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_form_should_be_prefilled(self):
gpes = GenePanelEntrySnapshotFactory()
gpes.evaluation.all().delete()
url = reverse_lazy('panels:review_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
gene_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, gene_data)
url = reverse_lazy('panels:evaluation',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
res = self.client.get(url)
assert res.content.find(
str.encode('<option value="{}" selected>'.format(
gene_data['moi']))) != -1
def setUp(self):
super().setUp()
self.gpes = GenePanelEntrySnapshotFactory()
evidence = self.gpes.evidence.all()[0]
evidence.reviewer.user_type = 'GEL'
evidence.reviewer.save()
def test_gene_not_ready(self):
gpes = GenePanelEntrySnapshotFactory()
url = reverse_lazy('panels:mark_entity_as_not_ready',
args=(gpes.panel.panel.pk, 'gene',
gpes.gene.get('gene_symbol')))
r = self.client.post(url, {})
self.assertEqual(r.status_code, 302)
def test_old_pk_redirect(self):
gpes = GenePanelEntrySnapshotFactory()
gpes.panel.panel.old_pk = fake.password(length=24,
special_chars=False,
upper_case=False)
gpes.panel.panel.save()
res = self.client.get(
reverse_lazy('panels:old_code_url_redirect',
args=(
gpes.panel.panel.old_pk,
'',
)))
self.assertEqual(res.status_code, 301)
self.assertEqual(
res.url, reverse_lazy('panels:detail',
args=(gpes.panel.panel.pk, )))
res = self.client.get(
reverse_lazy('panels:old_code_url_redirect',
args=(gpes.panel.panel.old_pk,
'gene/' + gpes.gene.get('gene_symbol'))))
self.assertEqual(res.status_code, 301)
self.assertEqual(
res.url + '/',
reverse_lazy('panels:evaluation',
args=(gpes.panel.panel.id, 'gene',
gpes.gene.get('gene_symbol'))))
def test_update_publications(self):
gpes = GenePanelEntrySnapshotFactory()
gpes.evaluation.all().delete()
url = reverse_lazy('panels:update_entity_publications',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
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=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene.get('gene_symbol'))
assert res.json().get('status') == 200
assert Comment.objects.count() == 1
assert gene.publications == publications_array
assert gene.panel.version != gpes.panel.version
def test_remove_publication(self):
"""Remove a publication to a gene panel entry"""
gpes = GenePanelEntrySnapshotFactory(
penetrance=GenePanelEntrySnapshot.PENETRANCE.Incomplete)
gpes.publications = [fake.sentence(), fake.sentence()]
gpes.save()
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
gene_data = {
"gene": gpes.gene_core.pk,
"gene_name": "Gene name",
"source": set([ev.name for ev in gpes.evidence.all()]),
"tags": [tag.pk for tag in gpes.tags.all()],
"publications": ";".join(gpes.publications[:1]),
"phenotypes":
";".join([phenotype for phenotype in gpes.phenotypes]),
"moi": gpes.moi,
"mode_of_pathogenicity": gpes.mode_of_pathogenicity,
"penetrance": GenePanelEntrySnapshot.PENETRANCE.Complete,
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
gene = GenePanel.objects.get(
pk=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene_core.gene_symbol)
assert gene.publications == gpes.publications[:1]
def test_promote_panel(self):
gpes = GenePanelEntrySnapshotFactory()
data = {'version_comment': fake.sentence()}
url = reverse_lazy('panels:promote', args=(gpes.panel.panel.pk, ))
res = self.client.post(url, data)
self.assertEqual(res.status_code, 302)
def test_str_data_copied(self):
gpes = GenePanelEntrySnapshotFactory()
active_panel = gpes.panel
str_item = active_panel.add_str(self.gel_user, 'ABC', {
'gene': gpes.gene_core,
'chromosome': '1',
'position_37': (12345, 12346),
'position_38': (12345, 12346),
'repeated_sequence': 'ATAT',
'normal_repeats': '2',
'pathogenic_repeats': '5',
'panel': active_panel,
'moi': 'X-LINKED: hemizygous mutation in males, biallelic mutations in females',
'penetrance': 'Incomplete',
'publications': None,
'phenotypes': None,
'sources': [],
})
active_panel = active_panel.panel.active_panel
assert active_panel.has_str(str_item.name)
active_panel.increment_version()
active_panel = active_panel.panel.active_panel
assert active_panel.panel.active_panel.has_str(str_item.name)
def test_specific_versions(self):
gpes = GenePanelEntrySnapshotFactory()
res = self.client.get(
'/crowdsourcing/WebServices/get_panel/{}?version=0.0'.format(
gpes.panel.id))
self.assertIn('version=0.0', res.url)
self.assertEqual(res.status_code, 301)
def test_add_evaluation_error(self):
"""Add comments"""
gpes = GenePanelEntrySnapshotFactory()
current_version = gpes.panel.version
gpes.evaluation.all().delete()
url = reverse_lazy('panels:review_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
gene_data = {
"comments": fake.sentence(),
"publications": "1;",
"phenotypes": "2;",
}
res = self.client.post(url, gene_data)
assert res.status_code == 200
assert b'Make sure there is no ; if no value after: ' in res.content
gene_data = {
"comments": fake.sentence(),
"publications": "1",
"phenotypes": "2",
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
v01gene = gpes.panel.panel.active_panel.get_gene(
gpes.gene.get('gene_symbol'))
assert v01gene.evaluation.get(user=self.gel_user).comments.count() == 1
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_evaluation_comments_only(self):
"""Add comments"""
gpes = GenePanelEntrySnapshotFactory()
current_version = gpes.panel.version
gpes.evaluation.all().delete()
url = reverse_lazy('panels:review_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
gene_data = {
"comments": fake.sentence(),
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
v01gene = gpes.panel.panel.active_panel.get_gene(
gpes.gene.get('gene_symbol'))
assert v01gene.evaluation.get(user=self.gel_user).comments.count() == 1
gene_data = {
"comments": fake.sentence(),
}
res = self.client.post(url, gene_data)
assert v01gene.evaluation.get(user=self.gel_user).comments.count() == 2
assert current_version == gpes.panel.panel.active_panel.version
def test_delete_comment(self):
gpes = GenePanelEntrySnapshotFactory()
current_version = gpes.panel.version
evaluation_url = reverse_lazy('panels:review_entity',
kwargs={
'pk':
gpes.panel.panel.pk,
'entity_type':
'gene',
'entity_name':
gpes.gene.get('gene_symbol')
})
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=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene.get('gene_symbol'))
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':
gpes.panel.panel.pk,
'entity_type':
'gene',
'entity_name':
gpes.gene.get('gene_symbol'),
'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 == gpes.panel.panel.active_panel.version
def test_download_panel_contains_strs(self):
gpes = GenePanelEntrySnapshotFactory()
gps = gpes.panel
strs = STRFactory(repeated_sequence="ATATCGCGN", 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(strs.repeated_sequence.encode()) != 1)
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_view_edit_gene_in_panel(self):
gpes = GenePanelEntrySnapshotFactory()
url = reverse_lazy('panels:edit_entity',
args=(
gpes.panel.panel.pk,
'gene',
gpes.gene.get('gene_symbol'),
))
r = self.client.get(url)
self.assertEqual(r.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_gene_evaluation(self):
gpes = GenePanelEntrySnapshotFactory()
url = reverse_lazy('panels:evaluation',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
res = self.client.get(url)
assert res.status_code == 200
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_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_edit_gene_in_panel(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')
})
number_of_genes = gpes.panel.stats.get('number_of_genes')
# 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_evidence = Evidence.ALL_SOURCES[randint(0, 9)]
original_evidences = set([ev.name for ev in gpes.evidence.all()])
original_evidences.add(new_evidence)
gene_data = {
"gene":
gpes.gene_core.pk,
"gene_name":
"Gene name",
"source":
set([source, new_evidence]),
"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
gene = GenePanel.objects.get(
pk=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene_core.gene_symbol)
assert gpes.panel.panel.active_panel.version != gpes.panel.version
new_current_number = gpes.panel.panel.active_panel.stats.get(
'number_of_genes', 0)
assert number_of_genes == new_current_number
def test_update_panel_many_to_many(self):
gpes = GenePanelEntrySnapshotFactory()
url = reverse_lazy('panels:update', kwargs={'pk': gpes.panel.panel.pk})
data = self.create_panel_data()
self.client.post(url, data)
gp = GenePanel.objects.get(pk=gpes.panel.panel.pk)
active_snapshot = gp.active_panel
assert active_snapshot.major_version == 0
assert active_snapshot.minor_version == 1
assert gp.name == data['level4']
assert active_snapshot.get_all_genes.count() == 1
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_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 test_panel_types(self):
panel_type = PanelTypeFactory()
gpes = GenePanelEntrySnapshotFactory()
panel_data = self.panel_data
panel_data['types'] = [
panel_type.pk,
]
res = self.client.post(reverse_lazy('panels:create'), panel_data)
self.assertEqual(res.status_code, 302)
gp = GenePanel.objects.get(name=self.panel_data['level4'])
self.assertEqual(gp.types.first(), panel_type)
r = self.client.get(reverse_lazy('panels:detail', args=(gp.pk, )))
self.assertIn(panel_type.name.encode(), r.content)
def test_mark_as_ready(self):
gpes = GenePanelEntrySnapshotFactory()
gpes.evaluation.all().delete()
url = reverse_lazy('panels:mark_entity_as_ready',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
self.client.post(url, {'ready_comment': fake.sentence()})
gene = GenePanel.objects.get(
pk=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene.get('gene_symbol'))
assert gene.ready is True
def test_update_phenotypes_add_only(self):
gpes = GenePanelEntrySnapshotFactory()
phenotypes_array = [fake.word(), fake.word()]
old_phenotypes = gpes.phenotypes
data = {'phenotypes': phenotypes_array}
ap = GenePanel.objects.get(pk=gpes.panel.panel.pk).active_panel
ap.update_gene(self.gel_user,
gpes.gene.get('gene_symbol'),
data,
append_only=True)
gene = GenePanel.objects.get(
pk=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene.get('gene_symbol'))
assert gene.phenotypes == list(set(old_phenotypes + phenotypes_array))
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_add_tag_via_edit_details(self):
"""Set tags via edit gene detail section"""
gpes = GenePanelEntrySnapshotFactory(
penetrance=GenePanelEntrySnapshot.PENETRANCE.Incomplete)
url = reverse_lazy('panels:edit_entity',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
tag = TagFactory(name='some tag')
gene_data = {
"gene":
gpes.gene_core.pk,
"gene_name":
"Gene name",
"source":
set([ev.name for ev in gpes.evidence.all()]),
"tags": [tag.pk for tag in gpes.tags.all()] + [
tag.pk,
],
"publications":
";".join([publication for publication in gpes.publications]),
"phenotypes":
";".join([phenotype for phenotype in gpes.phenotypes]),
"moi":
gpes.moi,
"mode_of_pathogenicity":
gpes.mode_of_pathogenicity,
"penetrance":
GenePanelEntrySnapshot.PENETRANCE.Complete,
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
gene = GenePanel.objects.get(
pk=gpes.panel.panel.pk).active_panel.get_gene(
gpes.gene_core.gene_symbol)
assert sorted(list(gene.tags.values_list('pk'))) != sorted(
list(gpes.tags.values_list('pk')))