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cpicpgx / cpic-data

CPIC Data definitions and code to use that data
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Call API from inside R to get CSV results #10

Open vojtechhuser opened 3 years ago

vojtechhuser commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

@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 commented 3 years ago

@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.