def get_dot(G_orig):
"""Change labels and colors to be presented with graphviz"""
G = G_orig.copy()
cluster_networks.relabel_graph(G)
tr = {}
for node in G.nodes_iter():
tr[node] = '"{}"'.format(node)
nx.relabel_nodes(G, tr, copy=False)
for node in G.nodes_iter():
label = str(node)
if len(label) > MAX_LABEL:
label = u'{}..."'.format(label[:MAX_LABEL])
G.node[node]['label'] = label
for node in cluster_networks.get_leaf_nodes(G):
G.node[node]['color'] = "blue"
for node in cluster_networks.hybrid_nodes(G):
G.node[node]['color'] = "#7BFF74" # light green
G.node[node]['style'] = 'filled'
for node in cluster_networks.get_root_nodes(G):
G.node[node]['color'] = "orange"
for node in cluster_networks.problematic_treechild_nodes(G):
G.node[node]['color'] = "#FF77EB" # light pink
G.node[node]['style'] = 'filled'
for u, v in cluster_networks.removable_edges(G):
G.edge[u][v]['color'] = "red"
for root in cluster_networks.get_root_nodes(G):
G.node[root]['label'] = '"R"'
dot = nx.to_pydot(G).to_string()
return dot.strip()
G = network
return {
'cluster': cluster,
'network_dot': get_dot(G),
'network_ascii': network.nodes(),
'network_hard': hard,
'subtrees': subtrees,
'queue_key': q.key,
'soft_job_id': soft_job_id,
'soft_too_expensive': 1 if soft_too_expensive else 0,
'families_job_id': families_job_id,
'is_treechild': cluster_networks.is_treechild(G),
'number_nodes': len(G.nodes()),
'number_edges': len(G.edges()),
'number_hybrids': len(cluster_networks.hybrid_nodes(G)),
'number_leafs': len(cluster_networks.get_leaf_nodes(G)),
'number_conflictive_nodes': len(cluster_networks.problematic_treechild_nodes(G)),
'number_removable_edges': len(cluster_networks.removable_edges(G)),
'hybridization_degree': cluster_networks.hybridization_degree(G),
}
###
# Inputs
@post("/input/upload/")
def process_from_upload():
file_content = request.forms.optionsRadios
data = request.files.data
if file_content and data and data.file:
raw = data.file.read() # This is dangerous for big files
if file_content == 'cluster':
return process_clusters(raw)