def __init__(self,
cx=None,
server=None,
username=None,
password=None,
uuid=None,
data=None,
**attr):
'''There are generally four ways to create a graph.
1. An empty graph. G = NdexGraph()
2. Using a cx dictionary. G = NdexGraph(cx)
3. Loading it from an NDEx server.
G = NdexGraph(server='http://test.ndexbio.org' uuid='983a2b93-2c55-11e6-a7c5-0630eb0972a1')
4. Just like any other NetworkX MultiDiGraph().
'''
MultiDiGraph.__init__(self, data, **attr)
self.subnetwork_id = None
self.view_id = None
self.max_node_id = None
self.max_edge_id = None
self.pos = {}
self.unknown_cx = []
# Maps edge ids to node ids. e.g. { edge1: (source_node, target_node), edge2: (source_node, target_node) }
self.edgemap = {}
if not cx and server and uuid:
ndex = nc.Ndex(server, username, password)
cx = ndex.get_network_as_cx_stream(uuid).json()
if not cx:
raise RuntimeError("Failed to retrieve network with uuid " +
uuid + " from " + server)
# If there is no CX to process, just return.
if cx == None:
return
# First pass, get information about subnetworks.
for aspect in cx:
if 'subNetworks' in aspect:
for subnetwork in aspect['subNetworks']:
id = subnetwork['@id']
if self.subnetwork_id != None:
raise ValueError(
"networkn does not support collections!")
self.subnetwork_id = id
elif 'cyViews' in aspect:
for cyViews in aspect['cyViews']:
id = cyViews['@id']
if self.view_id != None:
raise ValueError(
"networkn does not support more than one view!")
self.view_id = id
elif 'metaData' in aspect:
# Strip metaData
continue
else:
self.unknown_cx.append(aspect)
cx = self.unknown_cx
# Second pass, just build basic graph.
self.unknown_cx = []
for aspect in cx:
if 'nodes' in aspect:
for node in aspect['nodes']:
id = node['@id']
name = node['n'] if 'n' in node else None
if name:
self.add_node(id, name=name)
else:
self.add_node(id)
represents = node['r'] if 'r' in node else None
if represents:
self.node[id]['represents'] = represents
elif 'edges' in aspect:
for edge in aspect['edges']:
id = edge['@id']
interaction = edge['i'] if 'i' in edge else None
s = edge['s']
t = edge['t']
self.edgemap[id] = (s, t)
if interaction:
self.add_edge(s, t, key=id, interaction=interaction)
else:
self.add_edge(s, t, key=id)
else:
self.unknown_cx.append(aspect)
cx = self.unknown_cx
# Third pass, handle attributes
# Notes. Not handled, datatypes.
self.unknown_cx = []
for aspect in cx:
if 'networkAttributes' in aspect:
for networkAttribute in aspect['networkAttributes']:
name = networkAttribute['n']
# special: ignore selected
if name == 'selected':
continue
value = networkAttribute['v']
if 'd' in networkAttribute:
d = networkAttribute['d']
if d == 'boolean':
value = value.lower() == 'true'
if 's' in networkAttribute or name not in self.graph:
self.graph[name] = value
elif 'nodeAttributes' in aspect:
for nodeAttribute in aspect['nodeAttributes']:
id = nodeAttribute['po']
name = nodeAttribute['n']
# special: ignore selected
if name == 'selected':
continue
value = nodeAttribute['v']
if 'd' in nodeAttribute:
d = nodeAttribute['d']
if d == 'boolean':
value = value.lower() == 'true'
if 's' in nodeAttribute or name not in self.node[id]:
self.node[id][name] = value
elif 'edgeAttributes' in aspect:
for edgeAttribute in aspect['edgeAttributes']:
id = edgeAttribute['po']
s, t = self.edgemap[id]
name = edgeAttribute['n']
# special: ignore selected and shared_name columns
if name == 'selected' or name == 'shared name':
continue
value = edgeAttribute['v']
if 'd' in edgeAttribute:
d = edgeAttribute['d']
if d == 'boolean':
value = value.lower() == 'true'
if 's' in edgeAttribute or name not in self[s][t][id]:
self[s][t][id][name] = value
else:
self.unknown_cx.append(aspect)
cx = self.unknown_cx
# Fourth pass, node locations
self.pos = {}
self.unknown_cx = []
for aspect in cx:
if 'cartesianLayout' in aspect:
for nodeLayout in aspect['cartesianLayout']:
id = nodeLayout['node']
x = nodeLayout['x']
y = nodeLayout['y']
self.pos[id] = np.array([x, y], dtype='float32')
else:
self.unknown_cx.append(aspect)
def __init__(self, cx=None, server=None, username=None, password=None, uuid=None, data=None, **attr):
'''There are generally four ways to create a graph.
1. An empty graph. G = NdexGraph()
2. Using a cx dictionary. G = NdexGraph(cx)
3. Loading it from an NDEx server.
G = NdexGraph(server='http://test.ndexbio.org' uuid='983a2b93-2c55-11e6-a7c5-0630eb0972a1')
4. Just like any other NetworkX MultiDiGraph().
'''
MultiDiGraph.__init__(self, data, **attr)
self.subnetwork_id = None
self.view_id = None
self.max_node_id = None
self.max_edge_id = None
self.pos = {}
self.unknown_cx = []
# Maps edge ids to node ids. e.g. { edge1: (source_node, target_node), edge2: (source_node, target_node) }
self.edgemap = {}
if not cx and server and uuid:
ndex = nc.Ndex(server,username,password)
cx = ndex.get_network_as_cx_stream(uuid).json()
if not cx:
raise RuntimeError("Failed to retrieve network with uuid " + uuid + " from " + server)
# If there is no CX to process, just return.
if cx == None:
return
# First pass, get information about subnetworks.
for aspect in cx:
if 'subNetworks' in aspect:
for subnetwork in aspect['subNetworks']:
id = subnetwork['@id']
if self.subnetwork_id != None:
raise ValueError("networkn does not support collections!")
self.subnetwork_id = id
elif 'cyViews' in aspect:
for cyViews in aspect['cyViews']:
id = cyViews['@id']
if self.view_id != None:
raise ValueError("networkn does not support more than one view!")
self.view_id = id
elif 'metaData' in aspect:
# Strip metaData
continue
else:
self.unknown_cx.append(aspect)
cx = self.unknown_cx
# Second pass, just build basic graph.
self.unknown_cx = []
for aspect in cx:
if 'nodes' in aspect:
for node in aspect['nodes']:
id = node['@id']
name = node['n'] if 'n' in node else None
if name:
self.add_node(id, name=name)
else:
self.add_node(id)
represents = node['r'] if 'r' in node else None
if represents:
self.node[id]['represents'] = represents
elif 'edges' in aspect:
for edge in aspect['edges']:
id = edge['@id']
interaction = edge['i'] if 'i' in edge else None
s = edge['s']
t = edge['t']
self.edgemap[id] = (s, t)
if interaction:
self.add_edge(s, t, key=id, interaction=interaction)
else:
self.add_edge(s, t, key=id)
else:
self.unknown_cx.append(aspect)
cx = self.unknown_cx
# Third pass, handle attributes
# Notes. Not handled, datatypes.
self.unknown_cx = []
for aspect in cx:
if 'networkAttributes' in aspect:
for networkAttribute in aspect['networkAttributes']:
name = networkAttribute['n']
# special: ignore selected
if name == 'selected':
continue
value = networkAttribute['v']
if 'd' in networkAttribute:
d = networkAttribute['d']
if d == 'boolean':
value = value.lower() == 'true'
if 's' in networkAttribute or name not in self.graph:
self.graph[name] = value
elif 'nodeAttributes' in aspect:
for nodeAttribute in aspect['nodeAttributes']:
id = nodeAttribute['po']
name = nodeAttribute['n']
# special: ignore selected
if name == 'selected':
continue
value = nodeAttribute['v']
if 'd' in nodeAttribute:
d = nodeAttribute['d']
if d == 'boolean':
value = value.lower() == 'true'
if 's' in nodeAttribute or name not in self.node[id]:
self.node[id][name] = value
elif 'edgeAttributes' in aspect:
for edgeAttribute in aspect['edgeAttributes']:
id = edgeAttribute['po']
s, t = self.edgemap[id]
name = edgeAttribute['n']
# special: ignore selected and shared_name columns
if name == 'selected' or name == 'shared name':
continue
value = edgeAttribute['v']
if 'd' in edgeAttribute:
d = edgeAttribute['d']
if d == 'boolean':
value = value.lower() == 'true'
if 's' in edgeAttribute or name not in self[s][t][id]:
self[s][t][id][name] = value
else:
self.unknown_cx.append(aspect)
cx = self.unknown_cx
# Fourth pass, node locations
self.pos = {}
self.unknown_cx = []
for aspect in cx:
if 'cartesianLayout' in aspect:
for nodeLayout in aspect['cartesianLayout']:
id = nodeLayout['node']
x = nodeLayout['x']
y = nodeLayout['y']
self.pos[id] = np.array([x,y], dtype='float32')
else:
self.unknown_cx.append(aspect)
