add a bit more bidirectionality to DnaSample/Sequence

[cdmlib.git] / .gitattributes

diff --git a/.gitattributes b/.gitattributes
index 1699806bbb763c98bca2d5ff48a69ee5ffa01ed0..7115efc8efe02fdb354b31443831b06680f2ae14 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -209,6 +209,7 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/IDbImportTransformed.
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/IDbImportTransformer.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/IInputTransformer.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/IMappingImport.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/IRdfMapper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/IXmlMapper.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/InputTransformerBase.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/MultipleAttributeMapperBase.java -text
@@ -442,6 +443,7 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.ja
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206ImportConfigurator.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206ImportState.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206XMLFieldGetter.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Identification.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/ExtensionTypeExcelImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/NamedAreaLevelExcelImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/NamedAreaLevellRow.java -text
@@ -476,6 +478,7 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXModsExtractor.java
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXTreatmentExtractor.java -text
 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
@@ -638,7 +641,9 @@ cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/sdd/varanusSDD_RatingExample_mo
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/sdd/wrongSDD.xml -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/ABCDImportTestCalvumPart1.xml -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/ABCDImportTestCalvumPart2.xml -text
+cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/Campanula_ABCD_import_3_taxa_11_units.xml -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportConfiguratorTest-input.xml -text
+cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportConfiguratorTest.doInvoke2.xml -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportConfiguratorTest.xml -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/excel/in/ExcelImportConfiguratorTest-input.xls -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/excel/in/ExcelSpecimenImportExampleTest-input.xls -text
@@ -777,6 +782,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/VocabularyEnum.java -te
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/WrongTermTypeException.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/init/ITermInitializer.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/init/ITermLoader.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/init/MockCdmCacher.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/init/TermLoader.java -text
 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
@@ -994,6 +1000,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/NomRefDefau
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/ReferenceDefaultCacheStrategy.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/SectionDefaultCacheStrategy.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/ThesisDefaultCacheStrategy.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/WebPageDefaultCacheStrategy.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/taxon/TaxonBaseDefaultCacheStrategy.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
@@ -1070,6 +1077,7 @@ cdmlib-model/src/main/resources/terms/InstitutionType.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/MeasurementUnit.csv -text
+cdmlib-model/src/main/resources/terms/MediaSpecimenKindOfUnit.csv -text
 cdmlib-model/src/main/resources/terms/Modifier.csv -text
 cdmlib-model/src/main/resources/terms/NameFeature.csv -text
 cdmlib-model/src/main/resources/terms/NameRelationshipType.csv -text
@@ -1555,6 +1563,7 @@ cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/hibenate/permissio
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/hibernate/CacheStrategyGeneratorTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/hibernate/CdmDeleteListenerTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/hibernate/replace/ReferringObjectMetadataFactoryTest.java -text
+cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/profiler/ProfileController.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/profiler/ProfilerController.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/test/function/Datasource.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/test/function/TestCdmApplicationUtils.java -text
@@ -1643,6 +1652,9 @@ cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.testFindDeleted.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.xml -text
+cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonNodeDaoHibernateImplTest.testSortindexForJavassist-result.xml -text
+cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonNodeDaoHibernateImplTest.testSortindexForJavassist.xml -text
+cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonNodeDaoHibernateImplTest.testSortindexForJavassist2-result.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonNodeDaoHibernateImplTest.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/dao/hibernate/view/AuditEventDaoTest.xml -text
 cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/persistence/hibernate/CacheStrategyGeneratorTest.testOnSaveOrUpdateAgents-result.xml -text
@@ -1716,6 +1728,9 @@ cdmlib-remote-webapp/ide/eclipse/cdmlib-remote[!!-~]-[!!-~]remote[!!-~]debug[!!-
 cdmlib-remote-webapp/ide/eclipse/cdmlib-remote-webapp[!!-~]-[!!-~]profile.launch -text
 cdmlib-remote-webapp/ide/eclipse/cdmlib-remote-webapp[!!-~]-[!!-~]run.launch -text
 cdmlib-remote-webapp/pom.xml -text
+cdmlib-remote-webapp/src/main/java/eu/etaxonomy/cdm/remote/config/PreloadedBeans.java -text
+cdmlib-remote-webapp/src/main/java/eu/etaxonomy/cdm/remote/config/SpringMVCConfig.java -text
+cdmlib-remote-webapp/src/main/java/eu/etaxonomy/cdm/remote/vaadin/redlist/wigetset/AppWidgetSet.gwt.xml -text
 cdmlib-remote-webapp/src/main/resources/log4j.properties -text
 cdmlib-remote-webapp/src/main/webapp/VAADIN/themes/mytheme/favicon.ico -text
 cdmlib-remote-webapp/src/main/webapp/VAADIN/themes/mytheme/icons/32/Thumbs.db -text
@@ -1785,7 +1800,6 @@ cdmlib-remote-webapp/src/main/webapp/WEB-INF/datasources/empty-default-datasourc
 cdmlib-remote-webapp/src/main/webapp/WEB-INF/datasources/p6spy.xml -text
 cdmlib-remote-webapp/src/main/webapp/WEB-INF/datasources/routing-datasource.xml -text
 cdmlib-remote-webapp/src/main/webapp/WEB-INF/json-views.xml -text
-cdmlib-remote-webapp/src/main/webapp/WEB-INF/jsp/index.jsp -text
 cdmlib-remote-webapp/src/main/webapp/WEB-INF/oai-views.xml -text
 cdmlib-remote-webapp/src/main/webapp/WEB-INF/rdf-views.xml -text
 cdmlib-remote-webapp/src/main/webapp/WEB-INF/web.xml -text
@@ -1808,6 +1822,7 @@ cdmlib-remote-webapp/src/main/webapp/css/jquery-ui/images/ui-icons_888888_256x24
 cdmlib-remote-webapp/src/main/webapp/css/jquery-ui/images/ui-icons_cd0a0a_256x240.png -text
 cdmlib-remote-webapp/src/main/webapp/css/jquery-ui/jquery-ui-1.8.23.custom.css -text
 cdmlib-remote-webapp/src/main/webapp/csv/csvExport.jsp -text
+cdmlib-remote-webapp/src/main/webapp/index.html -text
 cdmlib-remote-webapp/src/main/webapp/js/cdm_ws_progress.js -text
 cdmlib-remote-webapp/src/main/webapp/js/csv_export.js -text
 cdmlib-remote-webapp/src/main/webapp/js/jquery-1.7.2.min.js -text
@@ -1892,6 +1907,7 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonListControll
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonNodeController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonNodeListController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalController.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalListController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TermController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TermListController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/VocabularyController.java -text
@@ -2061,15 +2077,22 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/MetadataController.j
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/Utils.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
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/ClassificationSelectionForm.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/DemoTaxonTable.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/DetailWindow.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/DistributionSelectionForm.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/HorizontalToolbar.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/LoginForm.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/components/TaxonTableDTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/service/AuthenticationService.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/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
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/uiset/redlist/views/ClassificationSelectorView.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/uiset/redlist/views/DashBoardView.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/uiset/redlist/views/DistributionSelectorView.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/uiset/redlist/views/ErrorView.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/uiset/redlist/views/LoginView.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/vaadin/widgetset/AppWidgetSet.gwt.xml -text
@@ -2109,6 +2132,7 @@ cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote/dto/tdwg/mappings.xml -
 cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote/ehcache.xml -text
 cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote/json/jsonConfigurations.xml -text
 cdmlib-remote/src/main/resources/log4j.properties -text
+cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/controller/util/CdmAntPathMatcherTest.java -text
 cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/dto/assembler/lsid/AssemblerTest.java -text
 cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/service/AuthorityControllerTest.java -text
 cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/service/DataControllerTest.java -text
@@ -2138,6 +2162,7 @@ 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/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
@@ -2318,6 +2343,8 @@ cdmlib-services/src/main/resources/wsdl/LSIDDataServiceHTTPBindings.wsdl -text
 cdmlib-services/src/main/resources/wsdl/LSIDDataServiceSOAPBindings.wsdl -text
 cdmlib-services/src/main/resources/wsdl/LSIDPortTypes.wsdl -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/application/FirstDataInserterTest.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/cache/CdmCacherTest.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/cache/MockCdmCacher.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacadeCacheStrategyTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacadeFieldUnitCacheStrategyTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacadeTest.java -text
@@ -2327,6 +2354,7 @@ cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/CommonServiceImplTest
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/DescriptionServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/FeatureNodeServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/GroupServiceImplTest.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/HandlingCdmEntitiesTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/IdentifiableServiceBaseTest.java -text
 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
@@ -2346,6 +2374,7 @@ cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceSearchTes
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TermServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TransmissionEngineDistributionTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/UserAndGroupServiceImplTest.java -text
+cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/VocabularyServiceImplTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/lsid/LSIDAuthorityServiceTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/lsid/LSIDDataServiceTest.java -text
 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/lsid/LSIDMetadataServiceTest.java -text
@@ -2389,6 +2418,7 @@ cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/BlankDataSet.xml
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/ClassificationServiceImplTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/CommonServiceImplTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/FeatureNodeServiceImplTest-indexing.xml -text
+cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/HandlingCdmEntitiesTest.xml -text
 cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/IdentifiableServiceBaseTest.testUpdateTitleCache-result.xml -text
 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