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

* upstream/master: (155 commits) Update DEVELOPERS Update README.md [WIP] File link deletion dialog improvements (#3690) Update guava (#3692) Fix some FX Thread issue (#3691) Fixed typo, mayor to major (#3685) add Office xml test for latex free fields (#3680) Migrate importer tests to JUnit5 (#3665) fix typo Update slf4j-api from 1.8.0-beta0 -> 1.8.0-beta1 Update richtext from 0.8.1 -> 0.8.2 Update junit from 5.1.0-M1 -> 5.1.0-M2 Update checkstyle from 8.7 -> 8.8 Export all fields with their latex free equivalent (#3675) try around with exckluding tag (#3676) Fixes #3648: Chained modifiers work again (#3670) Update gradle from 4.4.1 to 4.5 and tweak .gitattributes Fix 2633 saving creates new database (#3674) New translations JabRef_en.properties (French) Implements #1664: group based on aux file (#3444) ... # Conflicts: # CHANGELOG.md # CONTRIBUTING.md # build.gradle # gradle/wrapper/gradle-wrapper.jar # gradle/wrapper/gradle-wrapper.properties # scripts/syncLang.py # src/main/java/org/jabref/FallbackExceptionHandler.java # src/main/java/org/jabref/Globals.java # src/main/java/org/jabref/JabRefMain.java # src/main/java/org/jabref/cli/ArgumentProcessor.java # src/main/java/org/jabref/cli/JabRefCLI.java # src/main/java/org/jabref/collab/EntryChange.java # src/main/java/org/jabref/collab/EntryDeleteChange.java # src/main/java/org/jabref/collab/FileUpdateListener.java # src/main/java/org/jabref/collab/StringAddChange.java # src/main/java/org/jabref/collab/StringChange.java # src/main/java/org/jabref/collab/StringNameChange.java # src/main/java/org/jabref/collab/StringRemoveChange.java # src/main/java/org/jabref/gui/BasePanel.java # src/main/java/org/jabref/gui/ClipBoardManager.java # src/main/java/org/jabref/gui/DefaultInjector.java # src/main/java/org/jabref/gui/DialogService.java # src/main/java/org/jabref/gui/EntryTypeDialog.java # src/main/java/org/jabref/gui/JabRefFrame.java # src/main/java/org/jabref/gui/actions/IntegrityCheckAction.java # src/main/java/org/jabref/gui/collab/ChangeScanner.java # src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java # src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java # src/main/java/org/jabref/gui/customjfx/CustomJFXPanel.java # src/main/java/org/jabref/gui/desktop/JabRefDesktop.java # src/main/java/org/jabref/gui/entryeditor/DeprecatedFieldsTab.java # src/main/java/org/jabref/gui/entryeditor/EntryEditor.css # src/main/java/org/jabref/gui/entryeditor/EntryEditor.java # src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java # src/main/java/org/jabref/gui/entryeditor/OptionalFields2Tab.java # src/main/java/org/jabref/gui/entryeditor/OptionalFieldsTab.java # src/main/java/org/jabref/gui/entryeditor/OtherFieldsTab.java # src/main/java/org/jabref/gui/entryeditor/RequiredFieldsTab.java # src/main/java/org/jabref/gui/entryeditor/SourceTab.java # src/main/java/org/jabref/gui/entryeditor/UserDefinedFieldsTab.java # src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java # src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java # src/main/java/org/jabref/gui/exporter/ExportAction.java # src/main/java/org/jabref/gui/exporter/ExportFileFilter.java # src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java # src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java # src/main/java/org/jabref/gui/fieldeditors/EditorValidator.java # src/main/java/org/jabref/gui/fieldeditors/FieldEditors.java # src/main/java/org/jabref/gui/fieldeditors/FileListEditorTransferHandler.java # src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java # src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java # src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java # src/main/java/org/jabref/gui/fieldeditors/MapBasedEditorViewModel.java # src/main/java/org/jabref/gui/groups/GroupDialog.java # src/main/java/org/jabref/gui/groups/GroupSidePane.java # src/main/java/org/jabref/gui/groups/GroupTreeController.java # src/main/java/org/jabref/gui/help/AboutDialogViewModel.java # src/main/java/org/jabref/gui/help/HelpAction.java # src/main/java/org/jabref/gui/importer/ImportFileFilter.java # src/main/java/org/jabref/gui/importer/ImportFormats.java # src/main/java/org/jabref/gui/maintable/MainTableSelectionListener.java # src/main/java/org/jabref/gui/preftabs/AppearancePrefsTab.java # src/main/java/org/jabref/gui/preftabs/EntryEditorPrefsTab.java # src/main/java/org/jabref/gui/preftabs/PreviewPrefsTab.java # src/main/java/org/jabref/gui/search/GlobalSearchBar.java # src/main/java/org/jabref/gui/util/BindingsHelper.java # src/main/java/org/jabref/gui/util/DefaultFileUpdateMonitor.java # src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java # src/main/java/org/jabref/gui/util/FileUpdateListener.java # src/main/java/org/jabref/gui/worker/CitationStyleToClipboardWorker.java # src/main/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGenerator.java # src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java # src/main/java/org/jabref/logic/citationstyle/CitationStyle.java # src/main/java/org/jabref/logic/citationstyle/CitationStyleCache.java # src/main/java/org/jabref/logic/citationstyle/CitationStyleGenerator.java # src/main/java/org/jabref/logic/exporter/BibTeXMLExporter.java # src/main/java/org/jabref/logic/exporter/ExportFormats.java # src/main/java/org/jabref/logic/exporter/IExportFormat.java # src/main/java/org/jabref/logic/exporter/MSBibExporter.java # src/main/java/org/jabref/logic/exporter/ModsExporter.java # src/main/java/org/jabref/logic/exporter/OpenDocumentSpreadsheetCreator.java # src/main/java/org/jabref/logic/exporter/OpenOfficeDocumentCreator.java # src/main/java/org/jabref/logic/exporter/TemplateExporter.java # src/main/java/org/jabref/logic/importer/ImportFormatReader.java # src/main/java/org/jabref/logic/importer/WebFetchers.java # src/main/java/org/jabref/logic/importer/fetcher/IacrEprintFetcher.java # src/main/java/org/jabref/logic/integrity/FieldCheckers.java # src/main/java/org/jabref/logic/integrity/IntegrityCheck.java # src/main/java/org/jabref/logic/journals/JournalAbbreviationRepository.java # src/main/java/org/jabref/logic/shared/DBMSProcessor.java # src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java # src/main/java/org/jabref/logic/util/FileType.java # src/main/java/org/jabref/logic/util/JavaVersion.java # src/main/java/org/jabref/logic/util/io/CiteKeyBasedFileFinder.java # src/main/java/org/jabref/logic/util/io/FileFinder.java # src/main/java/org/jabref/logic/util/io/FileUtil.java # src/main/java/org/jabref/logic/util/io/RegExpBasedFileFinder.java # src/main/java/org/jabref/model/auxparser/AuxParserResult.java # src/main/java/org/jabref/model/database/BibDatabaseContext.java # src/main/java/org/jabref/model/entry/FieldProperty.java # src/main/java/org/jabref/model/pdf/FileAnnotation.java # src/main/java/org/jabref/model/util/FileUpdateListener.java # src/main/java/org/jabref/preferences/CustomExportList.java # src/main/java/org/jabref/preferences/JabRefPreferences.java # src/test/java/org/jabref/TestArchitectureTests.java # src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java # src/test/java/org/jabref/gui/importer/EntryFromFileCreatorManagerTest.java # src/test/java/org/jabref/logic/bibtexkeypattern/BibtexKeyGeneratorTest.java # src/test/java/org/jabref/logic/bibtexkeypattern/MakeLabelWithDatabaseTest.java # src/test/java/org/jabref/logic/exporter/MsBibExportFormatTest.java # src/test/java/org/jabref/logic/importer/ImportFormatReaderTestParameterless.java # src/test/java/org/jabref/logic/importer/fetcher/ArXivTest.java # src/test/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystemTest.java # src/test/java/org/jabref/logic/importer/fetcher/CrossRefTest.java # src/test/java/org/jabref/logic/importer/fetcher/DBLPFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/DiVATest.java # src/test/java/org/jabref/logic/importer/fetcher/DoiFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/FulltextFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/GvkFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/IacrEprintFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/IsbnFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/IsbnViaChimboriFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/IsbnViaEbookDeFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/LibraryOfCongressTest.java # src/test/java/org/jabref/logic/importer/fetcher/MedlineFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/MrDLibFetcherTest.java # src/test/java/org/jabref/logic/importer/fetcher/SpringerLinkTest.java # src/test/java/org/jabref/logic/importer/fetcher/TitleFetcherTest.java # src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java # src/test/java/org/jabref/logic/importer/fileformat/FreeCiteImporterTest.java # src/test/java/org/jabref/logic/l10n/LocalizationConsistencyTest.java # src/test/java/org/jabref/logic/shared/DBMSConnectionTest.java # src/test/java/org/jabref/logic/shared/DBMSProcessorTest.java # src/test/java/org/jabref/logic/shared/DBMSSynchronizerTest.java # src/test/java/org/jabref/logic/shared/DBMSTypeTest.java # src/test/java/org/jabref/logic/shared/SynchronizationTestEventListener.java # src/test/java/org/jabref/logic/shared/SynchronizationTestSimulator.java # src/test/java/org/jabref/logic/shared/TestConnector.java # src/test/java/org/jabref/logic/util/BracketedPatternTest.java # src/test/java/org/jabref/logic/util/io/CiteKeyBasedFileFinderTest.java # src/test/java/org/jabref/logic/util/io/RegExpBasedFileFinderTests.java # src/test/java/org/jabref/testutils/category/FetcherTest.java
JabRef · Feb 6, 2018 · 06685dd · 06685dd
2 parents c91fe49 + e33bd58
commit 06685dd
Show file tree

Hide file tree

Showing 532 changed files with 7,095 additions and 6,819 deletions.
diff --git a/.gitattributes b/.gitattributes
@@ -1,8 +1,9 @@
 # unix  line endings at unix files
-gradlew eol=lf
-*.sh eol=lf
+gradlew text eol=lf
+*.sh text eol=lf
+*.bat text eol=crlf
 
-AUTHORS eol=lf
+AUTHORS text eol=lf
 
 # ensure that line endings of *.java and *.properties are normalized
 *.properties text

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.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`?
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,10 +12,30 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- 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 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 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)
+- 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)
 
 ### 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)
+- 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.
 
 ### 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.
 
 
 
@@ -68,7 +88,7 @@ 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)
@@ -77,6 +97,7 @@ 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)
@@ -111,7 +132,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - We fixed an issue where the same Java Look and Feel would be listed more than once in the Preferences. [#3391](https://github.com/JabRef/jabref/issues/3391)
  - We fixed an issue where errors in citation styles triggered an exception when opening the preferences dialog. [#3389](https://github.com/JabRef/jabref/issues/3389)
  - We fixed an issue where entries were displayed twice after insertion into a shared database. [#3164](https://github.com/JabRef/jabref/issues/3164)
- - We improved the auto link algorithm so that files starting with a similar key are no longer found (e.g, `Einstein1902` vs `Einstein1902a`). [#3472](https://github.com/JabRef/jabref/issues/3472) 
+ - We improved the auto link algorithm so that files starting with a similar key are no longer found (e.g, `Einstein1902` vs `Einstein1902a`). [#3472](https://github.com/JabRef/jabref/issues/3472)
  - We fixed an issue where special fields (such as `printed`) could not be cleared when syncing special fields via the keywords. [#3432](https://github.com/JabRef/jabref/issues/3432)
  - We fixed an issue where the tooltip of the global search bar showed html tags instead of formatting the text. [#3381](https://github.com/JabRef/jabref/issues/3381)
  - We fixed an issue where timestamps were not updated for changed entries. [#2810](https://github.com/JabRef/jabref/issues/2810)
@@ -124,6 +145,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - We fixed an issue where fetched entries from the ACM fetcher could not be imported. [#3500](https://github.com/JabRef/jabref/issues/3500)
  - We fixed an issue where custom data in combobox fields in the entry editor was not saved. [#3538](https://github.com/JabRef/jabref/issues/3538)
  - We fixed an issue where automatically found files were not added with a relative paths when the bib file is in the same directory as the files. [#3476](https://github.com/JabRef/jabref/issues/3476)
+ - We improved the key generator to remove certain illegal characters such as colons or apostrophes. [#3359](https://github.com/JabRef/jabref/issues/3359)
 
 
 ## [4.0] - 2017-10-04

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -6,6 +6,7 @@ Take a look at GitHub's excellent [help documentation] for a detailed explanatio
 We also have [code howtos](https://github.com/JabRef/jabref/wiki/Code-Howtos) and [guidelines for setting up a local workspace](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
 
 In case you have any question, do not hesitate to write one of our [JabRef developers](https://github.com/orgs/JabRef/teams/developers) an email.
+We should also be online at [gitter](https://gitter.im/JabRef/jabref).
 
 
 ## Formal requirements for a pull request
@@ -65,28 +66,45 @@ 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
+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/>.
+
+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).
 
 

diff --git a/DEVELOPERS b/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)