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divide up creation/population of temp pet table [VS-48] #7395

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merged 5 commits into from
Aug 13, 2021
Merged

divide up creation/population of temp pet table [VS-48] #7395

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7d9e17c
divide up creation/population of pet new table
rsasch Aug 6, 2021
d165300
cleanup
rsasch Aug 6, 2021
f8e3ace
reference updated docker image in GvsPrepareCallset
rsasch Aug 9, 2021
275d697
Merge branch 'ah_var_store' into rsa_divide_new_pet_db_calls
rsasch Aug 10, 2021
01d0dab
added query size compute back in and some formatting
rsasch Aug 10, 2021
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3 changes: 1 addition & 2 deletions scripts/variantstore/wdl/GvsPrepareCallset.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ workflow GvsPrepareCallset {
String? docker
}

String docker_final = select_first([docker, "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20210726"])
String docker_final = select_first([docker, "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20210806"])

if (localize_sample_names_with_service_account && defined(service_account_json_path)) {
call LocalizeFile {
Expand All @@ -46,7 +46,6 @@ workflow GvsPrepareCallset {
fq_destination_dataset = fq_destination_dataset,
temp_table_ttl_in_hours = temp_table_ttl_in_hours,
service_account_json_path = service_account_json_path,

docker = docker_final
}

Expand Down
44 changes: 23 additions & 21 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 @@ -107,7 +107,7 @@ def load_sample_names(sample_names_to_extract, fq_temp_table_dataset):
table = bigquery.Table(fq_sample_table, schema=schema)
expiration = datetime.datetime.utcnow() + datetime.timedelta(hours=TEMP_TABLE_TTL_HOURS)
table.expires = expiration
table = client.update_table(table, ["expires"])
table = client.update_table(table, ["expires"])

return fq_sample_table

Expand Down Expand Up @@ -193,34 +193,36 @@ def create_position_table(fq_temp_table_dataset, min_variant_samples):
def make_new_pet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids):
def get_pet_subselect(fq_pet_table, samples, id):
sample_stanza = ','.join([str(s) for s in samples])
sql = f" q_{id} AS (SELECT p.location, p.sample_id, p.state from `{fq_pet_table}` p " \
f" join `{fq_temp_table_dataset}.{VET_DISTINCT_POS_TABLE}` v on (p.location = v.location) WHERE p.sample_id IN ({sample_stanza})), "
sql = f" q_{id} AS (SELECT p.location, p.sample_id, p.state FROM `{fq_pet_table}` p \n" \
f" JOIN `{fq_temp_table_dataset}.{VET_DISTINCT_POS_TABLE}` v on (p.location = v.location) \n WHERE p.sample_id IN ({sample_stanza})), "
return sql

subs = {}
for i in range(1, PET_VET_TABLE_COUNT+1):
partition_samples = get_samples_for_partition(sample_ids, i)
partition_samples = get_samples_for_partition(sample_ids, i) #sample ids for the partition

# KCIBUL -- grr, should be fixed width
fq_pet_table = f"{fq_pet_vet_dataset}.{PET_TABLE_PREFIX}{i:03}"
if len(partition_samples) > 0:
subs = {}
create_or_insert = f"\nCREATE OR REPLACE TABLE `{fq_temp_table_dataset}.{PET_NEW_TABLE}` {TEMP_TABLE_TTL} AS \n WITH \n" if i == 1 \
else f"\nINSERT INTO `{fq_temp_table_dataset}.{PET_NEW_TABLE}` \n WITH \n"
fq_pet_table = f"{fq_pet_vet_dataset}.{PET_TABLE_PREFIX}{i:03}"
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j = 1

for samples in split_lists(partition_samples, 1000):
id = f"{i}_{j}"
subs[id] = get_pet_subselect(fq_pet_table, samples, id)
j = j + 1

sql = f"create or replace table `{fq_temp_table_dataset}.{PET_NEW_TABLE}` {TEMP_TABLE_TTL} AS \n" + \
"with\n" + \
("\n".join(subs.values())) + "\n" \
"q_all AS (" + (" union all ".join([ f"(SELECT * FROM q_{id})" for id in subs.keys()])) + ")\n" + \
f" (SELECT * FROM q_all)"
sql = create_or_insert + ("\n".join(subs.values())) + "\n" + \
"q_all AS (" + (" union all ".join([ f"(SELECT * FROM q_{id})" for id in subs.keys()])) + ")\n" + \
f" (SELECT * FROM q_all)"

print(sql)
print(f"PET Query is {utf8len(sql)/(1024*1024)} MB in length")
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results = execute_with_retry("insert pet new table", sql)
return results
print(sql)
if i == 1:
execute_with_retry("create and populate pet new table", sql)
else:
execute_with_retry("populate pet new table", sql)

return

def populate_final_extract_table(fq_temp_table_dataset, fq_destination_table_data, fq_sample_mapping_table):
# first, create the table structure
Expand Down Expand Up @@ -306,7 +308,7 @@ def make_extract_table(fq_pet_vet_dataset,
try:
fq_destination_table_data = f"{fq_destination_dataset}.{destination_table_prefix}__DATA"
fq_destination_table_samples = f"{fq_destination_dataset}.{destination_table_prefix}__SAMPLES"

global client
# this is where a set of labels are being created for the cohort extract
query_labels_map = {}
Expand All @@ -323,7 +325,7 @@ def make_extract_table(fq_pet_vet_dataset,

if not (bool(re.match(r"[a-z0-9_-]+$", key)) & bool(re.match(r"[a-z0-9_-]+$", value))):
raise ValueError(f"label key or value did not pass validation--format should be 'key1=val1, key2=val2'")

#Default QueryJobConfig will be merged into job configs passed in
#but if a specific default config is being updated (eg labels), new config must be added
#to the client._default_query_job_config that already exists
Expand All @@ -345,10 +347,10 @@ def make_extract_table(fq_pet_vet_dataset,

global PET_VET_TABLE_COUNT
PET_VET_TABLE_COUNT = max_tables

global TEMP_TABLE_TTL_HOURS
TEMP_TABLE_TTL_HOURS = temp_table_ttl_hours

global TEMP_TABLE_TTL
TEMP_TABLE_TTL = f" OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL {TEMP_TABLE_TTL_HOURS} HOUR)) "

Expand All @@ -367,7 +369,7 @@ def make_extract_table(fq_pet_vet_dataset,
# pull the sample ids back down
sample_ids = get_all_sample_ids(fq_destination_table_samples)
print(f"Discovered {len(sample_ids)} samples in {fq_destination_table_samples}...")

make_new_vet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids)

create_position_table(fq_temp_table_dataset, min_variant_samples)
Expand Down