def test_update_gene_collection(self):
gene_to_update = GeneFactory()
gene_to_delete = GeneFactory()
gene_to_update_symbol = GeneFactory()
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene_to_update,
panel=gps)
STRFactory.create_batch(2, panel=gps) # random STRs
STRFactory.create(gene_core=gene_to_update, panel=gps)
RegionFactory.create_batch(2, panel=gps) # random STRs
RegionFactory.create(gene_core=gene_to_update, panel=gps)
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
STRFactory.create_batch(2, panel=gps) # random STRs
GenePanelEntrySnapshotFactory.create(gene_core=gene_to_update_symbol,
panel=gps)
STRFactory.create(gene_core=gene_to_update_symbol, panel=gps)
RegionFactory.create_batch(2, panel=gps) # random STRs
RegionFactory.create(gene_core=gene_to_update_symbol, panel=gps)
to_insert = [
Gene(gene_symbol='A', ensembl_genes={
'inserted': True
}).dict_tr(),
Gene(gene_symbol='B', ensembl_genes={
'inserted': True
}).dict_tr(),
]
to_update = [
Gene(gene_symbol=gene_to_update.gene_symbol,
ensembl_genes={
'updated': True
}).dict_tr()
]
to_update_symbol = [(Gene(gene_symbol='C',
ensembl_genes={
'updated': True
}).dict_tr(),
gene_to_update_symbol.gene_symbol)]
to_delete = [gene_to_delete.gene_symbol]
migration = {
'insert': to_insert,
'update': to_update,
'delete': to_delete,
'update_symbol': to_update_symbol
}
update_gene_collection(migration)
self.assertTrue(GenePanelEntrySnapshot.objects.get_active().get(
gene_core__gene_symbol=gene_to_update.gene_symbol).gene.get(
'ensembl_genes')['updated'])
self.assertTrue(STR.objects.get_active().get(
gene_core__gene_symbol=gene_to_update.gene_symbol).gene.get(
'ensembl_genes')['updated'])
self.assertTrue(Region.objects.get_active().get(
gene_core__gene_symbol=gene_to_update.gene_symbol).gene.get(
'ensembl_genes')['updated'])
updated_not_updated = [
gpes.gene['ensembl_genes']
for gpes in GenePanelEntrySnapshot.objects.filter(
gene_core__gene_symbol=gene_to_update.gene_symbol)
]
self.assertNotEqual(updated_not_updated[0], updated_not_updated[1])
updated_not_updated = [
str_item.gene['ensembl_genes'] for str_item in STR.objects.filter(
gene_core__gene_symbol=gene_to_update.gene_symbol)
]
self.assertNotEqual(updated_not_updated[0], updated_not_updated[1])
updated_not_updated = [
region_item.gene['ensembl_genes']
for region_item in Region.objects.filter(
gene_core__gene_symbol=gene_to_update.gene_symbol)
]
self.assertNotEqual(updated_not_updated[0], updated_not_updated[1])
self.assertFalse(
GenePanelEntrySnapshot.objects.get(
gene_core__gene_symbol=gene_to_update_symbol.gene_symbol).
gene_core.active)
self.assertFalse(
STR.objects.get(gene_core__gene_symbol=gene_to_update_symbol.
gene_symbol).gene_core.active)
self.assertFalse(
Region.objects.get(gene_core__gene_symbol=gene_to_update_symbol.
gene_symbol).gene_core.active)
self.assertFalse(
Gene.objects.get(
gene_symbol=gene_to_update_symbol.gene_symbol).active)
self.assertFalse(
Gene.objects.get(gene_symbol=gene_to_delete.gene_symbol).active)
self.assertTrue(Gene.objects.get(gene_symbol='A').active)
self.assertTrue(
GenePanelEntrySnapshot.objects.get(gene_core__gene_symbol='C').
gene.get('ensembl_genes')['updated'])
self.assertTrue(
STR.objects.get(gene_core__gene_symbol='C').gene.get(
'ensembl_genes')['updated'])
self.assertTrue(
Region.objects.get(gene_core__gene_symbol='C').gene.get(
'ensembl_genes')['updated'])
def test_update_ensembl(self):
gene_symbol = 'FAM58A'
gene_to_update = GeneFactory(gene_symbol=gene_symbol)
ensembl_data = {
"GRch37": {
"82": {
"ensembl_id": "ENSG00000147382",
"location": "X:152853377-152865500"
}
},
"GRch38": {
"90": {
"ensembl_id": "ENSG00000262919",
"location": "X:153587919-153600045"
}
}
}
json_data = {gene_symbol: ensembl_data}
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene_to_update,
panel=gps)
STRFactory.create_batch(2, panel=gps) # random STRs
STRFactory.create(gene_core=gene_to_update, panel=gps)
RegionFactory.create_batch(2, panel=gps) # random STRs
RegionFactory.create(gene_core=gene_to_update, panel=gps)
gps_2 = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps_2) # random genes
STRFactory.create_batch(2, panel=gps_2) # random STRs
RegionFactory.create_batch(2, panel=gps_2) # random STRs
RegionFactory.create(gene_core=gene_to_update, panel=gps_2)
# make sure ensembl data doesn't match
for gene in GenePanelEntrySnapshot.objects.filter(
gene__gene_symbol=gene_symbol):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for str in STR.objects.filter(gene__gene_symbol=gene_symbol):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for region in Region.objects.filter(gene__gene_symbol=gene_symbol):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
gps_pk = gps.pk
gps_version = gps.version
gps_2_version = gps_2.version
process(json_data)
# make sure previous data didn't change
for gene in GenePanelEntrySnapshot.objects.filter(
gene__gene_symbol=gene_symbol, panel_id=gps_pk):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for str in STR.objects.filter(gene__gene_symbol=gene_symbol,
panel_id=gps_pk):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for region in Region.objects.filter(gene__gene_symbol=gene_symbol,
panel_id=gps_pk):
self.assertNotEqual(gene.gene.get('ensembl_genes'), ensembl_data)
gps = gps.panel.active_panel
gps_2 = gps_2.panel.active_panel
self.assertNotEqual(gps_version, gps.version)
self.assertNotEqual(gps_2_version, gps_2.version)
# make sure new data has changed
for gene in GenePanelEntrySnapshot.objects.filter(
gene__gene_symbol=gene_symbol, panel=gps):
self.assertEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for str in STR.objects.filter(gene__gene_symbol=gene_symbol,
panel=gps):
self.assertEqual(gene.gene.get('ensembl_genes'), ensembl_data)
for region in Region.objects.filter(gene__gene_symbol=gene_symbol,
panel=gps):
self.assertEqual(gene.gene.get('ensembl_genes'), ensembl_data)