/1450): EntryEditor is restored in the correct size after preference changes
+- Fixed [#421](https://github.com/JabRef/jabref/issues/421): Remove LaTeX commands from all BibTeX fields when exporting to Word Bibliography
 
 ### Removed
 - Removed possibility to export entries/databases to an `.sql` file, as the logic cannot easily use the correct escape logic
 - Removed support of old groups format, which was used prior to JabRef version 1.6. If you happen to have a 10 years old .bib file, then JabRef 3.3 can be used to convert it to the current format.
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+- Removed possibility to automatically add braces via Option - Preferences - File - Store the following fields with braces around capital letters. Please use save actions instead for adding braces automatically.
+- Removed button to refresh groups view. This button shouldn't be needed anymore. Please report any cases where the groups view is not updated automatically.
+- Medline and GVK importer no longer try to expand author initials (i.e.  `EH Wissler -> E. H. Wissler`).
+- Removed not-working option "Select Matches" under Groups -> Settings.
 
 
 ## [3.3] - 2016-04-17
@@ -105,9 +226,9 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 - Implemented [#672](https://github.com/JabRef/jabref/issues/672): FileList now distributes its space dependent on the width of its columns
 - Added missing German translations
 - Swedish is added as a language option (still not a complete translation)
+- [#969](https://github.com/JabRef/jabref/issues/969) Adding and replacing old event system mechanisms with Google Guava EventBus.
 
 ### Fixed
-- Alleviate multiuser concurrency issue when near simultaneous saves occur to a shared database file
 - Fixed [#318](https://github.com/JabRef/jabref/issues/318): Improve normalization of author names
 - Fixed [#598](https://github.com/JabRef/jabref/issues/598) and [#402](https://github.com/JabRef/jabref/issues/402): No more issues with invalid icons for ExternalFileTypes in global search or after editing the settings
 - Fixed [#883](https://github.com/JabRef/jabref/issues/883): No NPE during cleanup
@@ -350,10 +471,12 @@ Since much functionality has changed during development, a release of this versi
 
 The changelog of 2.11 and versions before is maintained as [text file](https://github.com/JabRef/jabref/blob/dev_2.11/CHANGELOG) in the [dev_2.11 branch](https://github.com/JabRef/jabref/tree/dev_2.11).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v3.3...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v3.5...HEAD
+[3.5]: https://github.com/JabRef/jabref/compare/v3.4...v3.5
+[3.4]: https://github.com/JabRef/jabref/compare/v3.3...v3.4
 [3.3]: https://github.com/JabRef/jabref/compare/v3.2...v3.3
 [3.2]: https://github.com/JabRef/jabref/compare/v3.1...v3.2
 [3.1]: https://github.com/JabRef/jabref/compare/v3.0...v3.1
 [3.0]: https://github.com/JabRef/jabref/compare/v2.11.1...v3.0
 [dev_2.11]: https://github.com/JabRef/jabref/compare/v2.11.1...dev_2.11
-[2.11.1]: https://github.com/JabRef/jabref/compare/v2.11...v2.11.1
+[2.11.1]: https://github.com/JabRef/jabref/compare/v2.11...v2.11.1

CONTRIBUTING.md

@@ -41,7 +41,7 @@ More information on this can be found via `man git-shortlog`.
 
 
 ### Modify the header
-The headers of each `.java` file states "JabREf contributors".
+The headers of each `.java` file states "JabRef contributors".
 Author credits are given using the `AUTHORS` file and by using the `git blame` functionality.
 
 For instance,
@@ -99,7 +99,7 @@ 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 -b localization.gradle generateMissingTranslationKeys` the "KEY" is added to the other translation files as well.
+With `gradlew generateMissingTranslationKeys` 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`