fixed issues for cran release

Author: explodecomputer

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ieugwasr
 Title: Interface to the 'OpenGWAS' Database API
-Version: 0.1.7
+Version: 0.2.0
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,7 @@
+# ieugwasr 0.2.0
+* Moving API address to https://api.opengwas.org/api/
+* Fixing issues for CRAN release
+
 # ieugwasr 0.1.7
 * Added functions to write LD scores files into compressed `.gz` files for each super-population and divided by chromosomes.
 * Added argument to output [gwasglue2](https://mrcieu.github.io/gwasglue2/) objects in `ieugwasr::tophits()` and `ieugwasr::associations()`.

R/api.R

@@ -9,7 +9,7 @@
 select_api <- function(where="public", silent=FALSE)
 {
 	url <- switch(where,
-		public = "http://gwas-api.mrcieu.ac.uk/",
+		public = "https://api.opengwas.io/api/",
 		private = "http://ieu-db-interface.epi.bris.ac.uk:8082/",
 		dev1 = "http://localhost:8019/",
 		dev2 = "http://127.0.0.1:5000/"

R/query.R

@@ -241,19 +241,9 @@ batches <- function(access_token = check_access_token())
 #' if not then does not perform authentication
 #'
 #' @export
-#' @return Dataframe. If `gwasglue = TRUE` then returns a gwasglue2 object.
+#' @return Dataframe
 associations <- function(variants, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold = 0.3, access_token=check_access_token()){
 
-	# Query specific variants from specific GWAS using associations_query internal function (old version)
-	out <- associations_query(variants=variants, id=id, proxies=proxies, r2=r2, align_alleles=align_alleles, palindromes=palindromes, maf_threshold=maf_threshold, access_token=access_token)
-	
-	return(out)
-}
-
-
-# Query specific variants from specific GWAS - associations internal function to allow for future gwasglue2 integration
-associations_query <- function(variants=variants, id=id, proxies=proxies, r2=r2, align_alleles=align_alleles, palindromes=palindromes, maf_threshold = maf_threshold, access_token=access_token)
-{
 	id <- legacy_ids(id)
 	out <- api_query("associations", query=list(
 		variant=variants,
@@ -265,7 +255,6 @@ associations_query <- function(variants=variants, id=id, proxies=proxies, r2=r2,
 		maf_threshold=maf_threshold
 	), access_token=access_token) %>% get_query_content()
 
-	if(inherits(out, "response"))
 	if(inherits(out, "response"))
 	{
 		return(out)
@@ -274,8 +263,11 @@ associations_query <- function(variants=variants, id=id, proxies=proxies, r2=r2,
 	} else {
 		return(dplyr::tibble())
 	}
+	
+	return(out)
 }
 
+
 #' Look up sample sizes when meta data is missing from associations
 #'
 #' @param d Output from [`associations`]
@@ -409,7 +401,6 @@ tophits_query <- function(id, pval=5e-8, clump = 1, r2 = 0.001, kb = 10000, pop=
 		pop=pop
 	), access_token=access_token) %>% get_query_content()
 	if(inherits(out, "response"))
-	if(inherits(out, "response"))
 	{
 		return(out)
 	} else if(is.data.frame(out)) {

R/zzz.R

@@ -17,7 +17,7 @@
 										"https://www.googleapis.com/auth/userinfo.email"),
 		googleAuthR.ok_content_types=c("application/json; charset=UTF-8", ("text/html; charset=UTF-8")),
 		googleAuthR.securitycode = 
-			paste0(sample(c(1:9, LETTERS, letters), 20, replace = T), collapse=''),
+			paste0(sample(c(1:9, LETTERS, letters), 20, replace = TRUE), collapse=''),
 		googleAuthR.tryAttempts = 5
 	)
 	# toset <- !(names(op.googleAuthR) %in% names(op))