def test_adding_gene_create_activity(self):
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(4, panel=gps)
gene = GeneFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene'
})
gene_data = {
"gene":
gene.pk,
"source":
Evidence.OTHER_SOURCES[0],
"phenotypes":
"{};{};{}".format(*fake.sentences(nb=3)),
"rating":
Evaluation.RATINGS.AMBER,
"moi":
[x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 12)][0],
"mode_of_pathogenicity":
[x for x in Evaluation.MODES_OF_PATHOGENICITY][randint(1, 2)][0],
"penetrance":
GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
req = self.client.post(url, gene_data)
self.assertEqual(Activity.objects.count(), 1)
def test_export_activities_functionality(self):
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(4, panel=gps)
gene = GeneFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene'
})
gene_data = {
"gene":
gene.pk,
"source":
Evidence.OTHER_SOURCES[0],
"phenotypes":
"{};{};{}".format(*fake.sentences(nb=3)),
"rating":
Evaluation.RATINGS.AMBER,
"moi":
[x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 12)][0],
"mode_of_pathogenicity":
[x for x in Evaluation.MODES_OF_PATHOGENICITY][randint(1, 2)][0],
"penetrance":
GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
self.client.post(url, gene_data)
activities_url = reverse(
'panels:activity') + '?format=csv&panel=' + str(gps.panel.pk)
res = self.client.get(activities_url)
self.assertTrue(gps.panel.name.encode() in res.content)
def test_adding_gene_save_source(self):
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(4, panel=gps)
gene = GeneFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene'
})
gene_data = {
"gene":
gene.pk,
"source":
Evidence.OTHER_SOURCES[0],
"phenotypes":
"{};{};{}".format(*fake.sentences(nb=3)),
"rating":
Evaluation.RATINGS.AMBER,
"moi":
[x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 12)][0],
"mode_of_pathogenicity":
[x for x in Evaluation.MODES_OF_PATHOGENICITY][randint(1, 2)][0],
"penetrance":
GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
self.client.post(url, gene_data)
gpes = gps.panel.active_panel.get_gene(gene.gene_symbol)
self.assertTrue(gene_data['source'] in gpes.evaluation.get(
user=self.verified_user).comments.first().comment)
def test_mark_all_genes_not_ready(self):
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(5, ready=True, panel=gps)
assert GenePanelEntrySnapshot.objects.filter(ready=True).count() == 5
url = reverse_lazy('panels:mark_not_ready',
kwargs={'pk': gps.panel.pk})
res = self.client.get(url)
assert GenePanelEntrySnapshot.objects.filter(ready=True).count() == 0
assert res.status_code == 302
def test_get_panels_for_a_gene(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps3 = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps3) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps3)
gps4 = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps4) # random genes
assert GenePanelEntrySnapshot.objects.get_gene_panels(
gene.gene_symbol).count() == 3
url = reverse_lazy('panels:entity_detail',
kwargs={'slug': gene.gene_symbol})
res = self.client.get(url)
assert len(res.context_data['entries']) == 3
def prepare_compare(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.internal)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps2 = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps2) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps2)
STRFactory(panel=gps, position_37=None)
return gene, gps, gps2
def test_delete_gene(self):
gps = GenePanelSnapshotFactory()
genes = GenePanelEntrySnapshotFactory.create_batch(5, panel=gps)
gene_symbol = genes[2].gene['gene_symbol']
number_of_genes = gps.stats.get('number_of_genes')
assert gps.has_gene(gene_symbol) is True
gps = gps.panel.active_panel
gps.delete_gene(gene_symbol)
gps = gps.panel.active_panel
assert gps.panel.active_panel.has_gene(gene_symbol) is False
assert number_of_genes - 1 == gps.panel.active_panel.stats.get(
'number_of_genes') # 4 is due to create_batch
old_gps = GenePanel.objects.get(
pk=gps.panel.pk).genepanelsnapshot_set.last()
assert old_gps.version != gps.version
assert old_gps.has_gene(gene_symbol) is True
new_gps = GenePanel.objects.get(pk=gps.panel.pk).active_panel
assert new_gps.has_gene(gene_symbol) is False
gene_symbol = genes[3].gene['gene_symbol']
assert new_gps.has_gene(gene_symbol) is True
new_gps.delete_gene(gene_symbol, False)
assert new_gps.has_gene(gene_symbol) is False
new_gps = GenePanel.objects.get(pk=gps.panel.pk).active_panel
assert new_gps.has_gene(gene_symbol) is False
def test_filter_by_panel_date_range(self):
gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(4, panel=gps)
gene = GeneFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene'
})
gene_data = {
"gene":
gene.pk,
"source":
Evidence.OTHER_SOURCES[0],
"phenotypes":
"{};{};{}".format(*fake.sentences(nb=3)),
"rating":
Evaluation.RATINGS.AMBER,
"moi":
[x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 12)][0],
"mode_of_pathogenicity":
[x for x in Evaluation.MODES_OF_PATHOGENICITY][randint(1, 2)][0],
"penetrance":
GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
self.client.post(url, gene_data)
now = timezone.now()
date_from = (now - timedelta(days=7)).strftime('%Y-%m-%d')
date_to = (now + timedelta(days=7)).strftime('%Y-%m-%d')
activities_url = reverse(
'panels:activity'
) + '?date_from=' + date_from + '&date_to=' + date_to
res = self.client.get(activities_url)
self.assertEqual(len(res.context['activities']), 1)
now = timezone.now() - timedelta(days=30)
date_from = (now - timedelta(days=7)).strftime('%Y-%m-%d')
date_to = (now + timedelta(days=7)).strftime('%Y-%m-%d')
activities_url = reverse(
'panels:activity'
) + '?date_from=' + date_from + '&date_to=' + date_to
res = self.client.get(activities_url)
self.assertEqual(len(res.context['activities']), 0)
def test_user_reviews(self):
gps = GenePanelSnapshotFactory()
gpes = GenePanelEntrySnapshotFactory.create_batch(10, panel=gps)
for g in gpes:
for evaluation in g.evaluation.all():
evaluation.user = self.verified_user
evaluation.save()
self.assertEqual(self.verified_user.get_recent_evaluations().count(),
35)
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_get_internal_panels_for_a_gene(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps2 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.internal)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps2) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps2)
gps3 = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps3) # random genes
self.assertEqual(
GenePanelEntrySnapshot.objects.get_gene_panels(
gene.gene_symbol).count(), 2)
self.assertEqual(
GenePanelSnapshot.objects.get_gene_panels(
gene.gene_symbol).count(), 1)
self.assertEqual(
GenePanelSnapshot.objects.get_gene_panels(gene.gene_symbol,
all=True,
internal=True).count(),
2)
url = reverse_lazy('panels:entity_detail',
kwargs={'slug': gene.gene_symbol})
res = self.client.get(url)
self.assertEqual(len(res.context_data['entries']), 2)
def test_filter_by_panel_entity(self):
gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(4, panel=gps)
gene = GeneFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene'
})
gene_data = {
"gene":
gene.pk,
"source":
Evidence.OTHER_SOURCES[0],
"phenotypes":
"{};{};{}".format(*fake.sentences(nb=3)),
"rating":
Evaluation.RATINGS.AMBER,
"moi":
[x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 12)][0],
"mode_of_pathogenicity":
[x for x in Evaluation.MODES_OF_PATHOGENICITY][randint(1, 2)][0],
"penetrance":
GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
self.client.post(url, gene_data)
activities_url = reverse(
'panels:activity'
) + '?entity=' + gene.gene_symbol + '&version=0.0&panel=' + str(
gps.panel.pk)
res = self.client.get(activities_url)
self.assertEqual(len(res.context['activities']), 1)
activities_url = reverse(
'panels:activity') + '?entity=ABCD&version=0.0&panel=' + str(
gps.panel.pk)
res = self.client.get(activities_url)
self.assertEqual(len(res.context['activities']), 0)
def test_delete_gene_ajax(self):
gps = GenePanelSnapshotFactory()
genes = GenePanelEntrySnapshotFactory.create_batch(5, panel=gps)
gene_symbol = genes[2].gene['gene_symbol']
number_of_genes = gps.stats.get('number_of_genes')
url = reverse_lazy('panels:delete_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene',
'entity_name': gene_symbol
})
res = self.client.get(url, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
new_gps = GenePanel.objects.get(pk=gps.panel.pk).active_panel
assert new_gps.has_gene(gene_symbol) is False
assert number_of_genes - 1 == new_gps.stats.get(
'number_of_genes') # 4 is due to create_batch
assert res.json().get('status') == 200
assert res.json().get('content').get('inner-fragments')
def test_list_genes(self):
GenePanelEntrySnapshotFactory.create_batch(3)
r = self.client.get(reverse_lazy('panels:entities_list'))
self.assertEqual(r.status_code, 200)
def test_download_genes(self):
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2, panel=gps)
res = self.client.get(reverse_lazy('panels:download_genes'))
self.assertEqual(res.status_code, 200)
def test_panel_index(self):
GenePanelEntrySnapshotFactory.create_batch(4)
r = self.client.get(reverse_lazy('panels:index'))
self.assertEqual(r.status_code, 200)
def test_update_gene_collection(self):
gene_to_update = GeneFactory()
gene_to_delete = GeneFactory()
gene_to_update_symbol = GeneFactory()
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene_to_update,
panel=gps)
STRFactory.create_batch(2, panel=gps) # random STRs
STRFactory.create(gene_core=gene_to_update, panel=gps)
RegionFactory.create_batch(2, panel=gps) # random STRs
RegionFactory.create(gene_core=gene_to_update, panel=gps)
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
STRFactory.create_batch(2, panel=gps) # random STRs
GenePanelEntrySnapshotFactory.create(gene_core=gene_to_update_symbol,
panel=gps)
STRFactory.create(gene_core=gene_to_update_symbol, panel=gps)
RegionFactory.create_batch(2, panel=gps) # random STRs
RegionFactory.create(gene_core=gene_to_update_symbol, panel=gps)
to_insert = [
Gene(gene_symbol='A', ensembl_genes={
'inserted': True
}).dict_tr(),
Gene(gene_symbol='B', ensembl_genes={
'inserted': True
}).dict_tr(),
]
to_update = [
Gene(gene_symbol=gene_to_update.gene_symbol,
ensembl_genes={
'updated': True
}).dict_tr()
]
to_update_symbol = [(Gene(gene_symbol='C',
ensembl_genes={
'updated': True
}).dict_tr(),
gene_to_update_symbol.gene_symbol)]
to_delete = [gene_to_delete.gene_symbol]
migration = {
'insert': to_insert,
'update': to_update,
'delete': to_delete,
'update_symbol': to_update_symbol
}
update_gene_collection(migration)
self.assertTrue(GenePanelEntrySnapshot.objects.get_active().get(
gene_core__gene_symbol=gene_to_update.gene_symbol).gene.get(
'ensembl_genes')['updated'])
self.assertTrue(STR.objects.get_active().get(
gene_core__gene_symbol=gene_to_update.gene_symbol).gene.get(
'ensembl_genes')['updated'])
self.assertTrue(Region.objects.get_active().get(
gene_core__gene_symbol=gene_to_update.gene_symbol).gene.get(
'ensembl_genes')['updated'])
updated_not_updated = [
gpes.gene['ensembl_genes']
for gpes in GenePanelEntrySnapshot.objects.filter(
gene_core__gene_symbol=gene_to_update.gene_symbol)
]
self.assertNotEqual(updated_not_updated[0], updated_not_updated[1])
updated_not_updated = [
str_item.gene['ensembl_genes'] for str_item in STR.objects.filter(
gene_core__gene_symbol=gene_to_update.gene_symbol)
]
self.assertNotEqual(updated_not_updated[0], updated_not_updated[1])
updated_not_updated = [
region_item.gene['ensembl_genes']
for region_item in Region.objects.filter(
gene_core__gene_symbol=gene_to_update.gene_symbol)
]
self.assertNotEqual(updated_not_updated[0], updated_not_updated[1])
self.assertFalse(
GenePanelEntrySnapshot.objects.get(
gene_core__gene_symbol=gene_to_update_symbol.gene_symbol).
gene_core.active)
self.assertFalse(
STR.objects.get(gene_core__gene_symbol=gene_to_update_symbol.
gene_symbol).gene_core.active)
self.assertFalse(
Region.objects.get(gene_core__gene_symbol=gene_to_update_symbol.
gene_symbol).gene_core.active)
self.assertFalse(
Gene.objects.get(
gene_symbol=gene_to_update_symbol.gene_symbol).active)
self.assertFalse(
Gene.objects.get(gene_symbol=gene_to_delete.gene_symbol).active)
self.assertTrue(Gene.objects.get(gene_symbol='A').active)
self.assertTrue(
GenePanelEntrySnapshot.objects.get(gene_core__gene_symbol='C').
gene.get('ensembl_genes')['updated'])
self.assertTrue(
STR.objects.get(gene_core__gene_symbol='C').gene.get(
'ensembl_genes')['updated'])
self.assertTrue(
Region.objects.get(gene_core__gene_symbol='C').gene.get(
'ensembl_genes')['updated'])
def test_activities(self):
GenePanelEntrySnapshotFactory.create_batch(4)
res = self.client.get(reverse_lazy('panels:activity'))
self.assertEqual(res.status_code, 200)
def test_update_ensembl(self):
gene_symbol = 'FAM58A'
gene_to_update = GeneFactory(gene_symbol=gene_symbol)
ensembl_data = {
"GRch37": {
"82": {
"ensembl_id": "ENSG00000147382",
"location": "X:152853377-152865500"
}
},
"GRch38": {
"90": {
"ensembl_id": "ENSG00000262919",
"location": "X:153587919-153600045"
}
}
}
json_data = {gene_symbol: ensembl_data}
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene_to_update,
panel=gps)
STRFactory.create_batch(2, panel=gps) # random STRs
STRFactory.create(gene_core=gene_to_update, panel=gps)
RegionFactory.create_batch(2, panel=gps) # random STRs
RegionFactory.create(gene_core=gene_to_update, panel=gps)
gps_2 = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps_2) # random genes
STRFactory.create_batch(2, panel=gps_2) # random STRs
RegionFactory.create_batch(2, panel=gps_2) # random STRs
RegionFactory.create(gene_core=gene_to_update, panel=gps_2)
# make sure ensembl data doesn't match
for gene in GenePanelEntrySnapshot.objects.filter(
gene__gene_symbol=gene_symbol):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for str in STR.objects.filter(gene__gene_symbol=gene_symbol):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for region in Region.objects.filter(gene__gene_symbol=gene_symbol):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
gps_pk = gps.pk
gps_version = gps.version
gps_2_version = gps_2.version
process(json_data)
# make sure previous data didn't change
for gene in GenePanelEntrySnapshot.objects.filter(
gene__gene_symbol=gene_symbol, panel_id=gps_pk):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for str in STR.objects.filter(gene__gene_symbol=gene_symbol,
panel_id=gps_pk):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for region in Region.objects.filter(gene__gene_symbol=gene_symbol,
panel_id=gps_pk):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
gps = gps.panel.active_panel
gps_2 = gps_2.panel.active_panel
self.assertNotEqual(gps_version, gps.version)
self.assertNotEqual(gps_2_version, gps_2.version)
# make sure new data has changed
for gene in GenePanelEntrySnapshot.objects.filter(
gene__gene_symbol=gene_symbol, panel=gps):
self.assertEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for str in STR.objects.filter(gene__gene_symbol=gene_symbol,
panel=gps):
self.assertEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for region in Region.objects.filter(gene__gene_symbol=gene_symbol,
panel=gps):
self.assertEqual(gene.gene.get('ensembl_genes'), ensembl_data)
