90 lines
2.7 KiB
Python
Executable File
90 lines
2.7 KiB
Python
Executable File
#!/usr/bin/env python
|
|
from fetch import wikidata
|
|
from neo4j import GraphDatabase
|
|
|
|
|
|
NEO4J_URI = "bolt://localhost:7687"
|
|
NEO4J_USR = "neo4j"
|
|
NEO4J_PSW = "test"
|
|
|
|
# Conection with Neo4j
|
|
driver = GraphDatabase.driver(NEO4J_URI, auth=(NEO4J_USR, NEO4J_PSW))
|
|
|
|
|
|
|
|
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)
|
|
|
|
|
|
|
|
# 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
|
|
)
|
|
|
|
# Close Neo4j connection
|
|
driver.close()
|