e_set_name = 'pipeline'
min_sub = 0.02
#ndex = nc.Ndex("http://dev2.ndexbio.org", "netpath", "netpath2015")
#response = ndex.get_network_as_cx_stream("961563b7-4633-11e7-a6ff-0660b7976219")
ndex = nc.Ndex(
config_data.get('sim_map_style').get('server'),
config_data.get('sim_map_style').get('user'),
config_data.get('sim_map_style').get('pass'))
#response = ndex.get_network_as_cx_stream("9eae5085-47c6-11e7-96f7-06832d634f41") # LIPID MAPS template
response = ndex.get_network_as_cx_stream(
config_data.get('sim_map_style').get('uuid')) # NCI PID Map template
template_cx = response.json()
template_network = networkn.NdexGraph(template_cx)
similarity_graph = smu.create_similarity_map_from_enrichment_files(
map_name, e_set_dir, e_set_name, min_sub, ext_link_paths=ext_link_map)
toolbox.apply_network_as_template(similarity_graph, template_network)
print "applied graphic style from " + str(template_network.get_name())
layouts.apply_directed_flow_layout(similarity_graph,
node_width=35,
iterations=50,
use_degree_edge_weights=True)
filename = getcwd() + "/" + similarity_graph.get_name() + ".cx"
print "writing map to: " + filename
#similarity_graph.upload_to('http://dev2.ndexbio.org', 'netpath', 'netpath2015')
__author__ = 'danielcarlin'
import argparse
import ndex.client as nc
import ndex.networkn as networkn
import demo_notebooks.causal_paths.causal_utilities as cu
from pandas import read_table
net_uuid='b04e406b-dc88-11e6-86b1-0ac135e8bacf'
G = networkn.NdexGraph(server='http://public.ndexbio.org', uuid=net_uuid)
probe_genes_mat=read_table('../genes.txt',na_values='none', header=None)
probe_genes=list(probe_genes_mat[0])
drug_desc=read_table('../drugs_hugo.txt',na_values='none')
drug_genes=list()
for target_string in list(drug_desc['HGNC target']):
targets=target_string.split(',')
drug_genes.extend(targets)
for affector_string in list(drug_desc['HGNC downstream']):
affectors=affector_string.split(',')
drug_genes.extend(affectors)
drug_genes=list(set(drug_genes))
npaths=1
def main():
parser = argparse.ArgumentParser(
description='create NDEx network from TSV, one edge per line')
parser.add_argument('username')
parser.add_argument('password')
parser.add_argument('server')
parser.add_argument('ndextsv')
parser.add_argument('plan')
parser.add_argument('name')
parser.add_argument('desc')
parser.add_argument(
'-t',
action='store',
dest='template_id',
help='network id for the network to use as a graphic template')
parser.add_argument('-l',
action='store',
dest='layout',
help='name of the layout to apply')
parser.add_argument('-u',
action='store',
dest='update_uuid',
help='uuid of the network to update')
# parser.add_argument('update_username' )
# parser.add_argument('update_password')
# parser.add_argument('update_server')
arg = parser.parse_args()
try:
# set up the ndex connection
# error thrown if cannot authenticate
my_ndex = nc.Ndex("http://" + arg.server, arg.username, arg.password)
# current_directory = os.path.dirname(os.path.abspath(__file__))
# plan_filename = os.path.join(current_directory, "import_plans", arg.plan)
print("loading plan from: " + arg.plan)
try:
import_plan = d2c.TSVLoadingPlan(arg.plan)
except jsonschema.ValidationError as e1:
print("Failed to parse the loading plan '" + arg.plan + "': " +
e1.message)
print('at path: ' + str(e1.absolute_path))
print("in block: ")
print(e1.instance)
return
# set up the ndextsv -> cx converter
print("parsing ndextsv file using loading plan ...")
tsv_converter = d2c.TSV2CXConverter(import_plan)
#print json.dumps(cx, indent=4)
template_network = None
if arg.template_id:
response = my_ndex.get_network_as_cx_stream(arg.template_id)
template_cx = response.json()
template_network = networkn.NdexGraph(template_cx)
# If update_uuid is set, then we get the existing network's attributes and provenance
if arg.update_uuid:
response = my_ndex.get_network_aspect_as_cx_stream(
arg.update_uuid, "networkAttributes")
network_attributes = response.json()
provenance = my_ndex.get_provenance(arg.update_uuid)
ng = tsv_converter.convert_tsv_to_cx(
arg.tsv,
network_attributes=network_attributes,
provenance=provenance)
if template_network:
toolbox.apply_network_as_template(ng, template_network)
else:
try:
response = my_ndex.get_network_aspect_as_cx_stream(
arg.update_uuid, "cyVisualProperties")
visual_properties = response.json()
if len(visual_properties) > 0:
ng.unclassified_cx.append(
{"cyVisualProperties": visual_properties})
except requests.HTTPError as err:
if err.response.status_code == 404:
print(
"No cyVisualProperties aspect found in old network, not adding it."
)
else:
raise
if arg.layout:
if arg.layout == "df_simple":
layouts.apply_directed_flow_layout(ng)
my_ndex.update_cx_network(ng.to_cx_stream(), arg.update_uuid)
else:
ng = tsv_converter.convert_tsv_to_cx(arg.tsv,
name=arg.name,
description=arg.desc)
if template_network:
toolbox.apply_network_as_template(ng, template_network)
if arg.layout:
if arg.layout == "df_simple":
layouts.apply_directed_flow_layout(ng)
my_ndex.save_cx_stream_as_new_network(ng.to_cx_stream())
print("Done.")
except jsonschema.exceptions.ValidationError as ve:
print(str(ve))
exit(1)
except requests.exceptions.RequestException as e:
print("error in request to NDEx server: " + str(e))
raise e