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 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/",