removing deprecated DTOs

[cdmlib.git] / .gitattributes

diff --git a/.gitattributes b/.gitattributes
index a1d476822db248e474821beeb61e1a392711d983..b7ca3835172c57dfdcced55227629da4ba2a7598 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,6 +1,7 @@
 * text=auto !eol
 /INSTALL.TXT -text
 /LICENSE.TXT -text
+app-import/build.xml -text
 app-import/pom.xml -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/abcdImport/SpecimenImport.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/abcdImport/SynthesysCacheActivator.java -text
@@ -1001,6 +1002,7 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/SimpleSpecimen.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXDescriptionImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXImportConfigurator.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXImportState.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXModsImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXNomenclatureImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXTransformer.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsrdf/CdmOneToManyXmlMapper.java -text
@@ -1380,11 +1382,11 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/JournalDefa
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/NomRefDefaultCacheStrategyBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/reference/StrictReferenceBaseDefaultCacheStrategy.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/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
 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/java/eu/etaxonomy/cdm/strategy/taxon/TaxonBaseDefaultCacheStrategy.java -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
@@ -1489,6 +1491,7 @@ cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/unit/EntityTestBase.java -text
 cdmlib-model/src/test/resources/log4j.properties -text
 cdmlib-persistence/LICENSE.TXT -text
 cdmlib-persistence/README.TXT -text
+cdmlib-persistence/build.xml -text
 cdmlib-persistence/pom.xml -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationUtils.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/CdmDataSource.java -text
@@ -1620,7 +1623,6 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/hibernate/SaveEnti
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/hibernate/UpdateEntityListener.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/query/MatchMode.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/query/OrderHint.java -text
-cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/query/SelectMode.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/view/IAuditEventDao.java -text
 cdmlib-persistence/src/main/java/org/hibernate/dialect/H2CorrectedDialect.java -text
 cdmlib-persistence/src/main/java/org/hibernate/dialect/HSQLCorrectedDialect.java -text
@@ -1774,6 +1776,7 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/FeatureListContro
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/FeatureTreeListController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/FeatureTreeListPortalController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/HttpStatusMessage.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/ManagementController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/MediaController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/MediaListController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/NameController.java -text
@@ -1787,55 +1790,13 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/ReferencePortalCo
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonListController.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/TaxonomicTreeController.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TermListConroller.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/interceptor/ContentNegociationHandlerInterceptor.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/interceptor/DatasourceContextHandlerInterceptor.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/interceptor/LocaleContextHandlerInterceptor.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/AnnotationElementSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/AnnotationSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/AnnotationTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/AssociationFeatureSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/BaseSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/BaseTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/DescriptionElementSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/DescriptionTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/DistributionSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/FeatureNodeTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/FeatureSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/FeatureTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/FeatureTreeSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/FeatureTreeTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/HomotypicTaxonGroupSTO.java -text
-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/LocalisedTermSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/MediaRepresenationPartSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/MediaRepresentationSTO.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
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/NameRelationshipTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/NameSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/NameTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/NameTypeDesignationSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/ReferenceSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/ReferenceTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/ReferencedEntityBaseSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/ResultSetPageSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/RightsSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/SpecimenSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/SpecimenTypeDesignationSTO.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/SynonymRelationshipTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/TagEnum.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/TaggedText.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/TaxonRelationshipTO.java -text
-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/TypeDesignationSTO.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/DozerBeanMapperFactoryBean.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/converter/DateTimeConverter.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/assembler/converter/HibernateProxyFieldMapper.java -text
@@ -1862,6 +1823,7 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/tdwg/voc/TaxonRelationsh
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/dto/tdwg/voc/Team.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/editor/LSIDAuthorityPropertyEditor.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/editor/LSIDPropertyEditor.java -text
+cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/editor/NamedAreaPropertyEditor.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/editor/RankPropertyEditor.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/editor/UUIDPropertyEditor.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/exception/CdmExceptionResolver.java -text
@@ -1892,7 +1854,6 @@ cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/l10n/LocaleContext.java -tex
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/AuthorityController.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/CdmObjectNonExisting.java -text
 cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/DataController.java -text
-cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/service/ManagementController.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/view/BaseView.java -text
@@ -1908,18 +1869,17 @@ cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote.xml -text
 cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote/dto/tdwg/mappings-deep.xml -text
 cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote/dto/tdwg/mappings-shallow.xml -text
 cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote/dto/tdwg/mappings.xml -text
-cdmlib-remote/src/main/resources/eu/etaxonomy/cdm/remote/log4j.properties -text
+cdmlib-remote/src/main/resources/log4j.properties -text
 cdmlib-remote/src/main/resources/spy.properties -text
 cdmlib-remote/src/main/webapp/WEB-INF/applicationContext.views.xml -text
 cdmlib-remote/src/main/webapp/WEB-INF/applicationContext.xml -text
 cdmlib-remote/src/main/webapp/WEB-INF/cdmrest-servlet.xml -text
-cdmlib-remote/src/main/webapp/WEB-INF/datasources/datasources-bgbm24-import.xml -text
 cdmlib-remote/src/main/webapp/WEB-INF/datasources/datasources-local.xml -text
-cdmlib-remote/src/main/webapp/WEB-INF/datasources/datasources-wp7virtual-import.xml -text
-cdmlib-remote/src/main/webapp/WEB-INF/datasources/datasources-wp7virtual-production-A.xml -text
-cdmlib-remote/src/main/webapp/WEB-INF/datasources/datasources-wp7virtual-production-B.xml -text
-cdmlib-remote/src/main/webapp/WEB-INF/datasources/empty-default-datasource-wp7virtual.xml -text
 cdmlib-remote/src/main/webapp/WEB-INF/datasources/empty-default-datasource.xml -text
+cdmlib-remote/src/main/webapp/WEB-INF/datasources/example.cdmlibrary/datasources-set-A.xml -text
+cdmlib-remote/src/main/webapp/WEB-INF/datasources/example.cdmlibrary/datasources-set-B.xml -text
+cdmlib-remote/src/main/webapp/WEB-INF/datasources/example.cdmlibrary/use-A-set.sh -text
+cdmlib-remote/src/main/webapp/WEB-INF/datasources/example.cdmlibrary/use-B-set.sh -text
 cdmlib-remote/src/main/webapp/WEB-INF/datasources/p6spy.xml -text
 cdmlib-remote/src/main/webapp/WEB-INF/datasources/routing-datasource.xml -text
 cdmlib-remote/src/main/webapp/WEB-INF/jsonConfigurations.xml -text
@@ -1927,7 +1887,8 @@ cdmlib-remote/src/main/webapp/WEB-INF/views.xml -text
 cdmlib-remote/src/main/webapp/WEB-INF/web.xml -text
 cdmlib-remote/src/main/webapp/favicon.ico -text svneol=unset#unset
 cdmlib-remote/src/main/webapp/index.jsp -text
-cdmlib-remote/src/main/webapp/jsp/error.jsp -text
+cdmlib-remote/src/main/webapp/jsp/datasources/list.jsp -text
+cdmlib-remote/src/main/webapp/jsp/index.jsp -text
 cdmlib-remote/src/main/webapp/robots.txt -text
 cdmlib-remote/src/site/site.xml -text
 cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/dto/assembler/lsid/AssemblerTest.java -text
@@ -2116,11 +2077,13 @@ eclipse-plugin/cglib-2.1.3.jar -text
 eclipse-plugin/commons-collections-2.1.1.jar -text
 eclipse-plugin/commons-collections-3.2-sources.jar -text
 eclipse-plugin/commons-collections-3.2.jar -text
+eclipse-plugin/commons-lang-2.4.jar -text
 eclipse-plugin/commons-logging-1.0.4.jar -text
 eclipse-plugin/dom4j-1.6.1.jar -text
 eclipse-plugin/ehcache-1.2.3.jar -text
 eclipse-plugin/ejb3-persistence.jar -text
 eclipse-plugin/h2-1.0.73.jar -text
+eclipse-plugin/h2-1.1.115.jar -text
 eclipse-plugin/hibernate-3.2.6.ga-sources.jar -text
 eclipse-plugin/hibernate-3.2.6.ga.jar -text
 eclipse-plugin/hibernate-annotations-3.3.1.GA.jar -text
@@ -2171,6 +2134,7 @@ eclipse-plugin/mssqlserver-2000.3.jar -text
 eclipse-plugin/msutil-2000.3.jar -text
 eclipse-plugin/mysql-connector-java-3.1.14-bin.jar -text
 eclipse-plugin/opencsv-1.8.jar -text
+eclipse-plugin/org.apache.commons.codec-1.3.0.jar -text
 eclipse-plugin/plugin.xml -text
 eclipse-plugin/poi-3.1-FINAL.jar -text
 eclipse-plugin/pom.xml -text
@@ -2331,6 +2295,18 @@ pluginTesterApplication/src/plugintesterapplication/View.java -text
 pluginTesterApplication/src/test/testClass.java -text
 /pom.xml -text
 /settings.xml -text
+src/docbkx/ReferenceDocumentation.xml -text
+src/docbkx/annotation-and-markers.xml -text
+src/docbkx/base-classes.xml -text
+src/docbkx/basic-persistence.xml -text
+src/docbkx/identifiable-entities.xml -text
+src/docbkx/resources/css/html.css -text
+src/docbkx/resources/images/ModelOverview20.gif -text
+src/docbkx/resources/images/cdmlib-arch3.png -text
+src/docbkx/resources/images/logo.png -text
+src/docbkx/resources/xsl/cdmlib.xsl -text
+src/docbkx/resources/xsl/fopdf.xsl -text
+src/docbkx/resources/xsl/html_chunk.xsl -text
 src/site/resources/images/logos/logo_edit.png -text
 src/site/resources/images/logos/logo_edit2.png -text
 src/site/site.xml -text