Loading Profiles and Cohort Generation in Atlas

t_abdul_basser · November 13, 2018, 10:44pm

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

hui_xing_tan · November 14, 2018, 9:36am

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

Chris_Knoll · November 14, 2018, 3:09pm

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?

pavgra · November 14, 2018, 4:16pm

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

Chris_Knoll · November 14, 2018, 4:31pm

Ok, for postgresql, those indexes are found here:

github.com

OHDSI/CommonDataModel/blob/master/PostgreSQL/OMOP CDM postgresql pk indexes.txt

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@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.

hui_xing_tan · November 16, 2018, 11:11pm

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

vkramdev · December 19, 2018, 1:35pm

@Chris_Knoll

I am trying to view the dashboard in atlas. I am unable to load the data.

When i tried to check the cause i could find below error :
org.postgresql.util.PSQLException: ERROR: relation “webapi.achilles_results” does not exist.

Indeed there is no table as such in the webapi schema. My question is where do i get the table structure or some DDL statements to create the table.

I am using WebAPI v 2.4.3 .

Thanks.

t_abdul_basser · January 8, 2019, 6:44pm

@vkramdev While you have probably already found an answer to your question, I just want to document the answer here for others who may be new to the OHDSI tools: Achilles results tables (e.g.achilles_results) are generated when you run Achilles against a CDM/source.