def assemble_cx(stmts, name):
ca = CxAssembler()
ca.network_name = name
ca.add_statements(stmts)
ca.make_model()
cx_str = ca.print_cx()
return cx_str
def upload_to_ndex(stmts, ndex_cred):
nd = ndex.client.Ndex('http://public.ndexbio.org',
username=ndex_cred.get('user'),
password=ndex_cred.get('password'))
network_id = ndex_cred.get('network')
ca = CxAssembler()
ca.network_name = 'rasmachine'
ca.add_statements(stmts)
ca.make_model()
cx_str = ca.print_cx()
try:
logger.info('Getting network summary...')
summary = nd.get_network_summary(network_id)
except Exception as e:
logger.error('Could not get NDEx network summary.')
logger.error(e)
return
try:
logger.info('Updating network...')
cx_stream = io.BytesIO(cx_str.encode('utf-8'))
with open('cx_upload.cx', 'wb') as fh:
fh.write(cx_str.encode('utf-8'))
nd.update_cx_network(cx_stream, network_id)
except Exception as e:
logger.error('Could not update NDEx network.')
logger.error(e)
return
ver_str = summary.get('version')
new_ver = _increment_ndex_ver(ver_str)
profile = {
'name': summary.get('name'),
'description': summary.get('description'),
'version': new_ver,
}
logger.info('Updating NDEx network (%s) profile to %s' %
(network_id, profile))
profile_retries = 5
for i in range(profile_retries):
try:
time.sleep(5)
nd.update_network_profile(network_id, profile)
break
except Exception as e:
logger.error('Could not update NDEx network profile.')
logger.error(e)
