update GHA- revert tp pkgdown

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.15.10
+Version: 1.15.11
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",

R/find_sumstats.R

@@ -4,6 +4,24 @@
 #' a case-insensitive substring search in the respective metadata column.
 #' Users can supply a single character string or a
 #' list/vector of character strings.
+#' 
+#' To authenticate, you need to generate a token from the OpenGWAS website. The 
+#' token behaves like a password, and it will be used to authorise the requests 
+#' you make to the OpenGWAS API. Here are the steps to generate the token and 
+#' then have `ieugwasr` automatically use it for your queries:
+#' 1. Login to https://api.opengwas.io/profile/
+#' 2. Generate a new token
+#' 3. Add `OPENGWAS_JWT=<token>` to your .Renviron file, thi can be edited in R
+#' by running `usethis::edit_r_environ()`
+#' 4. Restart your R session
+#' 5. To check that your token is being recognised, run 
+#' `ieugwasr::get_opengwas_jwt()`. If it returns a long random string then you 
+#' are authenticated.
+#' 6. To check that your token is working, run `ieugwasr::user()`. It will make a 
+#' a request to the API for your user information using your token. It should 
+#' return a list with your user information. If it returns an error, then your 
+#' token is not working.
+#' 7. Make sure you have submitted use
 #'
 #' By default, returns metadata for all studies currently in Open GWAS database.
 #'

README.Rmd

@@ -107,6 +107,25 @@ See the [OpenGWAS vignette website](https://al-murphy.github.io/MungeSumstats/ar
 for information on how to use MungeSumstats to access, standardise and perform
 quality control on GWAS Summary Statistics from the MRC IEU [Open GWAS Project](https://gwas.mrcieu.ac.uk/).
 
+**NOTE** to authenticate, you need to generate a token from the OpenGWAS website. 
+The token behaves like a password, and it will be used to authorise the requests 
+you make to the OpenGWAS API. Here are the steps to generate the token and then 
+have `ieugwasr` automatically use it for your queries:
+
+1. Login to https://api.opengwas.io/profile/
+2. Generate a new token
+3. Add `OPENGWAS_JWT=<token>` to your .Renviron file, thi can be edited in R by 
+running `usethis::edit_r_environ()`
+4. Restart your R session
+5. To check that your token is being recognised, run 
+`ieugwasr::get_opengwas_jwt()`. If it returns a long random string then you are 
+authenticated.
+6. To check that your token is working, run `ieugwasr::user()`. It will make a 
+request to the API for your user information using your token. It should return 
+a list with your user information. If it returns an error, then your token is 
+not working.
+7. Make sure you have submitted use
+
 Please read carefully through the [FAQ website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ) 
 for an queries about running MungeSumstats. If you have any outside of this 
 problems please do file an [Issue](https://github.com/al-murphy/MungeSumstats/issues)