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_get_internal_panels_for_a_gene(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps2 = GenePanelSnapshotFactory(
panel__status=GenePanel.STATUS.internal)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps2) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps2)
gps3 = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps3) # random genes
self.assertEqual(
GenePanelEntrySnapshot.objects.get_gene_panels(
gene.gene_symbol).count(), 2)
self.assertEqual(
GenePanelSnapshot.objects.get_gene_panels(
gene.gene_symbol).count(), 1)
self.assertEqual(
GenePanelSnapshot.objects.get_gene_panels(gene.gene_symbol,
all=True,
internal=True).count(),
2)
url = reverse_lazy('panels:entity_detail',
kwargs={'slug': gene.gene_symbol})
res = self.client.get(url)
self.assertEqual(len(res.context_data['entries']), 2)
def prepare_compare(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.internal)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps2 = GenePanelSnapshotFactory(panel__status=GenePanel.STATUS.public)
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps2) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps2)
STRFactory(panel=gps, position_37=None)
return gene, gps, gps2
def test_download_panel(self):
gene, gps, gps2 = self.prepare_compare()
grey_gene = 'gene2'
gene2 = GeneFactory(gene_symbol=grey_gene)
gpes = GenePanelEntrySnapshotFactory.create(gene_core=gene2, panel=gps)
gpes.saved_gel_status = 0
res = self.client.get(
reverse_lazy('panels:download_panel_tsv',
args=(gps.panel.pk, '01234')))
self.assertEqual(res.status_code, 200)
self.assertEqual(res.content.find(grey_gene.encode()), -1)
def test_import_reviews(self):
gene = GeneFactory(gene_symbol="ABCC5-AS1")
gps = GenePanelSnapshotFactory()
current_version = gps.version
gps.panel.name = "Panel One"
gps.panel.save()
GenePanelEntrySnapshotFactory.create(gene_core=gene,
panel=gps,
evaluation=(None, ))
file_path = os.path.join(os.path.dirname(__file__),
'import_reviews_data.tsv')
test_reviews_file = os.path.abspath(file_path)
with open(test_reviews_file) as f:
url = reverse_lazy('panels:upload_reviews')
self.client.post(url, {'review_list': f})
ap = GenePanel.objects.get(name="Panel One").active_panel
assert ap.get_gene(gene.gene_symbol).evaluation.count() == 1
assert current_version != ap.version
def test_get_panels_for_a_gene(self):
gene = GeneFactory()
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps)
gps3 = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps3) # random genes
GenePanelEntrySnapshotFactory.create(gene_core=gene, panel=gps3)
gps4 = GenePanelSnapshotFactory()
GenePanelEntrySnapshotFactory.create_batch(2,
panel=gps4) # random genes
assert GenePanelEntrySnapshot.objects.get_gene_panels(
gene.gene_symbol).count() == 3
url = reverse_lazy('panels:entity_detail',
kwargs={'slug': gene.gene_symbol})
res = self.client.get(url)
assert len(res.context_data['entries']) == 3
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)
