task #10009
closedCleanup dependencies in TaxEditor
100%
Description
Remove all unnecessary dependencies from TaxEditor.
Includes intensive testing if everything still works as expected.
Related issues
Updated by Andreas Müller over 1 year ago
- Related to task #9359: Update cdmlib, taxeditor, cdmserver etc. dependencies added
Updated by Andreas Müller over 1 year ago
- Due date set to 05/13/2022
- Start date set to 05/10/2022
Updated by Andreas Müller over 1 year ago
- Status changed from New to In Progress
- Assignee changed from Katja Luther to Andreas Müller
- % Done changed from 0 to 10
Updated by Andreas Müller over 1 year ago
- Related to task #10067: Update to hibernate 5.4 (or higher) and hibernate search 5.11 and lucene 5.5 added
Updated by Andreas Müller over 1 year ago
- Related to task #10055: Updates, upgrades and cleanup 2023 added
Updated by Andreas Müller over 1 year ago
- Status changed from In Progress to Resolved
- % Done changed from 10 to 70
Seems to work but still needs intensive testing and maybe some cleanup.
Updated by Andreas Müller over 1 year ago
The following dependencies were used in prior version but are currently not on the classpath:
lib/aspectjrt-1.9.7.jar,\ lib/ezmorph-1.0.6.jar,\ lib/itextpdf-5.5.13.3.jar,\ lib/jdom2-2.0.6.jar,\ lib/spring-expression-4.3.30.RELEASE.jar,\ lib/spring-oxm-4.3.30.RELEASE.jar,\ lib/spring-test-4.3.30.RELEASE.jar,\ lib/usertype.core-7.0.0.CR1.jar,\ lib/xalan-2.7.2.jar,\ lib/xmlbeans-3.1.0.jar,\ lib/javax.el-api-3.0.0.jar,\ lib/aopalliance-1.0.jar,\ lib/cglib-nodep-3.3.0.jar,\ lib/classmate-1.5.1.jar,\ lib/poi-4.1.2.jar,\ lib/poi-ooxml-4.1.2.jar,\ lib/poi-ooxml-schemas-4.1.2.jar,\ lib/JavaAPIforKml-2.2.1.jar,\ lib/iiif-apis-0.3.9.jar,\
Updated by Andreas Müller over 1 year ago
- Priority changed from Highest to Priority14
Updated by Andreas Müller over 1 year ago
For the following dependencies it is unclear if they are needed. They are marked as "Only added for correct package export" (except for commons-math which was below poi which is not needed anymore (as it looks like)):
lib/commons-collections-3.2.2.jar,\ lib/commons-imaging-1.0-alpha3.jar,\ lib/commons-logging-1.2.jar,\ lib/hibernate-commons-annotations-5.1.2.Final.jar,\ lib/hibernate-search-engine-5.11.10.Final.jar,\ lib/hibernate-search-orm-5.11.10.Final.jar,\ lib/spring-context-support-4.3.30.RELEASE.jar,\ lib/spring-jdbc-4.3.30.RELEASE.jar,\ lib/spring-orm-4.3.30.RELEASE.jar,\ lib/spring-security-config-4.2.20.RELEASE.jar,\ lib/json-lib-2.4-jdk15.jar,\ lib/commons-math3-3.6.1.jar
Updated by Andreas Müller over 1 year ago
Testing needs to be done in the "with java" verson.
Updated by Andreas Müller over 1 year ago
Andreas Müller wrote in #note-10:
For the following dependencies it is unclear if they are needed. They are marked as "Only added for correct package export" (except for commons-math which was below poi which is not needed anymore (as it looks like)):
lib/commons-collections-3.2.2.jar,\ lib/commons-imaging-1.0-alpha3.jar,\ lib/commons-logging-1.2.jar,\ lib/hibernate-commons-annotations-5.1.2.Final.jar,\ lib/hibernate-search-engine-5.11.10.Final.jar,\ lib/hibernate-search-orm-5.11.10.Final.jar,\ lib/spring-context-support-4.3.30.RELEASE.jar,\ lib/spring-jdbc-4.3.30.RELEASE.jar,\ lib/spring-orm-4.3.30.RELEASE.jar,\ lib/spring-security-config-4.2.20.RELEASE.jar,\ lib/json-lib-2.4-jdk15.jar,\ lib/commons-math3-3.6.1.jar
removed them all except for commons-imaging (required in store), spring-jdbc (required for test run), commons-math (required in editor). Still needs further testing.
Updated by Andreas Müller over 1 year ago
- Assignee changed from Andreas Müller to Katja Luther
- % Done changed from 70 to 90
Andreas Müller wrote in #note-7:
Seems to work but still needs intensive testing and maybe some cleanup.
Cleanup should be done (in v5.33-SNAPSHOT). Can you do some futher testing (e.g. imports like ABCD/biocase provider) but also others.
I already tested images and maps. They are shown. I also tested the datasource view. It works.
When ready with testing we may close the ticket.
Updated by Andreas Müller over 1 year ago
- Related to bug #10105: Fix logging in TaxEditor after migration to log4j 2 added
Updated by Katja Luther over 1 year ago
Online search and import works as expected, but importing from a file does not work anymore. I don't know whether this is related to this ticket, but in v5.32 it still works:
Using a file from test ressources of cdmlib-io, the following exception appears (running the tests works)
could not execute statement org.hibernate.exception.GenericJDBCException: could not execute statement at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:47) at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113) at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99) at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:200) at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3298) at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3825) at org.hibernate.action.internal.EntityInsertAction.execute(EntityInsertAction.java:107) at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:604) at org.hibernate.engine.spi.ActionQueue.lambda$executeActions$1(ActionQueue.java:478) at java.util.LinkedHashMap.forEach(LinkedHashMap.java:684) at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:475) at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:344) at org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:57) at org.hibernate.event.service.internal.EventListenerGroupImpl.fireEventOnEachListener(EventListenerGroupImpl.java:99) at org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1327) at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1870) at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:370) at eu.etaxonomy.cdm.persistence.dao.hibernate.name.TaxonNameDaoHibernateImpl.findByName(TaxonNameDaoHibernateImpl.java:585) at eu.etaxonomy.cdm.api.service.NameServiceImpl.findNamesByNameCache(NameServiceImpl.java:410) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy212.findNamesByNameCache(Unknown Source) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.getOrCreateTaxonName(SpecimenImportBase.java:130) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.addParentTaxon(SpecimenImportBase.java:793) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.addTaxonNode(SpecimenImportBase.java:1047) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.handleIdentifications(SpecimenImportBase.java:1027) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.handleSingleUnit(Abcd206Import.java:777) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:267) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:1) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.doInvoke(SpecimenImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmIoBase.invoke(CdmIoBase.java:104) at eu.etaxonomy.cdm.io.common.CdmImportBase.invoke(CdmImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.doImport(CdmApplicationAwareDefaultImport.java:221) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.invoke(CdmApplicationAwareDefaultImport.java:84) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importDataFromInputStream(IOServiceImpl.java:168) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importData(IOServiceImpl.java:120) at eu.etaxonomy.cdm.io.service.IOServiceImpl$1.doRun(IOServiceImpl.java:75) at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:43) Caused by: java.sql.SQLException: Incorrect string value: '\x8Auva P...' for column 'text' at row 1 at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:129) at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:122) at com.mysql.cj.jdbc.ClientPreparedStatement.executeInternal(ClientPreparedStatement.java:916) at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1061) at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1009) at com.mysql.cj.jdbc.ClientPreparedStatement.executeLargeUpdate(ClientPreparedStatement.java:1320) at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdate(ClientPreparedStatement.java:994) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:384) at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:197) ... 44 more --- Exception during import! Transaction rolled back because it has been marked as rollback-only org.springframework.transaction.UnexpectedRollbackException: Transaction rolled back because it has been marked as rollback-only at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:728) at eu.etaxonomy.cdm.io.common.CdmIoBase.commitTransaction(CdmIoBase.java:163) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:250) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:1) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.doInvoke(SpecimenImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmIoBase.invoke(CdmIoBase.java:104) at eu.etaxonomy.cdm.io.common.CdmImportBase.invoke(CdmImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.doImport(CdmApplicationAwareDefaultImport.java:221) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.invoke(CdmApplicationAwareDefaultImport.java:84) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importDataFromInputStream(IOServiceImpl.java:168) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importData(IOServiceImpl.java:120) at eu.etaxonomy.cdm.io.service.IOServiceImpl$1.doRun(IOServiceImpl.java:75) at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:43)
Updated by Andreas Müller about 1 year ago
- Related to bug #10175: IllegalStateException when more than 10 exceptions in UpdateResult added
Updated by Katja Luther 5 months ago
Katja Luther wrote in #note-15:
Online search and import works as expected, but importing from a file does not work anymore. I don't know whether this is related to this ticket, but in v5.32 it still works:
Using a file from test ressources of cdmlib-io, the following exception appears (running the tests works)
could not execute statement org.hibernate.exception.GenericJDBCException: could not execute statement at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:47) at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113) at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99) at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:200) at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3298) at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3825) at org.hibernate.action.internal.EntityInsertAction.execute(EntityInsertAction.java:107) at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:604) at org.hibernate.engine.spi.ActionQueue.lambda$executeActions$1(ActionQueue.java:478) at java.util.LinkedHashMap.forEach(LinkedHashMap.java:684) at org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:475) at org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:344) at org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:57) at org.hibernate.event.service.internal.EventListenerGroupImpl.fireEventOnEachListener(EventListenerGroupImpl.java:99) at org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1327) at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1870) at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:370) at eu.etaxonomy.cdm.persistence.dao.hibernate.name.TaxonNameDaoHibernateImpl.findByName(TaxonNameDaoHibernateImpl.java:585) at eu.etaxonomy.cdm.api.service.NameServiceImpl.findNamesByNameCache(NameServiceImpl.java:410) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy212.findNamesByNameCache(Unknown Source) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.getOrCreateTaxonName(SpecimenImportBase.java:130) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.addParentTaxon(SpecimenImportBase.java:793) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.addTaxonNode(SpecimenImportBase.java:1047) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.handleIdentifications(SpecimenImportBase.java:1027) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.handleSingleUnit(Abcd206Import.java:777) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:267) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:1) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.doInvoke(SpecimenImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmIoBase.invoke(CdmIoBase.java:104) at eu.etaxonomy.cdm.io.common.CdmImportBase.invoke(CdmImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.doImport(CdmApplicationAwareDefaultImport.java:221) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.invoke(CdmApplicationAwareDefaultImport.java:84) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importDataFromInputStream(IOServiceImpl.java:168) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importData(IOServiceImpl.java:120) at eu.etaxonomy.cdm.io.service.IOServiceImpl$1.doRun(IOServiceImpl.java:75) at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:43) Caused by: java.sql.SQLException: Incorrect string value: '\x8Auva P...' for column 'text' at row 1 at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:129) at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:122) at com.mysql.cj.jdbc.ClientPreparedStatement.executeInternal(ClientPreparedStatement.java:916) at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1061) at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1009) at com.mysql.cj.jdbc.ClientPreparedStatement.executeLargeUpdate(ClientPreparedStatement.java:1320) at com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdate(ClientPreparedStatement.java:994) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:384) at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:197) ... 44 more --- Exception during import! Transaction rolled back because it has been marked as rollback-only org.springframework.transaction.UnexpectedRollbackException: Transaction rolled back because it has been marked as rollback-only at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:728) at eu.etaxonomy.cdm.io.common.CdmIoBase.commitTransaction(CdmIoBase.java:163) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:250) at eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206Import.doInvoke(Abcd206Import.java:1) at eu.etaxonomy.cdm.io.specimen.SpecimenImportBase.doInvoke(SpecimenImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmIoBase.invoke(CdmIoBase.java:104) at eu.etaxonomy.cdm.io.common.CdmImportBase.invoke(CdmImportBase.java:1) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.doImport(CdmApplicationAwareDefaultImport.java:221) at eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport.invoke(CdmApplicationAwareDefaultImport.java:84) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importDataFromInputStream(IOServiceImpl.java:168) at eu.etaxonomy.cdm.io.service.IOServiceImpl.importData(IOServiceImpl.java:120) at eu.etaxonomy.cdm.io.service.IOServiceImpl$1.doRun(IOServiceImpl.java:75) at eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread.run(RemotingProgressMonitorThread.java:43)
I think this does not belong to this ticket because it is an error on cdmlib side. I will create a new ticket for this.
Updated by Katja Luther 5 months ago
- Status changed from Resolved to Closed
- Assignee changed from Katja Luther to Andreas Müller
So I think we can close this ticket.