Fix 2633 saving creates new database#3674
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tobiasdiez merged 5 commits intoJan 30, 2018
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lenhard
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Jan 30, 2018
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Thanks for your PR, this looks good to me!
Just one note: Could you please merge the current master into your branch? Some (unrelated) tests are still failing and these are repaired on master. I would like to see a successful travis build before we merge this.
koppor
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Jan 30, 2018
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@lenhard Thanks for your review. Have performed a merge so hopefully that should be fixed now. |
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The build still fails but so does the master (with the same failing tests). I thus merge this PR now. Thanks for your contribution! |
Siedlerchr
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Feb 6, 2018
* 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
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Fix #2633 using the method suggested by @koppor. Switching from Files.copy to Files.write now simply overwrites the content of the file, leaving any hard links intact.