def test_st_layout_full():
G = NdexGraph()
toolbox.load(G, 'st_layout_network2.txt', header=True)
toolbox.annotate(G, 'st_layout_annotate2.txt')
toolbox.apply_source_target_layout(G)
template_id = 'd1856d17-4937-11e6-a5c7-06603eb7f303'
toolbox.apply_template(G, template_id, 'http://public.ndexbio.org', 'scratch', 'scratch')
G.set_name('test_st_layout_wtf1')
# G.write_to('temp.cx')
G.upload_to('http://dev2.ndexbio.org', 'scratch', 'scratch')
def test_st_layout_full():
G = NdexGraph()
toolbox.load(G, 'st_layout_network2.txt', header=True)
toolbox.annotate(G, 'st_layout_annotate2.txt')
toolbox.apply_source_target_layout(G)
template_id = 'd1856d17-4937-11e6-a5c7-06603eb7f303'
toolbox.apply_template(G, template_id, 'http://public.ndexbio.org',
'scratch', 'scratch')
G.set_name('test_st_layout_wtf1')
# G.write_to('temp.cx')
G.upload_to('http://dev2.ndexbio.org', 'scratch', 'scratch')
def test_complex_layout():
G = NdexGraph()
s1 = G.add_new_node('S1', st_layout='Source')
s2 = G.add_new_node('S2', st_layout='Source')
s3 = G.add_new_node('S3', st_layout='Source')
t1 = G.add_new_node('T1', st_layout='Target')
t2 = G.add_new_node('T2', st_layout='Target')
f1 = G.add_new_node('F1', st_layout='Forward')
f2 = G.add_new_node('F2', st_layout='Forward')
f3 = G.add_new_node('F3', st_layout='Forward')
f4 = G.add_new_node('F4', st_layout='Forward')
f5 = G.add_new_node('F5', st_layout='Forward')
r1 = G.add_new_node('R1', st_layout='Reverse')
r2 = G.add_new_node('R2', st_layout='Reverse')
r3 = G.add_new_node('R3', st_layout='Reverse')
b = G.add_new_node('B1', st_layout='Both')
G.add_edge_between(r3,r2)
G.add_edge_between(r2,r1)
G.add_edge_between(r1,s1)
G.add_edge_between(r3,b)
G.add_edge_between(s2, f3)
G.add_edge_between(s3, f1)
G.add_edge_between(f1, f2)
G.add_edge_between(f2, t1)
G.add_edge_between(f1, b)
G.add_edge_between(f3, f4)
G.add_edge_between(f4, f5)
G.add_edge_between(f5, t2)
G.add_edge_between(b, t1)
G.add_edge_between(b, s2)
G.add_edge_between(b, r1)
G.add_edge_between(t1,r3)
toolbox.apply_source_target_layout(G)
template_id = 'd1856d17-4937-11e6-a5c7-06603eb7f303'
toolbox.apply_template(G, template_id)
G.set_name('experiment1')
G.upload_to('http://public.ndexbio.org', 'scratch', 'scratch')
def test_complex_layout():
G = NdexGraph()
s1 = G.add_new_node('S1', st_layout='Source')
s2 = G.add_new_node('S2', st_layout='Source')
s3 = G.add_new_node('S3', st_layout='Source')
t1 = G.add_new_node('T1', st_layout='Target')
t2 = G.add_new_node('T2', st_layout='Target')
f1 = G.add_new_node('F1', st_layout='Forward')
f2 = G.add_new_node('F2', st_layout='Forward')
f3 = G.add_new_node('F3', st_layout='Forward')
f4 = G.add_new_node('F4', st_layout='Forward')
f5 = G.add_new_node('F5', st_layout='Forward')
r1 = G.add_new_node('R1', st_layout='Reverse')
r2 = G.add_new_node('R2', st_layout='Reverse')
r3 = G.add_new_node('R3', st_layout='Reverse')
b = G.add_new_node('B1', st_layout='Both')
G.add_edge_between(r3, r2)
G.add_edge_between(r2, r1)
G.add_edge_between(r1, s1)
G.add_edge_between(r3, b)
G.add_edge_between(s2, f3)
G.add_edge_between(s3, f1)
G.add_edge_between(f1, f2)
G.add_edge_between(f2, t1)
G.add_edge_between(f1, b)
G.add_edge_between(f3, f4)
G.add_edge_between(f4, f5)
G.add_edge_between(f5, t2)
G.add_edge_between(b, t1)
G.add_edge_between(b, s2)
G.add_edge_between(b, r1)
G.add_edge_between(t1, r3)
toolbox.apply_source_target_layout(G)
template_id = 'd1856d17-4937-11e6-a5c7-06603eb7f303'
toolbox.apply_template(G, template_id)
G.set_name('experiment1')
G.upload_to('http://public.ndexbio.org', 'scratch', 'scratch')
def test_template():
template_id = 'f35fbfd3-4918-11e6-a5c7-06603eb7f303'
G = NdexGraph()
G.add_new_node('1', color='green')
G.add_new_node('2', color='red')
G.add_new_node('3', color='green')
G.add_new_node('4', color='green')
G.add_new_node('5', color='green')
G.add_new_node('6', color='red')
G.add_edge_between(1, 2)
G.add_edge_between(2, 3)
G.add_edge_between(3, 4)
G.add_edge_between(4, 5)
G.add_edge_between(5, 6)
toolbox.apply_template(G, template_id)
G.set_name('template apply')
G.upload_to('http://public.ndexbio.org', 'scratch', 'scratch')
def test_template():
template_id = 'f35fbfd3-4918-11e6-a5c7-06603eb7f303'
G = NdexGraph()
G.add_new_node('1', color='green')
G.add_new_node('2', color='red')
G.add_new_node('3', color='green')
G.add_new_node('4', color='green')
G.add_new_node('5', color='green')
G.add_new_node('6', color='red')
G.add_edge_between(1, 2)
G.add_edge_between(2, 3)
G.add_edge_between(3, 4)
G.add_edge_between(4, 5)
G.add_edge_between(5, 6)
toolbox.apply_template(G, template_id)
G.set_name('template apply')
G.upload_to('http://public.ndexbio.org', 'scratch', 'scratch')
def set_style(network_id, ndex_cred):
# Update network style
import ndex.beta.toolbox as toolbox
template_uuid = "ea4ea3b7-6903-11e7-961c-0ac135e8bacf"
server = 'http://public.ndexbio.org'
username = ndex_cred.get('user')
password = ndex_cred.get('password')
source_network = ndex.networkn.NdexGraph(server=server,
username=username,
password=password,
uuid=network_id)
toolbox.apply_template(source_network,
template_uuid,
server=server,
username=username,
password=password)
source_network.update_to(network_id,
server=server,
username=username,
password=password)
else:
(r1, g1, b1), (r2, g2, b2) = colors[i], colors[i+1]
return int(r1 + f*(r2-r1)), int(g1 + f*(g2-g1)), int(b1 + f*(b2-b1))
def convert_to_rgb_string(minval, maxval, val, colors):
r, g, b = convert_to_rgb(minval, maxval, val, colors)
return 'rbg(' + str(r) + ',' + str(g) + ', ' + str(b) + ')'
#with open(path.join(path.abspath(path.dirname(__file__)),'nci_pid_preview.cx'), 'r') as file_handler:
# network_in_cx_from_file = file_handler.read().replace('\n', '')
# G = NdexGraph(cx=json.loads(network_in_cx_from_file))
# print G.to_cx()
source_network = networkn.NdexGraph(server="http://dev.ndexbio.org", username="******", password="******", uuid="49eb81d9-665a-11e7-8e93-06832d634f41")
toolbox.apply_template(source_network, "4a78a6ab-665a-11e7-8e93-06832d634f41", server="http://dev.ndexbio.org", username="******", password="******")
source_network.upload_to(server="http://dev.ndexbio.org", username="******", password="******")
if False:
elastic_search_uri = 'http://ec2-107-21-1-214.compute-1.amazonaws.com/'
es = Elasticsearch([elastic_search_uri],send_get_body_as='POST',timeout=300) # Prod Clustered Server
search_body = {
'sort' : [
'_score'
],
'query': {
'bool': {
'must': [
{'match': {
'_id': '2020037526'
) # ndexebs.get('edge_table')[0].get('PATHWAY_NAMES')
network_summary = current_netpath_metadata.get(
sif_pathway_name)
# {'node_table': [], 'edge_table': []}
if len(ebs.get('node_table')) > 0:
network = ebs2cx.ebs_to_network(ebs, name=sif_pathway_name)
#network = trim_edges(network)
ebs2cx.ndex_edge_filter(network)
layouts.apply_directed_flow_layout(network)
#toolbox.apply_template(network, "c51cda49-6192-11e5-8ac5-06603eb7f303", server="http://dev2.ndexbio.org", username="******", password="******")
toolbox.apply_template(
network,
config_data.get('network_style').get('uuid'),
server=config_data.get('network_style').get('server'),
username=config_data.get('network_style').get('user'),
password=config_data.get('network_style').get(
'pass')) # NCI PID
#toolbox.apply_template(network, "4b63be4e-4716-11e7-96f7-06832d634f41", server="http://dev.ndexbio.org", username="******", password="******") # Lipid Maps
#toolbox.apply_template(network, "23aa48fe-4fb0-11e7-a8b5-06832d634f41", server="http://dev.ndexbio.org", username="******", password="******") # Lipid Maps
#toolbox.apply_template(network, "71f237da-4704-11e7-a6ff-0660b7976219", server="http://dev2.ndexbio.org", username="******", password="******") # Netpath
#if network.pos:
# if network.view_id is None:
# network.view_id = 1
# if network.subnetwork_id is None:
# network.subnetwork_id = 1
# SET NETWORK METADATA FROM CURRENT NETWORK IN NDEx
current_netpath_metadata_tmp = current_netpath_metadata.get(
print ebs
sif_pathway_name = sif.replace('.sif', '')
#if ndexebs.get('edge_table') and len(ndexebs.get('edge_table')) > 0:
#sif_pathway_name = file_title_mapping.get(sif_pathway_name) # ndexebs.get('edge_table')[0].get('PATHWAY_NAMES')
network_summary = current_netpath_metadata.get(sif_pathway_name)
# {'node_table': [], 'edge_table': []}
if len(ebs.get('node_table')) > 0:
network = ebs2cx.ebs_to_network(ebs, name=sif_pathway_name)
ebs2cx.ndex_edge_filter(network)
layouts.apply_directed_flow_layout(network)
toolbox.apply_template(network,
"2328cb9f-4d39-11e7-9a21-06832d634f41",
server="http://dev.ndexbio.org",
username="******",
password="******") # NCI PID
# SET NETWORK METADATA FROM CURRENT NETWORK IN NDEx
current_netpath_metadata_tmp = current_netpath_metadata.get(
sif_pathway_name)
network.set_name(sif_pathway_name)
network.namespaces = {
"KEGG Pathway": "http://identifiers.org/kegg.pathway/",
"Mouse Genome Database":
"http://www.informatics.jax.org/accession/",
"KEGG Compound": "http://identifiers.org/kegg.compound/",
"LIPID MAPS":
"http://www.lipidmaps.org/data/LMSDRecord.php?LMID=",
"cas": "http://identifiers.org/cas/",
