def test_increment_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)
del child2.panel.active_panel
child2 = child2.panel.active_panel
self.assertNotEqual(initial_child2_pk, child2.pk)
parent.child_panels.set([child1, child2])
parent.update_saved_stats()
self.assertEqual(child1, child1.panel.active_panel)
self.assertEqual(child2, child2.panel.active_panel)
new_data = {
'level2': fake.sentence(nb_words=6, variable_nb_words=True),
'level3': fake.sentence(nb_words=6, variable_nb_words=True),
'level4': fake.sentence(nb_words=6, variable_nb_words=True),
'description': fake.text(max_nb_chars=300),
'omim': fake.sentences(nb=3),
'orphanet': fake.sentences(nb=3),
'hpo': fake.sentences(nb=3),
'old_panels': fake.sentences(nb=3),
'status': GenePanel.STATUS.internal,
'child_panels': [child1.pk, child2.pk]
}
url = reverse_lazy('panels:update', kwargs={'pk': parent.panel_id})
res = self.client.post(url, new_data)
self.assertNotEqual(parent, parent.panel.active_panel)
self.assertEqual(parent.panel.active_panel.child_panels.count(), 2)
self.assertEqual(len(parent.panel.active_panel.get_all_entities_extra),
3)
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_multiple_parent_panels(self):
"""
Test updates to the test panels, and make sure parent panels are updated correctly
"""
gene1 = GeneFactory()
gene2 = GeneFactory()
gene3 = GeneFactory()
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[2],
],
"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,
}
gene3_data = {
"gene":
gene3.pk,
"sources": [
Evidence.OTHER_SOURCES[3],
],
"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":
True,
}
child1 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
child2 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
child3 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
parent = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
parent.child_panels.set([child1, child2])
parent.update_saved_stats()
self.assertEqual(parent.version, "0.0")
parent2 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.public)
parent2.child_panels.set([child2, child3])
parent2.update_saved_stats()
self.assertEqual(parent2.version, "0.0")
child1.add_gene(self.gel_user, gene1.gene_symbol, gene1_data)
child1.add_gene(self.gel_user, gene2.gene_symbol, gene2_data)
self.assertEqual(child1.version, "0.2")
parent = parent.panel.active_panel
self.assertEqual(parent.version, "0.2")
parent2 = parent2.panel.active_panel
self.assertEqual(parent2.version, "0.0")
child2.add_gene(self.gel_user, gene2.gene_symbol, gene2_data)
del child2.panel.active_panel
child2 = child2.panel.active_panel
self.assertEqual(child2.version, "0.1")
del parent.panel.active_panel
parent = parent.panel.active_panel
self.assertEqual(parent.version, "0.3")
del parent2.panel.active_panel
parent2 = parent2.panel.active_panel
self.assertEqual(parent2.version, "0.1")
child3.add_gene(self.gel_user, gene3.gene_symbol, gene3_data)
self.assertEqual(child3.version, "0.1")
del parent.panel.active_panel
parent = parent.panel.active_panel
old_stats = parent.stats
self.assertEqual(parent.version, "0.3")
del parent2.panel.active_panel
parent2 = parent2.panel.active_panel
self.assertEqual(parent2.version, "0.2")
child2.increment_version()
child2.update_gene(
self.gel_user, gene2.gene_symbol, {
"gene":
gene2,
"sources": [
Evidence.OTHER_SOURCES[1],
],
"phenotypes":
fake.sentences(nb=2),
"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":
True,
}).update_rating(3, self.gel_user, '')
child2.update_saved_stats()
self.assertEqual(child1.version, "0.2")
self.assertEqual(child2.version, "0.2")
self.assertEqual(child3.version, "0.1")
del parent.panel.active_panel
parent = parent.panel.active_panel
self.assertEqual(parent.version, "0.4")
self.assertNotEqual(old_stats, parent.stats)
del parent2.panel.active_panel
parent2 = parent2.panel.active_panel
self.assertEqual(parent2.version, "0.3")
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
