def finish(args, loader=None):
"""
all things that are performed by single core, multi, ipython
should be done here
"""
if loader is None:
loader = GeminiLoader(args, prepare_db=False)
print "storing version, header, etc."
loader.store_resources()
loader.store_version()
loader.store_vcf_header()
if not args.skip_gene_tables:
print "storing gene-detailed"
loader._get_gene_detailed()
print "storing gene-summary"
loader._get_gene_summary()
if not args.test_mode:
print "updating gene-table"
loader.update_gene_table()
if not args.test_mode:
print "building indices"
loader.build_indices_and_disconnect()
else:
import database
database.close_and_commit(loader.c)
def finish(args, loader=None):
"""
all things that are performed by single core, multi, ipython
should be done here
"""
if loader is None:
loader = GeminiLoader(args, prepare_db=False)
print "storing version, header, etc."
loader.store_resources()
loader.store_version()
loader.store_vcf_header()
if not args.skip_gene_tables:
print "storing gene-detailed"
loader._get_gene_detailed()
print "storing gene-summary"
loader._get_gene_summary()
if not args.test_mode:
print "updating gene-table"
loader.update_gene_table()
if not args.test_mode:
print "building indices"
loader.build_indices_and_disconnect()
else:
import database
database.close_and_commit(loader.c)
def build_indices_and_disconnect(self):
"""
Create the db table indices and close up
db connection
"""
# index our tables for speed
database.create_indices(self.c)
# commit data and close up
database.close_and_commit(self.c, self.conn)
def build_indices_and_disconnect(self):
"""
Create the db table indices and close up
db connection
"""
# index our tables for speed
database.create_indices(self.c)
# commit data and close up
database.close_and_commit(self.c, self.conn)
