Merge pull request #203 from broadinstitute/sn_update_wdl_to_wait_on_…

…validation Make WDL wait on validation
broadinstitute · Jan 29, 2025 · ab99565 · ab99565
2 parents 0009c13 + c6648a1
commit ab99565
Showing 1 changed file with 8 additions and 62 deletions.
diff --git a/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl b/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl
@@ -11,15 +11,6 @@ workflow GetTDRSchemaJson {
     }
     String docker_name = select_first([docker, "us-central1-docker.pkg.dev/operations-portal-427515/ops-toolbox/ops_terra_utils_slim:latest"])
 
-    call ValidateInputs {
-        input:
-            input_metadata_tsv = input_metadata_tsv,
-            billing_project = billing_project,
-            workspace_name = workspace_name,
-            terra_table_names = terra_table_names,
-            docker_name = docker_name
-    }
-
     call GenerateSchemaJson {
         input:
             input_metadata_tsv = input_metadata_tsv,
@@ -29,50 +20,12 @@ workflow GetTDRSchemaJson {
             docker_name = docker_name,
             force_disparate_rows_to_string = force_disparate_rows_to_string
     }
-}
 
-task ValidateInputs {
-    input {
-        File? input_metadata_tsv
-        String? billing_project
-        String? workspace_name
-        String? terra_table_names
-        String docker_name
+    output {
+        File tdr_schema_json = GenerateSchemaJson.tdr_schema_json
     }
-
-    command <<<
-    set -euo pipefail
-
-    python3 <<CODE
-    tsv = "~{input_metadata_tsv}"
-    billing_project = "~{billing_project}"
-    workspace_name = "~{workspace_name}"
-    terra_table_names = "~{terra_table_names}"
-
-    terra_params = [billing_project, workspace_name, terra_table_names]
-
-    if tsv and any(terra_params):
-        raise ValueError(
-            "If the 'input_metadata_tsv' is provided, none of the terra parameters can also be provided. Please "
-            "leave 'billing_project', 'workspace_name' and 'terra_table_name' all blank if providing a tsv as input."
-        )
-    elif not tsv and not all(terra_params):
-        raise ValueError(
-            "If using the Terra workspace table as input, the 'billing_project', 'workspace_name' and "
-            "'terra_table_names' must ALL be provided"
-        )
-    if (tsv and not any(terra_params)) or (not tsv and all(terra_params)):
-        print("Input parameters validated, continuing")
-
-    CODE
-    >>>
-
-    runtime {
-		docker: docker_name
-	}
 }
 
-
 task GenerateSchemaJson {
     input {
         File? input_metadata_tsv
@@ -84,19 +37,12 @@ task GenerateSchemaJson {
     }
 
     command <<<
-        if [ ! -z "~{input_metadata_tsv}" ]; then
-            python /etc/terra_utils/python/generate_tdr_schema_json.py \
-                        --input_tsv ~{input_metadata_tsv} \
-                        ~{if force_disparate_rows_to_string then "--force_disparate_rows_to_string" else ""}
-
-        else
-            python /etc/terra_utils/python/generate_tdr_schema_json.py \
-                        --billing_project ~{billing_project} \
-                        --workspace_name ~{workspace_name} \
-                        --terra_table_names ~{terra_table_names} \
-                        ~{if force_disparate_rows_to_string then "--force_disparate_rows_to_string" else ""}
-        fi
-
+        python /etc/terra_utils/python/generate_tdr_schema_json.py \
+            ~{"--input_tsv " + input_metadata_tsv} \
+            ~{"--billing_project " + billing_project} \
+            ~{"--workspace_name " + workspace_name} \
+            ~{"--terra_table_names " + terra_table_names} \
+            ~{if force_disparate_rows_to_string then "--force_disparate_rows_to_string" else ""}
     >>>
 
     output {