Improve import error message [VS-437] (#7855)

broadinstitute · May 18, 2022 · 6767947 · 6767947
1 parent 7388851
commit 6767947
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Showing 2 changed files with 34 additions and 21 deletions.
diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl
@@ -1,5 +1,7 @@
 version 1.0
 
+import "GvsUtils.wdl" as GvsUtils
+
 workflow GvsImportGenomes {
 
   input {
@@ -22,9 +24,11 @@ workflow GvsImportGenomes {
   Int input_length = length(input_vcfs)
   Int input_indexes_length = length(input_vcf_indexes)
   if ((input_length != length(external_sample_names)) || (input_indexes_length != length(external_sample_names))) {
-    call TerminateWorkflow {
+    call GvsUtils.TerminateWorkflow {
       input:
-        message = "The number of external_sample_names, sample input_vcfs and sample input_vcf_indexes are not the same."
+        message = "The lengths of workflow inputs `external_sample_names` (" + length(external_sample_names) +
+                  "), `input_vcfs` (" + input_length + ") and `input_vcf_indexes` (" + input_indexes_length + ") should be the same.\n\n" +
+                  "If any of these counts are zero an incorrect or non-existent attribute may have been referenced."
     }
   }
 
@@ -295,25 +299,6 @@ task LoadData {
 
 
 
-task TerminateWorkflow {
-  input {
-    String message
-  }
-
-  command <<<
-    set -e
-    echo ~{message}
-    exit 1
-  >>>
-  runtime {
-    docker: "python:3.8-slim-buster"
-    memory: "1 GB"
-    disks: "local-disk 10 HDD"
-    preemptible: 3
-    cpu: 1
-  }
-}
-
 task SetIsLoadedColumn {
   meta {
     volatile: true

diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl
@@ -294,3 +294,31 @@ task BuildGATKJarAndCreateDataset {
     disks: "local-disk 500 HDD"
   }
 }
+
+
+task TerminateWorkflow {
+  input {
+    String message
+  }
+
+  command <<<
+    set -o errexit
+
+    # To avoid issues with special characters within the message, write the message to a file.
+    cat > message.txt <<FIN
+    ~{message}
+    FIN
+
+    # cat the file to stderr as this task is going to fail due to the exit 1.
+    cat message.txt >&2
+    exit 1
+  >>>
+
+  runtime {
+    docker: "python:3.8-slim-buster"
+    memory: "1 GB"
+    disks: "local-disk 10 HDD"
+    preemptible: 3
+    cpu: 1
+  }
+}