Reformated error message when query fails.

Note, qhql has changed how it handles errors and users will get much more informative errors using the current devel version (>=0.1.1.93).
daynefiler · Dec 8, 2021 · eae66da · eae66da
1 parent 51f7517
commit eae66da
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Showing 6 changed files with 20 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,6 +16,7 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.2
 Imports: 
+    crayon,
     data.table,
     ghql,
     glue,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,failedQuery)
 export(DatasetIds)
 export(ReferenceGenomeIds)
 export(apiUrl)
@@ -12,6 +13,7 @@ export(getVariantPopData)
 export(getVariantsFromRegion)
 export(validDatasets)
 export(validGenomes)
+import(crayon)
 import(ghql)
 importFrom(data.table,":=")
 importFrom(data.table,.BY)

diff --git a/R/convertVariantIds.R b/R/convertVariantIds.R
@@ -33,7 +33,7 @@ convertVariantIds <- function(varids, genomes) {
     }}
   '
   rsp <- .makeAndEvalQuery(qfmt, environment())
-  if (is(rsp, 'try-error')) return(rsp)
+  if (is(rsp, 'failedQuery')) return(rsp)
   res <- fromJSON(rsp, flatten = TRUE)$data
   res
 }

diff --git a/R/getVariantPopData.R b/R/getVariantPopData.R
@@ -39,7 +39,7 @@ getVariantPopData <- function(varids, genomes) {
     }}
   '
   rsp <- .makeAndEvalQuery(qfmt, environment())
-  if (is(rsp, 'try-error')) return(rsp)
+  if (is(rsp, 'failedQuery')) return(rsp)
   resLst <- fromJSON(rsp, flatten = TRUE)$data
   procPopData <- function(x) {
     cbind(varid = x$variantId,

diff --git a/R/getVariantsFromRegion.R b/R/getVariantsFromRegion.R
@@ -38,7 +38,7 @@ getVariantsFromRegion <- function(genomes, chroms, starts, stops = starts) {
     }}
   '
   rsp <- .makeAndEvalQuery(qfmt, environment())
-  if (is(rsp, 'try-error')) return(rsp)
+  if (is(rsp, 'failedQuery')) return(rsp)
   res <- lapply(fromJSON(rsp)$data, "[[", 1)
   res
 }

diff --git a/R/utils.R b/R/utils.R
@@ -112,7 +112,7 @@ getLiftoverIdName <- function(genomes) {
 .makeAndEvalQuery <- function(qfmt, genv, maxTries = 3) {
   gmCon <- GraphqlClient$new(url = apiUrl())
   qryBody <- glue_collapse(glue(qfmt, .envir = genv), sep = "\n")
-  qry <- Query$new()$query('q', glue('query {{ {qryBody} }}'))
+  qry <- Query$new()$query('q', glue('query {{\n{qryBody}\n}}'))
   tries <- 1
   repeat {
     if (tries > maxTries) break
@@ -121,5 +121,18 @@ getLiftoverIdName <- function(genomes) {
     Sys.sleep(2*tries)
     tries <- tries + 1
   }
+  if (is(tryres, 'try-error')) {
+    tryres <- list(errorMessage = tryres[1], query = qry$q$query)
+    class(tryres) <- "failedQuery"
+  }
   tryres
 }
+
+#' @import crayon
+#' @export
+
+print.failedQuery <- function(x) {
+  cat("Query failed with the following message:\n" %+% red(x$errorMessage))
+  cat("Query string (stored as x$query):\n" %+% cyan(x$query))
+}
+