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Fix bool flag in prepare #7529

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merged 1 commit into from
Oct 29, 2021
Merged

Fix bool flag in prepare #7529

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8 changes: 4 additions & 4 deletions scripts/variantstore/wdl/GvsPrepareCallset.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ workflow GvsPrepareCallset {
String fq_destination_dataset = "~{destination_project}.~{destination_dataset}"

Int temp_table_ttl_in_hours = 72
Boolean skip_pet_insert = false
Boolean skip_vet_new_insert = false
String? service_account_json_path
String? docker
}
Expand All @@ -37,7 +37,7 @@ workflow GvsPrepareCallset {
fq_temp_table_dataset = fq_temp_table_dataset,
fq_destination_dataset = fq_destination_dataset,
temp_table_ttl_in_hours = temp_table_ttl_in_hours,
skip_pet_insert = skip_pet_insert,
skip_vet_new_insert = skip_vet_new_insert,
service_account_json_path = service_account_json_path,
docker = docker_final
}
Expand Down Expand Up @@ -65,7 +65,7 @@ task PrepareCallsetTask {
String fq_temp_table_dataset
String fq_destination_dataset
Int temp_table_ttl_in_hours
Boolean skip_pet_insert
Boolean skip_vet_new_insert

String? service_account_json_path
String docker
Expand Down Expand Up @@ -107,7 +107,7 @@ task PrepareCallsetTask {
~{sep=" " query_label_args} \
--fq_sample_mapping_table ~{fq_sample_mapping_table} \
--ttl ~{temp_table_ttl_in_hours} \
--skip_pet_insert ~{skip_pet_insert} \
--skip_vet_new_insert ~{skip_vet_new_insert} \
$SERVICE_ACCOUNT_STANZA
>>>

Expand Down
14 changes: 7 additions & 7 deletions scripts/variantstore/wdl/extract/create_cohort_extract_data_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,7 @@ def create_final_extract_table(fq_destination_table_data):
print(sql)
results = utils.execute_with_retry(client, "create-final-export-table", sql)

def populate_final_extract_table_with_vet_new(fq_temp_table_dataset, fq_destination_table_data, skip_pet_insert):
def populate_final_extract_table_with_vet_new(fq_temp_table_dataset, fq_destination_table_data, skip_vet_new_insert):
sql = f"""
INSERT INTO `{fq_destination_table_data}`
SELECT
Expand All @@ -247,7 +247,7 @@ def populate_final_extract_table_with_vet_new(fq_temp_table_dataset, fq_destinat
`{fq_temp_table_dataset}.{VET_NEW_TABLE}`
"""
print(sql)
if (not skip_pet_insert):
if (not skip_vet_new_insert):
results = utils.execute_with_retry(client, "populate-final-export-vet", sql)
print(f"\nFinal cohort extract data written to {fq_destination_table_data}\n")
else:
Expand All @@ -268,7 +268,7 @@ def make_extract_table(fq_pet_vet_dataset,
fq_sample_mapping_table,
sa_key_path,
temp_table_ttl_hours,
skip_pet_insert
skip_vet_new_insert
):
try:
fq_destination_table_data = f"{fq_destination_dataset}.{destination_table_prefix}__DATA"
Expand Down Expand Up @@ -340,7 +340,7 @@ def make_extract_table(fq_pet_vet_dataset,
create_position_table(fq_temp_table_dataset, min_variant_samples)
create_final_extract_table(fq_destination_table_data)
populate_final_extract_table_with_pet(fq_pet_vet_dataset, fq_temp_table_dataset, fq_destination_table_data, sample_ids)
populate_final_extract_table_with_vet_new(fq_temp_table_dataset, fq_destination_table_data, skip_pet_insert)
populate_final_extract_table_with_vet_new(fq_temp_table_dataset, fq_destination_table_data, skip_vet_new_insert)
finally:
dump_job_stats()

Expand All @@ -358,9 +358,9 @@ def make_extract_table(fq_pet_vet_dataset,
parser.add_argument('--sa_key_path',type=str, help='Path to json key file for SA', required=False)
parser.add_argument('--max_tables',type=int, help='Maximum number of PET/VET tables to consider', required=False, default=250)
parser.add_argument('--ttl',type=int, help='Temp table TTL in hours', required=False, default=72)
parser.add_argument('--skip_pet_insert',type=bool,
parser.add_argument('--skip_vet_new_insert', default=False, type=lambda x: (str(x).lower() == 'true'),
help='This will not execute the final sql query to insert the pet_new data into the DATA table, but will print out the command instead. Useful when flex slots need to be allocated.',
required=False, default=False)
required=False)
sample_args = parser.add_mutually_exclusive_group(required=True)
sample_args.add_argument('--sample_names_to_extract',type=str, help='File containing list of samples to extract, 1 per line')
sample_args.add_argument('--fq_cohort_sample_names',type=str, help='FQN of cohort table to extract, contains "sample_name" column')
Expand All @@ -382,4 +382,4 @@ def make_extract_table(fq_pet_vet_dataset,
args.fq_sample_mapping_table,
args.sa_key_path,
args.ttl,
args.skip_pet_insert)
args.skip_vet_new_insert)