def postToGS(alignededges, overlaps, leftcoords, graphid):
"""Post graph to graphspace
"""
import graphspace_interface as interface
maxleftcoord = max([leftcoords[c] for c in leftcoords])
minleftcoord = min([leftcoords[c] for c in leftcoords])
for c in leftcoords:
leftcoords[c] = int(float(leftcoords[c]-minleftcoord)\
/ float(maxleftcoord-minleftcoord)*255)
user = '******'
password = '******'
group = 'SVLocalAssembly'
outfile = graphid + '.json'
#Graph 1 (tmp): read edges in from a file.
#Take the first two columns of the file as the edges.
#Make a directed graph NetworkX object.
#A directed graph will work even if we
#want to show an undirected graph, since
#each edge has a "directed" attribute that
#determines whether the edge is drawn with an
#arrow or not.
graph = nx.DiGraph(alignededges, directed=False)
for n in graph.nodes():
label = '%s' % (n)
interface.add_node_label(graph, n, label)
interface.add_node_wrap(graph, n, 'wrap')
interface.add_node_color(
graph, n, rgb_to_hex((0, leftcoords[n], 255 - leftcoords[n])))
interface.add_node_shape(graph, n, 'ellipse')
interface.add_node_height(graph, n, None, label)
interface.add_node_width(graph, n, None, label)
trueedges = [[u, v] for u, v, t in overlaps]
for t, h in graph.edges():
interface.add_edge_directionality(graph, t, h, False)
if [t, h] in trueedges or [h, t] in trueedges:
# true edges are blue
#print 'Blue'
interface.add_edge_color(graph, t, h, '#6666FF')
else:
# false edges are black
interface.add_edge_color(graph, t, h, '#000000')
interface.add_edge_width(graph, t, h, 2)
metadata = {'description': 'example1', 'title': graphid, 'tags': []}
print(graph, graphid, outfile, user, password, metadata)
interface.postGraph(graph, graphid, outfile=outfile, user=user,\
password=password, metadata=metadata)
if group != None:
interface.shareGraph(graphid,
user=user,
password=password,
group=group)
return
def postToGS(alignededges, overlaps, leftcoords, graphid):
"""Post graph to graphspace
"""
import graphspace_interface as interface
maxleftcoord = max([leftcoords[c] for c in leftcoords])
minleftcoord = min([leftcoords[c] for c in leftcoords])
for c in leftcoords:
leftcoords[c] = int(float(leftcoords[c]-minleftcoord)\
/ float(maxleftcoord-minleftcoord)*255)
user = '******'
password = '******'
group = 'SVLocalAssembly'
outfile = graphid+'.json'
#Graph 1 (tmp): read edges in from a file.
#Take the first two columns of the file as the edges.
#Make a directed graph NetworkX object.
#A directed graph will work even if we
#want to show an undirected graph, since
#each edge has a "directed" attribute that
#determines whether the edge is drawn with an
#arrow or not.
graph = nx.DiGraph(alignededges, directed=False)
for n in graph.nodes():
label = '%s' % (n)
interface.add_node_label(graph, n, label)
interface.add_node_wrap(graph, n, 'wrap')
interface.add_node_color(graph, n, rgb_to_hex((0, leftcoords[n], 255-leftcoords[n])))
interface.add_node_shape(graph, n, 'ellipse')
interface.add_node_height(graph, n, None, label)
interface.add_node_width(graph, n, None, label)
trueedges = [[u, v] for u, v, t in overlaps]
for t, h in graph.edges():
interface.add_edge_directionality(graph, t, h, False)
if [t, h] in trueedges or [h, t] in trueedges:
# true edges are blue
#print 'Blue'
interface.add_edge_color(graph, t, h, '#6666FF')
else:
# false edges are black
interface.add_edge_color(graph, t, h, '#000000')
interface.add_edge_width(graph, t, h, 2)
metadata = {'description': 'example1', 'title': graphid, 'tags': []}
print(graph, graphid, outfile, user, password, metadata)
interface.postGraph(graph, graphid, outfile=outfile, user=user,\
password=password, metadata=metadata)
if group != None:
interface.shareGraph(graphid, user=user, password=password, group=group)
return
def runExample1(edgefile,user,password,group,graphid,outfile):
#Graph 1 (tmp): read edges in from a file.
#Take the first two columns of the file as the edges.
edges = []
with open(edgefile) as fin:
for line in fin:
if line[0] == '#': # skip comments
continue
row = line.strip().split()
edges.append((row[0],row[1]))
#Make a directed graph NetworkX object.
#A directed graph will work even if we
#want to show an undirected graph, since
#each edge has a "directed" attribute that
#determines whether the edge is drawn with an
#arrow or not.
G = nx.DiGraph(edges,directed=True)
for n in G.nodes():
label= 'node\n%s' % (n)
interface.add_node_label(G,n,label)
interface.add_node_wrap(G,n,'wrap')
interface.add_node_color(G,n,'#ACFA58')
interface.add_node_shape(G,n,'rectangle')
interface.add_node_height(G,n,None,label)
interface.add_node_width(G,n,None,label)
for t,h in G.edges():
interface.add_edge_directionality(G,t,h,True)
interface.add_edge_color(G,t,h,'#000000')
interface.add_edge_width(G,t,h,2)
metadata = {'description':'example1','title':'Example 1 Graph','tags':[]}
print G,graphid,outfile,user,password,metadata
interface.postGraph(G,graphid,outfile=outfile,user=user,password=password,metadata=metadata)
if group != None:
interface.shareGraph(graphid,user=user,password=password,group=group)
return
#arrow or not.
G = nx.DiGraph(edges,directed=True)
for n in G.nodes():
label= 'node\n%s' % (n)
interface.add_node_label(G,n,label)
interface.add_node_wrap(G,n,'wrap')
interface.add_node_color(G,n,'#ACFA58')
interface.add_node_shape(G,n,'rectangle')
interface.add_node_height(G,n,None,label)
interface.add_node_width(G,n,None,label)
for t,h in G.edges():
interface.add_edge_directionality(G,t,h,True)
interface.add_edge_color(G,t,h,'#000000')
interface.add_edge_width(G,t,h,2)
#Divit's Note: We should have a JSON validator at this step
#Divit: We should. I want to talk to Murali about possibly enhancing the validator.
interface.postGraph(G,graphid,outfile=outfile,user=user,password=password)
if group != None:
interface.shareGraph(graphid,user=user,password=password,group=group)
#############
## Graph 2 (tmp2): randomly generate nodes and edges.
graphid = 'gs-interface-example2'
outfile = 'gs-interface-example2.json'
G = nx.DiGraph(directed=True)
# add 10 nodes
#arrow or not.
G = nx.DiGraph(edges, directed=True)
for n in G.nodes():
label = 'node\n%s' % (n)
interface.add_node_label(G, n, label)
interface.add_node_wrap(G, n, 'wrap')
interface.add_node_color(G, n, '#ACFA58')
interface.add_node_shape(G, n, 'rectangle')
interface.add_node_height(G, n, None, label)
interface.add_node_width(G, n, None, label)
for t, h in G.edges():
interface.add_edge_directionality(G, t, h, True)
interface.add_edge_color(G, t, h, '#000000')
interface.add_edge_width(G, t, h, 2)
#Divit's Note: We should have a JSON validator at this step
#Divit: We should. I want to talk to Murali about possibly enhancing the validator.
interface.postGraph(G, graphid, outfile=outfile, user=user, password=password)
if group != None:
interface.shareGraph(graphid, user=user, password=password, group=group)
#############
## Graph 2 (tmp2): randomly generate nodes and edges.
graphid = 'gs-interface-example2'
outfile = 'gs-interface-example2.json'
G = nx.DiGraph(directed=True)
# add 10 nodes