Call API from inside R to get CSV results

[vojtechhuser]

To help users, can you please provide R code that calls theapi call and gets CSV back

e.g. for this call
https://api.cpicpgx.org/v1/guideline?select=*,publication(title,pmid,year)&order=name

The default format for API responses is JSON. However, PostgREST has built-in support for responding to any request in CSV format. Use the Accept HTTP header with a value of text/csv.

[vojtechhuser]

this can be closed.
I found a way.

Yet pagination of results is a problem. I want to get full publication table

url='https://api.cpicpgx.org/v1/guideline?select=*,publication(title,pmid,year)&order=name'
#url='https://api.cpicpgx.org/v1/guideline?select=*,publication(*)'

library(httr)

r=GET(url,add_headers(Accept = "text/csv"))
r
http_status(r)
df=content(r)
nrow(df)
df

[whaleyr]

@vojtechhuser The request you're currently working with is bascially saying "give me all the guideline records and include related publications inside those guidelines".

I think what you're asking for is "give me all the publication records that are associated with a guideline". That request would be:
https://api.cpicpgx.org/v1/publication?guidelineid=not.is.null

See in that request you're asking for /publication instead of /guideline and then filtering on the guidelineid property of the publication data model.

Does that get you what you want?

[whaleyr]

@vojtechhuser One other thing. I just saw that I already have an example call for this in the Postman "quickstart" examples:
https://documenter.getpostman.com/view/1446428/Szt78VUJ?version=latest#a9cee1e5-b041-4b01-8f07-8feee18380b2

I've been leaving language-specific exmaples of API calls to Postman since they have a good set of popular language/frameworks (see the "LANGUAGE" select box at the top of the Postman page). Unfortunately, they don't include R in there. I'll update the cpic-data wiki docs to include a link to the httr docs for R folks.