def test_import_panel_sources(self):
gene = GeneFactory(gene_symbol="ABCC5-AS1")
A1CF = GeneFactory(gene_symbol="A1CF")
GeneFactory(gene_symbol="STR_1")
gps = GenePanelSnapshotFactory()
gps.panel.name = "Panel One"
gps.level4title.name = gps.panel.name
gps.level4title.save()
gps.panel.save()
evidence = EvidenceFactory.create(name="Expert Review Amber")
GenePanelEntrySnapshotFactory.create(gene_core=gene,
panel=gps,
evaluation=(None, ),
evidence=(evidence, ))
self.assertEqual(
gps.get_gene(gene.gene_symbol).evidence.first().name,
"Expert Review Amber")
file_path = os.path.join(os.path.dirname(__file__),
'import_panel_data.tsv')
test_panel_file = os.path.abspath(file_path)
with open(test_panel_file) as f:
url = reverse_lazy('panels:upload_panels')
self.client.post(url, {'panel_list': f})
ap = GenePanel.objects.get(name="Panel One").active_panel
self.assertEqual(
ap.get_gene(gene.gene_symbol).evidence.first().name,
"Expert Review Green")
self.assertEqual(ap.get_gene(gene.gene_symbol).evidence.count(), 1)
self.assertEqual(sorted(ap.get_gene('A1CF').phenotypes),
sorted(['57h', 'wef']))
def test_import_gene(self):
"""
Test Gene import. This also tests CellBaseConnector, which actually makes
requests to the server. We can mock it later if necessary.
"""
file_path = os.path.join(os.path.dirname(__file__), 'test_import.json')
test_gene_file = os.path.abspath(file_path)
# Create genes to update
update_symbol = []
update = []
with open(test_gene_file) as f:
results = json.load(f)
for r in results['update']:
update.append(
GeneFactory(gene_symbol=r['gene_symbol']).gene_symbol)
for r in results['update_symbol']:
update_symbol.append(GeneFactory(gene_symbol=r[1]).gene_symbol)
with open(test_gene_file) as f:
url = reverse_lazy('panels:upload_genes')
self.client.post(url, {'gene_list': f})
for us in update_symbol:
self.assertFalse(Gene.objects.get(gene_symbol=us).active)
for u in update:
gene = Gene.objects.get(gene_symbol=u)
if gene.ensembl_genes:
self.assertTrue(gene.active)
else:
self.assertFalse(gene.active)
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_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_reviewer_source_visible(self):
"""When a reviewer adds a gene source should be displayed"""
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene'
})
gene_data = {
"gene":
gene.pk,
"source":
Evidence.OTHER_SOURCES[2],
"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)
url = reverse_lazy('panels:detail', kwargs={'pk': gps.panel.pk})
res = self.client.get(url)
self.assertContains(res, gene_data['source'])
def test_update_gene_preserves_comments_order(self):
gpes = GenePanelEntrySnapshotFactory()
comments = list(CommentFactory.create_batch(4,
user=self.verified_user))
for ev in gpes.evaluation.all():
ev.comments.add(comments.pop())
max_comments_num = max(
[e.comments.count() for e in gpes.evaluation.all()])
self.assertEqual(1, max_comments_num)
old_gene_symbol = gpes.gene.get('gene_symbol')
new_gene = GeneFactory()
ap = GenePanel.objects.get(pk=gpes.panel.panel.pk).active_panel
new_data = {"gene": new_gene, "gene_name": "Other name"}
ap.update_gene(self.verified_user, old_gene_symbol, new_data)
new_ap = GenePanel.objects.get(pk=gpes.panel.panel.pk).active_panel
gpes = new_ap.get_gene(new_gene.gene_symbol)
max_comments_num_after_update = max(
[e.comments.count() for e in gpes.evaluation.all()])
self.assertEqual(1, max_comments_num_after_update)
def test_add_gene_to_panel(self):
"""When a reviewer adds a gene it shouldn't increment the version of a panel"""
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
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)
panel = gps.panel.active_panel
assert panel.version == gps.version
def test_import_regions(self):
GeneFactory(gene_symbol="ABCC5-AS1")
GeneFactory(gene_symbol="A1CF")
GeneFactory(gene_symbol="STR_1")
file_path = os.path.join(os.path.dirname(__file__),
'import_panel_data.tsv')
test_panel_file = os.path.abspath(file_path)
with open(test_panel_file) as f:
url = reverse_lazy('panels:upload_panels')
res = self.client.post(url, {'panel_list': f})
gp = GenePanel.objects.get(name="Panel One")
active_panel = gp.active_panel
self.assertEqual(active_panel.get_all_regions.count(), 1)
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 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_gel_curator_str_red(self):
"""When gene is added by a GeL currator it should be marked as red"""
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
url = reverse_lazy('panels:add_entity', kwargs={'pk': gps.panel.pk, 'entity_type': 'str'})
str_data = {
'name': 'SomeSTR',
'chromosome': '1',
'position_37_0': '12345',
'position_37_1': '12346',
'position_38_0': '12345',
'position_38_1': '123456',
'repeated_sequence': 'ATAT',
'normal_repeats': '2',
'pathogenic_repeats': '5',
"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, str_data)
panel = gps.panel.active_panel
assert panel.get_str('SomeSTR').saved_gel_status == 1
def test_reviewer_gene_grey(self):
"""When a reviewer adds a gene it should be marked as grey gene"""
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
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)
panel = gps.panel.active_panel
self.assertEqual(panel.get_gene(gene.gene_symbol).saved_gel_status, 0)
def test_region_review_view(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
region = RegionFactory(panel=gps, gene_core=gene)
url = reverse_lazy('panels:review_entity', args=(region.panel.panel.pk, 'region', region.name,))
r = self.client.get(url)
self.assertEqual(r.status_code, 200)
def test_gene_review_view(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
gpes = GenePanelEntrySnapshotFactory(panel=gps, gene_core=gene)
url = reverse_lazy('panels:review_entity',
args=(
gpes.panel.panel.pk,
'gene',
gene.gene_symbol,
))
r = self.client.get(url)
self.assertEqual(r.status_code, 200)
def test_download_panel(self):
gene, gps, gps2 = self.prepare_compare()
grey_gene = 'gene2'
gene2 = GeneFactory(gene_symbol=grey_gene)
gpes = GenePanelEntrySnapshotFactory.create(gene_core=gene2, panel=gps)
gpes.saved_gel_status = 0
res = self.client.get(
reverse_lazy('panels:download_panel_tsv',
args=(gps.panel.pk, '01234')))
self.assertEqual(res.status_code, 200)
self.assertEqual(res.content.find(grey_gene.encode()), -1)
def test_str_review_view(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
str_item = STRFactory(panel=gps, gene_core=gene)
url = reverse_lazy('panels:review_entity',
args=(
str_item.panel.panel.pk,
'str',
str_item.name,
))
r = self.client.get(url)
self.assertEqual(r.status_code, 200)
def test_add_region_to_panel(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
number_of_regions = gps.stats.get('number_of_regions')
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'region'
})
region_data = {
'name': 'SomeRegion',
'chromosome': '1',
'position_37_0': '',
'position_37_1': '',
'position_38_0': '12345',
'position_38_1': '123456',
'haploinsufficiency_score':
choice(Region.DOSAGE_SENSITIVITY_SCORES)[0],
'triplosensitivity_score':
choice(Region.DOSAGE_SENSITIVITY_SCORES)[0],
'required_overlap_percentage': randint(0, 100),
"gene": gene.pk,
"source": Evidence.ALL_SOURCES[randint(0, 9)],
"tags": [
TagFactory().pk,
],
"publications": "{};{};{}".format(*fake.sentences(nb=3)),
"phenotypes": "{};{};{}".format(*fake.sentences(nb=3)),
"rating": Evaluation.RATINGS.AMBER,
"comments": fake.sentence(),
"moi":
[x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 12)][0],
"penetrance": Region.PENETRANCE.Incomplete,
"current_diagnostic": "True",
"type_of_variants": Region.VARIANT_TYPES.small,
}
res = self.client.post(url, region_data)
new_current_number = gps.panel.active_panel.stats.get(
'number_of_regions')
assert gps.panel.active_panel.version != gps.version
assert res.status_code == 302
assert number_of_regions + 1 == new_current_number
# make sure tags are added
new_region = GenePanel.objects.get(
pk=gps.panel.pk).active_panel.get_region(region_data['name'])
assert sorted(list(new_region.tags.all().values_list(
'pk', flat=True))) == sorted(region_data['tags'])
def test_edit_gene_name_ajax(self):
gpes = GenePanelEntrySnapshotFactory()
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
old_gene_symbol = gpes.gene.get('gene_symbol')
# make sure new data has at least 1 of the same items
source = gpes.evidence.last().name
publication = gpes.publications[0]
phenotype = gpes.publications[1]
new_gene = GeneFactory()
gene_data = {
"gene":
new_gene.pk,
"gene_name":
"Other name",
"source":
set([source, Evidence.ALL_SOURCES[randint(0, 9)]]),
"tags": [
TagFactory().pk,
] + [tag.pk for tag in gpes.tags.all()],
"publications":
";".join([publication, fake.sentence()]),
"phenotypes":
";".join([phenotype, fake.sentence(),
fake.sentence()]),
"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,
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
new_gps = GenePanel.objects.get(pk=gpes.panel.panel.pk).active_panel
old_gps = GenePanelSnapshot.objects.get(pk=gpes.panel.pk)
# check panel has no previous gene
assert new_gps.has_gene(old_gene_symbol) is False
# test previous panel contains old gene
assert old_gps.has_gene(old_gene_symbol) is True
def test_gel_curator_region_red(self):
"""When gene is added by a GeL currator it should be marked as red"""
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'region'
})
region_data = {
'name':
'SomeRegion',
'chromosome':
'1',
'position_37_0':
'12345',
'position_37_1':
'12346',
'position_38_0':
'12345',
'position_38_1':
'123456',
'haploinsufficiency_score':
choice(Region.DOSAGE_SENSITIVITY_SCORES)[0],
'triplosensitivity_score':
choice(Region.DOSAGE_SENSITIVITY_SCORES)[0],
'required_overlap_percentage':
randint(0, 100),
"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":
Region.PENETRANCE.Incomplete,
"type_of_variants":
Region.VARIANT_TYPES.small,
}
self.client.post(url, region_data)
panel = gps.panel.active_panel
assert panel.get_region('SomeRegion').saved_gel_status == 1
def test_edit_gene_name_unit(self):
gpes = GenePanelEntrySnapshotFactory()
old_gene_symbol = gpes.gene.get('gene_symbol')
new_gene = GeneFactory()
ap = GenePanel.objects.get(pk=gpes.panel.panel.pk).active_panel
assert ap.has_gene(old_gene_symbol) is True
new_data = {"gene": new_gene, "gene_name": "Other name"}
ap.update_gene(self.verified_user, old_gene_symbol, new_data)
new_ap = GenePanel.objects.get(pk=gpes.panel.panel.pk).active_panel
assert new_ap.has_gene(old_gene_symbol) is False
assert new_ap.has_gene(new_gene.gene_symbol) is True
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_import_incorrect_position(self):
GeneFactory(gene_symbol="STR_1")
file_path = os.path.join(os.path.dirname(__file__),
'import_panel_data_error.tsv')
test_panel_file = os.path.abspath(file_path)
with open(test_panel_file) as f:
url = reverse_lazy('panels:upload_panels')
res = self.client.post(url, {'panel_list': f})
messages = [str(m) for m in res.wsgi_request._messages]
expected_messages = [
'Line: 3, 4, 5 is not properly formatted, please check it and try again.'
]
self.assertEqual(expected_messages, messages)
self.assertEqual(GenePanel.objects.count(), 0)
def test_activate_genes_output(self):
out = StringIO()
GeneFactory.create_batch(3, active=True)
GeneFactory.create_batch(4, active=False, ensembl_genes='{}')
GeneFactory.create_batch(5,
active=False,
ensembl_genes='{"hello": "world"}')
call_command('activate_genes', stdout=out)
self.assertIn('5 genes should be active', out.getvalue())
self.assertEqual(8, Gene.objects.filter(active=True).count())
def test_add_gene_to_panel(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
number_of_genes = gps.stats.get('number_of_genes', 0)
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'gene'
})
gene_data = {
"gene":
gene.pk,
"source":
Evidence.ALL_SOURCES[randint(0, 9)],
"tags": [
TagFactory().pk,
],
"publications":
"{};{};{}".format(*fake.sentences(nb=3)),
"phenotypes":
"{};{};{}".format(*fake.sentences(nb=3)),
"rating":
Evaluation.RATINGS.AMBER,
"comments":
fake.sentence(),
"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,
"current_diagnostic":
"True"
}
res = self.client.post(url, gene_data)
new_current_number = gps.panel.active_panel.stats.get(
'number_of_genes', 0)
assert gps.panel.active_panel.version != gps.version
assert res.status_code == 302
assert number_of_genes + 1 == new_current_number
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_mitochondrial_gene(self):
gene = GeneFactory(gene_symbol="MT-LORUM")
gpes = GenePanelEntrySnapshotFactory(gene_core=gene)
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
# make sure new data has at least 1 of the same items
gpes.publications[0]
gpes.publications[1]
gene_data = {
"gene":
gpes.gene_core.pk,
"gene_name":
"Gene name",
"source": [ev.name for ev in gpes.evidence.all()],
"tags": [
TagFactory().pk,
] + [tag.pk for tag in gpes.tags.all()],
"publications":
";".join(gpes.publications),
"phenotypes":
";".join(gpes.phenotypes),
"moi":
gpes.moi,
"mode_of_pathogenicity":
[x for x in Evaluation.MODES_OF_PATHOGENICITY][randint(1, 2)][0],
"penetrance":
GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
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.moi == "MITOCHONDRIAL"
def test_import_reviews(self):
gene = GeneFactory(gene_symbol="ABCC5-AS1")
gps = GenePanelSnapshotFactory()
current_version = gps.version
gps.panel.name = "Panel One"
gps.panel.save()
GenePanelEntrySnapshotFactory.create(gene_core=gene,
panel=gps,
evaluation=(None, ))
file_path = os.path.join(os.path.dirname(__file__),
'import_reviews_data.tsv')
test_reviews_file = os.path.abspath(file_path)
with open(test_reviews_file) as f:
url = reverse_lazy('panels:upload_reviews')
self.client.post(url, {'review_list': f})
ap = GenePanel.objects.get(name="Panel One").active_panel
assert ap.get_gene(gene.gene_symbol).evaluation.count() == 1
assert current_version != ap.version
def test_add_str_to_panel(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
number_of_strs = gps.stats.get('number_of_strs', 0)
url = reverse_lazy('panels:add_entity', kwargs={'pk': gps.panel.pk, 'entity_type': 'str'})
gene_data = {
'name': 'SomeSTR',
'chromosome': '1',
'position_37_0': '',
'position_37_1': '',
'position_38_0': '12345',
'position_38_1': '123456',
'repeated_sequence': 'ATAT',
'normal_repeats': '2',
'pathogenic_repeats': '5',
"gene": gene.pk,
"source": Evidence.ALL_SOURCES[randint(0, 9)],
"tags": [TagFactory().pk, ],
"publications": "{};{};{}".format(*fake.sentences(nb=3)),
"phenotypes": "{};{};{}".format(*fake.sentences(nb=3)),
"rating": Evaluation.RATINGS.AMBER,
"comments": fake.sentence(),
"moi": [x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 12)][0],
"penetrance": GenePanelEntrySnapshot.PENETRANCE.Incomplete,
"current_diagnostic": "True"
}
res = self.client.post(url, gene_data)
new_current_number = gps.panel.active_panel.stats.get('number_of_strs')
assert gps.panel.active_panel.version != gps.version
assert res.status_code == 302
assert number_of_strs + 1 == new_current_number
# make sure tags are added
new_str = GenePanel.objects.get(pk=gps.panel.pk).active_panel.get_str(gene_data['name'])
assert sorted(list(new_str.tags.all().values_list('pk', flat=True))) == sorted(gene_data['tags'])
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)
