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_add_evaluation_comments_only(self):
"""Add comments"""
region = RegionFactory()
current_version = region.panel.version
region.evaluation.all().delete()
url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
region_data = {
"comments": fake.sentence(),
}
res = self.client.post(url, region_data)
assert res.status_code == 302
v01gene = region.panel.panel.active_panel.get_region(region.name)
assert v01gene.evaluation.get(user=self.gel_user).comments.count() == 1
region_data = {
"comments": fake.sentence(),
}
res = self.client.post(url, region_data)
assert v01gene.evaluation.get(user=self.gel_user).comments.count() == 2
assert current_version == region.panel.panel.active_panel.version
def test_add_evaluation(self):
"""Add an evaluation"""
region = RegionFactory()
region.evaluation.all().delete()
region.panel.update_saved_stats()
url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
current_version = region.panel.version
number_of_evaluated_genes = region.panel.stats.get('number_of_evaluated_regions')
region_data = {
"rating": Evaluation.RATINGS.AMBER,
"current_diagnostic": True,
"comments": fake.sentence(),
"publications": ";".join([fake.sentence(), fake.sentence()]),
"phenotypes": ";".join([fake.sentence(), 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],
}
res = self.client.post(url, region_data)
assert res.status_code == 302
assert number_of_evaluated_genes + 1 == region.panel.panel.active_panel.stats.get('number_of_evaluated_regions')
assert current_version == region.panel.panel.active_panel.version
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_form_should_be_prefilled(self):
region = RegionFactory()
region.evaluation.all().delete()
url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
region_data = {
"rating": Evaluation.RATINGS.AMBER,
"current_diagnostic": True,
"publications": ";".join([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],
}
self.client.post(url, region_data)
url = reverse_lazy('panels:evaluation', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
res = self.client.get(url)
assert res.content.find(str.encode('<option value="{}" selected>'.format(region_data['moi']))) != -1
def test_edit_region_in_panel(self):
region = RegionFactory()
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
number_of_regions = region.panel.stats.get('number_of_regions')
# make sure new data has at least 1 of the same items
source = region.evidence.last().name
publication = region.publications[0]
phenotype = region.publications[1]
new_evidence = Evidence.ALL_SOURCES[randint(0, 9)]
original_evidences = set([ev.name for ev in region.evidence.all()])
original_evidences.add(new_evidence)
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':
choice(Region.DOSAGE_SENSITIVITY_SCORES)[0],
'required_overlap_percentage': randint(0, 100),
"gene": region.gene_core.pk,
"gene_name": "Gene name",
"source": set([source, new_evidence]),
"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],
"penetrance": Region.PENETRANCE.Incomplete,
"type_of_variants": Region.VARIANT_TYPES.small,
}
res = self.client.post(url, region_data)
assert res.status_code == 302
new_region = GenePanel.objects.get(
pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert region.panel.panel.active_panel.version != region.panel.version
new_current_number = new_region.panel.panel.active_panel.stats.get(
'number_of_regions')
assert number_of_regions == new_current_number
self.assertEqual(int(region_data['position_37_1']),
new_region.position_37.upper)
def test_delete_evaluation(self):
region = RegionFactory()
region.evaluation.all().delete()
evaluation_url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
gene_data = {
"rating": Evaluation.RATINGS.AMBER,
"current_diagnostic": True,
"comments": fake.sentence(),
"publications": ";".join([fake.sentence(), fake.sentence()]),
"phenotypes": ";".join([fake.sentence(), 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],
}
self.client.post(evaluation_url, gene_data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert gene.panel.version == region.panel.version
assert gene.is_reviewd_by_user(self.gel_user) is True
delete_evaluation_url = reverse_lazy('panels:delete_evaluation_by_user', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name,
'evaluation_pk': region.evaluation.get(user=self.gel_user).pk
})
res = self.client.get(delete_evaluation_url, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
last_gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert last_gene.is_reviewd_by_user(self.gel_user) is False
assert gene.panel.version == last_gene.panel.version
def test_change_evaluation(self):
region = RegionFactory()
current_version = region.panel.version
region.evaluation.all().delete()
url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
old_phenotypes = [fake.sentence(), fake.sentence(), fake.sentence()]
gene_data = {
"rating": Evaluation.RATINGS.AMBER,
"current_diagnostic": True,
"comments": fake.sentence(),
"publications": ";".join([fake.sentence(), fake.sentence()]),
"phenotypes": ";".join(old_phenotypes),
"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],
}
self.client.post(url, gene_data)
assert Evaluation.objects.filter(user=self.gel_user).count() == 1
gene_data = {
"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],
}
self.client.post(url, gene_data)
assert Evaluation.objects.filter(user=self.gel_user).count() == 1
assert Evaluation.objects.get(user=self.gel_user).phenotypes == old_phenotypes
assert current_version == region.panel.panel.active_panel.version
def test_add_tag_via_edit_details(self):
"""Set tags via edit gene detail section"""
region = RegionFactory(penetrance=Region.PENETRANCE.Incomplete)
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
tag = TagFactory(name='some tag')
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':
choice(Region.DOSAGE_SENSITIVITY_SCORES)[0],
'required_overlap_percentage':
randint(0, 100),
"gene":
region.gene_core.pk,
"gene_name":
"Gene name",
"source":
set([ev.name for ev in region.evidence.all()]),
"tags": [tag.pk for tag in region.tags.all()] + [
tag.pk,
],
"publications":
";".join([publication for publication in region.publications]),
"phenotypes":
";".join([phenotype for phenotype in region.phenotypes]),
"type_of_variants":
Region.VARIANT_TYPES.small,
"moi":
region.moi,
"penetrance":
Region.PENETRANCE.Complete,
}
res = self.client.post(url, region_data)
assert res.status_code == 302
new_region = GenePanel.objects.get(
pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert sorted(list(new_region.tags.all())) != sorted(
list(region.tags.all()))
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_download_all_regions(self):
gpes = GenePanelEntrySnapshotFactory()
gps = gpes.panel
region = RegionFactory(panel=gps)
res = self.client.get(reverse_lazy('panels:download_regions'))
self.assertEqual(res.status_code, 200)
self.assertTrue(b"".join(res.streaming_content).find(
region.verbose_name.encode()) != 1)
def test_edit_region_name_ajax(self):
region = RegionFactory()
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
old_region_name = region.name
# make sure new data has at least 1 of the same items
source = region.evidence.last().name
publication = region.publications[0]
phenotype = region.publications[1]
gene_data = {
'name': 'NewRegion',
'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": 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, gene_data)
assert res.status_code == 302
new_gps = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel
old_gps = GenePanelSnapshot.objects.get(pk=region.panel.pk)
# check panel has no previous gene
assert new_gps.has_region(old_region_name) is False
# test previous panel contains old gene
assert old_gps.has_region(old_region_name) is True
def test_region_evaluation(self):
region = RegionFactory()
url = reverse_lazy('panels:evaluation',
kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
res = self.client.get(url)
assert res.status_code == 200
def test_download_panel_contains_regions(self):
gpes = GenePanelEntrySnapshotFactory()
gps = gpes.panel
RegionFactory(panel=gps)
res = self.client.get(
reverse_lazy('panels:download_panel_tsv',
args=(gps.panel.pk, '01234')))
self.assertEqual(res.status_code, 200)
self.assertTrue(res.content.find(b'region') != 1)
def test_remove_publication(self):
"""Remove a publication to a gene panel entry"""
region = RegionFactory(penetrance=Region.PENETRANCE.Incomplete)
region.publications = [fake.sentence(), fake.sentence()]
region.save()
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
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':
choice(Region.DOSAGE_SENSITIVITY_SCORES)[0],
'required_overlap_percentage': randint(0, 100),
"gene": region.gene_core.pk,
"gene_name": "Gene name",
"source": set([ev.name for ev in region.evidence.all()]),
"tags": [tag.name for tag in region.tags.all()],
"publications": ";".join(region.publications[:1]),
"phenotypes":
";".join([phenotype for phenotype in region.phenotypes]),
"type_of_variants": Region.VARIANT_TYPES.small,
"moi": region.moi,
"penetrance": Region.PENETRANCE.Complete,
}
res = self.client.post(url, region_data)
assert res.status_code == 302
new_region = GenePanel.objects.get(
pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert new_region.publications == region.publications[:1]
def test_mark_as_ready_no_gene(self):
region = RegionFactory(gene=None)
region.evaluation.all().delete()
url = reverse_lazy('panels:mark_entity_as_ready', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
self.client.post(url, {'ready_comment': fake.sentence()})
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert gene.ready is True
def test_edit_region_name_unit(self):
region = RegionFactory()
old_region_name = region.name
ap = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel
assert ap.has_region(old_region_name) is True
new_data = {"name": 'NewRegion'}
ap.update_region(self.verified_user, old_region_name, new_data)
new_ap = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel
assert new_ap.has_region(old_region_name) is False
assert new_ap.has_region('NewRegion') is True
def test_edit_comment(self):
region = RegionFactory()
current_version = region.panel.version
evaluation_url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
comment = fake.sentence()
gene_data = {
"rating": Evaluation.RATINGS.AMBER,
"current_diagnostic": True,
"comments": comment,
"publications": ";".join([fake.sentence(), fake.sentence()]),
"phenotypes": ";".join([fake.sentence(), 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],
}
self.client.post(evaluation_url, gene_data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
evaluation = gene.evaluation.get(user=self.gel_user)
assert evaluation.comments.first().comment == comment
get_comment_url = reverse_lazy('panels:edit_comment_by_user', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name,
'comment_pk': evaluation.comments.first().pk
})
res = self.client.get(get_comment_url, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
self.assertEqual(res.status_code, 200)
new_comment = fake.sentence()
edit_comment_url = reverse_lazy('panels:submit_edit_comment_by_user', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name,
'comment_pk': evaluation.comments.first().pk
})
res = self.client.post(edit_comment_url, {'comment': new_comment})
assert res.status_code == 302
assert evaluation.comments.first().comment == new_comment
assert current_version == region.panel.panel.active_panel.version
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_curator_comment_added(self):
region = RegionFactory()
region.evaluation.all().delete()
url = reverse_lazy('panels:update_entity_rating', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
new_status = 0
data = {'comment': fake.sentence(), 'status': new_status}
res = self.client.post(url, data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.content.find(str.encode(data['comment'])) != -1
assert gene.evaluation.count() > 0
def test_update_rating(self):
region = RegionFactory()
region.evaluation.all().delete()
url = reverse_lazy('panels:update_entity_rating', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
new_status = 0
data = {'comment': fake.sentence(), 'status': new_status}
res = self.client.post(url, data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert Comment.objects.count() == 1
assert res.content.find(str.encode(data['comment'])) != -1
assert gene.saved_gel_status == new_status
new_status = 1
data = {'comment': fake.sentence(), 'status': new_status}
res = self.client.post(url, data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert Comment.objects.count() == 3
assert gene.saved_gel_status == new_status
new_status = 2
data = {'comment': fake.sentence(), 'status': new_status}
res = self.client.post(url, data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert Comment.objects.count() == 6
assert gene.saved_gel_status == new_status
new_status = 3
data = {'comment': fake.sentence(), 'status': new_status}
res = self.client.post(url, data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert Comment.objects.count() == 10
assert gene.saved_gel_status == new_status
assert gene.panel.version != region.panel.version
def test_update_tags(self):
region = RegionFactory()
current_version = region.panel.version
region.evaluation.all().delete()
url = reverse_lazy('panels:update_entity_tags', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
tag1 = TagFactory()
tag2 = TagFactory()
res = self.client.post(url, {'tags': [tag1.pk, tag2.pk]}, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert gene.tags.count() == 2
assert current_version == region.panel.panel.active_panel.version
def test_update_moi(self):
region = RegionFactory()
region.evaluation.all().delete()
url = reverse_lazy('panels:update_entity_moi', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
moi = [x for x in Evaluation.MODES_OF_INHERITANCE][randint(1, 2)]
data = {'comment': fake.sentence(), 'moi': moi[1]}
res = self.client.post(url, data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert Comment.objects.count() == 1
assert gene.moi == moi[1]
assert gene.panel.version != region.panel.version
def test_update_publications(self):
region = RegionFactory()
region.evaluation.all().delete()
url = reverse_lazy('panels:update_entity_publications', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
publications_array = [fake.word(), fake.word()]
publications = "{}; {}".format(publications_array[0], publications_array[1])
data = {'comment': fake.sentence(), 'publications': publications}
res = self.client.post(url, data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
assert res.json().get('status') == 200
assert Comment.objects.count() == 1
assert gene.publications == publications_array
assert gene.panel.version != region.panel.version
def test_update_region_preserves_comments_order(self):
region = RegionFactory()
comments = list(CommentFactory.create_batch(4,
user=self.verified_user))
for ev in region.evaluation.all():
ev.comments.add(comments.pop())
max_comments_num = max(
[e.comments.count() for e in region.evaluation.all()])
self.assertEqual(1, max_comments_num)
old_region_name = region.name
ap = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel
new_data = {"name": 'NewRegion'}
ap.update_region(self.verified_user, old_region_name, new_data)
new_ap = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel
new_region = new_ap.get_region('NewRegion')
max_comments_num_after_update = max(
[e.comments.count() for e in new_region.evaluation.all()])
self.assertEqual(1, max_comments_num_after_update)
def test_delete_comment(self):
region = RegionFactory()
current_version = region.panel.version
evaluation_url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
gene_data = {
"rating": Evaluation.RATINGS.AMBER,
"current_diagnostic": True,
"comments": fake.sentence(),
"publications": ";".join([fake.sentence(), fake.sentence()]),
"phenotypes": ";".join([fake.sentence(), 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],
}
self.client.post(evaluation_url, gene_data, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
gene = GenePanel.objects.get(pk=region.panel.panel.pk).active_panel.get_region(region.name)
evaluation = gene.evaluation.get(user=self.gel_user)
assert evaluation.comments.count() == 1
delete_comment_url = reverse_lazy('panels:delete_comment_by_user', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name,
'comment_pk': evaluation.comments.first().pk
})
res = self.client.get(delete_comment_url, HTTP_X_REQUESTED_WITH='XMLHttpRequest')
assert res.json().get('status') == 200
assert evaluation.comments.count() == 0
assert res.content.find(str.encode('Your review')) != -1
assert current_version == region.panel.panel.active_panel.version
def test_add_review_after_comment(self):
"""When you add a comment and then want to add a review it should be logged"""
region = RegionFactory()
current_version = region.panel.version
region.evaluation.all().delete()
url = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
gene_data = {
"comments": fake.sentence(),
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
v01gene = region.panel.panel.active_panel.get_region(region.name)
assert v01gene.evaluation.get(user=self.gel_user).comments.count() == 1
review_data = {
"rating": Evaluation.RATINGS.AMBER,
"current_diagnostic": True,
"comments": fake.sentence(),
"publications": ";".join([fake.sentence(), fake.sentence()]),
}
url_review = reverse_lazy('panels:review_entity', kwargs={
'pk': region.panel.panel.pk,
'entity_type': 'region',
'entity_name': region.name
})
self.client.post(url_review, review_data)
res_review = self.client.get(url_review)
assert res_review.content.find(str.encode(review_data['publications'])) != -1
assert current_version == region.panel.panel.active_panel.version
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)
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'])
