def test_active_panel(self):
"""
Make sure GenePanel.active_panel returns correct panel
"""
gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
gps2 = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
gps.panel.active_panel.increment_version()
gps.panel.active_panel.increment_version()
gps.panel.active_panel.increment_version()
gps.panel.active_panel.increment_version()
gps.panel.active_panel.increment_version()
gps = gps.panel.active_panel
assert gps.minor_version == 5
gp = GenePanel.objects.get(pk=gps.panel.pk)
assert gp.active_panel == gps
gps2.panel.active_panel.increment_version()
del gps2.panel.active_panel
gps2.panel.active_panel.increment_version()
del gps2.panel.active_panel
gps2 = gps2.panel.active_panel
assert gps2.minor_version == 2
gp2 = GenePanel.objects.get(pk=gps2.panel.pk)
assert gp2.active_panel == 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_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_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 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_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 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_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_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_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_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_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_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_user_reviews(self):
gps = GenePanelSnapshotFactory()
region = RegionFactory.create_batch(10, panel=gps)
for g in region:
for evaluation in g.evaluation.all():
evaluation.user = self.verified_user
evaluation.save()
self.assertEqual(self.verified_user.get_recent_evaluations().count(), 35)
def test_update_status(self):
gps = GenePanelSnapshotFactory()
url = reverse_lazy('panels:update', kwargs={'pk': gps.panel.pk})
data = self.create_panel_data()
data['status'] = GenePanel.STATUS.public
self.client.post(url, data)
gp = GenePanel.objects.get(pk=gps.panel.pk)
assert gp.status == data['status']
def test_update_panel(self):
gps = GenePanelSnapshotFactory()
url = reverse_lazy('panels:update', kwargs={'pk': gps.panel.pk})
data = self.create_panel_data()
self.client.post(url, data)
gp = GenePanel.objects.get(pk=gps.panel.pk)
assert gp.active_panel.major_version == 0
assert gp.active_panel.minor_version == 1
assert gp.name == data['level4']
def test_evaluation_single_panel(self):
gps = GenePanelSnapshotFactory()
gpes = GenePanelEntrySnapshotFactory(panel=gps)
gps.panel.active_panel.increment_version()
gps.panel.active_panel.increment_version()
gps = gps.panel.active_panel
gene_symbol = gpes.gene_core.gene_symbol
# check we copy evaluation rather than assign it
current_count = gps.panel.active_panel.get_all_genes[
0].evaluation.first().genepanelentrysnapshot_set.count()
self.assertEqual(current_count, 1)
# check if deleting gene preserves it in the previous versions
gp = gps.panel
gps.delete_gene(gene_symbol)
v1 = gp.genepanelsnapshot_set.get(major_version=0, minor_version=1)
self.assertTrue(v1.has_gene(gene_symbol))
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_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_evaluation_stays(self):
gps = GenePanelSnapshotFactory()
gpes = GenePanelEntrySnapshotFactory(panel=gps)
evaluations = gpes.evaluation.all()
gpes2 = GenePanelEntrySnapshotFactory(panel=gps)
evaluations2 = sorted(gpes2.evaluation.all().values_list('pk',
flat=True))
gps = gps.increment_version()
gps.update_gene(self.gel_user, gpes.gene_core.gene_symbol,
{'phenotypes': [
'abra',
]})
del gps.panel.active_panel
current_ev2 = sorted(
gps.panel.active_panel.get_gene(
gpes2.gene_core.gene_symbol).evaluation.all().values_list(
'pk', flat=True))
self.assertNotEqual(evaluations2, current_ev2)
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_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_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_type_of_variants_added(self):
region = RegionFactory()
gps = GenePanelSnapshotFactory()
url = reverse_lazy('panels:add_entity',
kwargs={
'pk': gps.panel.pk,
'entity_type': 'region'
})
source = region.evidence.last().name
publication = region.publications[0]
phenotype = region.publications[1]
region_data = {
'name': region.name,
'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': '',
'required_overlap_percentage': randint(0, 100),
"gene": region.gene_core.pk,
"gene_name": "Other name",
"source": set([source, Evidence.ALL_SOURCES[randint(0, 9)]]),
"tags": [
TagFactory().pk,
] + [tag.name for tag in region.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],
"type_of_variants": Region.VARIANT_TYPES.small,
"penetrance": Region.PENETRANCE.Incomplete,
}
res = self.client.post(url, region_data)
self.assertEqual(res.status_code, 302)
panel = gps.panel.active_panel
assert panel.get_region(
region.name).type_of_variants == region_data['type_of_variants']
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_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')
