OHDSI Home | Forums | Wiki | Github

ATLAS: posting concept set

I am having trouble using ROhdsiWebApi call postConceptSetDefinition.
Here is a brief bit of code, where I retrieve an existing concept set definition, then try to post it to the server under a different name. I am not including the code to authenticate against ATLAS because that works well, and it has my password in it.

conceptSet ← getConceptSetDefinition(conceptSetId = 518, baseUrl = webapi_root)
postConceptSetDefinition(name = “BS Test concept”, conceptSetDefinition = conceptSet, baseUrl = webapi_root)

Here is what the console returns after running it:

Error in .request(url, method = “PUT”, config = config, handle = handle, :
Bad Request (HTTP 400).

Is there a permission problem? Is our ATLAS instance misconfigured?
I have been using R programs to post cohort definitions and that code is working well.

Thanks for any suggestions on what I should do differently.

Bradley Slavik

A member of the OHDSI community suggested that I try the “develop” branch of this library. This proved to be a most useful suggestion. This branch worked fine with the postConceptSetDefinition call. I find it curious that the “fix” for this function is over a year old, but the “fix” is still in the “develop” branch and has not been merged into the “master” branch. Does anyone have any insight as to why this merge did not happen many months ago? What is the process for moving code fixes into “master” branch in the OHDSI community? Our team is very interested in using this function. I hope someone can inform me what requests, meetings, tests, etc., need to be performed before this useful code is part of the main branch.


OK. I tried again today to run code for posting concept sets. I tried several version of ROhdsiWebApi from the “master” branch and several from the “develop” branch. None have worked so far. We are running version 2.7.8 of ATLAS. If I can help by writing some tests needed to move the correct code to “master” branch, I am happy to do so. We need the ability to create concept sets from R. There is no alternative. Please offer some guidance.