Create cohort/concept set from Circe JSON? about capr

[anthonysena]

Part of my question is answered in the vignette: https://ohdsi.github.io/Capr/articles/CAPR_tutorial.html#importing-existing-json-cohorts

cd2 <- readInCirce("~/Documents/NetworkStudy/COVID/inpatientCovid.json")

I didn't see the option to do this from a ConceptSet JSON but just wanted to note that part of my list above is already addressed. Also, looking at the signature for readInCirce the parameters to connect to the vocabulary is required. I'm wondering why those are required for reading in the Circe JSON?

[mdlavallee92]

Sorry for the delay @anthonysena, github issues were linked to an old email and I missed some of this.

To answer your question about why vocabuaryDatabaseSchema is needed for the readInCirce, the function requires a lookup of the conceptId in the vocabulary tables. The reason for this is because I am using metaprogramming in R to create a series of calls to recreate the inputs of the json. In essence it is doing the getConceptIdDetails command behind the scenes to get the conceptId input in the right format to build a conceptSetExpression. Admittedly it is a bit redundant but it also provides a bug trace to check the R code is compiling properly. Does that make sense?

As for a conceptSetExpression json output, I am happy to render that if there is a standard format I can follow. I will check the circe-be structures. I will work on it in a test branch

[mdlavallee92]

Closing issue since it will no longer apply to capr v2