Broke out building & executing the query

This cleaned up the code and allowed easy repeat query attempts when a query fails.
daynefiler · Dec 3, 2021 · 2495105 · 2495105
1 parent e2bfe04
commit 2495105
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Showing 4 changed files with 30 additions and 33 deletions.
diff --git a/R/convertVariantIds.R b/R/convertVariantIds.R
@@ -11,17 +11,14 @@
 #' convertVariantIds(varids = '1-89388944-A-C', genomes = "GRCh37")
 #' }
 #'
-#' @import ghql
-#' @importFrom glue glue glue_collapse
 #' @importFrom jsonlite fromJSON
 #' @export
 
 convertVariantIds <- function(varids, genomes) {
   stopifnot(validGenomes(genomes))
-  gmCon <- GraphqlClient$new(url = apiUrl())
   datasets <- getDatasets(genomes)
   idnames <- getLiftoverIdName(genomes)
-  tmp <-
+  qfmt <-
   '
     {genomes}_{gsub("-", "_", varids)}:
     liftover({idnames}: "{varids}", reference_genome: {genomes}) {{
@@ -35,15 +32,9 @@ convertVariantIds <- function(varids, genomes) {
       }}
     }}
   '
-  qryBody <- glue_collapse(glue(tmp), sep = "\n")
-  qry <- Query$new()$query('convertIds',
-                           glue('query convertIds {{ {qryBody} }}'))
-  tryres <- try(jsn <- gmCon$exec(qry$convertIds), silent = TRUE)
-  if (is(tryres, 'try-error')) {
-    warning(qfailmessage)
-    return(tryres)
-  }
-  res <- fromJSON(jsn, flatten = TRUE)$data
+  rsp <- .makeAndEvalQuery(qfmt)
+  if (is(rsp, 'try-error')) return(rsp)
+  res <- fromJSON(rsp, flatten = TRUE)$data
   res
 }
 
diff --git a/R/getVariantPopData.R b/R/getVariantPopData.R
@@ -20,7 +20,7 @@ getVariantPopData <- function(varids, genomes) {
   stopifnot(validGenomes(genomes))
   gmCon <- GraphqlClient$new(url = apiUrl())
   datasets <- getDatasets(genomes)
-  tmp <-
+  qfmt <-
     '
     {genomes}_{gsub("-", "_", varids)}:
     variant(variantId: "{varids}", dataset: {datasets}) {{
@@ -38,15 +38,9 @@ getVariantPopData <- function(varids, genomes) {
       }}
     }}
   '
-  qryBody <- glue_collapse(glue(tmp), sep = "\n")
-  qry <- Query$new()$query('convertIds',
-                           glue('query convertIds {{ {qryBody} }}'))
-  tryres <- try(jsn <- gmCon$exec(qry$convertIds), silent = TRUE)
-  if (is(tryres, 'try-error')) {
-    warning(qfailmessage)
-    return(tryres)
-  }
-  resLst <- fromJSON(jsn, flatten = TRUE)$data
+  rsp <- .makeAndEvalQuery(qfmt)
+  if (is(rsp, 'try-error')) return(rsp)
+  resLst <- fromJSON(rsp, flatten = TRUE)$data
   procPopData <- function(x) {
     cbind(varid = x$variantId,
           chrom = x$chrom,

diff --git a/R/getVariantsFromRegion.R b/R/getVariantsFromRegion.R
@@ -22,7 +22,7 @@ getVariantsFromRegion <- function(genomes, chroms, starts, stops = starts) {
   stopifnot(validGenomes(genomes))
   gmCon <- GraphqlClient$new(url = apiUrl())
   datasets <- getDatasets(genomes)
-  tmp <-
+  qfmt <-
   '
     {genomes}_{chroms}_{starts}_{stops}:
     region(chrom: "{chroms}",
@@ -37,15 +37,9 @@ getVariantsFromRegion <- function(genomes, chroms, starts, stops = starts) {
       }}
     }}
   '
-  qryBody <- glue_collapse(glue(tmp), sep = "\n")
-  qry <- Query$new()$query('getRegion',
-                           glue('query getRegion {{ {qryBody} }}'))
-  tryres <- try(jsn <- gmCon$exec(qry$getRegion), silent = TRUE)
-  if (is(tryres, 'try-error')) {
-    warning(qfailmessage)
-    return(tryres)
-  }
-  res <- lapply(fromJSON(jsn)$data, "[[", 1)
+  rsp <- .makeAndEvalQuery(qfmt)
+  if (is(rsp, 'try-error')) return(rsp)
+  res <- lapply(fromJSON(rsp)$data, "[[", 1)
   res
 }
 
diff --git a/R/utils.R b/R/utils.R
@@ -105,3 +105,21 @@ getLiftoverIdName <- function(genomes) {
   stopifnot(validGenomes(genomes))
   attr(ReferenceGenomeIds, "liftoverIdName")[match(genomes, ReferenceGenomeIds)]
 }
+
+#' @importFrom glue glue glue_collapse
+#' @import ghql
+
+.makeAndEvalQuery <- function(qfmt, maxTries = 3) {
+  gmCon <- GraphqlClient$new(url = apiUrl())
+  qryBody <- glue_collapse(glue(qfmt), sep = "\n")
+  qry <- Query$new()$query('q', glue('query {{ {qryBody} }}'))
+  tries <- 1
+  repeat {
+    if (tries > maxTries) break
+    tryres <- try(gmCon$exec(qry$q), silent = TRUE)
+    if (!is(tryres, 'try-error')) break
+    Sys.sleep(2*tries)
+    tries <- tries + 1
+  }
+  tryres
+}