fix SQL

broadinstitute · Nov 30, 2023 · a2a0028 · a2a0028
1 parent 02a0c5b
commit a2a0028
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/scripts/variantstore/wdl/GvsUtils.wdl b/scripts/variantstore/wdl/GvsUtils.wdl
@@ -72,7 +72,7 @@ task GetToolVersions {
     # GVS generally uses the smallest `alpine` version of the Google Cloud SDK as it suffices for most tasks, but
     # there are a handlful of tasks that require the larger GNU libc-based `slim`.
     String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:435.0.0-slim"
-    String variants_docker = "us.gcr.io/broad-dsde-methods/variantstore:2023-11-30-alpine-38a6c5ce9"
+    String variants_docker = "us.gcr.io/broad-dsde-methods/variantstore:2023-11-30-alpine-02a0c5bd7"
     String gatk_docker = "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_2023_10_31_e7746ce7c38a8226bcac5b89284782de2a4cdda1"
     String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
     String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"

diff --git a/scripts/variantstore/wdl/extract/create_ranges_cohort_extract_data_table.py b/scripts/variantstore/wdl/extract/create_ranges_cohort_extract_data_table.py
@@ -110,20 +110,19 @@ def get_all_sample_ids(fq_destination_table_samples, only_output_vet_tables, fq_
 
 def create_extract_samples_table(control_samples, fq_destination_table_samples, fq_sample_name_table,
                                  fq_sample_mapping_table, honor_withdrawn, extract_table_ttl):
-
     ttl = ""
     if extract_table_ttl:
         ttl = "OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL 14 DAY))"
 
     sql = f"""
-
-    CREATE OR REPLACE TABLE `{fq_destination_table_samples}` AS (
+    CREATE OR REPLACE TABLE `{fq_destination_table_samples}` 
+    {ttl}
+    AS (
         SELECT m.sample_id, m.sample_name, m.is_loaded, {"m.withdrawn," if honor_withdrawn else "NULL as withdrawn,"} m.is_control FROM `{fq_sample_name_table}` s JOIN
         `{fq_sample_mapping_table}` m ON (s.sample_name = m.sample_name) WHERE
              m.is_loaded IS TRUE AND m.is_control = {control_samples}
              {"AND m.withdrawn IS NULL" if honor_withdrawn else ""}
     )
-    {ttl}
     """
     print(sql)
 
@@ -164,6 +163,7 @@ def create_final_extract_ref_table(fq_destination_table_ref_data, extract_table_
     ttl = ""
     if extract_table_ttl:
         ttl = "OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL 14 DAY))"
+
     sql = f"""
         CREATE OR REPLACE TABLE `{fq_destination_table_ref_data}` 
         (