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add test
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@hanars
hanars committed Feb 13, 2024
1 parent 0b3a872 commit e81d795
Showing 1 changed file with 41 additions and 11 deletions.
52 changes: 41 additions & 11 deletions seqr/utils/search/hail_search_utils_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,15 @@
from hail_search.test_utils import get_hail_search_body, EXPECTED_SAMPLE_DATA, FAMILY_1_SAMPLE_DATA, \
FAMILY_2_ALL_SAMPLE_DATA, ALL_AFFECTED_SAMPLE_DATA, CUSTOM_AFFECTED_SAMPLE_DATA, HAIL_BACKEND_VARIANTS, \
LOCATION_SEARCH, EXCLUDE_LOCATION_SEARCH, VARIANT_ID_SEARCH, RSID_SEARCH, GENE_COUNTS, FAMILY_2_VARIANT_SAMPLE_DATA, \
FAMILY_2_MITO_SAMPLE_DATA, EXPECTED_SAMPLE_DATA_WITH_SEX, VARIANT_LOOKUP_VARIANT, MULTI_PROJECT_SAMPLE_DATA
FAMILY_2_MITO_SAMPLE_DATA, EXPECTED_SAMPLE_DATA_WITH_SEX, VARIANT_LOOKUP_VARIANT, MULTI_PROJECT_SAMPLE_DATA, \
GCNV_VARIANT4, SV_VARIANT2
MOCK_HOST = 'http://test-hail-host'

SV_WGS_SAMPLE_DATA = [{
'individual_guid': 'I000018_na21234', 'family_guid': 'F000014_14', 'project_guid': 'R0004_non_analyst_project',
'affected': 'A', 'sample_id': 'NA21234',
}]


@mock.patch('seqr.utils.search.hail_search_utils.HAIL_BACKEND_SERVICE_HOSTNAME', MOCK_HOST)
class HailSearchUtilsTests(SearchTestHelper, TestCase):
Expand All @@ -28,11 +34,12 @@ def setUp(self):
'results': HAIL_BACKEND_VARIANTS, 'total': 5,
})

def _test_minimal_search_call(self, expected_search_body=None, **kwargs):
def _test_minimal_search_call(self, expected_search_body=None, call_offset=-1, url_path='search', **kwargs):
expected_search = expected_search_body or get_hail_search_body(genome_version='GRCh37', **kwargs)

executed_request = responses.calls[-1].request
executed_request = responses.calls[call_offset].request
self.assertEqual(executed_request.headers.get('From'), '[email protected]')
self.assertEqual(executed_request.url.split('/')[-1], url_path)
self.assertDictEqual(json.loads(executed_request.body), expected_search)

def _test_expected_search_call(self, search_fields=None, gene_ids=None, intervals=None, exclude_intervals= None,
Expand Down Expand Up @@ -149,8 +156,7 @@ def test_query_variants(self):
query_variants(self.results_model, user=self.user)
sv_sample_data = {
'SV_WES': FAMILY_2_VARIANT_SAMPLE_DATA['SNV_INDEL'],
'SV_WGS': [{'individual_guid': 'I000018_na21234', 'family_guid': 'F000014_14',
'project_guid': 'R0004_non_analyst_project', 'affected': 'A', 'sample_id': 'NA21234'}],
'SV_WGS': SV_WGS_SAMPLE_DATA,
}
self._test_expected_search_call(search_fields=['annotations'], dataset_type='SV', sample_data=sv_sample_data)

Expand Down Expand Up @@ -208,34 +214,58 @@ def test_get_variant_query_gene_counts(self):
gene_counts = get_variant_query_gene_counts(self.results_model, self.user)
self.assertDictEqual(gene_counts, GENE_COUNTS)
self.assert_cached_results({'gene_aggs': gene_counts})
self._test_expected_search_call(sort=None)
self._test_expected_search_call(url_path='gene_counts', sort=None)

@responses.activate
def test_variant_lookup(self):
responses.add(responses.POST, f'{MOCK_HOST}:5000/lookup', status=200, json=VARIANT_LOOKUP_VARIANT)
variant = variant_lookup(self.user, '1-10439-AC-A', genome_version='37', foo='bar')
self.assertListEqual(variant, [VARIANT_LOOKUP_VARIANT])
self._test_minimal_search_call(expected_search_body={
self._test_minimal_search_call(url_path='lookup', expected_search_body={
'variant_id': ['1', 10439, 'AC', 'A'], 'genome_version': 'GRCh37', 'foo': 'bar', 'data_type': 'SNV_INDEL',
})

variant_lookup(self.user, '1-10439-AC-A', genome_version='37', families=self.families)
self._test_minimal_search_call(expected_search_body={
self._test_minimal_search_call(url_path='lookup', expected_search_body={
'variant_id': ['1', 10439, 'AC', 'A'], 'genome_version': 'GRCh37',
'sample_data': ALL_AFFECTED_SAMPLE_DATA['SNV_INDEL'], 'data_type': 'SNV_INDEL',
})

with self.assertRaises(InvalidSearchException) as cm:
variant_lookup(self.user, 'prefix_123_DEL')
variant_lookup(self.user, 'suffix_140608_DUP')
self.assertEqual(str(cm.exception), 'Sample type must be specified to look up a structural variant')
# TODO add test for SVs

responses.add(responses.POST, f'{MOCK_HOST}:5000/lookup', status=200, json=GCNV_VARIANT4)
variant_lookup(self.user, 'suffix_140608_DUP', sample_type='WES')
self._test_minimal_search_call(url_path='lookup', expected_search_body={
'variant_id': 'suffix_140608_DUP', 'genome_version': 'GRCh38', 'data_type': 'SV_WES',
})

sv_families = Family.objects.filter(id__in=[2, 14])
variant_lookup(self.user, 'suffix_140608_DUP', sample_type='WES', families=sv_families)
self._test_minimal_search_call(url_path='lookup', call_offset=-2, expected_search_body={
'variant_id': 'suffix_140608_DUP', 'genome_version': 'GRCh38', 'data_type': 'SV_WES',
'sample_data': ALL_AFFECTED_SAMPLE_DATA['SV_WES']
})
self._test_minimal_search_call(expected_search_body={
'genome_version': 'GRCh38', 'data_type': 'SV_WES', 'annotations': {'structural': ['DEL', 'gCNV_DEL']},
'intervals': ['17:38718997-38738487'], 'sample_data': {'SV_WGS': SV_WGS_SAMPLE_DATA},
})

# No second lookup call is made for non DELs/DUPs
responses.add(responses.POST, f'{MOCK_HOST}:5000/lookup', status=200, json=SV_VARIANT2)
variant_lookup(self.user, 'cohort_2911.chr1.final_cleanup_INS_chr1_160', sample_type='WGS', families=sv_families)
self._test_minimal_search_call(url_path='lookup', expected_search_body={
'variant_id': 'cohort_2911.chr1.final_cleanup_INS_chr1_160', 'genome_version': 'GRCh38', 'data_type': 'SV_WGS',
'sample_data': SV_WGS_SAMPLE_DATA
})

responses.add(responses.POST, f'{MOCK_HOST}:5000/lookup', status=404)
with self.assertRaises(HTTPError) as cm:
variant_lookup(self.user, '1-10439-AC-A')
self.assertEqual(cm.exception.response.status_code, 404)
self.assertEqual(str(cm.exception), 'Variant not present in seqr')
self._test_minimal_search_call(expected_search_body={
self._test_minimal_search_call(url_path='lookup', expected_search_body={
'variant_id': ['1', 10439, 'AC', 'A'], 'genome_version': 'GRCh38', 'data_type': 'SNV_INDEL',
})

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