def upload_model(self, ndex_cred=None, private=True, style='default'):
"""Creates a new NDEx network of the assembled CX model.
To upload the assembled CX model to NDEx, you need to have
a registered account on NDEx (http://ndexbio.org/) and have
the `ndex` python package installed. The uploaded network
is private by default.
Parameters
----------
ndex_cred : Optional[dict]
A dictionary with the following entries:
'user': NDEx user name
'password': NDEx password
private : Optional[bool]
Whether or not the created network will be private on NDEX.
style : Optional[str]
This optional parameter can either be (1)
The UUID of an existing NDEx network whose style should be applied
to the new network. (2) Unspecified or 'default' to use
the default INDRA-assembled network style. (3) None to
not set a network style.
Returns
-------
network_id : str
The UUID of the NDEx network that was created by uploading
the assembled CX model.
"""
cx_str = self.print_cx()
if not ndex_cred:
username, password = ndex_client.get_default_ndex_cred({})
ndex_cred = {'user': username, 'password': password}
network_id = ndex_client.create_network(cx_str, ndex_cred, private)
if network_id and style:
template_id = None if style == 'default' else style
nretries = 3
for retry_idx in range(nretries):
time.sleep(3)
try:
ndex_client.set_style(network_id, ndex_cred, template_id)
break
except Exception:
msg = 'Style setting failed, '
if retry_idx + 1 < nretries:
logger.info(msg + 'retrying %d more times' %
(nretries - (retry_idx + 1)))
else:
logger.info(msg + 'the network will be missing style '
'information.')
return network_id
def upload_model(self, ndex_cred=None, private=True, style='default'):
"""Creates a new NDEx network of the assembled CX model.
To upload the assembled CX model to NDEx, you need to have
a registered account on NDEx (http://ndexbio.org/) and have
the `ndex` python package installed. The uploaded network
is private by default.
Parameters
----------
ndex_cred : Optional[dict]
A dictionary with the following entries:
'user': NDEx user name
'password': NDEx password
private : Optional[bool]
Whether or not the created network will be private on NDEX.
style : Optional[str]
This optional parameter can either be (1)
The UUID of an existing NDEx network whose style should be applied
to the new network. (2) Unspecified or 'default' to use
the default INDRA-assembled network style. (3) None to
not set a network style.
Returns
-------
network_id : str
The UUID of the NDEx network that was created by uploading
the assembled CX model.
"""
cx_str = self.print_cx()
if not ndex_cred:
username, password = ndex_client.get_default_ndex_cred({})
ndex_cred = {'user': username,
'password': password}
network_id = ndex_client.create_network(cx_str, ndex_cred, private)
if network_id and style:
template_id = None if style == 'default' else style
ndex_client.set_style(network_id, ndex_cred, template_id)
return network_id
def upload_model(self, ndex_cred=None, private=True, style='default'):
"""Creates a new NDEx network of the assembled CX model.
To upload the assembled CX model to NDEx, you need to have
a registered account on NDEx (http://ndexbio.org/) and have
the `ndex` python package installed. The uploaded network
is private by default.
Parameters
----------
ndex_cred : Optional[dict]
A dictionary with the following entries:
'user': NDEx user name
'password': NDEx password
private : Optional[bool]
Whether or not the created network will be private on NDEX.
style : Optional[str]
This optional parameter can either be (1)
The UUID of an existing NDEx network whose style should be applied
to the new network. (2) Unspecified or 'default' to use
the default INDRA-assembled network style. (3) None to
not set a network style.
Returns
-------
network_id : str
The UUID of the NDEx network that was created by uploading
the assembled CX model.
"""
cx_str = self.print_cx()
if not ndex_cred:
username, password = ndex_client.get_default_ndex_cred({})
ndex_cred = {'user': username, 'password': password}
network_id = ndex_client.create_network(cx_str, ndex_cred, private)
if network_id and style:
template_id = None if style == 'default' else style
ndex_client.set_style(network_id, ndex_cred, style)
return network_id
import sys
import pickle
from indra.databases import ndex_client
from indra.assemblers.cx import CxAssembler
from indra.assemblers.cx.hub_layout import add_semantic_hub_layout
if __name__ == '__main__':
kinase = sys.argv[1]
with open('dark_kinase_statements_assembled.pkl', 'rb') as fh:
stmts = pickle.load(fh)
cxa = CxAssembler(stmts[kinase])
cxa.make_model()
add_semantic_hub_layout(cxa.cx, kinase)
model_id = cxa.upload_model()
ndex_client.set_style(model_id)