OHDSI Home | Forums | Wiki | Github

Tip: Achilles RC/PC/DRC/DPC counts in Atlas

Implementers
#1

Hello Atlas implementers,

I didn’t realize this until today that we had this officially available: if you are using Atlas 2.11.0 or greater, you can populate the results table “achilles_result_concept_count” for showing record count / person count / desc RC / desc PC in concept results using this endpoint:

/WebAPI/ddl/achilles
(demo site: https://atlas-demo.ohdsi.org/WebAPI/ddl/achilles)

This was originally going to be in Achilles package, but now is simply a script that you can grab and run.

Thank you @Sergey and @Anton_Abushkevich for adding this!

Thanks,
Ajit

4 Likes
#2

if atlas ver is under 2.11 , can not execute scirpt that you make?

Record counts and Patient counts on non-stand concepts
Patient Counts on Non-Standard Concepts?
#3

Great work! Can Achilles also still be used to calculate and show the RC/DRC? Or do we have to use the new achilles_result_concept_count table?

#4

Achilles computes RC/DRC if optimizeAtlasCache = TRUE. But then this endpoint drops it and recreates it with PC/DPC.

I think we may want to drop optimizeAtlasCache from Achilles altogether in favor of this WebAPI endpoint to avoid overlap.

1 Like
#5

I believe only in 2.11.0 and beyond.

#6

@Ajit_Londhe

We have Atlas/WebAPI 2.11.1, but the endpoint /WebAPI/ddl/achilles doesn’t work. However, the endpoint /WebAPI/info returns expected values.

Any idea where the issue might be?

Thanks
Jack

#7

Do you have security enabled? If so, it is not directly accessible from the browser, you’d need to authenticate with a security token. This is fixed in the new 2.12.1 release (https://github.com/OHDSI/WebAPI/issues/2183).

#8

@Ajit_Londhe Thanks, it explains. I will keep an eye on it when the new upgrades are in place.

#9

My workaround is to use the Atlas Demo site. Here’s my R code:

 achillesTablesUrl <- sprintf("%s/ddl/achilles?dialect=%s&schema=%s&vocabSchema=%s",
                            "https://atlas-demo.ohdsi.org/WebAPI",
                            connectionDetails$dbms,
                            resultsDatabaseSchema,
                            cdmDatabaseSchema)


response <- httr::GET(url = achillesTablesUrl)
achillesRcSql <- httr::content(response)
#10

However, even this needs a workaround if you’re on Redshift. This SQL includes some casting to varchar that then don’t play nice with the inserts: https://github.com/OHDSI/WebAPI/issues/2194.

Changing the final insert to cast the concept ids back to ints avoids cast errors.

t