reinstating google oauth temporarily

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ieugwasr
 Title: Interface to the 'OpenGWAS' Database API
-Version: 0.2.2-9000
+Version: 0.2.2-9001
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-0920-1055")),
@@ -25,6 +25,7 @@ Imports:
     jsonlite,
     magrittr,
     rlang,
+    googleAuthR,
     stats
 Suggests: 
     knitr,

NAMESPACE

@@ -11,8 +11,10 @@ export(api_status)
 export(associations)
 export(batch_from_id)
 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)
@@ -25,6 +27,7 @@ export(ld_reflookup)
 export(legacy_ids)
 export(logging_info)
 export(phewas)
+export(revoke_access_token)
 export(select_api)
 export(tophits)
 export(user)

R/api.R

@@ -62,3 +62,59 @@ logging_info <- function()
 		"c) to monitor inappropriate or unfair usage.\n",
 		"We do NOT log the queries that are being performed, and we do NOT share your email address with anybody else.")
 }
+
+
+#' Get access token for OAuth2 access to MR Base
+#'
+#'
+#' @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.
+#'
+#' @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)
+	}
+}
+
+
+#' 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

@@ -27,6 +27,8 @@
 #' 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 
@@ -36,7 +38,7 @@
 #' @export
 #' @return Data frame
 ld_clump <- function(dat=NULL, clump_kb=10000, clump_r2=0.001, clump_p=0.99, 
-                     pop = "EUR", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL)
+                     pop = "EUR", access_token=check_access_token(),opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL)
 {
 
 	stopifnot("rsid" %in% names(dat))
@@ -77,7 +79,7 @@ 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, opengwas_jwt=opengwas_jwt)
+				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)
 			} 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)
 			}
@@ -97,9 +99,11 @@ 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", opengwas_jwt=get_opengwas_jwt())
+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())
 {
 	res <- api_query('ld/clump',
 			query = list(
@@ -110,7 +114,7 @@ ld_clump_api <- function(dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR",
 				kb = clump_kb,
 				pop = pop
 			),
-			opengwas_jwt=opengwas_jwt
+			access_token=access_token, opengwas_jwt=opengwas_jwt
 		) %>% get_query_content()
 	y <- subset(dat, !dat[["rsid"]] %in% res)
 	if(nrow(y) > 0)
@@ -186,18 +190,20 @@ 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', opengwas_jwt=get_opengwas_jwt())
+ld_reflookup <- function(rsid, pop='EUR', access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt())
 {
 	res <- api_query('ld/reflookup',
 			query = list(
 				rsid = rsid,
 				pop = pop
 			),
-			opengwas_jwt=opengwas_jwt
+			access_token=access_token, opengwas_jwt=opengwas_jwt
 		) %>% get_query_content()
 	if(length(res) == 0)
 	{

R/ld_matrix.R

@@ -26,14 +26,16 @@
 #' 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", opengwas_jwt=get_opengwas_jwt(), bfile=NULL, plink_bin=NULL) {
+ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", access_token=check_access_token(), 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.")
@@ -50,7 +52,7 @@ ld_matrix <- function(variants, with_alleles=TRUE, pop="EUR", opengwas_jwt=get_o
 		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), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	res <- api_query('ld/matrix', query = list(rsid=variants, pop=pop), access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
 
 	if(all(is.na(res))) stop("None of the requested variants were found")
 	variants2 <- res$snplist

R/query.R

@@ -5,6 +5,8 @@
 #'
 #' @param path Either a full query path (e.g. for get) or an endpoint (e.g. for post) queries
 #' @param query If post query, provide a list of arguments as the payload. `NULL` by default
+#' @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 method `"GET"` (default) or `"POST"`, `"DELETE"` etc
 #' @param silent `TRUE`/`FALSE` to be passed to httr call. `TRUE` by default
@@ -14,13 +16,14 @@
 #'
 #' @export
 #' @return httr response object
-api_query <- function(path, query=NULL, opengwas_jwt=get_opengwas_jwt(), 
+api_query <- function(path, query=NULL, access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt(), 
                       method="GET", silent=TRUE, encode="json", timeout=300)
 {
 	ntry <- 0
 	ntries <- 5
 	headers <- httr::add_headers(
 		# 'Content-Type'='application/json; charset=UTF-8',
+		'X-Api-Token'=access_token,
 		'Authorization'=paste("Bearer", opengwas_jwt=opengwas_jwt),
 		'X-Api-Source'=ifelse(is.null(options()$mrbase.environment), 'R/TwoSampleMR', 'mr-base-shiny'),
 		'X-TEST-MODE-KEY'=Sys.getenv("OPENGWAS_X_TEST_MODE_KEY")
@@ -157,19 +160,21 @@ print.ApiStatus <- function(x, ...)
 #'
 #' @param id List of MR-Base IDs to retrieve. If `NULL` (default) retrieves all 
 #' available datasets
+#' @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.
 #'
 #' @export
 #' @return Dataframe of details for all available studies
-gwasinfo <- function(id=NULL, opengwas_jwt=get_opengwas_jwt())
+gwasinfo <- function(id=NULL, access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt())
 {
 	id <- legacy_ids(id)
 	if(!is.null(id))
 	{
 		stopifnot(is.vector(id))
-		out <- api_query('gwasinfo', query = list(id=id), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+		out <- api_query('gwasinfo', query = list(id=id), access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
 	} else {
-		out <- api_query('gwasinfo', opengwas_jwt=opengwas_jwt) %>% get_query_content()
+		out <- api_query('gwasinfo', access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
 	}
 	if(length(out) == 0)
 	{
@@ -204,14 +209,15 @@ batch_from_id <- function(id)
 
 #' Get list of data batches in IEU GWAS database
 #'
-#'
+#' @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.
 #'
 #' @export
 #' @return data frame
-batches <- function(opengwas_jwt=get_opengwas_jwt())
+batches <- function(access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt())
 {
-	api_query('batches', opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	api_query('batches', access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
 }
 
 #' Query specific variants from specific GWAS
@@ -232,11 +238,13 @@ batches <- function(opengwas_jwt=get_opengwas_jwt())
 #' `1` = yes (default), `0` = no
 #' @param palindromes Allow palindromic SNPs (if `proxies = 1`). `1` = yes (default), `0` = no
 #' @param maf_threshold MAF threshold to try to infer palindromic SNPs. Default = `0.3`.
+#' @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.
 #'
 #' @export
 #' @return Dataframe
-associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold = 0.3, opengwas_jwt=get_opengwas_jwt()) {
+associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold = 0.3, access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt()) {
 	id <- legacy_ids(id)
 	out <- api_query("associations", query=list(
 		variant=variants,
@@ -246,7 +254,7 @@ associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palin
 		align_alleles=align_alleles,
 		palindromes=palindromes,
 		maf_threshold=maf_threshold
-	), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	), access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
 
 	if(inherits(out, "response"))
 	{
@@ -307,17 +315,19 @@ fix_n <- function(d)
 #' @param variants Array of variants e.g. `c("rs234", "7:105561135-105563135")`
 #' @param pval p-value threshold. Default = `0.00001`
 #' @param batch Vector of batch IDs to search across. If `c()` (default) then returns all batches
+#' @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.
 #'
 #' @export
 #' @return Dataframe
-phewas <- function(variants, pval = 0.00001, batch=c(), opengwas_jwt=get_opengwas_jwt())
+phewas <- function(variants, pval = 0.00001, batch=c(), access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt())
 {
 	out <- api_query("phewas", query=list(
 		variant=variants,
 		pval=pval,
 		index_list=batch
-	), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	), access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
 
 	if(!inherits(out, "response")) {
 		out <- out %>% dplyr::as_tibble() %>% fix_n()
@@ -349,12 +359,14 @@ phewas <- function(variants, pval = 0.00001, batch=c(), opengwas_jwt=get_opengwa
 #' If force_server = `TRUE` then will recompute using server side LD reference panel.
 #' @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.
 #'
 #' @export
 #' @return Dataframe
 tophits <- function(id, pval=5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR", 
-                    force_server = FALSE, opengwas_jwt=get_opengwas_jwt()) {
+                    force_server = FALSE, access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt()) {
 	id <- legacy_ids(id)
 	if(clump == 1 & r2 == 0.001 & kb == 10000 & pval == 5e-8)
 	{
@@ -374,7 +386,7 @@ tophits <- function(id, pval=5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR",
 		r2=r2,
 		kb=kb,
 		pop=pop
-	), opengwas_jwt=opengwas_jwt) %>% get_query_content()
+	), access_token=access_token, opengwas_jwt=opengwas_jwt) %>% get_query_content()
 	if(inherits(out, "response"))
 	{
 		return(out)
@@ -391,15 +403,17 @@ tophits <- function(id, pval=5e-8, clump = 1, r2 = 0.001, kb = 10000, pop="EUR",
 #' Check datasets that are in process of being uploaded
 #'
 #' @param id ID
+#' @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.
 #'
 #' @export
 #' @return Dataframe
-editcheck <- function(id, opengwas_jwt=get_opengwas_jwt())
+editcheck <- function(id, access_token=check_access_token(), opengwas_jwt=get_opengwas_jwt())
 {
 	api <- options()[["ieugwasr_api"]]
 	select_api("private")
-	out <- api_query(paste0("edit/check/", id), opengwas_jwt=opengwas_jwt) %>%
+	out <- api_query(paste0("edit/check/", id), access_token=access_token, opengwas_jwt=opengwas_jwt) %>%
 		get_query_content()
 	options(ieugwasr_api=api)
 	return(out)