def test_query_variants(self, mock_get_variants, mock_get_gene_counts,
mock_error_logger, mock_analyst_group):
url = reverse(query_variants_handler, args=['abc'])
self.check_collaborator_login(
url, request_data={'projectFamilies': PROJECT_FAMILIES})
url = reverse(query_variants_handler, args=[SEARCH_HASH])
# add a locus list
LocusList.objects.get(guid=LOCUS_LIST_GUID).projects.add(
Project.objects.get(guid=PROJECT_GUID))
# Test invalid inputs
response = self.client.get(url)
self.assertEqual(response.status_code, 400)
self.assertEqual(response.reason_phrase,
'Invalid search hash: {}'.format(SEARCH_HASH))
mock_error_logger.assert_not_called()
response = self.client.post(url,
content_type='application/json',
data=json.dumps({'search': SEARCH}))
self.assertEqual(response.status_code, 400)
self.assertEqual(response.reason_phrase,
'Invalid search: no projects/ families specified')
mock_error_logger.assert_not_called()
mock_get_variants.side_effect = InvalidIndexException('Invalid index')
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 400)
self.assertEqual(response.json()['error'], 'Invalid index')
mock_error_logger.assert_called_with('Invalid index', extra=mock.ANY)
mock_get_variants.side_effect = InvalidSearchException(
'Invalid search')
mock_error_logger.reset_mock()
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 400)
self.assertEqual(response.json()['error'], 'Invalid search')
mock_error_logger.assert_not_called()
mock_get_variants.side_effect = ConnectionTimeout(
'', '', ValueError('Timeout'))
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 504)
self.assertEqual(response.json()['error'],
'ConnectionTimeout caused by - ValueError(Timeout)')
mock_error_logger.assert_not_called()
mock_get_variants.side_effect = TransportError(
'N/A', 'search_phase_execution_exception', {'error': 'Invalid'})
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 400)
self.assertEqual(
response.json()['error'],
"TransportError: N/A - 'search_phase_execution_exception' - 'Invalid'"
)
self.assertEqual(response.json()['detail'], {'error': 'Invalid'})
mock_error_logger.assert_not_called()
error_info_json = {
'error': {
'root_cause': [{
'type':
'response_handler_failure_transport_exception'
}]
}
}
mock_get_variants.side_effect = TransportError(
'401', 'search_phase_execution_exception', error_info_json)
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 401)
self.assertEqual(
response.json()['error'],
"TransportError: 401 - 'search_phase_execution_exception' - response_handler_failure_transport_exception"
)
self.assertEqual(response.json()['detail'], error_info_json)
mock_error_logger.assert_not_called()
mock_get_variants.side_effect = _get_es_variants
# Test new search
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()), {
'searchedVariants', 'savedVariantsByGuid', 'genesById',
'search', 'variantTagsByGuid', 'variantNotesByGuid',
'variantFunctionalDataByGuid', 'locusListsByGuid'
})
self.assertListEqual(response_json['searchedVariants'], VARIANTS)
self.assertDictEqual(
response_json['search'], {
'search':
SEARCH,
'projectFamilies': [{
'projectGuid': PROJECT_GUID,
'familyGuids': mock.ANY
}],
'totalResults':
3,
})
self.assertSetEqual(
set(response_json['search']['projectFamilies'][0]['familyGuids']),
{'F000001_1', 'F000002_2'})
self.assertSetEqual(set(response_json['savedVariantsByGuid'].keys()), {
'SV0000001_2103343353_r0390_100', 'SV0000002_1248367227_r0390_100'
})
self.assertSetEqual(
set(response_json['genesById'].keys()),
{'ENSG00000227232', 'ENSG00000268903', 'ENSG00000233653'})
gene_fields = {'locusListGuids'}
gene_fields.update(GENE_VARIANT_FIELDS)
self.assertSetEqual(
set(response_json['genesById']['ENSG00000227232'].keys()),
gene_fields)
self.assertListEqual(
response_json['genesById']['ENSG00000227232']['locusListGuids'],
[LOCUS_LIST_GUID])
self.assertSetEqual(set(response_json['locusListsByGuid'].keys()),
{LOCUS_LIST_GUID})
intervals = response_json['locusListsByGuid'][LOCUS_LIST_GUID][
'intervals']
self.assertEqual(len(intervals), 2)
self.assertSetEqual(
set(intervals[0].keys()), {
'locusListGuid', 'locusListIntervalGuid', 'genomeVersion',
'chrom', 'start', 'end'
})
results_model = VariantSearchResults.objects.get(
search_hash=SEARCH_HASH)
mock_get_variants.assert_called_with(results_model,
sort='xpos',
page=1,
num_results=100,
skip_genotype_filter=False)
mock_error_logger.assert_not_called()
# Test pagination
response = self.client.get('{}?page=3'.format(url))
self.assertEqual(response.status_code, 200)
mock_get_variants.assert_called_with(results_model,
sort='xpos',
page=3,
num_results=100,
skip_genotype_filter=False)
mock_error_logger.assert_not_called()
# Test sort
response = self.client.get('{}?sort=pathogenicity'.format(url))
self.assertEqual(response.status_code, 200)
mock_get_variants.assert_called_with(results_model,
sort='pathogenicity',
page=1,
num_results=100,
skip_genotype_filter=False)
mock_error_logger.assert_not_called()
# Test export
export_url = reverse(export_variants_handler, args=[SEARCH_HASH])
response = self.client.get(export_url)
self.assertEqual(response.status_code, 200)
expected_content = [
[
'chrom', 'pos', 'ref', 'alt', 'gene', 'worst_consequence',
'1kg_freq', 'exac_freq', 'gnomad_genomes_freq',
'gnomad_exomes_freq', 'topmed_freq', 'cadd', 'revel', 'eigen',
'polyphen', 'sift', 'muttaster', 'fathmm', 'rsid', 'hgvsc',
'hgvsp', 'clinvar_clinical_significance', 'clinvar_gold_stars',
'filter', 'family_id_1', 'tags_1', 'notes_1', 'family_id_2',
'tags_2', 'notes_2', 'sample_1', 'num_alt_alleles_1', 'gq_1',
'ab_1', 'sample_2', 'num_alt_alleles_2', 'gq_2', 'ab_2'
],
[
'21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '',
'', '', '', '', '', '', '', '', '', '', '', '',
'ENST00000623083.3:c.1075G>A', 'ENSP00000485442.1:p.Gly359Ser',
'', '', '', '1',
'Tier 1 - Novel gene and phenotype (None)|Review (None)', '',
'2', '', '', 'NA19675', '1', '46.0', '0.702127659574',
'NA19679', '0', '99.0', '0.0'
],
[
'3', '835', 'AAAG', 'A', '', '', '', '', '', '', '', '', '',
'', '', '', '', '', '', '', '', '', '', '', '1', '', '', '',
'', '', 'NA19679', '0', '99.0', '0.0', '', '', '', ''
],
[
'12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '',
'', '', '', '', '', '', '', '', '', '', '', '', '2',
'Known gene for phenotype (None)|Excluded (None)',
'test n\xf8te (None)', '', '', '', '', '', '', '', '', '', '',
''
]
]
self.assertEqual(
response.content,
('\n'.join(['\t'.join(line)
for line in expected_content]) + '\n').encode('utf-8'))
mock_get_variants.assert_called_with(results_model,
page=1,
load_all=True)
mock_error_logger.assert_not_called()
# Test gene breakdown
gene_counts = {
'ENSG00000227232': {
'total': 2,
'families': {
'F000001_1': 2,
'F000002_2': 1
}
},
'ENSG00000268903': {
'total': 1,
'families': {
'F000002_2': 1
}
}
}
mock_get_gene_counts.return_value = gene_counts
gene_breakdown_url = reverse(get_variant_gene_breakdown,
args=[SEARCH_HASH])
response = self.client.get(gene_breakdown_url)
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(set(response_json.keys()),
{'searchGeneBreakdown', 'genesById'})
self.assertDictEqual(response_json['searchGeneBreakdown'],
{SEARCH_HASH: gene_counts})
self.assertSetEqual(set(response_json['genesById'].keys()),
{'ENSG00000227232', 'ENSG00000268903'})
gene_fields = {
'constraints', 'omimPhenotypes', 'mimNumber', 'cnSensitivity'
}
gene_fields.update(GENE_FIELDS)
self.assertSetEqual(
set(response_json['genesById']['ENSG00000227232'].keys()),
gene_fields)
# Test compound hets
mock_get_variants.side_effect = _get_compound_het_es_variants
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()), {
'searchedVariants', 'savedVariantsByGuid', 'genesById',
'search', 'variantTagsByGuid', 'variantNotesByGuid',
'variantFunctionalDataByGuid', 'locusListsByGuid'
})
self.assertListEqual(response_json['searchedVariants'],
COMP_HET_VARAINTS)
self.assertSetEqual(set(response_json['savedVariantsByGuid'].keys()),
{'SV0000002_1248367227_r0390_100'})
self.assertSetEqual(set(response_json['genesById'].keys()),
{'ENSG00000233653'})
mock_error_logger.assert_not_called()
# Test cross-project discovery for analyst users
self.login_analyst_user()
mock_get_variants.side_effect = _get_es_variants
response = self.client.get('{}?sort=pathogenicity'.format(url))
self.assertEqual(response.status_code, 403)
mock_analyst_group.__bool__.return_value = True
mock_analyst_group.resolve_expression.return_value = 'analysts'
response = self.client.get('{}?sort=pathogenicity'.format(url))
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()), {
'searchedVariants', 'savedVariantsByGuid', 'genesById',
'search', 'variantTagsByGuid', 'variantNotesByGuid',
'variantFunctionalDataByGuid', 'familiesByGuid',
'locusListsByGuid'
})
self.assertListEqual(response_json['searchedVariants'],
VARIANTS_WITH_DISCOVERY_TAGS)
self.assertSetEqual(set(response_json['familiesByGuid'].keys()),
{'F000011_11'})
mock_get_variants.assert_called_with(results_model,
sort='pathogenicity_hgmd',
page=1,
num_results=100,
skip_genotype_filter=False)
mock_error_logger.assert_not_called()
# Test no results
mock_get_variants.side_effect = _get_empty_es_variants
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertDictEqual(
response_json, {
'searchedVariants': [],
'search': {
'search': SEARCH,
'projectFamilies': PROJECT_FAMILIES,
'totalResults': 0,
}
})
mock_error_logger.assert_not_called()
def test_query_variants(self, mock_get_variants, mock_get_gene_counts):
url = reverse(query_variants_handler, args=[SEARCH_HASH])
_check_login(self, url)
# add a locus list
response = self.client.post(reverse(add_project_locus_lists,
args=[PROJECT_GUID]),
content_type='application/json',
data=json.dumps(
{'locusListGuids': [LOCUS_LIST_GUID]}))
self.assertEqual(response.status_code, 200)
# Test invalid inputs
response = self.client.get(url)
self.assertEqual(response.status_code, 400)
self.assertEqual(response.reason_phrase,
'Invalid search hash: {}'.format(SEARCH_HASH))
response = self.client.post(url,
content_type='application/json',
data=json.dumps({'search': SEARCH}))
self.assertEqual(response.status_code, 400)
self.assertEqual(response.reason_phrase,
'Invalid search: no projects/ families specified')
mock_get_variants.side_effect = InvalidIndexException('Invalid index')
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 400)
self.assertEqual(response.reason_phrase, 'Invalid index')
mock_get_variants.side_effect = _get_es_variants
# Test new search
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()), {
'searchedVariants', 'savedVariantsByGuid', 'genesById',
'search', 'variantTagsByGuid', 'variantNotesByGuid',
'variantFunctionalDataByGuid', 'familiesByGuid'
})
self.assertListEqual(response_json['searchedVariants'],
EXPECTED_VARIANTS_WITH_DISCOVERY_TAGS)
self.assertDictEqual(
response_json['search'], {
'search': SEARCH,
'projectFamilies': PROJECT_FAMILIES,
'totalResults': 3,
})
self.assertSetEqual(set(response_json['savedVariantsByGuid'].keys()), {
'SV0000001_2103343353_r0390_100', 'SV0000002_1248367227_r0390_100'
})
self.assertSetEqual(
set(response_json['genesById'].keys()),
{'ENSG00000227232', 'ENSG00000268903', 'ENSG00000233653'})
self.assertListEqual(
response_json['genesById']['ENSG00000227232']['locusListGuids'],
[LOCUS_LIST_GUID])
self.assertSetEqual(set(response_json['familiesByGuid'].keys()),
{'F000011_11'})
results_model = VariantSearchResults.objects.get(
search_hash=SEARCH_HASH)
mock_get_variants.assert_called_with(results_model,
sort='xpos',
page=1,
num_results=100)
# Test pagination
response = self.client.get('{}?page=3'.format(url))
self.assertEqual(response.status_code, 200)
mock_get_variants.assert_called_with(results_model,
sort='xpos',
page=3,
num_results=100)
# Test sort
response = self.client.get('{}?sort=consequence'.format(url))
self.assertEqual(response.status_code, 200)
mock_get_variants.assert_called_with(results_model,
sort='consequence',
page=1,
num_results=100)
# Test export
export_url = reverse(export_variants_handler, args=[SEARCH_HASH])
response = self.client.get(export_url)
self.assertEqual(response.status_code, 200)
export_content = [
row.split('\t')
for row in response.content.rstrip('\n').split('\n')
]
self.assertEqual(len(export_content), 4)
self.assertListEqual(export_content[0], [
'chrom', 'pos', 'ref', 'alt', 'gene', 'worst_consequence',
'1kg_freq', 'exac_freq', 'gnomad_genomes_freq',
'gnomad_exomes_freq', 'topmed_freq', 'cadd', 'revel', 'eigen',
'polyphen', 'sift', 'muttaster', 'fathmm', 'rsid', 'hgvsc',
'hgvsp', 'clinvar_clinical_significance', 'clinvar_gold_stars',
'filter', 'family_id_1', 'tags_1', 'notes_1', 'family_id_2',
'tags_2', 'notes_2', 'sample_1:num_alt_alleles:gq:ab',
'sample_2:num_alt_alleles:gq:ab'
])
self.assertListEqual(export_content[1], [
'21', '3343400', 'GAGA', 'G', 'WASH7P', 'missense_variant', '', '',
'', '', '', '', '', '', '', '', '', '', '',
'ENST00000623083.3:c.1075G>A', 'ENSP00000485442.1:p.Gly359Ser', '',
'', '', '1',
'Tier 1 - Novel gene and phenotype (None)|Review (None)', '', '2',
'', '', 'NA19675:1:46.0:0.702127659574', 'NA19679:0:99.0:0.0'
])
self.assertListEqual(export_content[3], [
'12', '48367227', 'TC', 'T', '', '', '', '', '', '', '', '', '',
'', '', '', '', '', '', '', '', '', '', '', '2', 'Review (None)',
'test n\xc3\xb8te (None)', '', '', '', '', ''
])
mock_get_variants.assert_called_with(results_model,
page=1,
load_all=True)
# Test gene breakdown
gene_counts = {
'ENSG00000227232': {
'total': 2,
'families': {
'F000001_1': 2,
'F000002_2': 1
}
},
'ENSG00000268903': {
'total': 1,
'families': {
'F000002_2': 1
}
}
}
mock_get_gene_counts.return_value = gene_counts
gene_breakdown_url = reverse(get_variant_gene_breakdown,
args=[SEARCH_HASH])
response = self.client.get(gene_breakdown_url)
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(set(response_json.keys()),
{'searchGeneBreakdown', 'genesById'})
self.assertDictEqual(response_json['searchGeneBreakdown'],
{SEARCH_HASH: gene_counts})
self.assertSetEqual(set(response_json['genesById'].keys()),
{'ENSG00000227232', 'ENSG00000268903'})
# Test no cross-project discovery for non-staff users
login_non_staff_user(self)
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()), {
'searchedVariants', 'savedVariantsByGuid', 'genesById',
'search', 'variantTagsByGuid', 'variantNotesByGuid',
'variantFunctionalDataByGuid'
})
self.assertListEqual(response_json['searchedVariants'],
EXPECTED_VARIANTS)
# Test no results
mock_get_variants.side_effect = _get_empty_es_variants
response = self.client.post(url,
content_type='application/json',
data=json.dumps({
'projectFamilies': PROJECT_FAMILIES,
'search': SEARCH
}))
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertDictEqual(
response_json, {
'searchedVariants': [],
'genesById': {},
'search': {
'search': SEARCH,
'projectFamilies': PROJECT_FAMILIES,
'totalResults': 0,
}
})