wikimedica-disease-search/data/wikimedica/alignement.py

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import requests
import rdflib
SIGNES_ET_SYMPTOMES_WIKIMEDICA_PAGE = (
'http://wikimedi.ca/wiki/Sp%C3%A9cial:'
'Export_RDF/Concept:Signes_et_sympt%C3%B4mes'
)
PREFIX_PROPERTY = "http://wikimedi.ca/wiki/Special:URIResolver/Property-3A"
WIKIDATA_SPARQL_ENDPOINT = "https://query.wikidata.org/sparql"
USER_AGENT = "WikimedicaDiseaseSearch/0.1 (https://gitlab.com/matteodelabre/wikimedica-disease-search)"
session = requests.Session()
session.headers = {'User-Agent': USER_AGENT}
def make_sparql_request_wikimedica(page, request):
"""
Effectue une requête SPARQL sur une page de WikiMedica
:param page: Page de WikiMedica ciblé
:param request: Requête SPARQL appliqué
"""
data = session.get(page, stream=True)
g = rdflib.Graph()
g.parse(data.raw)
qres = g.query(request)
return [row.asdict() for row in qres]
def make_sparql_request_endpoint(endpoint, request):
"""
Effectue une requête SPARQL sur point d'accés
:param page: Adresse du point d'accés
:param request: Requête SPARQL appliqué
"""
res = session.get(endpoint, params={'format': 'json' ,'query': request})
if res.status_code != 200:
raise Exception('Erreur {}'.format(res.status_code))
return res.json()
nb_wikimedica_entity = 0
nb_align_by_property = 0
nb_align_by_name = 0
nb_align_conflict = 0
# get name and URI from WikiMedica
request_name_uri = """
SELECT ?name ?uri
WHERE {
?el rdfs:label ?name .
?el rdfs:isDefinedBy ?uri
}
"""
entitys_dic = make_sparql_request_wikimedica(
SIGNES_ET_SYMPTOMES_WIKIMEDICA_PAGE,
request_name_uri
)
nb_wikimedica_entity = len(entitys_dic)
# Try align entity with Wikidata
for entity in entitys_dic:
print()
print("="*10 + " " + entity['name'] + " " + "="*10)
print(entity['uri'])
# use Wikidata_id property
request_prop_Wikidata_id = """
PREFIX property: <{}>
SELECT ?wikidata_id
WHERE {{
?el property:Wikidata_id ?wikidata_id .
}}
""".format(PREFIX_PROPERTY)
prop_Wikidata_id = make_sparql_request_wikimedica(
entity['uri'],
request_prop_Wikidata_id
)
if len(prop_Wikidata_id) == 1:
nb_align_by_property = nb_align_by_property + 1
entity.update(prop_Wikidata_id[0])
print("align with 'property:Wikidata_id'")
elif len(prop_Wikidata_id) > 1:
print("Attention : il y a plus de 1 lien 'property:wikidata_id'")
# use name of entity
else:
request_search_by_name = """
SELECT ?entity
WHERE {{
?entity rdfs:label ?entityLabel;
wdt:P31 ?type.
VALUES ?entityLabel {{"{}"@fr "{}"@fr}}
VALUES ?type {{wd:Q12136 wd:Q1441305 wd:Q169872}}
}}
""".format((entity['name']).lower(), (entity['name']).capitalize())
list_wikidata_pages_uri = (make_sparql_request_endpoint(
WIKIDATA_SPARQL_ENDPOINT,
request_search_by_name
))['results']['bindings']
if len(list_wikidata_pages_uri) == 1:
nb_align_by_name = nb_align_by_name + 1
wikidata_uri = list_wikidata_pages_uri[0]
entity['wikidata_id'] = rdflib.term.URIRef(wikidata_uri)
print("align with 'name', 1 response")
print(wikidata_uri['entity']['value'])
elif len(list_wikidata_pages_uri) > 1:
nb_align_conflict = nb_align_conflict + 1
print("align with 'name', multi response")
print(list_wikidata_pages_uri)
print()
print("nb_wikimedica_entity : ", nb_wikimedica_entity)
print("nb_align_by_property : ", nb_align_by_property)
print("nb_align_by_name : ", nb_align_by_name)
print("nb_align_conflict : ", nb_align_conflict)