Fixed bug in .makeAndEvalQuery

Function now receives environment from calling function.
daynefiler · Dec 3, 2021 · 51f7517 · 51f7517
1 parent 2495105
commit 51f7517
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/R/convertVariantIds.R b/R/convertVariantIds.R
@@ -32,7 +32,7 @@ convertVariantIds <- function(varids, genomes) {
       }}
     }}
   '
-  rsp <- .makeAndEvalQuery(qfmt)
+  rsp <- .makeAndEvalQuery(qfmt, environment())
   if (is(rsp, 'try-error')) return(rsp)
   res <- fromJSON(rsp, flatten = TRUE)$data
   res

diff --git a/R/getVariantPopData.R b/R/getVariantPopData.R
@@ -21,7 +21,7 @@ getVariantPopData <- function(varids, genomes) {
   gmCon <- GraphqlClient$new(url = apiUrl())
   datasets <- getDatasets(genomes)
   qfmt <-
-    '
+  '
     {genomes}_{gsub("-", "_", varids)}:
     variant(variantId: "{varids}", dataset: {datasets}) {{
       variantId
@@ -38,7 +38,7 @@ getVariantPopData <- function(varids, genomes) {
       }}
     }}
   '
-  rsp <- .makeAndEvalQuery(qfmt)
+  rsp <- .makeAndEvalQuery(qfmt, environment())
   if (is(rsp, 'try-error')) return(rsp)
   resLst <- fromJSON(rsp, flatten = TRUE)$data
   procPopData <- function(x) {

diff --git a/R/getVariantsFromRegion.R b/R/getVariantsFromRegion.R
@@ -37,7 +37,7 @@ getVariantsFromRegion <- function(genomes, chroms, starts, stops = starts) {
       }}
     }}
   '
-  rsp <- .makeAndEvalQuery(qfmt)
+  rsp <- .makeAndEvalQuery(qfmt, environment())
   if (is(rsp, 'try-error')) return(rsp)
   res <- lapply(fromJSON(rsp)$data, "[[", 1)
   res

diff --git a/R/utils.R b/R/utils.R
@@ -109,9 +109,9 @@ getLiftoverIdName <- function(genomes) {
 #' @importFrom glue glue glue_collapse
 #' @import ghql
 
-.makeAndEvalQuery <- function(qfmt, maxTries = 3) {
+.makeAndEvalQuery <- function(qfmt, genv, maxTries = 3) {
   gmCon <- GraphqlClient$new(url = apiUrl())
-  qryBody <- glue_collapse(glue(qfmt), sep = "\n")
+  qryBody <- glue_collapse(glue(qfmt, .envir = genv), sep = "\n")
   qry <- Query$new()$query('q', glue('query {{ {qryBody} }}'))
   tries <- 1
   repeat {