def test_remove_publication(self):
"""Remove a publication to a gene panel entry"""
gpes = GenePanelEntrySnapshotFactory(
penetrance=GenePanelEntrySnapshot.PENETRANCE.Incomplete)
gpes.publications = [fake.sentence(), fake.sentence()]
gpes.save()
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
gene_data = {
"gene": gpes.gene_core.pk,
"gene_name": "Gene name",
"source": set([ev.name for ev in gpes.evidence.all()]),
"tags": [tag.pk for tag in gpes.tags.all()],
"publications": ";".join(gpes.publications[:1]),
"phenotypes":
";".join([phenotype for phenotype in gpes.phenotypes]),
"moi": gpes.moi,
"mode_of_pathogenicity": gpes.mode_of_pathogenicity,
"penetrance": GenePanelEntrySnapshot.PENETRANCE.Complete,
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
gene = GenePanel.objects.get(
pk=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene_core.gene_symbol)
assert gene.publications == gpes.publications[:1]
class TestWebservices(TransactionTestCase):
def setUp(self):
super().setUp()
self.gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
self.gps_public = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
self.gpes = GenePanelEntrySnapshotFactory(panel=self.gps_public)
self.gpes_internal = GenePanelEntrySnapshotFactory(panel__panel__status=GenePanel.STATUS.internal)
self.gpes_retired = GenePanelEntrySnapshotFactory(panel__panel__status=GenePanel.STATUS.retired)
self.gpes_deleted = GenePanelEntrySnapshotFactory(panel__panel__status=GenePanel.STATUS.deleted)
self.genes = GenePanelEntrySnapshotFactory.create_batch(4, panel=self.gps)
self.str = STRFactory(panel__panel__status=GenePanel.STATUS.public)
self.region = RegionFactory(panel__panel__status=GenePanel.STATUS.public)
self.region2 = RegionFactory(panel__panel__status=GenePanel.STATUS.public, position_37=None)
def test_list_panels(self):
r = self.client.get(reverse_lazy('webservices:list_panels'))
self.assertEqual(r.status_code, 200)
def test_list_panels_name(self):
url = reverse_lazy('webservices:list_panels')
r = self.client.get("{}?Types=all".format(url))
self.assertEqual(len(r.json()['result']), 5)
self.assertEqual(r.status_code, 200)
def test_list_100k_rd_type(self):
panel_type = PanelTypeFactory(slug='rare-disease-100k')
self.gps.panel.types.add(panel_type)
url = reverse_lazy('webservices:list_panels')
r = self.client.get(url)
self.assertEqual(len(r.json()['result']), 1)
self.assertEqual(r.status_code, 200)
def test_list_panels_filter_type(self):
panel_type = PanelTypeFactory()
self.gps.panel.types.add(panel_type)
url = reverse_lazy('webservices:list_panels')
r = self.client.get(url + '?Types=' + panel_type.slug)
self.assertEqual(len(r.json()['result']), 1)
self.assertEqual(r.json()['result'][0]['Name'], self.gps.panel.name)
self.assertEqual(r.status_code, 200)
def test_retired_panels(self):
url = reverse_lazy('webservices:list_panels')
self.gps.panel.status = GenePanel.STATUS.deleted
self.gps.panel.save()
r = self.client.get("{}?Types=all".format(url))
self.assertEqual(len(r.json()['result']), 4)
self.assertEqual(r.status_code, 200)
# Test deleted panels
url = reverse_lazy('webservices:list_panels')
r = self.client.get("{}?Retired=True&Types=all".format(url))
self.assertEqual(len(r.json()['result']), 5) # one for gpes via factory, 2nd - retired
self.assertEqual(r.status_code, 200)
# Test for unapproved panels
self.gps_public.panel.status = GenePanel.STATUS.internal
self.gps_public.panel.save()
url = reverse_lazy('webservices:list_panels')
r = self.client.get("{}?Retired=True&Types=all".format(url))
self.assertEqual(len(r.json()['result']), 4) # only retired panel will be visible
self.assertEqual(r.status_code, 200)
def test_internal_panel(self):
self.gps.panel.status = GenePanel.STATUS.internal
self.gps.panel.save()
url = reverse_lazy('webservices:get_panel', args=(self.gps.panel.pk, ))
r = self.client.get(url)
self.assertEqual(r.status_code, 200)
self.assertEqual(r.json(), ["Query Error: {} not found.".format(self.gps.panel.pk)])
self.gps.panel.active_panel.increment_version()
del self.gps.panel.active_panel
self.gps.panel.active_panel.increment_version()
r = self.client.get("{}?version=0.1".format(url))
self.assertEqual(r.status_code, 200)
self.assertIsNot(type(r.json()), list)
self.assertIsNotNone(r.json().get('result'))
def test_get_panel_name(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.gpes.panel.panel.name,)))
self.assertEqual(r.status_code, 200)
def test_get_panel_name_deleted(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.gpes_deleted.panel.panel.name,)))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.json(), ["Query Error: {} not found.".format(self.gpes_deleted.panel.panel.name)])
def test_get_panel_internal(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.gpes_internal.panel.panel.name,)))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.json(), ["Query Error: {} not found.".format(self.gpes_internal.panel.panel.name)])
def test_get_panel_retired(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.gpes_retired.panel.panel.name,)))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.json(), ["Query Error: {} not found.".format(self.gpes_retired.panel.panel.name)])
def test_get_panel_pk(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.gpes.panel.panel.pk,)))
self.assertEqual(r.status_code, 200)
def test_get_panel_version(self):
self.gpes.panel.increment_version()
del self.gpes.panel.panel.active_panel
self.gpes.panel.panel.active_panel.increment_version()
url = reverse_lazy('webservices:get_panel', args=(self.gpes.panel.panel.pk,))
r = self.client.get("{}?version=0.1".format(url))
self.assertEqual(r.status_code, 200)
self.gps.panel.status = GenePanel.STATUS.retired
self.gps.panel.save()
url = reverse_lazy('webservices:get_panel', args=(self.gpes.panel.panel.pk,))
r = self.client.get("{}?version=0.1".format(url))
self.assertEqual(r.status_code, 200)
self.assertTrue(b'Query Error' not in r.content)
def test_panel_created_timestamp(self):
self.gpes.panel.increment_version()
url = reverse_lazy('webservices:list_panels')
res = self.client.get("{}?Types=all".format(url))
# find gps panel
title = self.gps_public.panel.name
current_time = str(self.gps_public.created).replace('+00:00', 'Z').replace(' ', 'T')
gps_panel = [r for r in res.json()['result'] if r['Name'] == title][0]
self.assertEqual(gps_panel['CurrentCreated'], current_time)
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.gps_public.panel.name,))).json()
self.assertEqual(r['result']['Created'], current_time)
def test_get_search_gene(self):
url = reverse_lazy('webservices:search_genes', args=(self.gpes.gene_core.gene_symbol,))
r = self.client.get(url)
self.assertEqual(r.status_code, 200)
def test_search_by_gene(self):
url = reverse_lazy('webservices:search_genes', args=(self.gpes.gene_core.gene_symbol,))
r = self.client.get(url)
self.assertEqual(r.status_code, 200)
r = self.client.get("{}?ModeOfInheritance={}".format(url, self.gpes.moi))
self.assertEqual(r.status_code, 200)
r = self.client.get("{}?ModeOfPathogenicity={}".format(url, self.gpes.mode_of_pathogenicity))
self.assertEqual(r.status_code, 200)
r = self.client.get("{}?LevelOfConfidence={}".format(url, self.gpes.saved_gel_status))
self.assertEqual(r.status_code, 200)
r = self.client.get("{}?Penetrance={}".format(url, self.gpes.penetrance))
self.assertEqual(r.status_code, 200)
r = self.client.get("{}?Evidences={}".format(url, self.gpes.evidence.first().name))
self.assertEqual(r.status_code, 200)
r = self.client.get("{}?panel_name={}".format(url, self.gps.panel.name))
self.assertEqual(r.status_code, 200)
multi_genes_arg = "{},{}".format(self.genes[0].gene_core.gene_symbol, self.genes[1].gene_core.gene_symbol)
multi_genes_url = reverse_lazy('webservices:search_genes', args=(multi_genes_arg,))
r = self.client.get(multi_genes_url)
self.assertEqual(r.status_code, 200)
def test_strs_in_panel(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.str.panel.panel.pk,)))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.json()['result']['STRs'][0]['Name'], self.str.name)
self.assertEqual(r.json()['result']['STRs'][0]['GRCh37Coordinates'],
[self.str.position_37.lower, self.str.position_37.upper])
self.assertEqual(r.json()['result']['STRs'][0]['GRCh38Coordinates'],
[self.str.position_38.lower, self.str.position_38.upper])
self.assertEqual(r.json()['result']['STRs'][0]['PathogenicRepeats'], self.str.pathogenic_repeats)
def test_super_panel(self):
super_panel = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
super_panel.child_panels.set([self.gps_public, ])
r_direct = self.client.get(reverse_lazy('webservices:get_panel', args=(self.gps_public.panel.pk,)))
result_genes = list(sorted(r_direct.json()['result']['Genes'], key=lambda x: x.get('GeneSymbol')))
r = self.client.get(reverse_lazy('webservices:get_panel', args=(super_panel.panel.pk,)))
self.assertEqual(r.status_code, 200)
self.assertEqual(result_genes, list(sorted(r.json()['result']['Genes'], key=lambda x: x.get('GeneSymbol'))))
def test_no_loss_of_function(self):
url = reverse_lazy('webservices:search_genes', args=(self.gpes.gene_core.gene_symbol,))
r = self.client.get("{}?ModeOfPathogenicity={}".format(url, 'no_loss_of_function'))
self.assertEqual(len(r.json()['results']), 0)
self.gpes.mode_of_pathogenicity = convert_mop('no_loss_of_function', back=True)
self.gpes.save()
r = self.client.get("{}?ModeOfPathogenicity={}".format(url, 'no_loss_of_function'))
self.assertEqual(len(r.json()['results']), 1)
self.assertEqual(r.json()['results'][0]['GeneSymbol'], self.gpes.gene.get('gene_symbol'))
def test_region_in_panel(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.region.panel.panel.pk,)))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.json()['result']['Regions'][0]['Name'], self.region.name)
self.assertEqual(r.json()['result']['Regions'][0]['GRCh37Coordinates'],
[self.region.position_37.lower, self.region.position_37.upper])
self.assertEqual(r.json()['result']['Regions'][0]['GRCh38Coordinates'],
[self.region.position_38.lower, self.region.position_38.upper])
self.assertEqual(r.json()['result']['Regions'][0]['TriplosensitivityScore'], self.region.triplosensitivity_score)
self.assertEqual(r.json()['result']['Regions'][0]['TypeOfVariants'], self.region.type_of_variants)
def test_region_in_panel_empty_pos37(self):
r = self.client.get(reverse_lazy('webservices:get_panel', args=(self.region2.panel.panel.pk,)))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.json()['result']['Regions'][0]['Name'], self.region2.name)
self.assertEqual(r.json()['result']['Regions'][0]['GRCh37Coordinates'], None)
self.assertEqual(r.json()['result']['Regions'][0]['GRCh38Coordinates'],
[self.region2.position_38.lower, self.region2.position_38.upper])
self.assertEqual(r.json()['result']['Regions'][0]['TriplosensitivityScore'], self.region2.triplosensitivity_score)
self.assertEqual(r.json()['result']['Regions'][0]['TypeOfVariants'], self.region2.type_of_variants)
def test_region_filters(self):
url = reverse_lazy('webservices:get_panel', args=(self.region.panel.panel.pk,))
r = self.client.get("{}?HaploinsufficiencyScore={}".format(url, self.region.haploinsufficiency_score)).json()
self.assertEqual(r['result']['Regions'][0]['HaploinsufficiencyScore'], self.region.haploinsufficiency_score)
r = self.client.get("{}?TriplosensitivityScore={}".format(url, self.region.triplosensitivity_score)).json()
self.assertEqual(r['result']['Regions'][0]['TriplosensitivityScore'], self.region.triplosensitivity_score)
def test_list_entities(self):
url = reverse_lazy('webservices:list_entities')
r = self.client.get(url)
self.assertEqual(r.status_code, 200)
res = r.json()
self.assertEqual(len(res['results']), 8)
self.assertEqual(len([r for r in res['results'] if r['EntityType'] == 'str']), 1)
self.assertEqual(len([r for r in res['results'] if r['EntityType'] == 'region']), 2)
