# n = batch.create(node)
nodes.add(compound_id)
if compound.id not in compoundDict:
compoundDict[compound.id] = compound_id
currentNodes.add(compound_id)
importer.done_nodes()
for reaction in pathway.reactions:
if reaction.name in reactionToNode:
gene_ids = reactionToNode[reaction.name]
for gene_id in gene_ids:
for substrate in reaction.substrates:
substrate_id = substrate.name[4:]
if substrate_id in nodes:
importer.add_edge('Edge', substrate_id, gene_id, {'_isNetworkEdge': True})
currentEdges[substrate_id + '_' + gene_id] = {'source': substrate_id, 'target': gene_id}
# create_pathway_edge(edgeDict, substrateNode, node)
if reaction.type == 'reversible':
importer.add_edge('Edge', gene_id, substrate_id, {'_isNetworkEdge': True})
currentEdges[gene_id + '_' + substrate_id] = {'source': gene_id, 'target': substrate_id}
# create_pathway_edge(edgeDict, node, substrateNode)
for product in reaction.products:
product_id = product.name[4:]
if product_id in nodes:
importer.add_edge('Edge', gene_id, product_id, {'_isNetworkEdge': True})
currentEdges[gene_id + '_' + product_id] = {'source': gene_id, 'target': product_id}
# create_pathway_edge(edgeDict, node, productNode)
if node["Label"] in set_ids:
setId = set_ids[node["Label"]]
else:
current_set_id += 1
setId = str(current_set_id)
set_ids[node["Label"]] = setId
importer.add_node(['_Network_Node', 'Structure'],
str(node["StructureID"]), {
'name': str(node["StructureID"]),
'labels': [setId]
})
importer.add_node(['_Set_Node', 'Label'], setId,
{'name': str(node["Label"])})
importer.add_edge('ConsistsOf', setId, str(node["StructureID"]),
{}, 'Label')
else:
importer.add_node(['_Network_Node', 'Structure'],
str(node["StructureID"]), {
'name': str(node["StructureID"]),
'labels': []
})
edges = doc["edges"]
for edge in edges:
importer.add_edge('Edge', str(edge["SourceStructureID"]),
str(edge["TargetStructureID"]), {
'_isNetworkEdge': True,
'Type': edge["Type"],
'Label': edge["Label"]
for node in nodes:
if node["Label"] is not None:
if node["Label"] in set_ids:
setId = set_ids[node["Label"]]
else:
current_set_id += 1
setId = str(current_set_id)
set_ids[node["Label"]] = setId
importer.add_node(['_Network_Node', 'Structure'], str(node["StructureID"]),
{'name': str(node["StructureID"]), 'labels': [setId]})
importer.add_node(['_Set_Node', 'Label'], setId,
{'name': str(node["Label"])})
importer.add_edge('ConsistsOf', setId, str(node["StructureID"]), {}, 'Label')
else:
importer.add_node(['_Network_Node', 'Structure'], str(node["StructureID"]),
{'name': str(node["StructureID"]), 'labels': []})
edges = doc["edges"]
for edge in edges:
importer.add_edge('Edge', str(edge["SourceStructureID"]), str(edge["TargetStructureID"]), {'_isNetworkEdge': True,
'Type': edge["Type"],
'Label': edge["Label"]})
# importer.add_node(['_Network_Node', 'Compound'], compound_id,
# {'name': cpdName, 'idType': 'KEGG_COMPOUND',
# 'url': 'http://www.kegg.jp/dbget-bin/www_bget?cpd:' + compound_id})
# n = batch.create(node)
nodes.add(compound_id)
if compound.id not in compoundDict:
compoundDict[compound.id] = compound_id
currentNodes.add(compound_id)
importer.done_nodes()
for reaction in pathway.reactions:
if reaction.name in reactionToNode:
gene_ids = reactionToNode[reaction.name]
for gene_id in gene_ids:
for substrate in reaction.substrates:
substrate_id = substrate.name[4:]
if substrate_id in nodes:
importer.add_edge('Edge', substrate_id, gene_id,
{'_isNetworkEdge': True})
currentEdges[substrate_id + '_' + gene_id] = {
'source': substrate_id,
'target': gene_id
}
# create_pathway_edge(edgeDict, substrateNode, node)
if reaction.type == 'reversible':
importer.add_edge('Edge', gene_id,
substrate_id,
{'_isNetworkEdge': True})
currentEdges[gene_id + '_' + substrate_id] = {
'source': gene_id,
'target': substrate_id
}
# create_pathway_edge(edgeDict, node, substrateNode)
