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Merged
hanars merged 4 commits into from
Aug 17, 2026
Merged

Dev #5550

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bb75752
lazy import models for clickhouse reload command
hanars Aug 13, 2026
16ddba2
codacy clean up
hanars Aug 13, 2026
1a12fbc
codacy fix
hanars Aug 13, 2026
0ed5795
Merge pull request #5546 from broadinstitute/reload-clinvar-model-imp…
hanars Aug 17, 2026
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8 changes: 6 additions & 2 deletions clickhouse_search/management/commands/reload_clinvar_all_variants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,6 @@
from typing import Optional, Union

from clickhouse_backend import models
from clickhouse_search.models.reference_data_models import ClinvarAllVariantsGRCh37SnvIndel, ClinvarAllVariantsSnvIndel, ClinvarAllVariantsMito, \
ClinvarMvGRCh37SnvIndel, ClinvarMvSnvIndel, ClinvarMvMito, ClinvarSearchMvGRCh37SnvIndel, ClinvarSearchMvSnvIndel, ClinvarSearchMvMito
from clickhouse_search.constants import \
CLINVAR_ASSERTIONS as CORE_CLINVAR_ASSERTIONS, CLINVAR_PATHOGENICITIES as CORE_CLINVAR_PATHOGENICITIES, CLINVAR_DEFAULT_PATHOGENICITY as CORE_CLINVAR_DEFAULT_PATHOGENICITY, \
CLINVAR_CONFLICTING_CLASSICATIONS_OF_PATHOGENICITY as CORE_CLINVAR_CONFLICTING_CLASSICATIONS_OF_PATHOGENICITY
Expand Down Expand Up @@ -200,6 +198,8 @@ def parse_submitters_and_conditions(classified_record_node: xml) -> [list[str],
return submitters, conditions

def extract_variant_info(elem: xml.etree.ElementTree.Element, new_version: str, unenumerated_value_alerts: Optional[list] = None) -> tuple[models.ClickhouseModel, models.ClickhouseModel, models.ClickhouseModel]:
from clickhouse_search.models.reference_data_models import ClinvarAllVariantsGRCh37SnvIndel, ClinvarAllVariantsSnvIndel, ClinvarAllVariantsMito

# Cannot use regular bool-falseyness here, as:
# "An element with no child elements (even if it exists and has text) will be falsey."
classified_record_node = elem.find('ClassifiedRecord')
Expand Down Expand Up @@ -249,6 +249,8 @@ def extract_variant_info(elem: xml.etree.ElementTree.Element, new_version: str,
)

def parse_clinvar_file(gzipped_file, existing_version_obj, model_to_batch, unenumerated_value_alerts):
from clickhouse_search.models.reference_data_models import ClinvarAllVariantsSnvIndel

for event, elem in ET.iterparse(gzipped_file, events=('start', 'end')):
# Handle parsing the current date.
if event == 'start' and elem.tag == 'ClinVarVariationRelease':
Expand Down Expand Up @@ -286,6 +288,8 @@ class Command(BaseCommand):
help = 'Reload all clinvar variants from weekly NCBI xml release'

def handle(self, *args, **options):
from clickhouse_search.models.reference_data_models import ClinvarAllVariantsGRCh37SnvIndel, ClinvarAllVariantsSnvIndel, ClinvarAllVariantsMito, \
ClinvarMvGRCh37SnvIndel, ClinvarMvSnvIndel, ClinvarMvMito, ClinvarSearchMvGRCh37SnvIndel, ClinvarSearchMvSnvIndel, ClinvarSearchMvMito
model_to_batch = {
ClinvarAllVariantsGRCh37SnvIndel: [],
ClinvarAllVariantsSnvIndel: [],
Expand Down
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