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_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_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_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_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_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_tags(self):
gpes = GenePanelEntrySnapshotFactory()
current_version = gpes.panel.version
gpes.evaluation.all().delete()
url = reverse_lazy('panels:update_entity_tags',
kwargs={
'pk': gpes.panel.panel.pk,
'entity_type': 'gene',
'entity_name': gpes.gene.get('gene_symbol')
})
tag1 = TagFactory()
tag2 = TagFactory()
res = self.client.post(url, {'tags': [tag1.pk, tag2.pk]},
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 gene.tags.count() == 2
assert current_version == gpes.panel.panel.active_panel.version
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_remove_gene_from_str(self):
"""We need ability to remove genes from STRs"""
str_item = STRFactory()
url = reverse_lazy('panels:edit_entity', kwargs={
'pk': str_item.panel.panel.pk,
'entity_type': 'str',
'entity_name': str_item.name
})
number_of_strs = str_item.panel.stats.get('number_of_strs', 0)
# make sure new data has at least 1 of the same items
source = str_item.evidence.last().name
publication = str_item.publications[0]
phenotype = str_item.publications[1]
new_evidence = Evidence.ALL_SOURCES[randint(0, 9)]
original_evidences = set([ev.name for ev in str_item.evidence.all()])
original_evidences.add(new_evidence)
str_data = {
'name': str_item.name,
'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_name": "Gene name",
"source": set([source, new_evidence]),
"tags": [TagFactory().pk, ] + [tag.pk for tag in str_item.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": GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
res = self.client.post(url, str_data)
assert res.status_code == 302
new_str = GenePanel.objects.get(pk=str_item.panel.panel.pk).active_panel.get_str(str_item.name)
assert not new_str.gene_core
assert not new_str.gene
assert str_item.panel.panel.active_panel.version != str_item.panel.version
new_current_number = new_str.panel.panel.active_panel.stats.get('number_of_strs')
assert number_of_strs == new_current_number
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_edit_str_name_ajax(self):
str_item = STRFactory()
url = reverse_lazy('panels:edit_entity', kwargs={
'pk': str_item.panel.panel.pk,
'entity_type': 'str',
'entity_name': str_item.name
})
old_str_name = str_item.name
# make sure new data has at least 1 of the same items
source = str_item.evidence.last().name
publication = str_item.publications[0]
phenotype = str_item.publications[1]
gene_data = {
'name': 'NewSTR',
'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": str_item.gene_core.pk,
"gene_name": "Other name",
"source": set([source, Evidence.ALL_SOURCES[randint(0, 9)]]),
"tags": [TagFactory().pk, ] + [tag.pk for tag in str_item.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": GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
res = self.client.post(url, gene_data)
assert res.status_code == 302
new_gps = GenePanel.objects.get(pk=str_item.panel.panel.pk).active_panel
old_gps = GenePanelSnapshot.objects.get(pk=str_item.panel.pk)
# check panel has no previous gene
assert new_gps.has_str(old_str_name) is False
# test previous panel contains old gene
assert old_gps.has_str(old_str_name) is True
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')))
def test_edit_incorrect_repeated_sequence(self):
str_item = STRFactory()
url = reverse_lazy('panels:edit_entity', kwargs={
'pk': str_item.panel.panel.pk,
'entity_type': 'str',
'entity_name': str_item.name
})
number_of_strs = str_item.panel.stats.get('number_of_strs')
# make sure new data has at least 1 of the same items
source = str_item.evidence.last().name
publication = str_item.publications[0]
phenotype = str_item.publications[1]
new_evidence = Evidence.ALL_SOURCES[randint(0, 9)]
original_evidences = set([ev.name for ev in str_item.evidence.all()])
original_evidences.add(new_evidence)
str_data = {
'name': str_item.name,
'chromosome': '1',
'position_37_0': '12345',
'position_37_1': '12346',
'position_38_0': '12345',
'position_38_1': '123456',
'repeated_sequence': 'ATATBC',
'normal_repeats': '2',
'pathogenic_repeats': '5',
"gene": str_item.gene_core.pk,
"gene_name": "Gene name",
"source": set([source, new_evidence]),
"tags": [TagFactory().pk, ] + [tag.pk for tag in str_item.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": GenePanelEntrySnapshot.PENETRANCE.Incomplete,
}
res = self.client.post(url, str_data)
assert res.status_code == 200
assert res.content.find(b'Repeated sequence contains incorrect nucleotides') != -1
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_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_remove_tag_via_edit_details(self):
"""Remove tags via edit gene detail section"""
str_item = STRFactory(
penetrance=GenePanelEntrySnapshot.PENETRANCE.Incomplete
)
tag = TagFactory(name='some tag')
str_item.tags.add(tag)
url = reverse_lazy('panels:edit_entity', kwargs={
'pk': str_item.panel.panel.pk,
'entity_type': 'str',
'entity_name': str_item.name
})
str_data = {
'name': str_item.name,
'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": str_item.gene_core.pk,
"gene_name": "Gene name",
"source": set([ev.name for ev in str_item.evidence.all()]),
"tags": [],
"publications": ";".join([publication for publication in str_item.publications]),
"phenotypes": ";".join([phenotype for phenotype in str_item.phenotypes]),
"moi": str_item.moi,
"penetrance": GenePanelEntrySnapshot.PENETRANCE.Complete,
}
res = self.client.post(url, str_data)
assert res.status_code == 302
new_str = GenePanel.objects.get(pk=str_item.panel.panel.pk).active_panel.get_str(str_item.name)
assert list(new_str.tags.all()) == []
