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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
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Error messages I do not understand #56

Closed jcabrerazuniga closed 3 years ago

jcabrerazuniga commented 3 years ago

Hi again I started the latest version of the ETL-CDMBuilder and I got the next error messages. Can someone tell me what to look at? I am trying to convert a Truven mdcr database and my configuration file is at:

org.ohdsi.cdm.presentation.builder.dll.config.zip

Could this be related to the number of chunks or "Degree of Parallelism"?

My truven_mdcr database has an enrollment_detail table that is descried as:

Truven_mdcr dbo enrollment_detail age 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 1 YES 38 Truven_mdcr dbo enrollment_detail agegrp -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 2 YES 39 Truven_mdcr dbo enrollment_detail datatyp 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 3 YES 38 Truven_mdcr dbo enrollment_detail dobyr 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 4 YES 38 Truven_mdcr dbo enrollment_detail dtend -9 date 10 20 NULL NULL 1 NULL NULL -9 NULL NULL 5 YES 0 Truven_mdcr dbo enrollment_detail dtstart -9 date 10 20 NULL NULL 1 NULL NULL -9 NULL NULL 6 YES 0 Truven_mdcr dbo enrollment_detail eeclass -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 7 YES 39 Truven_mdcr dbo enrollment_detail eestatu -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 8 YES 39 Truven_mdcr dbo enrollment_detail efamid 4 int 10 4 0 10 1 NULL NULL 4 NULL NULL 9 YES 38 Truven_mdcr dbo enrollment_detail egeoloc -8 nchar 2 4 NULL NULL 1 NULL NULL -8 NULL 4 10 YES 39 Truven_mdcr dbo enrollment_detail empcty 4 int 10 4 0 10 1 NULL NULL 4 NULL NULL 11 YES 38 Truven_mdcr dbo enrollment_detail emprel -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 12 YES 39 Truven_mdcr dbo enrollment_detail empzip 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 13 YES 38 Truven_mdcr dbo enrollment_detail enrolid -5 bigint 19 8 0 10 1 NULL NULL -5 NULL NULL 14 YES 108 Truven_mdcr dbo enrollment_detail hlthplan -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 15 YES 39 Truven_mdcr dbo enrollment_detail indstry -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 16 YES 39 Truven_mdcr dbo enrollment_detail memdays 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 17 YES 38 Truven_mdcr dbo enrollment_detail mhsacovg -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 18 YES 39 Truven_mdcr dbo enrollment_detail msa 4 int 10 4 0 10 1 NULL NULL 4 NULL NULL 19 YES 38 Truven_mdcr dbo enrollment_detail phyflag -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 20 YES 39 Truven_mdcr dbo enrollment_detail plankey 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 21 YES 38 Truven_mdcr dbo enrollment_detail plantyp 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 22 YES 38 Truven_mdcr dbo enrollment_detail region -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 23 YES 39 Truven_mdcr dbo enrollment_detail rx -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 24 YES 39 Truven_mdcr dbo enrollment_detail seqnum -5 bigint 19 8 0 10 1 NULL NULL -5 NULL NULL 25 YES 108 Truven_mdcr dbo enrollment_detail sex -8 nchar 1 2 NULL NULL 1 NULL NULL -8 NULL 2 26 YES 39 Truven_mdcr dbo enrollment_detail version -8 nchar 2 4 NULL NULL 1 NULL NULL -8 NULL 4 27 YES 39 Truven_mdcr dbo enrollment_detail wgtkey 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 28 YES 38 Truven_mdcr dbo enrollment_detail year 5 smallint 5 2 0 10 1 NULL NULL 5 NULL NULL 29 YES 38

and my Vocab database does not show any Enrollment_Detail table

Thanks Jose

ERRROR MESSAGES: 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: org.ohdsi.cdm.presentation.builder Message: Input string was not in a correct format. Type: System.FormatException 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'.) ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'.) (ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'.) (ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'.) (ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'.) (ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'.) (ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'.) (ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: One or more errors occurred. (Input string was not in a correct format.) (ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.AggregateException 12/14/2020 10:29:39 AM| 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.Data.Odbc.OdbcException 12/14/2020 10:29:39 AM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 12/14/2020 10:29:39 AM| 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.Data.Odbc.OdbcException 12/14/2020 10:29:35 AM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 12/14/2020 10:29:35 AM| 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.Data.Odbc.OdbcException 12/14/2020 10:29:34 AM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 12/14/2020 10:29:34 AM| 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.Data.Odbc.OdbcException 12/14/2020 10:29:31 AM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 12/14/2020 10:29:30 AM| 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.Data.Odbc.OdbcException 12/14/2020 10:29:27 AM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 12/14/2020 10:29:27 AM| 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.Data.Odbc.OdbcException 12/14/2020 10:29:26 AM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 12/14/2020 10:29:26 AM| 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 [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'ethnicity_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_concept_id'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'race_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'vendor'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_source_value'. ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'observation_concept_id'. Message: ERROR [42S22] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid column name 'payersource'. Type: System.Data.Odbc.OdbcException 12/14/2020 10:29:24 AM| Exception Found:

Query: File name=ENROLLMENT_DETAIL SourceConnectionString= 12/14/2020 10:29:24 AM| SourceEngine=org.ohdsi.cdm.framework.desktop.Databases.MssqlDatabaseEngine

bradanton commented 3 years ago

Hi Jose,

I just added hot fix for the MDCR and MS SQL. (../ETL/IBM/Definitions/ENROLLMENT_DETAIL.xml - was updated) Please try latest version.

Thanks, Anton

jcabrerazuniga commented 3 years ago

I am now using the latest version you posted and the posted error messages are not showing up anymore. I am also crossing my fingers as my conversion from mdcr to cdm is running at present. With the previous version the conversion from mdcr->cdm failed at the "Copying Dictionary Section" so I am still expecting another problem.

Thanks Jose