{"action":"created","issue":{"url":"https://api.github.com/repos/lexevs/lexevs/issues/19","labels_url":"https://api.github.com/repos/lexevs/lexevs/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/lexevs/lexevs/issues/19/comments","events_url":"https://api.github.com/repos/lexevs/lexevs/issues/19/events","html_url":"https://github.com/lexevs/lexevs/issues/19","id":73331010,"number":19,"title":"(Possible) Issues Loading UMLS/SNOMEDCT_US w/LexEVS 6.2","user":{"login":"mkitchin","id":11393563,"avatar_url":"https://avatars.githubusercontent.com/u/11393563?v=3","gravatar_id":"","url":"https://api.github.com/users/mkitchin","html_url":"https://github.com/mkitchin","followers_url":"https://api.github.com/users/mkitchin/followers","following_url":"https://api.github.com/users/mkitchin/following{/other_user}","gists_url":"https://api.github.com/users/mkitchin/gists{/gist_id}","starred_url":"https://api.github.com/users/mkitchin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkitchin/subscriptions","organizations_url":"https://api.github.com/users/mkitchin/orgs","repos_url":"https://api.github.com/users/mkitchin/repos","events_url":"https://api.github.com/users/mkitchin/events{/privacy}","received_events_url":"https://api.github.com/users/mkitchin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-05-05T14:30:29Z","updated_at":"2015-05-05T17:36:41Z","closed_at":null,"body":"Hi there,\r\n\r\nI'm trying to load (what appears to be) the latest SNOMEDCT_US terminology via a UMLS subset and am getting pretty far in the process (8+hrs) before getting a great number of exceptions such as the one below.\r\n\r\nIn this case, I had to terminate the load after ~20hrs to make an appointment, so I can't say if it would've run to completion. At that point these exceptions had been coming steadily for ~8hrs.\r\n\r\nPer another issue, I've updated UMLS_SAB_ISO_Map.txt to the set from master and that got me past an initial URN problem.\r\n\r\nConfiguration:\r\n- 8 core (i7), 2.9GHz\r\n- 16GB RAM, 8GB heap configured for libgui or loader script (tried both)\r\n- SSD HD, plenty of space\r\n- MySQL 5.5\r\n- LexEVS 6.2 (release download)\r\n\r\nThoughts?\r\n\r\nLB_WARN_LOGGER WARN - 2015-05-05 04:57:47,457 - [LOG_ID 26019] Error inserting Transitive closure item.\r\norg.springframework.dao.DuplicateKeyException: SqlMapClient operation; SQL [];   \r\n--- The error occurred in ibatis/v20/entityAssnsToEntity.xml.  \r\n--- The error occurred while applying a parameter map.  \r\n--- Check the Association.insertTransitiveClosure-InlineParameterMap.  \r\n--- Check the statement (update failed).  \r\n--- Cause: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry '360969006-SNOMED Clinical Terms US Edition-78548001-SNOMED Clini' for key 'lbaaapUQ_etet_stid'; nested exception is com.ibatis.common.jdbc.exception.NestedSQLException:   \r\n--- The error occurred in ibatis/v20/entityAssnsToEntity.xml.  \r\n--- The error occurred while applying a parameter map.  \r\n--- Check the Association.insertTransitiveClosure-InlineParameterMap.  \r\n--- Check the statement (update failed).  \r\n--- Cause: com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationException: Duplicate entry '360969006-SNOMED Clinical Terms US Edition-78548001-SNOMED Clini' for key 'lbaaapUQ_etet_stid'\r\n\tat org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator.doTranslate(SQLErrorCodeSQLExceptionTranslator.java:241)\r\n\tat org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:72)\r\n\tat org.springframework.orm.ibatis.SqlMapClientTemplate.execute(SqlMapClientTemplate.java:203)\r\n\tat org.springframework.orm.ibatis.SqlMapClientTemplate.insert(SqlMapClientTemplate.java:364)\r\n\tat org.lexevs.dao.database.ibatis.batch.SqlMapClientTemplateInserter.insert(SqlMapClientTemplateInserter.java:47)\r\n\tat org.lexevs.dao.database.ibatis.association.IbatisAssociationDao.doInsertIntoTransitiveClosure(IbatisAssociationDao.java:660)\r\n\tat org.lexevs.dao.database.ibatis.association.IbatisAssociationDao.insertIntoTransitiveClosure(IbatisAssociationDao.java:677)\r\n\tat org.lexevs.dao.database.ibatis.association.IbatisAssociationDao$$FastClassByCGLIB$$25bd0256.invoke(<generated>)\r\n\tat net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)\r\n\tat org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib2AopProxy.java:689)\r\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)\r\n\tat org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)\r\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)\r\n\tat org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:622)\r\n\tat org.lexevs.dao.database.ibatis.association.IbatisAssociationDao$$EnhancerByCGLIB$$2d7f074f.insertIntoTransitiveClosure(<generated>)\r\n\tat org.lexevs.dao.database.operation.transitivity.DefaultTransitivityBuilder$BatchInsertController$3.execute(DefaultTransitivityBuilder.java:684)\r\n\tat org.lexevs.dao.database.service.daocallback.DaoManagerDaoCallbackService.executeInDaoLayer(DaoManagerDaoCallbackService.java:41)\r\n\tat org.lexevs.dao.database.service.daocallback.DaoManagerDaoCallbackService$$FastClassByCGLIB$$ea2683ff.invoke(<generated>)\r\n\tat net.sf.cglib.proxy.MethodProxy.invoke(MethodProxy.java:191)\r\n\tat org.springframework.aop.framework.Cglib2AopProxy$CglibMethodInvocation.invokeJoinpoint(Cglib2AopProxy.java:689)\r\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)\r\n\tat org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)\r\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)\r\n\tat org.springframework.aop.framework.Cglib2AopProxy$DynamicAdvisedInterceptor.intercept(Cglib2AopProxy.java:622)\r\n\tat org.lexevs.dao.database.service.daocallback.DaoManagerDaoCallbackService$$EnhancerByCGLIB$$c82b333.executeInDaoLayer(<generated>)\r\n\tat org.lexevs.dao.database.operation.transitivity.DefaultTransitivityBuilder$BatchInsertController.flush(DefaultTransitivityBuilder.java:680)\r\n\tat org.lexevs.dao.database.operation.transitivity.DefaultTransitivityBuilder$BatchInsertController.insertIntoTransitiveClosure(DefaultTransitivityBuilder.java:658)\r\n\tat org.lexevs.dao.database.operation.transitivity.DefaultTransitivityBuilder$BatchInsertController.access$300(DefaultTransitivityBuilder.java:620)\r\n\tat org.lexevs.dao.database.operation.transitivity.DefaultTransitivityBuilder.insertIntoTransitiveClosure(DefaultTransitivityBuilder.java:355)\r\n\tat org.lexevs.dao.database.operation.transitivity.DefaultTransitivityBuilder.processTransitive(DefaultTransitivityBuilder.java:297)\r\n\tat org.lexevs.dao.database.operation.transitivity.DefaultTransitivityBuilder.computeTransitivityTable(DefaultTransitivityBuilder.java:199)\r\n\tat org.lexevs.dao.database.operation.DefaultLexEvsDatabaseOperations.computeTransitiveTable(DefaultLexEvsDatabaseOperations.java:421)\r\n\tat org.lexgrid.loader.lexbigadmin.TransitivityBuildingTasklet.doExecute(TransitivityBuildingTasklet.java:68)\r\n\tat org.lexgrid.loader.lexbigadmin.AbstractLexEvsUtilityTasklet.execute(AbstractLexEvsUtilityTasklet.java:49)\r\n\tat org.lexgrid.loader.lexbigadmin.TransitivityBuildingTasklet.execute(TransitivityBuildingTasklet.java:47)\r\n\tat org.springframework.batch.core.step.tasklet.TaskletStep$ChunkTransactionCallback.doInTransaction(TaskletStep.java:347)\r\n\tat org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:130)\r\n\tat org.springframework.batch.core.step.tasklet.TaskletStep$2.doInChunkContext(TaskletStep.java:261)\r\n\tat org.springframework.batch.core.scope.context.StepContextRepeatCallback.doInIteration(StepContextRepeatCallback.java:76)\r\n\tat org.springframework.batch.repeat.support.RepeatTemplate.getNextResult(RepeatTemplate.java:367)\r\n\tat org.springframework.batch.repeat.support.RepeatTemplate.executeInternal(RepeatTemplate.java:214)\r\n\tat org.springframework.batch.repeat.support.RepeatTemplate.iterate(RepeatTemplate.java:143)\r\n\tat org.springframework.batch.core.step.tasklet.TaskletStep.doExecute(TaskletStep.java:247)\r\n\tat org.springframework.batch.core.step.AbstractStep.execute(AbstractStep.java:196)\r\n\tat org.springframework.batch.core.job.SimpleStepHandler.handleStep(SimpleStepHandler.java:115)\r\n\tat org.springframework.batch.core.job.flow.JobFlowExecutor.executeStep(JobFlowExecutor.java:61)\r\n\tat org.springframework.batch.core.job.flow.support.state.StepState.handle(StepState.java:60)\r\n\tat org.springframework.batch.core.job.flow.support.SimpleFlow.resume(SimpleFlow.java:144)\r\n\tat org.springframework.batch.core.job.flow.support.SimpleFlow.start(SimpleFlow.java:124)\r\n\tat org.springframework.batch.core.job.flow.support.state.SplitState$1.call(SplitState.java:83)\r\n\tat org.springframework.batch.core.job.flow.support.state.SplitState$1.call(SplitState.java:81)\r\n\tat java.util.concurrent.FutureTask.run(FutureTask.java:262)\r\n\tat org.springframework.core.task.SimpleAsyncTaskExecutor$ConcurrencyThrottlingRunnable.run(SimpleAsyncTaskExecutor.java:229)\r\n\tat java.lang.Thread.run(Thread.java:745)"},"comment":{"url":"https://api.github.com/repos/lexevs/lexevs/issues/comments/99154112","html_url":"https://github.com/lexevs/lexevs/issues/19#issuecomment-99154112","issue_url":"https://api.github.com/repos/lexevs/lexevs/issues/19","id":99154112,"user":{"login":"mkitchin","id":11393563,"avatar_url":"https://avatars.githubusercontent.com/u/11393563?v=3","gravatar_id":"","url":"https://api.github.com/users/mkitchin","html_url":"https://github.com/mkitchin","followers_url":"https://api.github.com/users/mkitchin/followers","following_url":"https://api.github.com/users/mkitchin/following{/other_user}","gists_url":"https://api.github.com/users/mkitchin/gists{/gist_id}","starred_url":"https://api.github.com/users/mkitchin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkitchin/subscriptions","organizations_url":"https://api.github.com/users/mkitchin/orgs","repos_url":"https://api.github.com/users/mkitchin/repos","events_url":"https://api.github.com/users/mkitchin/events{/privacy}","received_events_url":"https://api.github.com/users/mkitchin/received_events","type":"User","site_admin":false},"created_at":"2015-05-05T17:36:41Z","updated_at":"2015-05-05T17:36:41Z","body":"Hi there,\r\n\r\nThanks for getting back to me so quickly, again.\r\n\r\nGood news is I'm already importing the metathesaurus, so I ought to know in a few hours. I'll be sure to get back with you (here) about the results.\r\n\r\nOut of curiosity, do you have a sense of when LexEVS 6.3 would be released?"}}