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feat: empty new variants test #1113

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Merged
merged 4 commits into from
Jun 10, 2025
Merged

feat: empty new variants test #1113

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2e29058
empty new variants test
bpblanken Jun 8, 2025
21da3a8
Merge branch 'benb/gcnv' into benb/empty_new_variants_test
bpblanken Jun 10, 2025
dead126
fix merge conflicts
bpblanken Jun 10, 2025
2120869
ruff
bpblanken Jun 10, 2025
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104 changes: 65 additions & 39 deletions v03_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@
from v03_pipeline.lib.paths import (
new_variants_parquet_path,
new_variants_table_path,
remapped_and_subsetted_callset_path,
variant_annotations_table_path,
)
from v03_pipeline.lib.tasks.exports.write_new_variants_parquet import (
Expand All @@ -37,67 +36,62 @@


class WriteNewVariantsParquetTest(MockedDatarootTestCase):
def setUp(self) -> None:
super().setUp()
def test_empty_write_new_variants_parquet_test(
self,
) -> None:
ht = hl.read_table(
TEST_SNV_INDEL_ANNOTATIONS,
)
ht = ht.head(0)
ht.write(
new_variants_table_path(
ReferenceGenome.GRCh38,
DatasetType.SNV_INDEL,
TEST_RUN_ID,
),
)
ht = hl.read_table(
TEST_GRCH37_SNV_INDEL_ANNOTATIONS,
worker = luigi.worker.Worker()
task = WriteNewVariantsParquetTask(
reference_genome=ReferenceGenome.GRCh38,
dataset_type=DatasetType.SNV_INDEL,
sample_type=SampleType.WGS,
callset_path='fake_callset',
project_guids=[
'fake_project',
],
project_pedigree_paths=['fake_pedigree'],
skip_validation=True,
run_id=TEST_RUN_ID,
)
ht.write(
new_variants_table_path(
ReferenceGenome.GRCh37,
worker.add(task)
worker.run()
self.assertTrue(task.output().exists())
self.assertTrue(task.complete())
df = pd.read_parquet(
new_variants_parquet_path(
ReferenceGenome.GRCh38,
DatasetType.SNV_INDEL,
TEST_RUN_ID,
),
)
ht = hl.read_table(
TEST_MITO_ANNOTATIONS,
)
ht.write(
new_variants_table_path(
ReferenceGenome.GRCh38,
DatasetType.MITO,
TEST_RUN_ID,
),
self.assertEqual(
len(df),
0,
)

def test_snv_indel_write_new_variants_parquet_test(
self,
) -> None:
ht = hl.read_table(
TEST_SV_ANNOTATIONS,
TEST_SNV_INDEL_ANNOTATIONS,
)
ht.write(
new_variants_table_path(
ReferenceGenome.GRCh38,
DatasetType.SV,
DatasetType.SNV_INDEL,
TEST_RUN_ID,
),
)
ht = hl.read_table(TEST_GCNV_ANNOTATIONS)
ht.write(
variant_annotations_table_path(
ReferenceGenome.GRCh38,
DatasetType.GCNV,
),
)
ht.write(
remapped_and_subsetted_callset_path(
ReferenceGenome.GRCh38,
DatasetType.GCNV,
'fake_callset',
'fake_project',
),
)

def test_write_new_variants_parquet_test(
self,
) -> None:
worker = luigi.worker.Worker()
task = WriteNewVariantsParquetTask(
reference_genome=ReferenceGenome.GRCh38,
Expand Down Expand Up @@ -223,6 +217,16 @@ def test_write_new_variants_parquet_test(
def test_grch37_write_new_variants_parquet_test(
self,
) -> None:
ht = hl.read_table(
TEST_GRCH37_SNV_INDEL_ANNOTATIONS,
)
ht.write(
new_variants_table_path(
ReferenceGenome.GRCh37,
DatasetType.SNV_INDEL,
TEST_RUN_ID,
),
)
worker = luigi.worker.Worker()
task = WriteNewVariantsParquetTask(
reference_genome=ReferenceGenome.GRCh37,
Expand Down Expand Up @@ -334,6 +338,16 @@ def test_mito_write_new_variants_parquet_test(
self,
write_new_variants_table_task: Mock,
) -> None:
ht = hl.read_table(
TEST_MITO_ANNOTATIONS,
)
ht.write(
new_variants_table_path(
ReferenceGenome.GRCh38,
DatasetType.MITO,
TEST_RUN_ID,
),
)
write_new_variants_table_task.return_value = MockCompleteTask()
worker = luigi.worker.Worker()
task = WriteNewVariantsParquetTask(
Expand Down Expand Up @@ -422,6 +436,16 @@ def test_sv_write_new_variants_parquet_test(
self,
write_new_variants_table_task: Mock,
) -> None:
ht = hl.read_table(
TEST_SV_ANNOTATIONS,
)
ht.write(
new_variants_table_path(
ReferenceGenome.GRCh38,
DatasetType.SV,
TEST_RUN_ID,
),
)
write_new_variants_table_task.return_value = MockCompleteTask()
worker = luigi.worker.Worker()
task = WriteNewVariantsParquetTask(
Expand Down Expand Up @@ -494,12 +518,14 @@ def test_gcnv_write_new_variants_parquet_test(
get_callset_ht: Mock,
update_variant_annotations_task: Mock,
) -> None:
get_callset_ht.return_value = hl.read_table(
ht = hl.read_table(TEST_GCNV_ANNOTATIONS)
ht.write(
variant_annotations_table_path(
ReferenceGenome.GRCh38,
DatasetType.GCNV,
),
)
get_callset_ht.return_value = ht
update_variant_annotations_task.return_value = MockCompleteTask()
worker = luigi.worker.Worker()
task = WriteNewVariantsParquetTask(
Expand Down