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ETL-CDMBuilder Issues, part 2

Developers
#1

Seems like I was able to figure out the proper connection string for the builder database (which is inconsistent with the other configuration connection strings btw) form this issue (ETL-CDMBuilder documentation (or lack of it) questions). After looking into the source code for the builder. The build and target databases are properly created and now I am stuck in the chunk generation part with this error:

Builder: OHDSI-CONVERSIO
Time: Feb 9 2017 9:50PM
Error: Exception Found:
Type: System.Data.Odbc.OdbcException
Message: ERROR [42S02] [Microsoft][SQL Server Native Client 11.0][SQL Server]Invalid object name ‘dbo.ENROLLMENT_DETAIL’.
Source: sqlncli11.dll
Stacktrace: at System.Data.Odbc.OdbcConnection.HandleError(OdbcHandle hrHandle, RetCode retcode)
at System.Data.Odbc.OdbcCommand.ExecuteReaderObject(CommandBehavior behavior, String method, Boolean needReader, Object[] methodArguments, SQL_API odbcApiMethod)
at System.Data.Odbc.OdbcCommand.ExecuteReaderObject(CommandBehavior behavior, String method, Boolean needReader)
at System.Data.Odbc.OdbcCommand.ExecuteReader(CommandBehavior behavior)
at org.ohdsi.cdm.framework.data.DbLayer.DbSource.d__3.MoveNext()
at org.ohdsi.cdm.framework.core.Controllers.ChunkController.d__4.MoveNext()
at org.ohdsi.cdm.framework.core.Controllers.ChunkController.CreateChunks()
at org.ohdsi.cdm.framework.core.Controllers.BuilderController.PerformAction(Action act)

Seems like the table dbo.ENROLLMENT_DETAIL should contain the personId’s to put in the chunk (or something along those lines), but this is never generated by the builder program. I have looked in the code repository for this table, and see that in some tests this table is populated manually, but there is no single piece of code that shows this being done inside the builder on a regular basis for the regular build process. I am not a c# expert so I might be missing something.

Is this table supposed to be populated manually? if so, how? I don’t see any mention of this in any documentation other than the test cases on the code repository.

Any help would be greatly appreciated! @Patrick_Ryan, @ericaVoss seems like the github issues and the forum for the ETL-CDMBUILDER issues are a bit quiet.

#2

Hi @Juan_Banda,

enrollment_detail should be a part of the source Truven dataset; it is then used for building the CDM location, person, observation_period, and payer_plan_period tables.

Does your Truven dataset not include this table?

Thanks,
Ajit

#3

Hello,

We have that table, but not called like that. We basically loaded the sas
files with the same names, and have them separated by year. Do we have to
paste all the years together and rename the files? Documentation is not
clear about the input other than truven data on a mssql database.

Can you provide additional details on how the ETL-CDMbuilder expects the
data other the diagrams in the ETL documents?

Thanks in advance!

#4

@Juan_Banda - yes we concatenate all the year tables together in SQL Server and I believe there is some table renaming.

@Ajit_Londhe - I can’t remember, are we allowed to share the DB structure that we use? That might give @Juan_Banda enough information.

#5

Yes, we can share it with @Juan_Banda directly. I will email him with the DDLs we use for the native schema.

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