From 93038d41f3633a69eecf842e519de9015ee772c4 Mon Sep 17 00:00:00 2001
From: Sam Novod <samn@broadinstitute.org>
Date: Wed, 29 Jan 2025 09:58:25 -0500
Subject: [PATCH 1/2] Make WDL wait on validation

---
 wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl | 30 +++++++++++++----------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl b/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl
index 62bbf77..b7362ac 100644
--- a/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl
+++ b/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl
@@ -22,6 +22,8 @@ workflow GetTDRSchemaJson {
 
     call GenerateSchemaJson {
         input:
+            # Set so this step only runs if the input is validated
+            input_validated = ValidateInputs.validated,
             input_metadata_tsv = input_metadata_tsv,
             billing_project = billing_project,
             workspace_name = workspace_name,
@@ -29,6 +31,10 @@ workflow GetTDRSchemaJson {
             docker_name = docker_name,
             force_disparate_rows_to_string = force_disparate_rows_to_string
     }
+
+    output {
+        File tdr_schema_json = GenerateSchemaJson.tdr_schema_json
+    }
 }
 
 task ValidateInputs {
@@ -70,6 +76,10 @@ task ValidateInputs {
     runtime {
 		docker: docker_name
 	}
+
+    output {
+        Boolean validated = true
+    }
 }
 
 
@@ -81,22 +91,16 @@ task GenerateSchemaJson {
         String? terra_table_names
         String docker_name
         Boolean force_disparate_rows_to_string
+        Boolean input_validated
     }
 
     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 {

From c6648a11be4fc8b3c4e5f99575bcc3eba90e48c3 Mon Sep 17 00:00:00 2001
From: Sam Novod <samn@broadinstitute.org>
Date: Wed, 29 Jan 2025 10:21:46 -0500
Subject: [PATCH 2/2] remove validation step

---
 wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl | 58 -----------------------
 1 file changed, 58 deletions(-)

diff --git a/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl b/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl
index b7362ac..2d4cf45 100644
--- a/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl
+++ b/wdl/GetTdrSchemaJson/GetTdrSchemaJson.wdl
@@ -11,19 +11,8 @@ 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:
-            # Set so this step only runs if the input is validated
-            input_validated = ValidateInputs.validated,
             input_metadata_tsv = input_metadata_tsv,
             billing_project = billing_project,
             workspace_name = workspace_name,
@@ -37,52 +26,6 @@ workflow GetTDRSchemaJson {
     }
 }
 
-task ValidateInputs {
-    input {
-        File? input_metadata_tsv
-        String? billing_project
-        String? workspace_name
-        String? terra_table_names
-        String docker_name
-    }
-
-    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
-	}
-
-    output {
-        Boolean validated = true
-    }
-}
-
-
 task GenerateSchemaJson {
     input {
         File? input_metadata_tsv
@@ -91,7 +34,6 @@ task GenerateSchemaJson {
         String? terra_table_names
         String docker_name
         Boolean force_disparate_rows_to_string
-        Boolean input_validated
     }
 
     command <<<