OHDSI Home | Forums | Wiki | Github

Loading Profiles and Cohort Generation in Atlas

(Taha Abdul-Basser) #21

Thank you. Try running the concept hierarchy table creation SQL that @Chris_Knoll point to you and restarting.

(mintmountain89) #22

Thanks. Query has been running for one day in pgAdminIII and still the query isn’t completed. Any advice?

(Chris Knoll) #23

Could be a hardware performance problem, or lack of indexes on the vocabulary table. I understand that there are a set of PostgreSQL indexes published somewhere. @pavgra, do you have a set of indexes that you use on the vocabulary tables?

(Pavel Grafkin) #24

I think that we were always satisfied with the set of indexes provided by CommonDataModel repo.

(Chris Knoll) #25

Ok, for postgresql, those indexes are found here:

@hui_xing_tan: It shouldn’t take that long (under an hour) to create that concept hierarchy table. So, I’d kill the job, and apply the indexes that are described under the ‘standardized vocabulary’ section of the above link.

(mintmountain89) #26

Thank you! I tried out the query to apply the indexes. It has been running for a few hours as well…

Is there a site you can direct me to get the ddl for all the achilles results tables? I have the sample results data and can import the concept_hierarchy directly too to see if Atlas works once the table is inserted into the results schema