OHDSI Home | Forums | Wiki | Github

Atlas trying to read vocabulary-schema tables in the cdm-schema


(Javier Gracia-Tabuenca) #1

A company is trying set up Atlas in our enviroment.

The system is up and working, but Atlas triggers multiple errors in when calling the webAPI.
For example:

Caused by: com.simba.googlebigquery.support.exceptions.GeneralException: [Simba][BigQueryJDBCDriver](100032) Error executing query job. Message: 404 Not Found
{
  "code" : 404,
  "errors" : [ {
    "domain" : "global",
    "message" : "Not found: Table fg-dev3-library:finngen_omop_cdm.concept was not found in location europe-north1",
    "reason" : "notFound"
  } ],
  "message" : "Not found: Table fg-dev3-library:finngen_omop_cdm.concept was not found in location europe-north1",
  "status" : "NOT_FOUND"
}
        ... 113 more

It seems Atlas tryies to access the table concept in the cdm_schema. However, the table concept should be in the cdm_schema.

They follow the instructions in https://github.com/OHDSI/WebAPI/wiki/CDM-Configuration and configure 4 schemas in BigQuiery.

Is there any configuration we are missing by which in BigQuiery the tables should be defien diferently ?? Or any other clue ??

(from what i’v seen on post @mgkahn seems to have experience in installing CDM on BigQuiery)

Thanks.


(Javier Gracia-Tabuenca) #2

In case someone run on the same problem

we solved this by combining the schemas of vocab and cdm and reconfiguring source daimons for Atlas to recognize them from the same dataset .


(Gregory Klebanov) #3

hi @Javier - the vocabulary tables are a part of CDM and should be always siting in the same schema together with data that these vocabs were used to convert.


(Javier Gracia-Tabuenca) #4

thanks @gregk,

I speak on behalf of the thechnical person installing this:
I think that what was confusing for him is that
webAPI configuration documentation ( here ) uses one schema name for each giving the feeling that these should be in separated schemas.


(Chris Knoll) #5

@Javier,
You are correct that the webAPI documentation does describe multiple schemas when setting up a source:

schema permissions
cdm read-only
vocabulary read-only
results insert/delete/select/update
temp full control (create/remove tables & data)

Depending on your version of WebAPI and Atlas, the ability to use an external vocabulary schema for a WebAPI process may not be completely supported. A stand-alone vocabulary schema makes sense if you want to set up a data source only for vocabulary browsing (so only the vocabulary tables of the CDM schema would be populated).

But, @gregk is correct that the CDM schema encapsulates the vocabulary tables. So, for simplicity, when you are setting up a CDM schema, you should populate it with the vocabulary tables as well.


t