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Need help finding documentation for how to populate cdm_source for DQD

I’m following the instructions at the link below to set up DQD for my local instance of OMOP.

I’m getting this error:
Error in DataQualityDashboard::executeDqChecks(connectionDetails = connectionDetails, :
Please populate the cdm_source table before executing data quality checks.
In addition: Warning message:
In for (i in 1:length(args)) { : closing unused connection 3 ()

I’m not seeing documentation that indicates how to populate this table.

Does this documentation exist somewhere?

How do I figure out what values to use to populate this table?

These are the columns of cdm_source I’m seeing:

cdm_source_name
cdm_source_abbreviation
cdm_holder
source_description,
source_documentation_references,
cdm_etl_reference,
source_release_date,
cdm_release_date,
cdm_version,
cdm_version_concept_id,
vocabulary_version

Ouch, I’m not seeing 5.4 as a cdm version in the concept table I have. Am I looking in the correct place?

My vocab version is v5.0 04-FEB-22 (downloaded from Athena last week)

select * from concept
where lower(concept_name) like ‘%vocab%version%’
order by concept_name
;

Here is what I see in Athena

The cdm_source table is documented on the CommonDataModel page.

Hi,

Thanks for the link but for beginners like me its difficult to make out certain things of setting up this tool for the very first time.

With the in-adequate and unavailable documentation of DQD, it makes the work bit more annoying and time taking.

Apologies for the tone but would really appreciate if a documentation of CDM_SOURCE containing some examples of “what kind of values” goes for each row might help the new comers as well. This can be made as a new column with header like “Example values”.

Would be great if this is available as I still have issues as to what to fill in those columns in my Redshift database tables.

Thanks in advance.

Hi @ranatech. The DQD documentation is actually very detailed, if you know where to find it: Execute and View Data Quality Checks on OMOP CDM Database • DataQualityDashboard.
As a tip: nearly all OHDSI R packages have such an ‘github.io’ documentation page that can be found from Github repository.

And I agree that an example row for all OMOP CDM tables might be a nice addition to the CDM documentation. There is actually an example of how you can populate the CDM Source table on the CommonDataModel documentation.

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Thanks a ton @MaximMoinat . Please allow me sometime to go through the shared material. Appreciate your prompt response!!

You’re welcome. While browsing the CDM documentation, I also stumbled across an example of the CDM Source: sqlScripts.knit.

I will update my original response as well for future reference.

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Hi Maxim,

Not sure if this is the right thread to ping the issue but need 2 cents on the below issue.
Using the link shared by you above, I had inserted the values of cdm_source using the query editor in my Redshift database table. However, upon successfully establishing the connection from Rstudio to Redshift, I don’t seem to have the data in the cdm_source table. But if I query directly in Redshift query editor, I could see the 1 entry in cdm_source. Can you please advise?

Alternatively, I then manually inserted the data from within the Rstudio using the below command, post which I could execute the DQ checks.

dbGetQuery(conn,"insert into synthea100k.cdm_source (......) select .....")

Thanks in advance.

t