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_have_child_entities(self):
gene1 = GeneFactory()
gene2 = GeneFactory()
parent = GenePanelSnapshotFactory()
gene1_data = {
"gene":
gene1.pk,
"sources": [
Evidence.OTHER_SOURCES[0],
],
"phenotypes":
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,
"current_diagnostic":
False,
}
gene2_data = {
"gene":
gene2.pk,
"sources": [
Evidence.OTHER_SOURCES[0],
],
"phenotypes":
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,
"current_diagnostic":
False,
}
child1 = GenePanelSnapshotFactory()
child1.add_gene(self.gel_user, gene1.gene_symbol, gene1_data)
child1.panel.active_panel.add_gene(self.gel_user, gene2.gene_symbol,
gene2_data)
child1 = child1.panel.active_panel
child2 = GenePanelSnapshotFactory()
child2.add_gene(self.gel_user, gene1.gene_symbol, gene1_data)
child2 = child2.panel.active_panel
parent.child_panels.set([child1, child2])
parent.update_saved_stats()
del parent.is_super_panel
self.assertEqual(len(parent.get_all_entities_extra), 3)
self.assertTrue(parent.is_super_panel)
self.assertTrue(child1.is_child_panel)
self.assertTrue(child2.is_child_panel)
self.assertIn(child1.get_gene(gene1.gene_symbol),
parent.get_all_entities_extra)
self.assertIn(child1.get_gene(gene2.gene_symbol),
parent.get_all_entities_extra)
self.assertTrue(parent.genepanelentrysnapshot_set.count() == 0)
def test_increment_child_version(self):
gene1 = GeneFactory()
gene2 = GeneFactory()
parent = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
gene1_data = {
"gene":
gene1.pk,
"sources": [
Evidence.OTHER_SOURCES[0],
],
"phenotypes":
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,
"current_diagnostic":
False,
}
gene2_data = {
"gene":
gene2.pk,
"sources": [
Evidence.OTHER_SOURCES[0],
],
"phenotypes":
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,
"current_diagnostic":
False,
}
child1 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
initial_child1_pk = child1.pk
child1.add_gene(self.gel_user, gene1.gene_symbol, gene1_data)
child1 = child1.panel.active_panel
child1.add_gene(self.gel_user, gene2.gene_symbol, gene2_data)
child1 = child1.panel.active_panel
self.assertNotEqual(initial_child1_pk, child1.pk)
child2 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
initial_child2_pk = child2.pk
child2.add_gene(self.gel_user, gene1.gene_symbol, gene1_data)
child2 = child2.panel.active_panel
self.assertNotEqual(initial_child2_pk, child2.pk)
parent.child_panels.set([child1, child2])
parent.update_saved_stats()
old_parent = parent
child1.increment_version()
child1 = child1.panel.active_panel
child1.update_gene(
self.gel_user, gene2.gene_symbol, {
"gene":
gene2,
"sources": [
Evidence.OTHER_SOURCES[1],
],
"phenotypes":
fake.sentences(nb=3),
"rating":
Evaluation.RATINGS.GREEN,
"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":
False,
})
child1.get_gene(gene2.gene_symbol).update_rating(3, self.gel_user, '')
child1 = child1.panel.active_panel
parent = parent.panel.active_panel
parent.update_saved_stats()
self.assertNotEqual(parent, old_parent)
self.assertNotEqual(old_parent.stats, parent.stats)
self.assertIn(child1, parent.child_panels.all())
self.assertIn(child2, parent.child_panels.all())
self.assertEqual(child1.genepanelsnapshot_set.count(), 1)
self.assertEqual(
child2.genepanelsnapshot_set.count(),
2) # contains reference to two versions of parent panel
