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Changed exception handling
[cdmlib.git] / .gitattributes
diff --git a/.gitattributes b/.gitattributes
index 24aac9e1f5a3af5662cd91f975d175cbfb2bc2a1..1a49f8509dcc46f5ee613dc550239c39a6d33a0a 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -23,6 +23,7 @@ app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/EfloraSources.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/excelImport/distribution/CichorieaeDistributionActivator.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/excelImport/taxa/NormalExplicitActivator.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/app/exel/NormalExplicitTestActivator.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/images/AbstractImageImporter.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/images/ImageImportConfigurator.java -text
@@ -64,6 +65,7 @@ app-import/src/main/java/eu/etaxonomy/cdm/app/synthesysImport/SynthesysCacheActi
 app-import/src/main/java/eu/etaxonomy/cdm/app/tcs/TcsRdfTestActivator.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/tcs/TcsSources.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/tcs/TcsXmlTestActivator.java -text
+app-import/src/main/java/eu/etaxonomy/cdm/app/testUpdate/EricaceaeTestUpdateActivator.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestDatabase.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestTransaction.java -text
 app-import/src/main/java/eu/etaxonomy/cdm/app/viennaImport/ViennaActivator.java -text
@@ -122,6 +124,7 @@ app-import/src/main/resources/AsteraceaeSpecimenImagesVienna.mdb -text
 app-import/src/main/resources/arecaceae.rdf -text
 app-import/src/main/resources/collections/Acronyms.tab -text
 app-import/src/main/resources/distribution/distribution_cich.xls -text
+app-import/src/main/resources/excel/NormalExplicit.xls -text
 app-import/src/main/resources/globis.rdf.xml -text
 app-import/src/main/resources/globis_valid.rdf.xml -text
 app-import/src/main/resources/images/images_cich.xls -text
@@ -138,6 +141,7 @@ app-import/src/main/resources/sdd/Erythroneura.sdd11.xml -text
 app-import/src/main/resources/sdd/LIAS_Main.sdd11.xml -text
 app-import/src/main/resources/sdd/SDD-Test-Simple.xml -text
 app-import/src/main/resources/sdd/Val-Rosandra-FRIDA-Key.sdd11.xml -text
+app-import/src/main/resources/sdd/Xper2-import-export.sdd.xml -text
 app-import/src/main/resources/sdd/cichorieae-Xper2.xml -text
 app-import/src/main/resources/specimenABCD/CDMtabular9c04a474e2_23_09_08.xls -text
 app-import/src/main/resources/specimenABCD/multiABCD.xml -text
@@ -1187,7 +1191,8 @@ app-import/src/main/resources/taxonX/palm_tc_98853.xml -text
 app-import/src/main/resources/taxonX/palm_tc_98863.xml -text
 app-import/src/main/resources/taxonX/palm_tc_98882.xml -text
 app-import/src/main/resources/taxonX/palm_tc_98886.xml -text
-app-import/src/main/resources/tcsXmlTest.xml -text
+app-import/src/main/resources/tcs/Cichorium_tcs.xml -text
+app-import/src/main/resources/tcs/tcsXmlTest.xml -text
 cdm-server/LICENSE.TXT -text
 cdm-server/ide/eclipse/Bootloader[!!-~]-[!!-~]Help.launch -text
 cdm-server/ide/eclipse/Bootloader.launch -text
@@ -1203,7 +1208,7 @@ cdm-server/src/main/installer/linux/copyright -text
 cdm-server/src/main/installer/linux/postinst -text
 cdm-server/src/main/installer/linux/postrm -text
 cdm-server/src/main/installer/templates/.cdmLibrary/datasources.xml -text
-cdm-server/src/main/installer/templates/copyright -text
+cdm-server/src/main/installer/templates/copyright.txt -text
 cdm-server/src/main/installer/win32/Launch4JavaCDMSERVER.xml -text
 cdm-server/src/main/installer/win32/cdmserver.nsi -text
 cdm-server/src/main/installer/win32/cdmserver/bin/cdmserver.bat -text
@@ -1229,6 +1234,7 @@ cdmlib-commons/README.TXT -text
 cdmlib-commons/pom.xml -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/AccountStore.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/CdmUtils.java -text
+cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/DefaultProgressMonitor.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/DoubleResult.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/ExcelUtils.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/FileCopy.java -text
@@ -1237,6 +1243,7 @@ cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/NullProgressMonitor.java -t
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/ResultWrapper.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/Tree.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/TreeNode.java -text
+cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/UriUtils.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/XmlHelp.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/mediaMetaData/AudioMetaData.java -text
 cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/mediaMetaData/ImageMetaData.java -text
@@ -1570,16 +1577,17 @@ cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/endnote/in/EndnoteImportCo
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/endnote/in/EndnoteImportState.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/endnote/in/EndnoteRecordsImport.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/endnote/in/IEndnotePlaceholderClass.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDCdmExporter.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDDataSet.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDDescriptionIO.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDDocumentBuilder.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDExportConfigurator.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDExportState.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDImportConfigurator.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDImportState.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDIoBase.java -text
-cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenIoBase.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDTransformer.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImportConfigurator.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImportState.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/out/SDDCdmExporter.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/out/SDDDataSet.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/out/SDDDocumentBuilder.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/out/SDDExportConfigurator.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/out/SDDExportState.java -text
+cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/UnitsGatheringArea.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/UnitsGatheringEvent.java -text
 cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206DataHolder.java -text
@@ -1664,8 +1672,8 @@ cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/jaxb/TermTest.java -text
 cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/jaxb/TestCdmSchemaGenerator.java -text
 cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/jaxb/URIEncoder.java -text
 cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/reference/EndnoteRecordsImportTest.java -text
-cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/sdd/SDDCdmExporterTest.java -text
-cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/sdd/SDDDescriptionIOTest.java -text
+cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/sdd/in/SDDImportTest.java -text
+cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/sdd/out/SDDCdmExporterTest.java -text
 cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/specimen/abcd206/SpecimenImportConfiguratorTest.java -text
 cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/taxonx/TaxonXImportConfiguratorTest.java -text
 cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/tcsrdf/TcsRdfImportConfiguratorTest.java -text
@@ -1678,6 +1686,7 @@ cdmlib-io/src/test/resources/eu/etaxonomy/cdm/applicationContext-test.xml -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/dataset.dtd -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/excel/taxa/DenormalExplicit.xls -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/excel/taxa/DenormalImplied.xls -text
+cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImportTest-input-original.xls -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImportTest-input.xls -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImportTest.xml -text
 cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/excel/taxa/NormalImplied.xls -text
@@ -1758,6 +1767,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ExtensionType.java -tex
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Figure.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/GrantedAuthorityImpl.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/Group.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IAnnotatableEntity.java -text svneol=unset#text/plain
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/ICdmBase.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IDefinedTerm.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IEvent.java -text
@@ -1769,6 +1779,7 @@ 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/ISourceable.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IVersionableEntity.java -text svneol=unset#text/plain
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableEntity.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/IdentifiableSource.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/LSID.java -text
@@ -1819,6 +1830,7 @@ cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/Feature.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/FeatureNode.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/FeatureTree.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/IIdentificationKey.java -text
+cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/IModifiable.java -text svneol=unset#text/plain
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/IndividualsAssociation.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/MeasurementUnit.java -text
 cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/MediaKey.java -text
@@ -2247,6 +2259,21 @@ cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/PostgreSQLDatab
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/SqlServer2000DatabaseType.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/SqlServer2005DatabaseType.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/types/SybaseDatabaseType.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/CdmUpdater.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ColumnAdder.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ColumnNameChanger.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ISchemaUpdater.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ISchemaUpdaterStep.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/ITermUpdater.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SchemaUpdaterBase.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SchemaUpdaterStepBase.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SchemaUpdater_24_25.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SimpleSchemaUpdaterStep.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SingleTermUpdater.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/SortIndexUpdater.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TableNameChanger.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TermUpdaterBase.java -text
+cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/TermUpdater_24_25.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/AbstractBeanInitializer.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/AutoPropertyInitializer.java -text
 cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/BeanInitializer.java -text
@@ -2378,6 +2405,7 @@ cdmlib-persistence/src/main/java/org/hibernate/dialect/H2CorrectedDialect.java -
 cdmlib-persistence/src/main/java/org/hibernate/dialect/HSQLCorrectedDialect.java -text
 cdmlib-persistence/src/main/java/org/hibernate/dialect/MySQL5InnoDBUtf8Dialect.java -text
 cdmlib-persistence/src/main/java/org/hibernate/dialect/MySQL5MyISAMUtf8Dialect.java -text
+cdmlib-persistence/src/main/resources/c3p0-config.xml -text
 cdmlib-persistence/src/main/resources/eu/etaxonomy/cdm/cdm.datasources.xml -text
 cdmlib-persistence/src/main/resources/eu/etaxonomy/cdm/h2-datasource.xml -text
 cdmlib-persistence/src/main/resources/eu/etaxonomy/cdm/hibernate.cfg.xml -text
@@ -2398,6 +2426,7 @@ cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/database/types/PostgreSQLDatab
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/database/types/SqlServer2000DatabaseTypeTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/database/types/SqlServer2005DatabaseTypeTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/database/types/SybaseDatabaseTypeTest.java -text
+cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/database/update/CdmUpdaterTest.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/datagenerator/TaxonGenerator.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/BeanInitializerIntegration.java -text
 cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/MethodCacheImplTest.java -text
@@ -3390,9 +3419,6 @@ 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
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/conversation/ConversationHolder.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/conversation/IConversationEnabled.java -text
 cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacade.java -text