def test_variant_filters_from_request(self):
filters = [
('filter', 'in_dbsnp'),
('filter', 'quality<=1000'),
('filter', 'aaf_1kg_all<=0.5'),
('filter', 'aaf_max_all>0.4'),
]
expected = [
DbsnpFilter(name='in_dbsnp', op='=', val='1'),
QualityFilter(name='quality', op='<=', val='1000'),
ContinuousFilter(name='aaf_1kg_all', op='<=', val='0.5'),
ContinuousFilter(name='aaf_max_all', op='>', val='0.4'),
]
request = RequestFactory().get('', filters)
fc = variant_filters_from_request(request, db='test')
self.assertIsInstance(fc, FiltersCollection)
self.assertTrue(len(fc) == len(filters))
def check(ff, expect):
self.assertEqual(ff.val, expect.val)
self.assertEqual(ff.name, expect.name)
self.assertEqual(ff.op, expect.op)
for f in expected:
check(fc[f.name], f)
def test_genotypes_filter_from_request_with_default_ss(self):
"""With no samples selection given, makes them from PED phenotype."""
request = RequestFactory().get('', [('filter', 'genotype=dominant')])
fc = variant_filters_from_request(request, db='test')
gf = fc['genotype']
self.assertIsInstance(gf, GenotypesFilterDominant)
self.assertEqual(sorted(gf.ss.groups.keys()), ['affected','not_affected'])
def __init__(self, request, db):
"""Extract filters etc. information from http request."""
self.db = db
self.sort = sort_from_request(request)
self.pg = pagination_from_request(request)
self.ss = samples_selection_from_request(request, db)
self.fc = variant_filters_from_request(request, db, self.ss)
self.stats = stats_service(db)
def test_genotypes_filter_from_request_with_default_ss(self):
"""With no samples selection given, makes them from PED phenotype."""
request = RequestFactory().get('', [('filter', 'genotype=dominant')])
fc = variant_filters_from_request(request, db='test')
gf = fc['genotype']
self.assertIsInstance(gf, GenotypesFilterDominant)
self.assertEqual(sorted(gf.ss.groups.keys()),
['affected', 'not_affected'])
def __init__(self, request, db):
"""Extract filters etc. information from http request."""
self.db = db
self.sort = sort_from_request(request)
self.pg = pagination_from_request(request)
self.ss = samples_selection_from_request(request, db)
self.fc = variant_filters_from_request(request, db, self.ss)
self.stats = stats_service(db)
def test_genotypes_Active_filter_from_request_with_ss_from_request(self):
"""With a sound grouping passed by url."""
samples = [('samples', 'group1=09818,09819')]
filters = [('filter', 'genotype=active')]
request = RequestFactory().get('', samples + filters)
fc = variant_filters_from_request(request, db='test')
gf = fc['genotype']
self.assertIsInstance(gf, GenotypesFilterActive)
var = gf.apply(self.variants).variants # no need for self.genotypes, it will be created on the fly
for v in var:
gts = self.genotypes[v.pk-1]
self.assertTrue(gts[S09818] > 1 or gts[S09819] > 1)
def test_genotypes_Active_filter_from_request_with_ss_from_request(self):
"""With a sound grouping passed by url."""
samples = [('samples', 'group1=09818,09819')]
filters = [('filter', 'genotype=active')]
request = RequestFactory().get('', samples + filters)
fc = variant_filters_from_request(request, db='test')
gf = fc['genotype']
self.assertIsInstance(gf, GenotypesFilterActive)
var = gf.apply(
self.variants
).variants # no need for self.genotypes, it will be created on the fly
for v in var:
gts = self.genotypes[v.pk - 1]
self.assertTrue(gts[S09818] > 1 or gts[S09819] > 1)
def test_genotypes_Nothing_filter_from_request_with_ss_from_request(self):
"""With a sound grouping passed by url."""
samples = [('samples', 'A=09818,09819'), ('samples', 'B=09960,09961')]
filters = [('filter', 'genotype=nothing')]
request = RequestFactory().get('', samples + filters)
fc = variant_filters_from_request(request, db='test')
self.assertIsInstance(fc, FiltersCollection)
self.assertTrue(len(fc) == len(filters))
gf = fc['genotype']
self.assertEqual(sorted(gf.ss.groups.keys()), ['A', 'B'])
self.assertEqual(gf.name, 'genotype')
self.assertEqual(gf.val, 'nothing')
self.assertEqual(gf.op, '=')
self.assertIsInstance(gf, GenotypesFilterDoNothing)
def test_genotypes_Nothing_filter_from_request_with_ss_from_request(self):
"""With a sound grouping passed by url."""
samples = [('samples', 'A=09818,09819'), ('samples', 'B=09960,09961')]
filters = [('filter', 'genotype=nothing')]
request = RequestFactory().get('', samples + filters)
fc = variant_filters_from_request(request, db='test')
self.assertIsInstance(fc, FiltersCollection)
self.assertTrue(len(fc) == len(filters))
gf = fc['genotype']
self.assertEqual(sorted(gf.ss.groups.keys()), ['A','B'])
self.assertEqual(gf.name, 'genotype')
self.assertEqual(gf.val, 'nothing')
self.assertEqual(gf.op, '=')
self.assertIsInstance(gf, GenotypesFilterDoNothing)
def test_genotypes_Dominant_filter_from_request_with_ss_from_request(self):
"""With a sound grouping passed by url."""
samples = [('samples', 'not_affected=09960,09961'),
('samples', 'affected=09818,09819')]
filters = [('filter', 'genotype=dominant')]
request = RequestFactory().get('', samples + filters)
fc = variant_filters_from_request(request, db='test')
gf = fc['genotype']
self.assertIsInstance(gf, GenotypesFilterDominant)
var = gf.apply(self.variants).variants
for v in var:
gts = self.genotypes[v.pk - 1]
self.assertGreater(gts[S09818], 1)
self.assertGreater(gts[S09819], 1)
self.assertEqual(gts[S09960], 1)
self.assertEqual(gts[S09961], 1)
def test_genotypes_Dominant_filter_from_request_with_ss_from_request(self):
"""With a sound grouping passed by url."""
samples = [('samples', 'not_affected=09960,09961'),
('samples', 'affected=09818,09819')]
filters = [('filter', 'genotype=dominant')]
request = RequestFactory().get('', samples + filters)
fc = variant_filters_from_request(request, db='test')
gf = fc['genotype']
self.assertIsInstance(gf, GenotypesFilterDominant)
var = gf.apply(self.variants).variants
for v in var:
gts = self.genotypes[v.pk-1]
self.assertGreater(gts[S09818], 1)
self.assertGreater(gts[S09819], 1)
self.assertEqual(gts[S09960], 1)
self.assertEqual(gts[S09961], 1)
def test_variant_filters_from_request(self):
filters = [('filter', 'in_dbsnp'),
('filter', 'quality<=1000'),
('filter', 'aaf_1kg_all<=0.5'),
('filter', 'aaf_max_all>0.4'),
]
expected = [DbsnpFilter(name='in_dbsnp', op='=', val='1'),
QualityFilter(name='quality', op='<=', val='1000'),
ContinuousFilter(name='aaf_1kg_all', op='<=', val='0.5'),
ContinuousFilter(name='aaf_max_all', op='>', val='0.4'),
]
request = RequestFactory().get('', filters)
fc = variant_filters_from_request(request, db='test')
self.assertIsInstance(fc, FiltersCollection)
self.assertTrue(len(fc) == len(filters))
def check(ff, expect):
self.assertEqual(ff.val, expect.val)
self.assertEqual(ff.name, expect.name)
self.assertEqual(ff.op, expect.op)
for f in expected:
check(fc[f.name], f)
