wikimedica-disease-search/data/build_graph.py

#!/usr/bin/env python
from fetch import wikidata, wikimedica
from neo4j import GraphDatabase
import json


NEO4J_URI = "bolt://localhost:7687"
NEO4J_USR = "neo4j"
NEO4J_PSW = "test"

ALIGNEMENT_FILE_PATH = "data/alignment_result.json"



def define_link_from_type(link_id):
    """
    Define typy of link from ID

    :param link_id: id of link
    :return: type corresponding
    """
    if link_id in ["P780","P1542"]:
        return "Sign_symsymptoms"
    elif link_id == "P5642":
        return "Risk_factor"
    else:
        raise Exception("Error : unknow link id: " + link_id)



def create_graph():
    """
    Build and insert graph from wikidata to neo4j
    """
    # Create indexes
    with driver.session() as session:
            session.run("CREATE INDEX ON :Disease(id);")
            session.run("CREATE INDEX ON :Sign_symsymptoms(id);")
            session.run("CREATE INDEX ON :Risk_factor(id);")

    # Get all diseases, links, symptoms
    request_disease_links = (wikidata.request("""
        SELECT ?maladie ?maladieLabel ?link ?linkLabel ?signe_symptome ?signe_symptomeLabel
        WHERE {
        ?maladie ?link ?signe_symptome.
        SERVICE wikibase:label { bd:serviceParam wikibase:language "fr"}.
        VALUES ?link {wdt:P780 wdt:p1542 wdt:P5642}
        }
        ORDER BY ?maladie
    """
    ))['results']['bindings']

    for link in request_disease_links:
        disease_id = link["maladie"]["value"].split("/")[-1]
        disease_label = link["maladieLabel"]["value"].lower()
        disease_type = "Disease"

        link_id = link["link"]["value"].split("/")[-1]
        link_label = link["linkLabel"]["value"].lower()
        link_type = "link_"+define_link_from_type(link_id)

        signe_symptome_id = link["signe_symptome"]["value"].split("/")[-1]
        signe_symptome_label = link["signe_symptomeLabel"]["value"].split("/")[-1].lower()
        signe_symptome_type = define_link_from_type(link_id)

        with driver.session() as session:
            # add dieadiseases
            session.run(
                "MERGE (d:" + disease_type + " {id:$disease_id, label:$disease_label})",
                disease_id=disease_id,
                disease_label=disease_label,
            )

            # add symptoms
            session.run(
                "MERGE (s:" + signe_symptome_type + " {id:$signe_symptome_id, label:$signe_symptome_label})",
                signe_symptome_id=signe_symptome_id,
                signe_symptome_label=signe_symptome_label,
            )

            # add link
            session.run(
                "MATCH (d:" + disease_type + " {id:$disease_id})"
                "MATCH (s:" + signe_symptome_type + " {id:$signe_symptome_id})"
                "MERGE (d)-[l:" + link_type + " {id:$link_id, label:$link_label}]->(s)",
                link_id=link_id,
                link_label=link_label,
                disease_id=disease_id,
                signe_symptome_id=signe_symptome_id
            )



def align_with_wikimedica():
    """
    Align neo4j graph and Wikidata
    """
    with open(ALIGNEMENT_FILE_PATH, "r") as align_file:
        align = json.loads(align_file.read())
        
        for entity in align:
            if 'wikidata_id' in entity:
                
                with driver.session() as session:
                    wikidata_id = entity['wikidata_id']
                    wikidata_page = wikimedica.get_web_page(entity['wikimedica_uri'])

                    session.run(
                        "MATCH (d {id:$wikidata_id})"
                        "SET d.wikimedia_id = $wikimedica_uri",
                        wikidata_id=wikidata_id,
                        wikimedica_uri=wikidata_page,
                    )



# Conection with Neo4j
driver = GraphDatabase.driver(NEO4J_URI, auth=(NEO4J_USR, NEO4J_PSW))

create_graph()
align_with_wikimedica()

# Close Neo4j connection
driver.close()