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OHDSI / ETL-CDMBuilder

ETL-CDMBuilder is a repo containing a .NET Core application to perform ETL to OMOP CDM for multiple databases
Apache License 2.0
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"Ambiguous column" messages #58

Closed jcabrerazuniga closed 3 years ago

jcabrerazuniga commented 3 years ago

Hi While processing my mdcr db I am getting the next errors: at System.Threading.Tasks.TaskReplicator.Replica.Execute() at System.Threading.Tasks.TaskReplicator.Replica1.ExecuteAction(Boolean& yieldedBeforeCompletion) at System.Threading.Tasks.Parallel.<>c__DisplayClass19_01.b1(RangeWorker& currentWorker, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion) at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw(Exception source) --- End of stack trace from previous location where exception was thrown --- at System.Threading.Tasks.Parallel.<>cDisplayClass19_01.<ForWorker>b__1(RangeWorker& currentWorker, Int32 timeout, Boolean& replicationDelegateYieldedBeforeCompletion) at org.ohdsi.cdm.presentation.builder.Controllers.BuilderController.<>c__DisplayClass18_0.<Build>b__2(Int32 chunkId, ParallelLoopState state) in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Controllers\BuilderController.cs:line 303 Stacktrace: at org.ohdsi.cdm.presentation.builder.Base.DatabaseChunkBuilder.Process(IDatabaseEngine sourceEngine, String sourceSchemaName, List1 sourceQueryDefinitions, OdbcConnection sourceConnection, String vendor) in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Base\DatabaseChunkBuilder.cs:line 48 Source: sqlncli11.dll ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. Message: ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. Type: System.Data.Odbc.OdbcException Inner Exception Found: at org.ohdsi.cdm.presentation.builder.Controllers.BuilderController.PerformAction(Action act) in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Controllers\BuilderController.cs:line 55 at org.ohdsi.cdm.presentation.builder.Controllers.BuilderController.<>c__DisplayClass18_0.b__0() in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Controllers\BuilderController.cs:line 289 at System.Threading.Tasks.Parallel.For(Int32 fromInclusive, Int32 toExclusive, ParallelOptions parallelOptions, Action2 body) at System.Threading.Tasks.Parallel.ForWorker[TLocal](Int32 fromInclusive, Int32 toExclusive, ParallelOptions parallelOptions, Action1 body, Action2 bodyWithState, Func4 bodyWithLocal, Func1 localInit, Action1 localFinally) at System.Threading.Tasks.Parallel.ThrowSingleCancellationExceptionOrOtherException(ICollection exceptions, CancellationToken cancelToken, Exception otherException) at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw(Exception source) --- End of stack trace from previous location where exception was thrown --- at System.Threading.Tasks.Parallel.ForWorker[TLocal](Int32 fromInclusive, Int32 toExclusive, ParallelOptions parallelOptions, Action1 body, Action2 bodyWithState, Func4 bodyWithLocal, Func1 localInit, Action1 localFinally) Stacktrace: at System.Threading.Tasks.TaskReplicator.Run[TState](ReplicatableUserAction1 action, ParallelOptions options, Boolean stopOnFirstFailure) Source: System.Threading.Tasks.Parallel ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'.) ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'.) (ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'.) (ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'.) (ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. Message: One or more errors occurred. (ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. Type: System.AggregateException 9/20/2021 5:48:17 PM| Exception Found: Stacktrace: at org.ohdsi.cdm.presentation.builder.Base.DatabaseChunkBuilder.Process(IDatabaseEngine sourceEngine, String sourceSchemaName, List`1 sourceQueryDefinitions, OdbcConnection sourceConnection, String vendor) in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Base\DatabaseChunkBuilder.cs:line 48 Source: sqlncli11.dll ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. Message: ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. Type: System.Data.Odbc.OdbcException 9/20/2021 5:48:17 PM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 9/20/2021 5:48:17 PM| SourceEngine=org.ohdsi.cdm.framework.desktop.Databases.MssqlDatabaseEngine Stacktrace: at org.ohdsi.cdm.presentation.builder.Base.DatabaseChunkBuilder.Process(IDatabaseEngine sourceEngine, String sourceSchemaName, List`1 sourceQueryDefinitions, OdbcConnection sourceConnection, String vendor) in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Base\DatabaseChunkBuilder.cs:line 48 Source: sqlncli11.dll ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. Message: ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. Type: System.Data.Odbc.OdbcException 9/20/2021 5:45:57 PM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 9/20/2021 5:45:57 PM| SourceEngine=org.ohdsi.cdm.framework.desktop.Databases.MssqlDatabaseEngine Stacktrace: at org.ohdsi.cdm.presentation.builder.Base.DatabaseChunkBuilder.Process(IDatabaseEngine sourceEngine, String sourceSchemaName, List`1 sourceQueryDefinitions, OdbcConnection sourceConnection, String vendor) in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Base\DatabaseChunkBuilder.cs:line 48 Source: sqlncli11.dll ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. Message: ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. Type: System.Data.Odbc.OdbcException 9/20/2021 4:24:46 PM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 9/20/2021 4:24:46 PM| SourceEngine=org.ohdsi.cdm.framework.desktop.Databases.MssqlDatabaseEngine Stacktrace: at org.ohdsi.cdm.presentation.builder.Base.DatabaseChunkBuilder.Process(IDatabaseEngine sourceEngine, String sourceSchemaName, List`1 sourceQueryDefinitions, OdbcConnection sourceConnection, String vendor) in E:\repo\ohdsi\ETL-CDMBuilder\source\org.ohdsi.cdm.presentation.builder\Base\DatabaseChunkBuilder.cs:line 48 Source: sqlncli11.dll ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'ethnicity_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_concept_id'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'race_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'vendor'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_source_value'. ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'observation_concept_id'. Message: ERROR [42000] [Microsoft][SQL Server Native Client 11.0][SQL Server]Ambiguous column name 'payersource'. Type: System.Data.Odbc.OdbcException 9/20/2021 4:06:25 PM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 9/20/2021 4:06:24 PM| SourceEngine=org.ohdsi.cdm.framework.desktop.Databases.MssqlDatabaseEngine 9/20/2021 3:39:24 PM| ==================== Conversion to CDM was started ==================== 9/20/2021 3:39:24 PM| DONE - 2997 ms | KeysCount=952 9/20/2021 3:39:21 PM| Units - Loading into RAM... 9/20/2021 3:39:21 PM| DONE - 1260856 ms | KeysCount=247242 9/20/2021 3:18:20 PM| Lab - Loading into RAM... 9/20/2021 3:18:20 PM| DONE - 1586 ms | KeysCount=538 9/20/2021 3:18:19 PM| Revenue - Loading into RAM... 9/20/2021 3:18:19 PM| DONE - 92 ms | KeysCount=0 9/20/2021 3:18:18 PM| DischargeTo - Loading into RAM... 9/20/2021 3:18:18 PM| DONE - 128 ms | KeysCount=16 9/20/2021 3:18:18 PM| Visits - Loading into RAM... 9/20/2021 3:18:18 PM| DONE - 1196 ms | KeysCount=400 9/20/2021 3:18:17 PM| Modifier - Loading into RAM... 9/20/2021 3:18:17 PM| DONE - 93 ms | KeysCount=0 9/20/2021 3:18:17 PM| Drg - Loading into RAM... 9/20/2021 3:18:17 PM| DONE - 94 ms | KeysCount=0 9/20/2021 3:18:17 PM| HRA - Loading into RAM... 9/20/2021 3:18:17 PM| DONE - 10 ms | KeysCount=0 9/20/2021 3:18:17 PM| Death - Loading into RAM... 9/20/2021 3:18:17 PM| DONE - 581128 ms | KeysCount=108062 9/20/2021 3:08:36 PM| Procedure - Loading into RAM... 9/20/2021 3:08:36 PM| DONE - 680052 ms | KeysCount=96308 9/20/2021 2:57:16 PM| Condition_icd10 - Loading into RAM... 9/20/2021 2:57:16 PM| DONE - 113603 ms | KeysCount=17564 9/20/2021 2:55:22 PM| Condition - Loading into RAM... 9/20/2021 2:55:22 PM| DONE - 5814763 ms | KeysCount=970434 9/20/2021 1:18:27 PM| Drug - Loading into RAM...

What could be the problem?

jcabrerazuniga commented 3 years ago

Columns did not need to be included in the table's definition.