Need help finding documentation for how to populate cdm_source for DQD

Implementers
1

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

2 Likes
2

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
;

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3

Here is what I see in Athena

4

The cdm_source table is documented on the CommonDataModel page.

1 Like
5

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.

2 Likes
6

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.

2 Likes
7

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

8

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.

1 Like
9

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.