- change visibility of createTestDataSet to public

[cdmlib.git] / .gitattributes

diff --git a/.gitattributes b/.gitattributes
index a7a2fbefc11667ce69120fe32062cc8f42b07cd9..0afd937fddfdbccfd75b3994e225026dec9a860f 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -479,7 +479,6 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXXMLFieldGetter.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/CdmOneToManyXmlMapper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/CdmSingleAttributeRDFMapperBase.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/CdmSingleAttributeXmlMapperBase.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/CdmTextElementMapper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/CdmUnclearMapper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfImportBase.java -text
@@ -491,6 +490,7 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTaxonNameImport.java -t
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTaxonNameRelationsImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTaxonRelationsImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfTransformer.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/CdmSingleAttributeXmlMapperBase.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/DefaultTcsXmlPlaceholders.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/ITcsXmlPlaceholderClass.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/TcsXmlTransformer.java -text
@@ -661,10 +661,12 @@ cdmlib-model/LICENSE.TXT -text
 cdmlib-model/README.TXT -text
 cdmlib-model/pom.xml -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/aspectj/PropertyChangeAspect.aj -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/BigDecimalUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/DOIUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/EnumUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/HibernateProxyHelper.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/PartialUserType.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/ShiftUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/URIUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/UUIDUserType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/WSDLDefinitionUserType.java -text
@@ -761,6 +763,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MarkerType.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageText.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/MultilanguageTextHelper.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/OrderedTerm.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/OriginalSourceBase.java -text
@@ -788,7 +791,6 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/init/TermLoader.java -t
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/init/TermNotFoundException.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/package-info.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/package.html -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/AbsenceTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/CategoricalData.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/CommonTaxonName.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/DescriptionBase.java -text
@@ -810,8 +812,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/MultiAccessKey.jav
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/NaturalLanguageTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/PolytomousKey.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/PolytomousKeyNode.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTermBase.java -text
-cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/PresenceTerm.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/QuantitativeData.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/SpecimenDescription.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/State.java -text
@@ -852,6 +853,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/metadata/CdmPreference.java -t
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/metadata/PreferencePredicate.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/metadata/PreferenceSubject.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Amplification.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/AmplificationResult.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Cloning.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaQuality.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java -text
@@ -861,6 +863,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Sequence.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/SequenceDirection.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/SequenceString.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/SingleRead.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/SingleReadAlignment.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/package-info.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/package.html -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/BacterialName.java -text
@@ -1067,7 +1070,6 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/validation/constraint/StubValidator.
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/validation/constraint/TaxonNameCannotBeAcceptedAndSynonymValidator.java -text
 cdmlib-model/src/main/resources/ValidationMessages.properties -text
 cdmlib-model/src/main/resources/log4j.properties -text
-cdmlib-model/src/main/resources/terms/AbsenceTerm.csv -text
 cdmlib-model/src/main/resources/terms/AnnotationType.csv -text
 cdmlib-model/src/main/resources/terms/Continent.csv -text
 cdmlib-model/src/main/resources/terms/Country.csv -text
@@ -1075,6 +1077,7 @@ cdmlib-model/src/main/resources/terms/DerivationEventType.csv -text
 cdmlib-model/src/main/resources/terms/DeterminationModifier.csv -text
 cdmlib-model/src/main/resources/terms/DnaMarkerChloroplast.csv -text
 cdmlib-model/src/main/resources/terms/DnaMarkerEukaryote.csv -text
+cdmlib-model/src/main/resources/terms/DnaQualityType.csv -text
 cdmlib-model/src/main/resources/terms/ExtensionType.csv -text
 cdmlib-model/src/main/resources/terms/Feature.csv -text
 cdmlib-model/src/main/resources/terms/FormerCountries -text
@@ -1097,7 +1100,7 @@ cdmlib-model/src/main/resources/terms/NomenclaturalCode.csv -text
 cdmlib-model/src/main/resources/terms/NomenclaturalStatusType.csv -text
 cdmlib-model/src/main/resources/terms/NomenclaturalStatusTypeIczn.csv -text
 cdmlib-model/src/main/resources/terms/PlantKindOfUnit.csv -text
-cdmlib-model/src/main/resources/terms/PresenceTerm.csv -text
+cdmlib-model/src/main/resources/terms/PresenceAbsenceTerm.csv -text
 cdmlib-model/src/main/resources/terms/PreservationMethod.csv -text
 cdmlib-model/src/main/resources/terms/README.TXT -text
 cdmlib-model/src/main/resources/terms/Rank.csv -text
@@ -1121,6 +1124,7 @@ cdmlib-model/src/main/resources/update/update_r2.1.2.2_r2.4.1.2.mysql.sql -text
 cdmlib-model/src/main/resources/update/update_term_r2.4.2.1-r2.4.2.2.mysql.sql -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/aspectj/PropertyChangeTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/datagenerator/TaxonGenerator.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/hibernate/BigDecimalUserTypeTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/DatabaseInitialiser.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/agent/AgentValidationTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/agent/InstitutionalMembershipTest.java -text
@@ -1149,7 +1153,7 @@ cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/description/DescriptionElement
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/description/FeatureTreeTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/description/PolytomousKeyNodeTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/description/PolytomousKeyTest.java -text
-cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTermBaseTest.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/description/PresenceAbsenceTermTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/description/TextDataTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/NamedAreaTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/PointTest.java -text
@@ -1159,6 +1163,7 @@ cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/media/MediaUtilsTest.java -tex
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/metadata/CdmMetaDataTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/metadata/CdmPreferenceTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/metadata/PreferenceSubjectTest.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/molecular/AmplificationTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/molecular/MolecularTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BacterialNameTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/name/BotanicalNameTest.java -text
@@ -1207,6 +1212,7 @@ cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserIm
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/ParserProblemTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/TimePeriodParserTest.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/location/CoordinateConverterTest.java -text
+cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/BigDecimalTesting.java -text
 cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/TestFullReferenceParser.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/TestRegExs.java -text
@@ -1323,6 +1329,7 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/Specime
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/TermUpdater_31_33.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v31_33/TermVocabularyRepresentationUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v33_34/SchemaUpdater_331_34.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v33_34/SchemaUpdater_34_341.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v33_34/TermUpdater_33_34.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v33_34/UsernameConstraintUpdater.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/IAlternativeSpellingSuggestionParser.java -text
@@ -2086,6 +2093,7 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/CdmObjectNonExisting
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/DataController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/MetadataController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/Utils.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/SpringContextHelper.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/VaadinConfigurer.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/VaadinUI.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/CellRendererTable.java -text
@@ -2098,6 +2106,7 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/LoginForm.
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/TaxonTableDTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/data/LazyLoadedContainer.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/data/LazyLoadedIndexedContainer.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/service/CdmVaadinServlet.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/service/VaadinAuthenticationService.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/uiset/disabled/DefaultView.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/uiset/redlist/views/BfnView.java -text
@@ -2173,7 +2182,7 @@ cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/ICdmApplicationCo
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/MonitoredGenericApplicationContext.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/MonitoredListableBeanFactory.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/cache/CdmCacher.java -text
-cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/cache/CdmDaoCacher.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/cache/CdmTermCacher.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/conversation/ConversationHolder.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/conversation/ConversationHolderMock.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/conversation/IConversationEnabled.java -text
@@ -2276,6 +2285,7 @@ cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/IdentifiableSe
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/IncludedTaxonConfiguration.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/MatchingTaxonConfigurator.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/NameDeletionConfigurator.java -text
+cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/SpecimenDeleteConfigurator.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/SynonymDeletionConfigurator.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/TaxonBaseDeletionConfigurator.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/config/TaxonDeletionConfigurator.java -text
@@ -2371,7 +2381,7 @@ cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/IdentifiableServiceBa
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/IdentificationKeyGeneratorTTT.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/NameServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/NaturalLanguageGeneratorTest.java -text
-cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/OccurenceServiceTest.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/PolytomousKeyNodeServiceTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/PolytomousKeyServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/PreferenceServiceImplTest.java -text
@@ -2435,6 +2445,9 @@ cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/IdentifiableServ
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/IdentifiableServiceBaseTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/MediaDaoImplTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/NameServiceImplTest.xml -text
+cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/OccurenceServiceTest.move.xml -text
+cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/OccurrenceService.loadData.xml -text
+cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/OccurrenceServiceTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/OregonScientificDS6639-DSC_0307-small.jpg -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/OregonScientificDS6639-DSC_0307-small.tif -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/PolytomousKeyServiceImplTest.xml -text