For the R2D2-C3PO (COVID-19 research collaboration with pSCANNER), we setting up a shared project Atlas for internal project work, and we like to download from the atlas-ohdsi.org and upload into our project Atlas. We know we can do this one by one but is there a way can we do this in bulk? @krfeeney has been teaching some Atlas tricks, I’m including her to. Thanks! Lisa
Yes, it should be fairly simple since you can talk to both systems over HTTP. Assuming you have a list of concept IDs or cohort IDs, you would:
Fetch the expression from the atlas-ohdsi.org WebAPI instance via HTTP.
POST/PUT the content bak to your own instance.
You need to keep track of the IDs between them. atlas-ohdsi.org cohortID of 1717 will not be your imported cohort ID.
This website provides the complete HTTP API to access webapi: http://webapidoc.ohdsi.org/index.html#home. You can navigate to the end points by navigation on the right. Each endpoint will tell you what the path is, and what datastructure it expects.
I suggest starting out writing a simple R script that pulls a given cohort definition from WebAPI. Then try to forward that expression into a POST (create) request on the other WebAPI. After you get those maneuvers down, it’s a simple matter to just feed it a big list and loop through them.
- I think a concept of CohortGroup should be included in our informatics universe. (and supported by all core tools).
related issue https://github.com/OHDSI/CohortDiagnostics/issues/14
- did you mean url without - ? like https://atlas.ohdsi.org/
Thank you so much for that information. Since the API at https://atlas.ohdsi.org/WebAPI is secured with Google authentication would anyone have any sample code to generate and use the tokens for this purpose?
It’s an open question, and there is discussion on accessing a security-enabled WebAPI here. Since this is directly related to the topic raised (communicating with WebAPI in order to perform batch operations) I have no problem discussing it here, but specific conversations related to secured access should probably go there.
Thank you very much for your quick reply, this is helpful. I did pose the question regarding sample code for Google authentication on the other thread you mentioned.