def get_entities(self):
self.logger.info('getting genes')
attempts = 0
while attempts < 3:
try:
# get S288C genes
gene_ids_so = DBSession.query(
Dnasequenceannotation.dbentity_id,
Dnasequenceannotation.so_id).filter(
Dnasequenceannotation.taxonomy_id == 274901).all()
dbentity_ids_to_so = {}
dbentity_ids = set([])
so_ids = set([])
for gis in gene_ids_so:
dbentity_ids.add(gis[0])
so_ids.add(gis[1])
dbentity_ids_to_so[gis[0]] = gis[1]
all_genes = DBSession.query(Locusdbentity).filter(
Locusdbentity.dbentity_id.in_(list(dbentity_ids)),
Locusdbentity.dbentity_status == 'Active').all()
break
except StatementError:
traceback.print_exc()
log.info(
'DB error corrected. Rollingback previous error in db connection'
)
DBSession.rollback()
attempts += 1
return all_genes
def get_entities(self):
self.logger.info('getting gos')
attempts = 0
while attempts < 3:
try:
gos = DBSession.query(Go).all()
break
except:
traceback.print_exc()
DBSession.rollback()
attempts += 1
return gos
def get_entities(self):
self.log('getting phenotypes')
attempts = 0
while attempts < 3:
try:
phenotypes = DBSession.query(Phenotype).all()
break
except:
traceback.print_exc()
DBSession.rollback()
attempts += 1
return phenotypes
def get_entities(self):
self.logger.info('getting observables')
attempts = 0
while attempts < 3:
try:
observables = DBSession.query(Apo).filter_by(
apo_namespace="observable").all()
break
except:
traceback.print_exc()
DBSession.rollback()
attempts += 1
return observables