Programatically creating edges in Neo4j with python

Question

I'm trying to generate nodes and edges for some chemicals and associated reactions in neo4j with python but am hitting a problem with node/relationship creation...

My code...

from neo4j.v1 import GraphDatabase, basic_auth

driver = GraphDatabase.driver("bolt://localhost", auth=basic_auth("neo4j", "password"))
session = driver.session()

def addReactionNeo4j(reagents, products, reaction):
    cypher = "CREATE (%s:Reaction {RXNid:\"%s\", name:\"%s\"})" % (reaction[0],reaction[1],reaction[2])
    session.run(cypher)
    print cypher

    for reagent in reagents:
        cypher = "CREATE (%s:Molecule {CHMid: \"%s\", smiles:\"%s\"})" % (reagent[0], reagent[1], reagent[2])
        session.run(cypher)
        print cypher
        cypher = "CREATE (%s)-[:REAGENT]->(%s)" %(reagent[0], reaction[0])
        print cypher
        session.run(cypher)

    for product in products:            
        cypher = "CREATE (%s:Molecule {CHMid: \"%s\", smiles:\"%s\"})" % (product[0], product[1], product[2])
        session.run(cypher)
        print cypher
        cypher = "CREATE (%s)-[:PRODUCT]->(%s)" %(reaction[0], product[0])
        session.run(cypher)   
        print cypher

reagents1 = []
reagents1.append(["Chem2","nbutylamine","CCCCN"])
reagents1.append(["Chem3","butanoicAcid","CCCCOO"])

products1 =[]
products1.append(["Chem1","Nbutylbutanamide","CCCCNC(O)CCCC"])

reaction1 = ["Reaction1", "reaction1", "AmideFormation"]

addReactionNeo4j(reagents1, products1, reaction1)


session.close()

This code should write cypher code and execute it in Neo4j.

It gives the following cypher code as output

CREATE (Reaction1:Reaction {RXNid:"reaction1", name:"AmideFormation"})
CREATE (Chem2:Molecule {CHMid: "nbutylamine", smiles:"CCCCN"})
CREATE (Chem2)-[:REAGENT]->(Reaction1)
CREATE (Chem3:Molecule {CHMid: "butanoicAcid", smiles:"CCCCOO"})
CREATE (Chem3)-[:REAGENT]->(Reaction1)
CREATE (Chem1:Molecule {CHMid: "Nbutylbutanamide ", smiles:"CCCCNC(O)CCCC"})
CREATE (Reaction1)-[:PRODUCT]->(Chem1)

This code works as expected when pasted into Neo4J

But if I look the graph created by the code (which in theory should be executing the same cypher code) I get the nodes created but it has problems linking the nodes together with edges - leaving the nodes unconnected.

Can anyone advise me on what I am doing wrong ?

Thanks

Chris

Answer 1

I have a solution.

It appears if in neo4j I run

CREATE (Reaction1:Reaction {RXNid:"reaction1", name:"AmideFormation"})
CREATE (Chem2:Molecule {CHMid: "nbutylamine", smiles:"CCCCN"})
CREATE (Chem3:Molecule {CHMid: "butanoicAcid", smiles:"CCCCOO"})
CREATE (Chem1:Molecule {CHMid: "Nbutylbutanamide", smiles:"CCCCNC(O)CCCC"})

and then run ...

CREATE (Chem2)-[:REAGENT]->(Reaction1)
CREATE (Chem3)-[:REAGENT]->(Reaction1)
CREATE (Reaction1)-[:PRODUCT]->(Chem1)

I can replicate the problems with connecting nodes. However if I run them at the same time everything is fine.

Changing my code therefore to use MATCH and MERGE instead of simply create gets round the problem....

from neo4j.v1 import GraphDatabase, basic_auth

driver = GraphDatabase.driver("bolt://localhost", auth=basic_auth("neo4j", "arthuc01"))
session = driver.session()


def addReactionNeo4j(reagents, products, reaction):
    reagents = reagents1
    products = products1
    reaction = reaction1

    cypher = "MERGE (%s:Reaction {RXNid:\"%s\", name:\"%s\"})" % (reaction[0],reaction[1],reaction[2])
    session.run(cypher)
    print cypher

    for reagent in reagents:
        #USe MERGE to only add reagent/product or reaction in already if not:
        cypher = "MERGE (%s:Molecule {CHMid: \"%s\", smiles:\"%s\"})" % (reagent[0], reagent[1], reagent[2])
        session.run(cypher)
        print cypher

        cypher = "MATCH (m:Molecule {CHMid: \"%s\"} ), (r:Reaction {RXNid:\"%s\"})  \
                  MERGE (m)-[:REAGENT]->(r)" %(reagent[0], reaction[0])

        print cypher
        session.run(cypher)


    for product in products:
        #Check if product in already if not:
        cypher = "MERGE (%s:Molecule {CHMid: \"%s\", smiles:\"%s\"})" % (product[0], product[1], product[2])
        print cypher
        session.run(cypher)


        cypher = "MATCH (m:Molecule {CHMid: \"%s\"}), (r:Reaction {RXNid:\"%s\"}) \
                  MERGE (r)-[:PRODUCT]->(m)" %(product[0], reaction[0])
        print cypher
        session.run(cypher)


#        temp =""
#        for cypher in nodes:
#            temp = temp + cypher
#        session.run(temp)    
#            
reagents1 = []
reagents1.append(["Chem2","Chem2","CCCCN"])
reagents1.append(["Chem3","Chem3","CCCCOO"])

products1 =[]
products1.append(["Chem1","Chem1","CCCCNC(O)CCCC"])

reaction1 = ["reaction1", "reaction1", "AmideFormation"]

addReactionNeo4j(reagents1, products1, reaction1)


session.close()