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_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