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mock something else
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-70
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3 files changed

+16
-70
lines changed

v03_pipeline/lib/tasks/write_sample_qc_json_test.py

Lines changed: 11 additions & 69 deletions
Original file line numberDiff line numberDiff line change
@@ -8,85 +8,27 @@
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from v03_pipeline.lib.model import DatasetType, ReferenceGenome, SampleType
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from v03_pipeline.lib.tasks.write_sample_qc_json import WriteSampleQCJsonTask
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from v03_pipeline.lib.test.mock_complete_task import MockCompleteTask
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from v03_pipeline.lib.test.mocked_dataroot_testcase import MockedDatarootTestCase
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TEST_VCF = 'v03_pipeline/var/test/callsets/1kg_30variants.vcf'
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TEST_TDR_METRICS_FILE = 'v03_pipeline/var/test/tdr_metrics.tsv'
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TEST_RUN_ID = 'manual__2024-04-03'
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class WriteSampleQCJsonTaskTest(MockedDatarootTestCase):
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@patch('v03_pipeline.lib.tasks.write_tdr_metrics_files.gen_bq_table_names')
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@patch('v03_pipeline.lib.tasks.write_tdr_metrics_file.bq_metrics_query')
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@patch('v03_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask')
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@patch('v03_pipeline.lib.tasks.write_sample_qc_json.hfs.ls')
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def test_call_sample_qc(
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self,
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mock_bq_metrics_query: Mock,
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mock_gen_bq_table_names: Mock,
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mock_ls_tdr_dir: Mock,
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mock_tdr_task: Mock,
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) -> None:
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mock_gen_bq_table_names.return_value = ['datarepo-7242affb.datarepo_RP_0113']
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mock_bq_metrics_query.side_effect = [
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iter(
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[
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google.cloud.bigquery.table.Row(
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(
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'HG00731',
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'Unknown',
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Decimal('5.1'),
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Decimal('93.69'),
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Decimal('29.31'),
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),
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{
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'collaborator_sample_id': 0,
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'predicted_sex': 1,
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'contamination_rate': 2,
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'percent_bases_at_20x': 3,
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'mean_coverage': 4,
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},
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),
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google.cloud.bigquery.table.Row(
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(
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'HG00732',
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'Female',
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Decimal('5'),
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Decimal('90'),
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Decimal('28'),
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),
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{
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'collaborator_sample_id': 0,
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'predicted_sex': 1,
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'contamination_rate': 2,
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'percent_bases_at_20x': 3,
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'mean_coverage': 4,
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},
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),
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google.cloud.bigquery.table.Row(
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(
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'HG00733',
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'Male',
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Decimal('6'),
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Decimal('85'),
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Decimal('36.4'),
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),
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{
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'collaborator_sample_id': 0,
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'predicted_sex': 1,
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'contamination_rate': 2,
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'percent_bases_at_20x': 3,
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'mean_coverage': 4,
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},
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),
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google.cloud.bigquery.table.Row(
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('NA19675', 'Male', Decimal('0'), Decimal('80'), Decimal('30')),
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{
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'collaborator_sample_id': 0,
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'predicted_sex': 1,
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'contamination_rate': 2,
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'percent_bases_at_20x': 3,
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'mean_coverage': 4,
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},
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),
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],
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),
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]
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mock_tdr_task.return_value = MockCompleteTask()
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mock_tdr_table = Mock()
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mock_tdr_table.path = TEST_TDR_METRICS_FILE
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mock_ls_tdr_dir.return_value = [mock_tdr_table]
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worker = luigi.worker.Worker()
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task = WriteSampleQCJsonTask(
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reference_genome=ReferenceGenome.GRCh38,

v03_pipeline/var/test/sample_qc_1.json

Lines changed: 0 additions & 1 deletion
This file was deleted.

v03_pipeline/var/test/tdr_metrics.tsv

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
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collaborator_sample_id predicted_sex contamination_rate percent_bases_at_20x mean_coverage
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HG00731 Unknown 5.1 93.69 29.31
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HG00732 Female 5 90 28
4+
HG00733 Male 6 85 36.4
5+
NA19675 Male 0 80 30

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