harriscw commented 5 months ago

This warning kicks off for run_all_checks even when there is no issue for roche users who use roche_covid_df().

https://github.com/pharmaverse/sdtmchecks/blob/44f42f775635bcb4f1b1c3a7aab914868a398c88/R/run_all_checks.R#L98

I ran run_all_checks just now using the correct pipeline and get this warning even though covid related checks run. roche_covid_df looks at TS to get meddra version then uses appropriate terms from a bunch of files that are assumed to have been read in. So covid_df itself is not needed for run_all_checks, just whatever roche_covid_df() needs.

I think the simplest update would be expand the if() condition of this warning to encompass roche_covid_df()'s input needs

sarabodach commented 5 months ago

Other covid_df() issues -- #220 , #234, #239

jimrothstein commented 1 month ago

306

The covid_df if
```
if(!("covid_df" %in% ls(envir = .GlobalEnv))){ 
```
in run_all_checks is run AFTER all the checks have been run with mcapply
So I think running the covid if (and any other critieria) BEFORE and then adjusting metads will help with this problem
Since I am new, this might be a bit much for me. But I would like to take look.

sarabodach commented 1 month ago

Hi @jimrothstein - thanks for taking a look at this issue! Before you spend more time on it, I think @harriscw is considering an alternate handling for covid_df and may deprecate this portion, so the issue may resolve itself. Thanks!

sarabodach commented 3 weeks ago

Hi @jimrothstein - for this covid_df() issue - please note that there is PR #339 soon to be merged in that will update the handling and pass a vector with a few default terms instead of expecting a dataframe.

pharmaverse / sdtmchecks

run_all_checks inaccurate warning #306

306