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[cdmlib.git] / .gitattributes
diff --git a/.gitattributes b/.gitattributes
index 81975046a2b4eaba78d8205776945160d6a47b9d..61db608181324cb628b7d154a162822cf0b6eda0 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -2,9 +2,11 @@
 /INSTALL.TXT -text
 /LICENSE.TXT -text
 app-import/pom.xml -text
-app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelImportActivator.java -text
-app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelSources.java -text
-app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/CdmDestinations.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/BerlinModelImportActivator.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/BerlinModelSources.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CdmDestinations.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/app/viennaImport/Activator.java -text
+app-import/src/main/resources/Asteraceae[!!-~]Specimen[!!-~]Images[!!-~]Vienna.xls -text
 app-import/src/main/resources/log4j.properties -text
 cdmlib-commons/LICENSE.TXT -text
 cdmlib-commons/README.TXT -text
@@ -30,6 +32,9 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelReferenceIO.j
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonIO.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonNameIO.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTransformer.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/CdmBooleanMapper.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/CdmIOMapperBase.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/CdmStringMapper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/ImportHelper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/MapWrapper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/source/Source.java -text
@@ -54,10 +59,8 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/TeamOrPersonBase.java -t
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/package.html -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/AnnotatableEntity.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Annotation.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/AudioFile.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/CdmBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/EmbeddableLanguageString.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/EventBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Extension.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ExtensionType.java -text
@@ -65,34 +68,28 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Figure.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ICdmBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IEvent.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ILoadableTerm.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IMediaDocumented.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IOriginalSource.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IParsable.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IReferencedEntity.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IRelated.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IdentifyableMediaEntity.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ImageFile.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Keyword.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Language.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/LanguageString.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/LanguageStringBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Marker.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MarkerType.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Media.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MediaInstance.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MovieFile.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageSet.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/NoDefinedTermClassException.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/OrderedTermBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/OrderedTermVocabulary.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/OriginalSource.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedEntityBase.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ReferencedMedia.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/RelationshipBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/RelationshipTermBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Representation.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Rights.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/RightsTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/TermBase.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/TermLanguageComparator.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/TermVocabulary.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/TimePeriod.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/VersionableEntity.java -text
@@ -140,6 +137,16 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/Point.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/ReferenceSystem.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/WaterbodyOrCountry.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/package.html -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/AudioFile.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/IMediaDocumented.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/IdentifyableMediaEntity.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/ImageFile.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/Media.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/MediaInstance.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/MovieFile.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/ReferencedMedia.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/Rights.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/RightsTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/GenBankAccession.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Locus.java -text
@@ -155,6 +162,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/HybridRelationshipType.ja
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationship.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NameRelationshipType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NameTypeDesignation.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalCode.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatus.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NomenclaturalStatusType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NonViralName.java -text
@@ -168,7 +176,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/package.html -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/Collection.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DerivationEvent.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DerivationEventType.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DerivedUnit.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DerivedUnitBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DeterminationEvent.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/DeterminationModifier.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/occurrence/FieldObservation.java -text
@@ -230,15 +238,17 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/TeamDefaultCacheStrat
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/ZooNameDefaultCacheStrategy.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/exceptions/StringNotParsableException.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/exceptions/UnknownCdmTypeException.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/ITaxonNameParser.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/TaxonNameParserBotanicalNameImpl.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/TaxonNameParserZoologicalNameImpl.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/INonViralNameParser.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java -text
+cdmlib-model/src/main/resources/log4j.properties -text
 cdmlib-model/src/main/resources/terms/Continent.csv -text
 cdmlib-model/src/main/resources/terms/DerivationEventType.csv -text
 cdmlib-model/src/main/resources/terms/HybridRelationshipType.csv -text
 cdmlib-model/src/main/resources/terms/Language.csv -text
 cdmlib-model/src/main/resources/terms/MarkerType.csv -text
 cdmlib-model/src/main/resources/terms/NameRelationshipType.csv -text
+cdmlib-model/src/main/resources/terms/NamedAreaType.csv -text
+cdmlib-model/src/main/resources/terms/NomenclaturalCode.csv -text
 cdmlib-model/src/main/resources/terms/NomenclaturalStatusType.csv -text
 cdmlib-model/src/main/resources/terms/README.TXT -text
 cdmlib-model/src/main/resources/terms/Rank.csv -text
@@ -288,8 +298,9 @@ cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonBaseTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/BotanicNameCacheStrategyTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/ZoologicalNameCacheStrategyTest.java -text
-cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/TaxonNameParserBotanicalNameImplTest.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImplTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/TestModel.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/TestSpecimen.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/strategy/TestNameCacheStrategies.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/strategy/TestTaxonNameParserBotanicalNameImpl.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/suite/CdmTestSuite.java -text
@@ -306,10 +317,12 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/DataSourceNotFoundExc
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/DatabaseTypeEnum.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/DbSchemaValidation.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/ICdmDataSource.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/LocalH2.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/LocalHsqldb.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/VocabularyStoreImpl.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/DatabaseTypeBase.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/Db2DatabaseType.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/H2DatabaseType.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/HSqlDbDatabaseType.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/IDatabaseType.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/MySQLDatabaseType.java -text
@@ -339,6 +352,7 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxo
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/name/ITaxonNameDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/reference/IReferenceDao.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/fetch/CdmFetch.java -text
 cdmlib-persistence/src/main/resources/eu/etaxonomy/cdm/cdm.datasources.xml -text
 cdmlib-persistence/src/main/resources/eu/etaxonomy/cdm/hsql-datasource.xml -text
 cdmlib-persistence/src/main/resources/eu/etaxonomy/cdm/persistence.xml -text
@@ -381,7 +395,7 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/IBaseSTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/IReferenceSTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/IdentifiedString.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/InteractionFeatureSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/LocalisedTermTO.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/LocalisedTermSTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/MediaInstanceSTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/MediaSTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/MediaTO.java -text
@@ -404,6 +418,7 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/TaxonSTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/TaxonTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/TreeNode.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/AssemblerBase.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/LocalisedTermAssembler.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/MediaAssembler.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/NameAssembler.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/ReferenceAssembler.java -text
@@ -434,6 +449,8 @@ cdmlib-services/LICENSE.TXT -text
 cdmlib-services/README.TXT -text
 cdmlib-services/pom.xml -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationController.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationDefaultConfiguration.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/ICdmApplicationConfiguration.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSaveFileSystemXmlApplicationContext.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSaveGenericApplicationContext.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSavePathMatchingResourcePatternResolver.java -text
@@ -462,6 +479,7 @@ cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/Datasource.java -te
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestDatabase.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestService.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestTaxonFunction.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/integration/CreateDataTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/integration/TermLoaderIntegrationTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/suite/CdmTestSuite.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/unit/CdmUnitTestBase.java -text
@@ -508,6 +526,7 @@ eclipse-plugin/hibernate-annotations.jar -text
 eclipse-plugin/hibernate-commons-annotations.jar -text
 eclipse-plugin/hibernate-validator.jar -text
 eclipse-plugin/hibernate3.jar -text
+eclipse-plugin/hibernate3src.zip -text
 eclipse-plugin/hsqldb.jar -text
 eclipse-plugin/javassist.jar -text
 eclipse-plugin/jaxb-api.jar -text
@@ -519,6 +538,7 @@ eclipse-plugin/jta.jar -text
 eclipse-plugin/jtds-1.2.2.jar -text
 eclipse-plugin/junit-4.4.jar -text
 eclipse-plugin/log4j-1.2.14.jar -text
+eclipse-plugin/log4j-1.2.14src.zip -text
 eclipse-plugin/msbase-2000.3.jar -text
 eclipse-plugin/mssqlserver-2000.3.jar -text
 eclipse-plugin/msutil-2000.3.jar -text
@@ -562,10 +582,6 @@ libraryTesterApplication/lib/aopalliance-1.0.jar -text
 libraryTesterApplication/lib/asm-attrs.jar -text
 libraryTesterApplication/lib/asm.jar -text
 libraryTesterApplication/lib/aspectjrt-1.5.2a.jar -text
-libraryTesterApplication/lib/cdmlib-commons-0.4.7.jar -text
-libraryTesterApplication/lib/cdmlib-model-0.4.7.jar -text
-libraryTesterApplication/lib/cdmlib-persistence-0.4.7.jar -text
-libraryTesterApplication/lib/cdmlib-services-0.4.7.jar -text
 libraryTesterApplication/lib/cglib-2.1.3.jar -text
 libraryTesterApplication/lib/commons-collections-2.1.1.jar -text
 libraryTesterApplication/lib/commons-logging-1.0.4.jar -text
@@ -603,6 +619,8 @@ libraryTesterApplication/lib/spring-test-2.5.jar -text
 libraryTesterApplication/lib/spring-tx-2.5.jar -text
 libraryTesterApplication/lib/xercesImpl.jar -text
 libraryTesterApplication/lib/xml-apis.jar -text
+libraryTesterApplication/src/CdmDestinations.java -text
+libraryTesterApplication/src/Profiling.java -text
 libraryTesterApplication/src/testJar/TestJarMain.java -text
 musiclib-hibernatetest/listAnnotatedClasses.py -text
 musiclib-hibernatetest/pom.xml -text