def db_add(
domain_id,
astral_id,
astral_sid,
domain_start,
domain_stop,
astral_start,
astral_stop,
pdb_id,
chain,
overlap,
session=None,
):
# Create a domain_to_astral ORM object and push it to the DB. Create a scoped session for push.
# Raise exception if push fails
# If session not given, create scoped session for the DB push
if not session:
print "db_add:: No session provided. Creating scoped session"
session = ScopedSession()
if astral_start == None or astral_stop == None:
dtoa_obj = DomainAstralOverlap(
domain_id=domain_id,
astral_id=astral_id,
astral_sid=astral_sid,
domain_start=domain_start,
domain_stop=domain_stop,
pdb_id=pdb_id,
chain=chain,
overlap=overlap,
)
else:
dtoa_obj = DomainAstralOverlap(
domain_id=domain_id,
astral_id=astral_id,
astral_sid=astral_sid,
domain_start=domain_start,
domain_stop=domain_stop,
astral_start=int(astral_start),
astral_stop=int(astral_stop),
pdb_id=pdb_id,
chain=chain,
overlap=overlap,
)
session.add(dtoa_obj)
try:
session.flush()
except IntegrityError:
print "DomainToAstral {0} object already in database. Skipping".format(dtoa_obj)
session.rollback()
except Exception as e:
print "Error in pushing DomainToAstral object {0} to database".format(dtoa_obj)
raise
return dtoa_obj
def output_db(list):
# Takes a list of HomologComparisonProteinPair objects to store in the DB,
# table hpf.homolog_structure_allvall[...]
session = ScopedSession()
for pair in list:
hsa_obj = HomologStructAllVAll(source_id=pair.source.query_id, target_id=pair.target.query_id, score=pair.similarity)
session.add(hsa_obj)
try:
session.flush()
except IntegrityError:
print "Object {0} already in database. Rolling back and skipping..".format(hsa_obj)
session.rollback()
continue
except:
print "Could not add protein comparison object {0} to DB".format(hsa_obj)
raise
