Error when running DataQualityDashorad /databaseconnector

Developers
1

Hi all,

We have a BigQuery V5.4 OMOP database.
I’m trying to run the dataqualitydashboard using this script :

script
script646×588 26.2 KB

I encountered this error :

image
image620×614 19.3 KB

More details :

R_logs
R_logs817×238 9.15 KB

Could anyone give me details on what’s going on ? How could I fix this error ?
Would highly appreciate any help.

Best,
Meriem

1 Like
2

The error message is not very helpful, are you able to check your database logs for more info?

One thing I noticed is you’re using createDbiConnectionDetails instead of createConnectionDetails. createDbiConnectionDetails is not fully supported, so that might be causing an issue (see Create DBI connection details — createDbiConnectionDetails • DatabaseConnector).

Also, are you sure your cdm_source table exists?

1 Like
3

Thank you so much for your reply.

  1. I’m working with google cloud platform where my bigquey databased is stored. Where could I find the database logs ?
  2. I will make a try with createConnectionDetails.
  3. cdm_source is named CDM_SOURCE in my database. Could it be the source of the issue ?

Thank you !

4

I have checked and bigquery is not supported by createConnectionDetails.

5

BigQuery is supported! Connecting to Various Database Platforms • DatabaseConnector

You’ll need to check with your IT team about database logs.

However - I think that maybe the table name is the issue as you’ve pointed out! DQD runs this query - https://github.com/OHDSI/DataQualityDashboard/blob/6ef7ee2dd1116741e3fe9907ef4d9cc98eccb96c/R/executeDqChecks.R#L134 - which puts the table name as lowercase. I checked and BigQuery table names are case sensitive by default. So this query will indeed fail for you if your table name is all uppercase and you don’t have case sensitivity disabled in your BigQuery database.

It seems this issue has come up before and folks decided to lowercase everything to be safe: Google BigQuery support update - #17 by cukarthik. The CommonDataModel DDL for BigQuery also does make the tablenames lowercase: https://github.com/OHDSI/CommonDataModel/blob/main/inst/ddl/5.4/bigquery/OMOPCDM_bigquery_5.4_ddl.sql

That said, a lot of OHDSI docs tend to refer to table names in all caps. And the DQD config files have the table names listed in all caps. As a community we should probably either:

  • Decide on one convention and document/encode it consistently everywhere
  • Explicitly allow any casing and build in support for this to all of our tools

I’m not sure if this has already been discussed - @clairblacketer do you know?

1 Like
6

Thank you so much for your reply. Very intersting !
I followed your recommandations by making my BigQuery case insensitive and my DataQualityDashboard is running.
That was vey helpfull!