def network_force_directed_layout(G):
'''POST the network to CyREST, then run layout algorithm,
finally return the coordinates and the cy_network.
'''
# Create Py2cytoscape client
cy = CyRestClient(ip=IP, port=PORT)
# Reset session
cy.session.delete()
# POST the graph to CyREST
G_cy = cy.network.create_from_networkx(G)
# Change the layout params
layout_parameters = [{
"name": "numIterations",
"value": 500
}, {
"name": "numIterationsEdgeRepulsive",
"value": 500
}]
resp = requests.put(BASE_URL +
'/apply/layouts/force-directed-cl/parameters',
data=json.dumps(layout_parameters),
headers=HEADERS)
cy.layout.apply(name='force-directed-cl', network=G_cy)
# Get current view
view = G_cy.get_first_view()
nodes = view['elements']['nodes']
# Get a coord matrix ordered by id_original
ids_original = np.array([n['data']['id_original']
for n in nodes]).astype(np.int32)
xs = [n['position']['x'] for n in nodes]
ys = [n['position']['y'] for n in nodes]
coords = np.array([xs, ys]).T
return coords[ids_original], G_cy
def cyview(query,
dataset='HMDB',
connections='targets',
name='',
database=DATABASE):
""" See HMDB/DrugBank graphs with Cytoscape runing on your local machine
`
:param query: Query to select HMDB or DrugBank entries
:param dataset: HMDB or DrugBank, not case sensitive
:param connections: Connection type for DrugBank entries
:param name: Name of the graph on Cytoscape, query is used as default value
:param database: Name of the MongoDB database to connect
"""
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import Style
qc = parseinputquery(query)
print(qc) # todo: tests with HMDB
if dataset.upper() == 'HMDB':
qry = QueryHMDB(index=database)
pairs = qry.getconnectedmetabolites(qc)
mn = qry.get_connections_graph(pairs, query)
else: # assume DrugBank
qry = QueryDrugBank(db, database, 'drugbank')
mn = qry.get_connections_graph(qc, connections)
crcl = CyRestClient()
mn.name = json.dumps(qc) if name == '' else name
cyn = crcl.network.create_from_networkx(mn)
crcl.layout.apply('kamada-kawai', network=cyn)
crcl.style.apply(Style('default'), network=cyn)
def view_in_cytoscape(self, force_add_nodename=False):
"""Ports graph to Cytoscape
Parameters
----------
force_add_nodename : bool
If True, a node attribute called `nodename` will be added.
This seems to fix the bug the py2cytoscape has where it would
ignore the node names.
"""
if not hasattr(self, "cyrest"):
self.cyrest = CyRestClient()
if force_add_nodename:
nodenames = {
n: d[self.node_name]
for n, d in self.get_node_attributes().items()
}
self.set_node_attributes({"nodename": nodenames},
namespace="nodeids")
hdl = self.cyrest.network.create_from_networkx(self.network)
self.cyrest.layout.apply(name='degree-circle', network=hdl)
return self
def draw_graph(page_links: List[PageLink], layout_name: str) -> None:
log.info(f"Создаю граф из {len(page_links)} ссылок")
graph_nodes: Set[str] = set()
graph_edges: List[Tuple[str, str]] = []
for link in page_links:
if link.from_url not in graph_nodes:
graph_nodes.add(link.from_url)
if link.to_url not in graph_nodes:
graph_nodes.add(link.to_url)
graph_edges.append((link.from_url, link.to_url))
log.info("Рисую граф ссылок с расположением " + layout_name)
cytospace_client: CyRestClient = CyRestClient()
graph: CyNetwork = cytospace_client.network.create()
node_suids: Dict[str, int] = graph.add_nodes(list(graph_nodes))
graph.add_edges(
list({
"source": node_suids[edge[0]],
"target": node_suids[edge[1]]
} for edge in graph_edges))
cytospace_client.layout.apply(layout_name, graph)
# 24000 пикселей — максимальная высота изображения; это ограничение накладывает Cytospace
image_height: int = min(max(len(graph_nodes) * 60, 600), 24000)
graph_image: bytes = graph.get_png(image_height)
with open(f"links-{layout_name}.png", "wb+") as png_file:
png_file.write(graph_image)
def setUp(self):
self.client = CyRestClient()
self.client.network.delete_all()
locations = ['http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif']
self.network = self.client.network.create_from(locations)
view_id_list = self.network.get_views()
self.view = self.network.get_view(view_id_list[0], format='view')
def graphml2cyto(col_filename, style_filename, outpath):
cy = CyRestClient()
cy.session.delete()
net = cy.network.create_from(col_filename[:-4] + '.graphml')
entireNetworkJson = requests.get('http://localhost:1234/v1/networks.json')
entireNetwork = json.loads(entireNetworkJson.text)
nodes = entireNetwork[0]['elements']['nodes']
numNodes = json.loads(requests.get('http://localhost:1234/v1/networks/' + str(entireNetwork[0]['data']['SUID']) + '/nodes/count').text)['count']
numEdges = json.loads(requests.get('http://localhost:1234/v1/networks/' + str(entireNetwork[0]['data']['SUID']) + '/edges/count').text)['count']
for d in merge_dicts:
merge_ids = [n['data']['SUID'] for n in nodes if n['data']['name'] in d['members']]
#pprint.pprint(nodes)
requests.post('http://127.0.0.1:1234/v1/networks/' +
str(entireNetwork[0]['data']['SUID']) + '/groups',
data=json.dumps({'name': d['group'], 'nodes': merge_ids}),
headers = {'Accept': 'application/json', 'Content-Type': 'application/json'})
#with open(style_filename, 'r') as fstyle:
# content = fstyle.read()[1:-1]
# content = json.loads(content)
# print(content)
# styleResp = requests.post('http://127.0.0.1:1234/v1/styles/',
# data=json.dumps(content),
# headers = {'Accept': 'application/json', 'Content-Type': 'application/json'})
# styleName = json.loads(styleResp.text)['title']
# print('style name is: ' + styleName)
# cy.style.apply(style=styleName, network=net)
cy.layout.apply(name='circular', network=net)
cy.session.save(outpath)
cy.session.delete()
return numNodes, numEdges
def display_in_cytoscape(graph, network_name: str):
"""
Displays the graph in Cytoscape - if it is running
:param graph: The graph to display
:param network_name: Name of the network in Cytoscape
"""
try:
cy = CyRestClient()
cytoscape_network = cy.network.create_from_networkx(
network=graph, name=network_name, collection="Cluster comparison")
# add the layout
cy.layout.apply(name='force-directed', network=cytoscape_network)
# add the style
# Step 6: Create Visual Style as code (or by hand if you prefer)
comparison_style = cy.style.create('Cluster Comparison')
basic_settings = {
# You can set default values as key-value pairs.
'NODE_FILL_COLOR': '#6AACB8',
'NODE_SIZE': 55,
'NODE_BORDER_WIDTH': 0,
'NODE_LABEL_COLOR': '#555555',
'EDGE_WIDTH': 2,
'EDGE_TRANSPARENCY': 100,
'EDGE_STROKE_UNSELECTED_PAINT': '#333333',
'NETWORK_BACKGROUND_PAINT': '#FFFFFF'
}
comparison_style.update_defaults(basic_settings)
# Create some mappings
min_cluster_size = min([graph.node[c]["size"] for c in graph.nodes])
max_cluster_size = max([graph.node[c]["size"] for c in graph.nodes])
cluster_size_to_node_size = StyleUtil.create_slope(
min=min_cluster_size, max=max_cluster_size, values=(30, 100))
comparison_style.create_continuous_mapping(
column='size',
vp='NODE_SIZE',
col_type='Double',
points=cluster_size_to_node_size)
comparison_style.create_discrete_mapping(column='source',
vp="NODE_FILL_COLOR",
col_type="String",
mappings={
"source1": "#FC8D62",
"source2": "#A6D854"
})
comparison_style.create_passthrough_mapping(column='weight',
vp="EDGE_WIDTH",
col_type="Integer")
# apply the style
cy.style.apply(style=comparison_style, network=cytoscape_network)
except Exception as e:
print("Please open Cytoscape to display the graph: " + str(e))
def cyview(query):
""" See metabolite networks with Cytoscape runing on your local machine """
from py2cytoscape.data.cyrest_client import CyRestClient
qc = parseinputquery(query)
qry = QueryModelSEED()
mn = qry.get_metabolite_network(qc)
client = CyRestClient()
client.network.create_from_networkx(mn)
def setUp(self):
self.client = CyRestClient()
self.client.style.delete_all()
styles = self.client.style.get_all()
self.assertEqual(1, len(styles))
self.style = self.client.style.create(STYLE_NAME)
self.assertEqual(STYLE_NAME, self.style.get_name())
def view_withcytoscape(inf):
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import Style
crcl = CyRestClient()
r = json.load(open(inf))
g = get_cytoscape_graph(r, name=inf)
cyn = crcl.network.create_from_networkx(g)
crcl.layout.apply('kamada-kawai', network=cyn)
crcl.style.apply(Style('default'), network=cyn)
def __init__(self, node_df, edge_df, interaction_or_edge):
self.node_df = node_df
self.edge_df = edge_df
self.interaction_or_edge = interaction_or_edge
self.json_file_name = 'json_file.json'
self.json_file_path = os.path.join('../SampleData/InteractionGraph/',
self.json_file_name)
self.cy = CyRestClient()
self.node_edge_network = None # = self.cy.network.create_from(self.json_file_path)
def view_in_cytoscape(self):
"""Ports graph to Cytoscape"""
if not hasattr(self, "cyrest"):
self.cyrest = CyRestClient()
hdl = self.cyrest.network.create_from_networkx(self.network)
self.cyrest.layout.apply(name='degree-circle', network=hdl)
return self
def create_network(infile):
cy = CyRestClient()
# Reset
cy.session.delete()
# Step 2: Load network from somewhere
## entire path is needed
net = cy.network.create_from(infile)
return (net)
def __init__(self, graph, layout="attributes-layout", style='Directed'):
# name='FromMAGINE'):
# force-directed
# attributes-layout
self.graph = graph
self.cy = CyRestClient()
self.cy.session.delete()
self.cy.layout2 = LayoutClient()
self.style = None
self.edge_name2id = None
self.node_name2id = None
self.g_cy = None
self.view1 = None
for n, (i, j) in enumerate(self.graph.edges()):
self.graph[i][j]['name'] = '{},{}'.format(i, j)
self.g_cy = self.cy.network.create_from_networkx(self.graph)
time.sleep(2)
view_id_list = self.g_cy.get_views()
self.view1 = self.g_cy.get_view(view_id_list[0], format='view')
# Marquee Directed Simple
self.style = self.cy.style.create(style)
# self.style = self.cy.style.create('Marquee')
options = {
'NODE_LABEL_FONT_SIZE': 24,
'EDGE_WIDTH': 2,
'EDGE_TRANSPARENCY': '150',
# 'NETWORK_HEIGHT' : '2800',
# 'NETWORK_WIDTH' : '2800',
'NODE_LABEL_COLOR': 'black',
'NODE_FILL_COLOR': 'red',
'NETWORK_BACKGROUND_PAINT': '#00FFFFFF',
'NODE_SIZE': 80,
# 'NODE_LABEL_POSITION': 'C,C,c,0.00,-60.00',
'NETWORK_CENTER_X_LOCATION': 0.0,
'NETWORK_CENTER_Y_LOCATION': 0.0,
}
self.style.update_defaults(options)
if layout == 'attributes-layout':
self.cy.layout2.apply(name=layout,
network=self.g_cy,
params={'column': 'color'})
else:
self.cy.layout2.apply(name=layout, network=self.g_cy)
self.node_name2id = util.name2suid(self.g_cy, 'node')
self.edge_name2id = util.name2suid(self.g_cy, 'edge')
def __visualize_outputs(self):
_annot_file = os.path.abspath(self.annotations.out_annot_file)
_style_file = os.path.abspath(self.annotations.out_style_file)
cyclient = cyrest.cyclient()
cy = CyRestClient()
#cy.session.delete()
cy.network.create_from(self.runner.output_files['network-file'])
time.sleep(2)
style = cyclient.vizmap.load_file(_style_file)
cyclient.vizmap.apply(style[0])
cyclient.table.import_file(afile=_annot_file,
firstRowAsColumnNames=True,
keyColumnIndex='1',
startLoadRow='0',
dataTypeList=self.data_types)
cyclient.session.save_as(session_file=self.save_file)
def _setup_graph(self):
self.cy = CyRestClient()
self.cy.session.delete()
self.CY_STYLE = self.cy.style.create("Sample3")
defaults = {
"NODE_BORDER_PAINT": "black",
"NODE_LABEL_COLOR": "#33FF33",
"NODE_LABEL_FONT_SIZE": "18",
"NODE_SIZE": "30",
"EDGE_SOURCE_ARROW_SHAPE": "arrow",
"EDGE_SOURCE_ARROW_UNSELECTED_PAINT": "#9999FF",
"EDGE_STROKE_COLOR": "#CCCCCC"
}
self.CY_STYLE.update_defaults(defaults)
self.g = nx.DiGraph()
def cyview(query, name='', limit=4000):
""" See IntEnz enzyme graphs with Cytoscape runing on your local machine
:param query: Query to select IntEnz entries
:param name: Name of the graph on Cytoscape, query is used as default value
:param limit
"""
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import Style
qc = parseinputquery(query)
qry = QueryIntEnz()
mn = qry.get_connections_graph(qc, limit)
crcl = CyRestClient()
mn.name = json.dumps(qc) if name == '' else name
cyn = crcl.network.create_from_networkx(mn)
crcl.layout.apply('kamada-kawai', network=cyn)
crcl.style.apply(Style('default'), network=cyn)
def colorGraphe(self,tableTuple):
if not self.isRunning():
self.alerte()
else:
cy = CyRestClient()
net1 = cy.network.create_from(self.grapheLoc2[self.graph_3.currentRow()])
net1.create_node_column("composant", data_type='Integer',is_immutable=False)
net1.create_node_column("signe",data_type='Integer',is_immutable=False)
table=net1.get_node_table()
nodeTable={}
nodes=net1.get_nodes()
for node in nodes:
nodeTable[net1.get_node_value(node)['name']]=node
for line in tableTuple:
table.set_value(nodeTable[line[0]],"composant",line[1])
table.set_value(nodeTable[line[0]],"signe",line[2])
net1.update_node_table(table,network_key_col='name', data_key_col='name')
style1 = cy.style.create('sample_style1')
points = [{
'value': '0.0',
'lesser':'blue',
'equal':'blue',
'greater': 'blue'
},{
'value': '1.0',
'lesser':'red',
'equal':'red',
'greater': 'red'
}]
points[1]["value"]=self.nbComposantes(tableTuple)-1
style1.create_continuous_mapping(column='composant', col_type='Integer', vp='NODE_FILL_COLOR',points=points)
cy.style.apply(style1,net1)
cy.layout.apply(name='organic',network=net1)
self.doneC()
def affichage(self):
if not self.isRunning():
self.alerte()
else:
cy = CyRestClient()
style1 = cy.style.create('sample_style1')
#feuille de style cytoscape
new_defaults = {
# Node defaults
'NODE_FILL_COLOR': '#ff5500',
'NODE_SIZE': 20,
'NODE_BORDER_WIDTH': 0,
'NODE_TRANSPARENCY': 120,
'NODE_LABEL_COLOR': 'white',
# Edge defaults
'EDGE_WIDTH': 3,
'EDGE_STROKE_UNSELECTED_PAINT': '#aaaaaa',
#'EDGE_LINE_TYPE': 'LONG_DASH',
'EDGE_TRANSPARENCY': 120,
# Network defaults
'NETWORK_BACKGROUND_PAINT': 'white'
}
# Update
style1.update_defaults(new_defaults)
kv_pair = {
'-1': 'T',
'1': 'Arrow'
}
style1.create_discrete_mapping(column='interaction',
col_type='String', vp='EDGE_SOURCE_ARROW_SHAPE', mappings=kv_pair)
self.fname = self.grapheLoc[self.graph.currentRow()]
net1 = cy.network.create_from(self.grapheLoc[self.graph.currentRow()])
cy.style.apply(style1,net1)
class CytoscapeClient:
"""This is a wrapper to the py2cytoscape wrapper. The local installation of Py2cytoscape has been modified for it to work"""
def __init__(self, host="localhost", port="1234", version="v1"):
self.cy = CyRestClient(ip=host, port=port, version=version)
def gc(self):
self.cy.gc()
def free_memory(self):
self.cy.gc()
X = self.cy.status()
return max(
X['memoryStatus']['maxMemory'] - X['memoryStatus']['usedMemory'],
X['memoryStatus']['freeMemory'])
def random_id(self, prefix="MY_"):
import random
s = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
return prefix + ''.join(
[s[random.randint(0,
len(s) - 1)] for i in range(10)])
def cynet_from_xgmml(self,
s_file,
name=None,
s_layout="force-directed",
l_bundle=True,
t_xy=None,
l_digraph=False):
"""If t_xy is provided, s_layout is ignored
return CyNetwork"""
import os
if not os.path.exists(s_file):
import util
util.warn_msg('Missing file: %s' % s_file)
return None
if not l_digraph:
net = xgmml.Network(s_file, name=name)
else:
import digraph
net = digraph.Digraph(s_file, name=name)
if t_xy is not None:
net.set_XY(t_xy)
s_layout = None
S = net.T_node.header()
#print "---------------->", S
#S=[x for x in S if x not in ('Gene','Name','Symbol')]
#net.T_node.drop(S, axis=1, inplace=True)
##############################
return self.cynet_from_network(net,
name=name,
s_layout=s_layout,
l_bundle=l_bundle)
def cynet_from_network(self,
net,
name=None,
s_layout="force-directed",
l_bundle=True):
"""Input net: xgmml.Network object
return CyNetwork"""
#print "====>>>>>>>>", net.T_node.header()
data = net.to_json()
if name is None:
name = data['data']['name']
#cynet=self.cy.create(suid=net)
cynet = None
for trial in range(
3): # something Cytoscape errors, try up to three times
try:
if cynet is None:
cynet = self.cy.network.create(name=name, data=data)
except:
cynet = None
print("Fail at trail %d" % (trial + 1))
print("JSON data>", data)
if cynet is None:
import sys
util.warn_msg('Error during plot_go_network(): %s' %
sys.exc_info()[0])
print(traceback.format_exc())
id = cynet.get_id()
if s_layout is not None:
#print "apply layout %s" % s_layout
self.cy.layout.apply(name=s_layout, network=cynet)
if l_bundle:
self.cy.edgebundling.apply(cynet)
#print "apply bundle %s" % s_layout
self.cy.layout.fit(cynet)
return cynet
def delete_cynet(self, cynet=None):
"""None means delete all networks"""
if cynet is None:
self.cy.network.delete_all()
else:
self.cy.network.delete(cynet)
def get_network(self, suid):
"""Get xgmml.Network with X,Y coordinates"""
cynet = self.cy.network.create(suid=suid)
net = xgmml.Network.from_json(cynet.to_json())
net.T_node.drop([
x for x in ['graphics_x', 'graphics_y', 'SUID', 'id_original']
if x in net.T_node.header()
],
axis=1,
inplace=True)
t_xy = self.cynet_get_XY(cynet)
if t_xy is not None:
t_xy.drop('Gene', axis=1, inplace=True)
t_xy.rename2({'x': 'graphics_x', 'y': 'graphics_y'})
net.T_node = net.T_node.merge(t_xy,
left_on='id',
right_on='id',
how='left')
return net
def get_cynet(self, cynet):
"""make sure we return a cynet object"""
if type(cynet) in (str, int):
return self.cy.network.create(suid=int(cynet))
return cynet
def cynet_get_XY(self, cynet):
cynet = self.get_cynet(cynet)
data = cynet.get_first_view()
if data is None: return None # view does not exist
nodes = data['elements']['nodes']
X = []
for node in nodes:
# id is an internal id, Gene is our key
X.append({
'id': str(node['data']['id']),
'x': node['position']['x'],
'y': node['position']['y'],
'Gene': node['data']['Gene']
})
t_xy = pd.DataFrame(X)
return t_xy
def cynet_save(self, cynet, s_file="x.png"):
def save_image(s_file, data):
f = open(s_file, 'wb')
f.write(data)
f.close()
cynet = self.get_cynet(cynet)
s_ext = s_file.upper()
if s_ext.endswith('.PNG'):
save_image(s_file, cynet.get_png())
elif s_ext.endswith('.PDF'):
save_image(s_file, cynet.get_pdf())
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
class CyRestClientTests(unittest.TestCase):
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def test_cyrest_client(self):
print('\n---------- Client status tests start -----------\n')
# Make sure CyREST server is running
status = self.client.status()
self.assertIsNotNone(status)
pp(status)
self.assertEqual('v1', status['apiVersion'])
print('\n---------- Client status tests finished! -----------\n')
def test_create_network(self):
print('\n---------- Create network Tests Start -----------\n')
# Create empty network
num_networks = 5
for i in range(num_networks):
self.client.network.create()
networks = self.client.network.get_all()
self.assertIsNotNone(networks)
self.assertEqual(num_networks, len(networks))
def test_create_from(self):
print('\n---------- Loading network tests start -----------\n')
# Create from URL
locations = [
'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif',
'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/'
+ 'webservices/current/search/interactor/brca2_human?format=xml25'
]
networks = self.client.network.create_from(locations)
print(networks)
self.assertIsNotNone(networks)
print('---------- Loading networks done! -----------\n')
def test_network_api(self):
print('\n---------- Network API Tests Start -----------\n')
# Create empty network
for i in range(5):
self.client.network.create()
networks = self.client.network.get_all(format='json')
self.assertIsNotNone(networks)
pp(networks)
def test_cynetwork(self):
print('\n---------- CyNetwork Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
self.assertIsNotNone(nd)
pp(nd)
edge = network.add_edge(nd['a'], nd['b'])
self.assertIsNotNone(edge)
print(edge)
new_edges = ((nd['a'], nd['b'], 'i1'), (nd['a'], nd['c'], 'i1'))
new_edges_result = network.add_edges(new_edges)
print(new_edges_result)
self.assertEqual(2, len(new_edges_result))
node_table = network.get_node_table()
print(node_table)
node_table = network.get_node_table(format='tsv')
print(node_table)
node_table = network.get_node_table(format='csv')
print(node_table)
edge_table = network.get_edge_table()
print(edge_table)
print('\n---------- CyNetwork Tests Finished! -----------\n')
def test_create_view(self):
print('\n---------- CyNetworkView Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
all_values = view1.get_values()
print(all_values)
def test_view_api(self):
print('\n---------- View API test start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
print(nd)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
self.assertEqual(0, view1.get_x())
view1.set_x(100)
self.assertEqual(100, view1.get_value('NODE_X_LOCATION'))
new_values = {}
for key in nd.keys():
suid = nd[key]
new_values[suid] = 'red'
view.update_node_views('NODE_FILL_COLOR', new_values)
new_values_name = {}
for node_name in new_nodes:
new_values_name[node_name] = 'pink'
print('---------- New Fill colors -----------')
print(new_values_name)
view.update_node_views('NODE_FILL_COLOR', new_values_name, key_type='name')
view.update_network_view('NETWORK_BACKGROUND_PAINT', 'red')
net_view = view.get_network_view_as_dict()
bg_paint = net_view['NETWORK_BACKGROUND_PAINT']
self.assertEqual('#FF0000', bg_paint)
def test_convert(self):
print('\n---------- DataFrame Conversion Tests Start -----------\n')
import os
import pandas as pd
# Clean up Cytoscape session
self.client.session.delete()
dir_name = os.path.dirname(os.path.realpath(__file__))
df = pd.read_csv(
dir_name + '/data/galFiltered.sif',
names=['source', 'interaction', 'target'], sep=' ')
print(df.head(3))
net = df_util.from_dataframe(df)
network = self.client.network.create(data=net, name='Created from DataFrame')
original_column_count = len(network.get_node_columns())
dir_name = os.path.dirname(os.path.realpath(__file__))
file_name = dir_name + '/data/galFiltered.nodeAttrTable.txt'
data_table = pd.read_csv(file_name, sep='\t')
network.update_node_table(df=data_table, data_key_col='ID')
table_column_count = len(data_table.columns)
total_column_count = len(network.get_node_columns())
self.assertEqual(total_column_count, (original_column_count+table_column_count-1))
print('\n---------- DataFrame Conversion Tests Finished! -----------\n')
def test_delete_network(self):
network = self.client.network.create()
suids = self.client.network.get_all()
self.assertEqual(1, len(suids))
self.client.network.delete(network)
suids = self.client.network.get_all()
self.assertEqual(0, len(suids))
def test_create_from_networkx(self):
networkx1 = nx.scale_free_graph(100)
network = self.client.network.create_from_networkx(networkx1)
self.assertIsNotNone(network)
def network(G, name, outfile):
#Connect with cytoscape
cy = CyRestClient()
# Reset
#cy.session.delete()
#To create the network in cytoscape
network = cy.network.create_from_networkx(G,
name=name,
collection=str(outfile))
#print('New network created with py2cytoscape. Its SUID is ' + str(network.get_id()))
#To get the SUID of all the components of the network
all_suid = cy.network.get_all()
net1 = cy.network.create(all_suid[0])
#print(net1.get_first_view())
#Styles
cy.layout.apply(name='hierarchical', network=network)
# Get all existing Visual Styles
styles = cy.style.get_all()
#print(json.dumps(styles, indent=4))
# Get a reference to the existing style
default_style = cy.style.create('default')
#print(default_style.get_name())
# Get all available Visual Properties
#print(len(cy.style.vps.get_all()))
node_vps = cy.style.vps.get_node_visual_props()
edge_vps = cy.style.vps.get_edge_visual_props()
network_vps = cy.style.vps.get_network_visual_props()
#print(pd.Series(edge_vps).head())
#print(pd.Series(node_vps).head())
# Create a new style
style1 = cy.style.create("My_style")
#print(style1.get_name())
new_defaults = {
# Node defaults
'NODE_FILL_COLOR': '#00ddee',
'NODE_SIZE': 20,
'NODE_BORDER_WIDTH': 0,
'NODE_LABEL_COLOR': 'black',
# Edge defaults
'EDGE_WIDTH': 3,
'EDGE_STROKE_UNSELECTED_PAINT': '#aaaaaa',
'EDGE_LINE_TYPE': 'LONG_DASH',
'EDGE_TARGET_ARROW_SHAPE': 'DELTA',
# Network defaults
'NETWORK_BACKGROUND_PAINT': 'white',
}
style1.update_defaults(new_defaults)
#Apply style
cy.style.apply(style1, network)
# Passthrough mapping to get node labels
style1.create_passthrough_mapping(column='name',
col_type='String',
vp='NODE_LABEL')
# Discrete mapping for node colours:
cat = {'reactant': '#4D833C', 'product': '#C04E5D'}
style1.create_discrete_mapping(column='category',
col_type='String',
vp='NODE_FILL_COLOR',
mappings=cat)
# Discrete mapping for node shape:
reac = {'reactions': 'RECTANGLE'}
style1.create_discrete_mapping(column='category',
col_type='String',
vp='NODE_SHAPE',
mappings=reac)
def identificationColor():
Dico = {}
DicoInverse = {}
# Charger Dico des nodes
file = open(
"D:\\Documents\\Centrale\\Ei2\PAPPL\\App\\graphe_0.2_MEF-hash.txt",
'r')
data = file.readlines()
file.close()
for i in data:
#print(i)
node = i.split(" : ")[0].split("\"")[1]
#print(node)
conversion = i.split(" : ")[1].split("\n")[0]
#print(conversion)
Dico[conversion] = node
DicoInverse[node] = conversion
# Charger le graphe
# convertir le graphe en graphe networkX
file = open(
"D:\\Documents\\Centrale\\Ei2\PAPPL\\App\\graphe-coloration-processed.txt",
'r')
data = file.readlines()
file.close()
#print(data)
G = nx.Graph()
# Pour chaque ligne :
for i in data:
# Identifier source & target : convertir
source = Dico[i.split("(")[1].split(",")[0]]
target = Dico[i.split(",")[1].split(")")[0]]
# Identifier le type de correlation : signe de l'arc
# cas positif
if (len(i.split("Positif")) == 2):
G.add_edge(source, target, edge_type=1)
# cas négatif
else:
G.add_edge(source, target, edge_type=-1)
listeTuples = []
listeNodes = []
#Identifier les noeuds hors graphe de corrélation : tuples simples ou non listés
for i in DicoInverse.keys():
if (i in G.nodes()):
listeNodes.append(i)
else:
listeTuples.append(i)
# Pour chaque noeud :
# Fonction recursive d'exploration : parametre : graphe, tuple actuel,
while (len(listeNodes) != 0):
for node in listeNodes:
#print(node)
nouveauTuple = node
listeNodes.remove(node)
# Appel fonction de recherche
nouveauTuple = rechercheTuple(G, node, nouveauTuple, listeNodes, 1)
listeTuples.append(nouveauTuple)
# Affichage des tuples
#for tuple in listeTuples:
# print(tuple)
# print(listeTuples)
tableTuple = []
for i in range(len(listeTuples)):
tuple = listeTuples[i]
tuple = tuple.split(",")
for node in tuple:
if (node.split(" ")[1] == '-'):
tableTuple.append([node.split(" ")[0], i, -1])
else:
tableTuple.append([node.split(" ")[0], i, 1])
# print(tableTuple)
cy = CyRestClient()
# net1 = cy.network.create_from("D:\\Documents\\Centrale\\Ei2\\PAPPL\\App\\graphe_0.2_MEF.sif")
# net1.create_node_column("composante", data_type='Integer',is_immutable=False)
# net1.create_node_column("signe",data_type='Integer',is_immutable=False)
# table=net1.get_node_table()
# nodeTable={}
# nodes=net1.get_nodes()
# for node in nodes:
# nodeTable[net1.get_node_value(node)['name']]=node
# for line in tableTuple:
# table.set_value(nodeTable[line[0]],"composante",line[1])
# table.set_value(nodeTable[line[0]],"signe",line[2])
# net1.update_node_table(table,network_key_col='name', data_key_col='name')
n = nbComposantes(tableTuple)
listeComposante = [[] for _ in range(n)]
for line in tableTuple:
listeComposante[line[1] - 1].append(line[0])
print(listeComposante)
file = open("D:\\Documents\\Centrale\\Ei2\\PAPPL\\App\\graphe_0.2_MEF.sif",
'r')
base = file.readlines()
file.close()
graphesComposantes = []
for compo in listeComposante:
current = []
for line in base:
lineSliced = line[:-1]
edge = lineSliced.split("\t")
if (edge[2] in compo and edge[2] in compo):
current.append(line)
graphesComposantes.append(current)
print(current)
directory = "D:\\Documents\\Centrale\\Ei2\\PAPPL\\App\\graph"
if not os.path.exists(directory):
os.makedirs(directory)
for i in range(len(graphesComposantes)):
strOpen = "D:\\Documents\\Centrale\\Ei2\\PAPPL\\App\\graph\\c" + str(
i + 1) + ".sif"
file = open(strOpen, 'w')
for line in graphesComposantes[i]:
file.write(line)
file.write("\n")
def main():
# -------------------------
# 1. キーワード文字列を取得
# -------------------------
keywords = __create_keywords_data()
# -------------------------
# 2. 共起単語行列を作成する
# -------------------------
Xc_norm, vocabulary, counter = __get_co_occurrence_matrix_from(keywords)
# -------------------------
# 3. networkx 描画データを作成
# -------------------------
# 3-1.初期ノードの追加
G = nx.from_scipy_sparse_matrix(
Xc_norm, parallel_edges=True, create_using=nx.DiGraph(), edge_attribute='weight')
# 3-2.nodeに、count にcount属性を設定
value_key_dict = {}
for key, value in vocabulary.items():
count = counter.get(key, 0)
nx.set_node_attributes(G, "score", {value: count})
value_key_dict.update({value: key})
# 3-3.エッジと、ノードの削除
# 同一ノードに引かれたエッジと、出現回数の少ないエッジを削除
for (u, v, d) in G.edges(data=True):
if u == v:
G.remove_edge(u, v)
if d["weight"] <= 0.0:
G.remove_edge(u, v)
# 出現回数の少ないノードを除去
for n, a in G.nodes(data=True):
if a["score"] <= 10:
G.remove_node(n)
# 3-4 ラベルの張り替え、from_scipy_sparse_matrix 設定時はラベルとして1,2,3 等の数値が設定されている
G = nx.relabel_nodes(G, value_key_dict)
# ------------------------------------------------------
# 4 描画のために調整と、HTMLへのExport
# ------------------------------------
# Cytoscape に送信して、描画する
# http://localhost:1234/v1/apply/layouts でレイアウトアルゴリズムのリストを取得できる
from py2cytoscape.data.cyrest_client import CyRestClient
cy = CyRestClient(ip='127.0.0.1', port=1234)
for layout_algorithm in ["attribute-circle", "stacked-node-layout", "degree-circle", "circular", "attributes-layout", "kamada-kawai", "force-directed", "cose", "grid", "hierarchical", "fruchterman-rheingold", "isom", "force-directed-cl"]:
print("plot start layout_algorithm [" + layout_algorithm + "]...")
g_cy = cy.network.create_from_networkx(G)
cy.layout.apply(name=layout_algorithm, network=g_cy)
directed = cy.style.create('Curved')
cy.style.apply(directed, network=g_cy)
# エッジを束ねて見やすくする
cy.edgebundling.apply(g_cy)
view = g_cy.get_first_view()
import exporter as exporter
exporter.exportHTML(
view, "html/" + layout_algorithm + "_export.html", 'custermizedCurved', background='radial-gradient(#898989 15%, #DDDDDD 105%)')
print("plot end")
"""
THis would be the way to go without py2cytoscape
# Standard JSON library
import json
# Basic Setup
PORT_NUMBER = 8080
BASE = 'http://localhost:' + str(PORT_NUMBER) + '/v1/'
# Header for posting data to the server as JSON
HEADERS = {'Content-Type': 'application/json'}
# Define dictionary of empty network
empty_network = {
'data': {
'name': 'I\'m empty!'
},
'elements': {
'nodes':[],
'edges':[]
}
}
res = requests.post(BASE + 'networks?collection=My%20Collection', data=json.dumps(empty_network), headers=HEADERS)
new_network_id = res.json()['networkSUID']
print('Empty network created: SUID = ' + str(new_network_id))
"""
cy = CyRestClient()
def plot_cool_network(nx_graph):
network = cy.network.create_from_networkx(
nx_graph, collection='Generated by NetworkX')
print(network.get_id())
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def __init__(self, host="localhost", port="1234", version="v1"):
self.cy = CyRestClient(ip=host, port=port, version=version)
g = Graph.Read_Adjacency('r_data_science_ch2_fig2.1.txt')
g.get_adjacency()
type(g.get_adjacency())
g.get_adjacency()._get_data()
type(g.get_adjacency()._get_data())
type(g.get_adjacency().data)
g.get_adjacency().data
g.get_adjacency()._hash_()
g.get_adjacency().__hash__()
g.get_adjacency().__hash__(h)
g.get_adjacency().__hash__(g)
g.get_adjacency().shape
pip install py2cytoscape
import json
from py2cytoscape.data.cyrest_client import CyRestClient
cy = CyRestClient()
print(json.dumps(cy.status(), indent=4))
from igraph import *
g = Graph.Read_Adjacency('r_data_science_ch2_fig2.1.txt')
cy.network.create_from_igraph(g)
help(Graph.Read_GML)
from lesmis import *
loadGraphFromGml()
g
from lesmis import LesMis as lm
lm._g
from lesmis import LesMis as lm
lm.getGraph()
from lesmis import LesMis as lm
from lesmis import LesMis
lm = LesMis()
def get_client():
"""Initialises connection with Cytoscape and returns client."""
return CyRestClient()
def cytoscape_successful(self, update):
cytoscape_successful = True
# Create client
cy = CyRestClient()
# Clear current session
cy.session.delete()
# Convert DataFrame to json file and save file
self.dataframe_to_json()
# Create network from json file
node_edge_network = cy.network.create_from(self.json_file_path)
cy.layout.apply(network=node_edge_network)
# Add styles to the network
my_style = cy.style.create('my_style')
# Discrete mappings for specific regions
order_colour_key_value_pair = {
'1': '#c99e10',
'2': '#9b4f0f',
'3': '#1e434c',
'4': '#8d230f'
}
edge_order_colour_key_value_pair = {
'2': '#9b4f0f',
'3': '#1e434c',
'4': '#8d230f'
}
edge_order_size_key_value_pair = {'2': '5.0', '3': '3.0', '4': '1.0'}
order_size_key_value_pair = {
'1': '25.0',
'2': '35.0',
'3': '40.0',
'4': '50.0'
}
order_shape_key_value_pair = {
'1': 'Ellipse',
'2': 'Diamond',
'3': 'Triangle',
'4': 'Hexagon'
}
# If the GUI is being loaded for the first time
# Then create network with 'default' styles
if not update:
new_styles = {
'NODE_FILL_COLOR': '#363636',
'NODE_SIZE': 10,
'NODE_BORDER_WIDTH': 0,
'NODE_TRANSPARENCY': 255,
'NODE_LABEL_COLOR': '#323334',
'EDGE_WIDTH': 3,
'EDGE_STROKE_UNSELECTED_PAINT': '#a9a9a9',
'EDGE_LINE_TYPE': 'SOLID',
'EDGE_TRANSPARENCY': 120,
'NETWORK_BACKGROUND_PAINT': 'white'
}
my_style.update_defaults(new_styles)
# Add these styles only if the network type is Interaction
if self.interaction_or_edge == 1:
my_style.create_discrete_mapping(
column='order',
col_type='String',
vp='NODE_FILL_COLOR',
mappings=order_colour_key_value_pair)
my_style.create_discrete_mapping(
column='order',
col_type='String',
vp='NODE_SIZE',
mappings=order_size_key_value_pair)
my_style.create_discrete_mapping(
column='order',
col_type='String',
vp='NODE_SHAPE',
mappings=order_shape_key_value_pair)
my_style.create_discrete_mapping(
column='order',
col_type='String',
vp='EDGE_STROKE_UNSELECTED_PAINT',
mappings=edge_order_colour_key_value_pair)
my_style.create_discrete_mapping(
column='order',
col_type='String',
vp='EDGE_WIDTH',
mappings=edge_order_size_key_value_pair)
# TODO write the code for other styles
# TODO If need to update then read the csv file with styles and tweak it as necessary
else:
print('No styles specified')
cy.style.apply(my_style, node_edge_network)
cy.layout.fit(network=node_edge_network)
Image(node_edge_network.get_png(height=400))
return cytoscape_successful
class CyRestClientTests(unittest.TestCase):
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def test_cyrest_client(self):
print('\n---------- Client status tests start -----------\n')
# Make sure CyREST server is running
status = self.client.status()
self.assertIsNotNone(status)
pp(status)
self.assertEqual('v1', status['apiVersion'])
print('\n---------- Client status tests finished! -----------\n')
def test_create_network(self):
print('\n---------- Create network Tests Start -----------\n')
# Create empty network
num_networks = 5
for i in range(num_networks):
self.client.network.create()
networks = self.client.network.get_all()
self.assertIsNotNone(networks)
self.assertEqual(num_networks, len(networks))
def test_create_from(self):
print('\n---------- Loading network tests start -----------\n')
# Create from URL
locations = [
'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif',
'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/'
+ 'webservices/current/search/interactor/brca2_human?format=xml25'
]
networks = self.client.network.create_from(locations)
print(networks)
self.assertIsNotNone(networks)
print('---------- Loading networks done! -----------\n')
def test_network_api(self):
print('\n---------- Network API Tests Start -----------\n')
# Create empty network
for i in range(5):
self.client.network.create()
networks = self.client.network.get_all(format='json')
self.assertIsNotNone(networks)
pp(networks)
def test_cynetwork(self):
print('\n---------- CyNetwork Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
self.assertIsNotNone(nd)
pp(nd)
edge = network.add_edge(nd['a'], nd['b'])
self.assertIsNotNone(edge)
pp(edge)
new_edges = ((nd['a'], nd['b'], 'i1'), (nd['a'], nd['c'], 'i1'))
new_edges_result = network.add_edges(new_edges)
print(new_edges_result)
self.assertEqual(2, len(new_edges_result))
node_table = network.get_node_table()
print(node_table)
node_table = network.get_node_table(format='tsv')
print(node_table)
node_table = network.get_node_table(format='csv')
print(node_table)
edge_table = network.get_edge_table()
print(edge_table)
print('\n---------- CyNetwork Tests Finished! -----------\n')
def test_convert(self):
print('\n---------- DataFrame Conversion Tests Start -----------\n')
import os
import pandas as pd
# Clean up Cytoscape session
self.client.session.delete()
dir_name = os.path.dirname(os.path.realpath(__file__))
df = pd.read_csv(
dir_name + '/data/galFiltered.sif',
names=['source', 'interaction', 'target'], sep=' ')
print(df.head(3))
net = df_util.from_dataframe(df)
network = self.client.network.create(data=net, name='Created from DataFrame')
original_column_count = len(network.get_node_columns())
dir_name = os.path.dirname(os.path.realpath(__file__))
file_name = dir_name + '/data/galFiltered.nodeAttrTable.txt'
data_table = pd.read_csv(file_name, sep='\t')
network.update_node_table(df=data_table, data_key_col='ID')
table_column_count = len(data_table.columns)
total_column_count = len(network.get_node_columns())
self.assertEqual(total_column_count, (original_column_count+table_column_count-1))
print('\n---------- DataFrame Conversion Tests Finished! -----------\n')
def test_delete_network(self):
network = self.client.network.create()
suids = self.client.network.get_all()
self.assertEqual(1, len(suids))
self.client.network.delete(network)
suids = self.client.network.get_all()
self.assertEqual(0, len(suids))
def test_create_from_networkx(self):
networkx1 = nx.scale_free_graph(100)
network = self.client.network.create_from_networkx(networkx1)
self.assertIsNotNone(network)
class CyRestClientTests(unittest.TestCase):
def setUp(self):
self.client = CyRestClient()
# cleanup
self.client.network.delete_all()
def test_cyrest_client(self):
print('\n---------- Client status tests start -----------\n')
# Make sure CyREST server is running
status = self.client.status()
self.assertIsNotNone(status)
pp(status)
self.assertEqual('v1', status['apiVersion'])
print('\n---------- Client status tests finished! -----------\n')
def test_create_network(self):
print('\n---------- Create network Tests Start -----------\n')
# Create empty network
num_networks = 5
for i in range(num_networks):
self.client.network.create()
networks = self.client.network.get_all()
self.assertIsNotNone(networks)
self.assertEqual(num_networks, len(networks))
def test_create_from(self):
print('\n---------- Loading network tests start -----------\n')
# Create from URL
locations = [
'http://chianti.ucsd.edu/cytoscape-data/galFiltered.sif',
'http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/' +
'webservices/current/search/interactor/brca2_human?format=xml25'
]
networks = self.client.network.create_from(locations)
print(networks)
self.assertIsNotNone(networks)
print('---------- Loading networks done! -----------\n')
def test_network_api(self):
print('\n---------- Network API Tests Start -----------\n')
# Create empty network
for i in range(5):
self.client.network.create()
networks = self.client.network.get_all(format='json')
self.assertIsNotNone(networks)
pp(networks)
def test_cynetwork(self):
print('\n---------- CyNetwork Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
self.assertIsNotNone(nd)
pp(nd)
edge = network.add_edge(nd['a'], nd['b'])
self.assertIsNotNone(edge)
pp(edge)
new_edges = ((nd['a'], nd['b'], 'i1'), (nd['a'], nd['c'], 'i1'))
new_edges_result = network.add_edges(new_edges)
print(new_edges_result)
self.assertEqual(2, len(new_edges_result))
node_table = network.get_node_table()
print(node_table)
node_table = network.get_node_table(format='tsv')
print(node_table)
node_table = network.get_node_table(format='csv')
print(node_table)
edge_table = network.get_edge_table()
print(edge_table)
print('\n---------- CyNetwork Tests Finished! -----------\n')
def test_create_view(self):
print('\n---------- CyNetworkView Tests Start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
all_values = view1.get_values()
print(all_values)
def test_view_api(self):
print('\n---------- View API test start -----------\n')
network = self.client.network.create()
self.assertIsNotNone(network)
nodes = network.get_nodes()
pp(nodes)
new_nodes = ['a', 'b', 'c']
nd = network.add_nodes(new_nodes)
print(nd)
views = network.get_views()
print('Views: ')
print(views)
view_id = views[0]
view = network.get_view(view_id, format='view')
self.assertIsNotNone(view)
self.assertEqual(view_id, view.get_id())
node_views = view.get_node_views()
self.assertIsNotNone(node_views)
self.assertEqual(3, len(node_views))
view1 = node_views[0]
self.assertIsNotNone(view1)
self.assertEqual(0, view1.get_x())
view1.set_x(100)
self.assertEqual(100, view1.get_value('NODE_X_LOCATION'))
new_values = {}
for key in nd.keys():
suid = nd[key]
new_values[suid] = 'red'
view.update_node_views('NODE_FILL_COLOR', new_values)
new_values_name = {}
for node_name in new_nodes:
new_values_name[node_name] = 'pink'
view.update_node_views('NODE_FILL_COLOR',
new_values_name,
key_type='name')
view.update_network_view('NETWORK_BACKGROUND_PAINT', 'red')
net_view = view.get_network_view_as_dict()
bg_paint = net_view['NETWORK_BACKGROUND_PAINT']
self.assertEqual('#FF0000', bg_paint)
def test_convert(self):
print('\n---------- DataFrame Conversion Tests Start -----------\n')
import os
import pandas as pd
# Clean up Cytoscape session
self.client.session.delete()
dir_name = os.path.dirname(os.path.realpath(__file__))
df = pd.read_csv(dir_name + '/data/galFiltered.sif',
names=['source', 'interaction', 'target'],
sep=' ')
print(df.head(3))
net = df_util.from_dataframe(df)
network = self.client.network.create(data=net,
name='Created from DataFrame')
original_column_count = len(network.get_node_columns())
dir_name = os.path.dirname(os.path.realpath(__file__))
file_name = dir_name + '/data/galFiltered.nodeAttrTable.txt'
data_table = pd.read_csv(file_name, sep='\t')
network.update_node_table(df=data_table, data_key_col='ID')
table_column_count = len(data_table.columns)
total_column_count = len(network.get_node_columns())
self.assertEqual(total_column_count,
(original_column_count + table_column_count - 1))
print(
'\n---------- DataFrame Conversion Tests Finished! -----------\n')
def test_delete_network(self):
network = self.client.network.create()
suids = self.client.network.get_all()
self.assertEqual(1, len(suids))
self.client.network.delete(network)
suids = self.client.network.get_all()
self.assertEqual(0, len(suids))
def test_create_from_networkx(self):
networkx1 = nx.scale_free_graph(100)
network = self.client.network.create_from_networkx(networkx1)
self.assertIsNotNone(network)
