removing google oauth2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ieugwasr
 Title: Interface to the 'OpenGWAS' Database API
-Version: 0.2.2-9003
+Version: 1.0.0
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-0920-1055")),
@@ -25,7 +25,6 @@ Imports:
     jsonlite,
     magrittr,
     rlang,
-    googleAuthR,
     stats
 Suggests: 
     knitr,

NAMESPACE

@@ -14,7 +14,6 @@ export(batches)
 export(check_access_token)
 export(editcheck)
 export(fill_n)
-export(get_access_token)
 export(get_opengwas_jwt)
 export(get_query_content)
 export(gwasinfo)
@@ -27,7 +26,6 @@ export(ld_reflookup)
 export(legacy_ids)
 export(logging_info)
 export(phewas)
-export(revoke_access_token)
 export(select_api)
 export(tophits)
 export(user)

NEWS.md

@@ -1,5 +1,6 @@
 # ieugwasr 1.0.0
 * Introducing JWT authorisation for the API
+* Phasing out Google Oauth2 authorisation
 * Added user() function to get user information
 * Fixing issue with anonymous functions and backwards compatibility
 * Bug in tophits when result is empty

R/afl2.r

@@ -7,14 +7,15 @@
 #'
 #' @param variantlist Choose pre-defined list. reduced = ~20k SNPs that are 
 #' common in all super populations (default). hapmap3 = ~1.3 million hm3 SNPs
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
-afl2_list <- function(variantlist=c("reduced", "hapmap3")[1])
+afl2_list <- function(variantlist=c("reduced", "hapmap3")[1], opengwas_jwt=get_opengwas_jwt())
 {
 	if(variantlist == "reduced")
 	{
-		api_query("variants/afl2/snplist") %>% 
+		api_query("variants/afl2/snplist", opengwas_jwt=opengwas_jwt) %>% 
 			get_query_content() %>%
 			dplyr::as_tibble() %>%
 			return()
@@ -33,12 +34,13 @@ afl2_list <- function(variantlist=c("reduced", "hapmap3")[1])
 #'
 #' @param rsid Vector of rsids
 #' @param reference Default=`"1000g"`
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
-afl2_rsid <- function(rsid, reference="1000g")
+afl2_rsid <- function(rsid, reference="1000g", opengwas_jwt=get_opengwas_jwt())
 {
-	out <- api_query("variants/afl2", list(rsid=rsid)) %>% get_query_content()
+	out <- api_query("variants/afl2", list(rsid=rsid), opengwas_jwt=opengwas_jwt) %>% get_query_content()
 	if(inherits(out, "response"))
 	{
 		return(out)
@@ -54,12 +56,13 @@ afl2_rsid <- function(rsid, reference="1000g")
 #' @param chrpos list of `<chr>:<pos>` in build 37, e.g. `c("3:46414943", "3:122991235")`. 
 #' Also allows ranges e.g `"7:105561135-105563135"`
 #' @param reference Default=`"1000g"`
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return Data frame containing ancestry specific LD scores and allele frequencies for each variant
-afl2_chrpos <- function(chrpos, reference="1000g")
+afl2_chrpos <- function(chrpos, reference="1000g", opengwas_jwt=get_opengwas_jwt())
 {
-	out <- api_query("variants/afl2", list(chrpos=chrpos)) %>% get_query_content()
+	out <- api_query("variants/afl2", list(chrpos=chrpos), opengwas_jwt=opengwas_jwt) %>% get_query_content()
 	if(inherits(out, "response"))
 	{
 		return(out)
@@ -79,14 +82,15 @@ afl2_chrpos <- function(chrpos, reference="1000g")
 #' e.g. output from associations
 #' @param snpinfo Output from [`afl2_list`], [`afl2_rsid`] or [`afl2_chrpos`]. 
 #' If `NULL` then [`afl2_list()`] is used by default
+#' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
 #'
 #' @export
 #' @return data frame ordered by most likely ancestry, each row represents a super population and cor column represents the correlation between the GWAS dataset and the 1000 genomes super population allele frequencies
-infer_ancestry <- function(d, snpinfo=NULL)
+infer_ancestry <- function(d, snpinfo=NULL, opengwas_jwt=get_opengwas_jwt())
 {
 	if(is.null(snpinfo))
 	{
-		snpinfo <- afl2_list()
+		snpinfo <- afl2_list(opengwas_jwt=opengwas_jwt)
 	}
 	snpinfo <- snpinfo %>%
 		dplyr::inner_join(., d, by="rsid")
@@ -100,30 +104,3 @@ infer_ancestry <- function(d, snpinfo=NULL)
 	return(out)
 }
 
-#' Look up sample sizes when meta data is missing from associations
-#'
-#' @param d Output from [`associations`]
-#'
-#' @export
-#' @return Data frame which is an updated version of the input but with sample sizes inferred where missing
-fill_n <- function(d)
-{
-	id <- d$id[1]
-	if(! "n" %in% names(d))
-	{
-		d$n <- NA
-	}
-	d$n <- as.numeric(d$n)
-	if(any(is.na(d$n)))
-	{
-		info <- gwasinfo(id)
-		if(!is.na(info$sample_size))
-		{
-			d$n <- info$sample_size
-		} else {
-			d$n <- info$ncase + info$ncontrol
-		}
-	}
-	return(d)	
-}
-

R/api.R

@@ -67,57 +67,14 @@ logging_info <- function()
 }
 
 
-#' Get access token for OAuth2 access to MR Base
+#' Check if authentication has been maded
 #'
-#'
-#' @export
-#' @return access token string
-get_access_token <- function()
-{
-	message("Using access token. For info on how this is used see logging_info()")
-	tf <- basename(tempfile())
-	check <- suppressWarnings(file.create(tf))
-	if(!check)
-	{
-		stop("You are currently in a directory which doesn't have write access.\n",
-			"  In order to authenticate we need to store the credentials in a file called '.httr-oauth'.\n",
-			"  Please setwd() to a different directory where you have write access.")
-	} else {
-		unlink(tf)
-	}
-	a <- googleAuthR::gar_auth(email=TRUE)
-	if(! a$validate())
-	{
-		a$refresh()
-	}
-	return(a$credentials$access_token)
-}
-
-
-#' Check if authentication has been made
-#'
-#' If a call to [`get_access_token()`] has been made then it will have generated `mrbase.oauth`. 
-#' Pass the token if it is present, if not, return `NULL` and do not authenticate.
+#' Deprectated. Use `get_opengwas_jwt()` instead. See https://mrcieu.github.io/ieugwasr/articles/guide.html#authentication for more information.
 #'
 #' @export
 #' @return NULL or access_token depending on current authentication state
 check_access_token <- function()
 {
-	if(file.exists("ieugwasr_oauth"))
-	{
-		return(get_access_token())
-	} else {
-		return(NULL)
-	}
+	message("Deprectated. Use `get_opengwas_jwt()` instead. See https://mrcieu.github.io/ieugwasr/articles/guide.html#authentication for more information.")
 }
 
-
-#' Revoke access token for MR Base
-#'
-#' @export
-#' @return No return value, called for side effects
-revoke_access_token <- function()
-{
-	a <- googleAuthR::gar_auth("mrbase.oauth")
-	a$revoke()
-}

R/ld_clump.R

@@ -27,8 +27,6 @@
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`. 
 #' `'legacy'` also available - which is a previously used verison of the EUR 
 #' panel with a slightly different set of markers
-#' @param access_token Google OAuth2 access token. 
-#' Used to authenticate level of access to data. By default, checks if already 
 #' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' 
 #' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @param plink_bin If `NULL` and `bfile` is not `NULL` then will detect 
@@ -38,7 +36,7 @@
 #' @export
 #' @return Data frame
 ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99, 
-                     pop = "EUR", access_token=check_access_token(),opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL)
+                     pop = "EUR", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL)
 {
 
 	stopifnot("rsid" %in% names(dat))
@@ -79,7 +77,7 @@ ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99,
 			message("Clumping ", ids[i], ", ", nrow(x), " variants, using ", pop, " population reference")
 			if(is.null(bfile))
 			{
-				res[[i]] <- ld_clump_api(x, clump_kb=clump_kb, clump_r2=clump_r2, clump_p=clump_p, pop=pop, access_token=access_token, opengwas_jwt=opengwas_jwt)
+				res[[i]] <- ld_clump_api(x, clump_kb=clump_kb, clump_r2=clump_r2, clump_p=clump_p, pop=pop, opengwas_jwt=opengwas_jwt)
 			} else {
 				res[[i]] <- ld_clump_local(x, clump_kb=clump_kb, clump_r2=clump_r2, clump_p=clump_p, bfile=bfile, plink_bin=plink_bin)
 			}
@@ -99,11 +97,9 @@ ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99,
 #' @param clump_p Clumping sig level for index variants. Default = `1` (i.e. no threshold)
 #' @param pop Super-population to use as reference panel. Default = `"EUR"`. 
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`
-#' @param access_token Google OAuth2 access token. 
-#' Used to authenticate level of access to data. By default, checks if already 
 #' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @return Data frame of only independent variants
-ld_clump_api <- function(dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR", access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt())
+ld_clump_api <- function(dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR", opengwas_jwt=get_opengwas_jwt())
 {
 	res <- api_query('ld/clump',
 			query = list(
@@ -114,7 +110,7 @@ ld_clump_api <- function(dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR",
 				kb = clump_kb,
 				pop = pop
 			),
-			access_token=access_token, opengwas_jwt=opengwas_jwt
+			opengwas_jwt=opengwas_jwt
 		) %>% get_query_content()
 	y <- subset(dat, !dat[["rsid"]] %in% res)
 	if(nrow(y) > 0)
@@ -190,20 +186,18 @@ random_string <- function(n=1, len=6)
 #' @param rsid Array of rsids to check
 #' @param pop Super-population to use as reference panel. Default = `"EUR"`. 
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`
-#' @param access_token Google OAuth2 access token. 
-#' Used to authenticate level of access to data. By default, checks if already 
 #' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
 #'
 #' @export
 #' @return Array of rsids that are present in the LD reference panel
-ld_reflookup <- function(rsid, pop='EUR', access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt())
+ld_reflookup <- function(rsid, pop='EUR', opengwas_jwt=get_opengwas_jwt())
 {
 	res <- api_query('ld/reflookup',
 			query = list(
 				rsid = rsid,
 				pop = pop
 			),
-			access_token=access_token, opengwas_jwt=opengwas_jwt
+			opengwas_jwt=opengwas_jwt
 		) %>% get_query_content()
 	if(length(res) == 0)
 	{

R/ld_matrix.R

@@ -26,16 +26,14 @@
 #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR"`. 
 #' `'legacy'` also available - which is a previously used verison of the EUR 
 #' panel with a slightly different set of markers
-#' @param access_token Google OAuth2 access token. 
-#' Used to authenticate level of access to data. By default, checks if already 
 #' @param opengwas_jwt Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.#' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @param bfile If this is provided then will use the API. Default = `NULL`
 #' @param plink_bin If `NULL` and bfile is not `NULL` then will detect packaged 
 #' plink binary for specific OS. Otherwise specify path to plink binary. Default = `NULL`
 #'
 #' @export
 #' @return Matrix of LD r values
-ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL) {
+ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL) {
 	if(length(variants) > 500 & is.null(bfile))
 	{
 		stop("SNP list must be smaller than 500. Try running locally by providing local ld reference with bfile argument. See vignettes for a guide on how to do this.")
@@ -52,7 +50,7 @@ ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", access_token=check
 		return(ld_matrix_local(variants, bfile=bfile, plink_bin=plink_bin, with_alleles=with_alleles))
 	}
 
-	res <- api_query('ld/matrix', query = list(rsid=variants, pop=pop), access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	res <- api_query('ld/matrix', query = list(rsid=variants, pop=pop), opengwas_jwt=opengwas_jwt) %>% get_query_content()
 
 	if(all(is.na(res))) stop("None of the requested variants were found")
 	variants2 <- res$snplist