Updated fail behavior

daynefiler · Dec 3, 2021 · 2a965c4 · 2a965c4
1 parent f5f8e34
commit 2a965c4
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Showing 3 changed files with 12 additions and 3 deletions.
diff --git a/R/convertVariantIds.R b/R/convertVariantIds.R
@@ -39,7 +39,10 @@ convertVariantIds <- function(varids, genomes) {
   qry <- Query$new()$query('convertIds',
                            glue('query convertIds {{ {qryBody} }}'))
   tryres <- try(jsn <- gmCon$exec(qry$convertIds), silent = TRUE)
-  if (is(tryres, 'try-error')) stop(qfailmessage)
+  if (is(tryres, 'try-error')) {
+    warning(qfailmessage)
+    return(tryres)
+  }
   res <- fromJSON(jsn, flatten = TRUE)$data
   res
 }

diff --git a/R/getVariantPopData.R b/R/getVariantPopData.R
@@ -42,7 +42,10 @@ getVariantPopData <- function(varids, genomes) {
   qry <- Query$new()$query('convertIds',
                            glue('query convertIds {{ {qryBody} }}'))
   tryres <- try(jsn <- gmCon$exec(qry$convertIds), silent = TRUE)
-  if (is(tryres, 'try-error')) stop(qfailmessage)
+  if (is(tryres, 'try-error')) {
+    warning(qfailmessage)
+    return(tryres)
+  }
   resLst <- fromJSON(jsn, flatten = TRUE)$data
   procPopData <- function(x) {
     cbind(varid = x$variantId,

diff --git a/R/getVariantsFromRegion.R b/R/getVariantsFromRegion.R
@@ -41,7 +41,10 @@ getVariantsFromRegion <- function(genomes, chroms, starts, stops = starts) {
   qry <- Query$new()$query('getRegion',
                            glue('query getRegion {{ {qryBody} }}'))
   tryres <- try(jsn <- gmCon$exec(qry$getRegion), silent = TRUE)
-  if (is(tryres, 'try-error')) stop(qfailmessage)
+  if (is(tryres, 'try-error')) {
+    warning(qfailmessage)
+    return(tryres)
+  }
   res <- lapply(fromJSON(jsn)$data, "[[", 1)
   res
 }