|
|
|
|
|
import wikipediaapi |
|
import urllib.parse |
|
import sys |
|
from SPARQLWrapper import SPARQLWrapper, JSON |
|
import json |
|
from tqdm import tqdm |
|
endpoint_url = "https://query.wikidata.org/sparql" |
|
|
|
query = """SELECT DISTINCT ?item ?itemLabel ?article ?icd10code WHERE { |
|
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE]". } |
|
{ |
|
SELECT DISTINCT ?item ?article ?icd10code WHERE { |
|
?item p:P4229 ?statement0. |
|
?statement0 (ps:P4229) _:anyValueP4229. |
|
FILTER(EXISTS { ?statement0 prov:wasDerivedFrom ?reference. }) |
|
OPTIONAL { |
|
?article schema:about ?item . |
|
?article schema:inLanguage "en" . |
|
FILTER (SUBSTR(str(?article), 1, 25) = "https://en.wikipedia.org/") |
|
} |
|
?item wdt:P4229 ?icd10code. |
|
} |
|
} |
|
} |
|
""" |
|
|
|
|
|
def get_results(endpoint_url, query): |
|
user_agent = "WDQS-example Python/%s.%s" % (sys.version_info[0], sys.version_info[1]) |
|
|
|
sparql = SPARQLWrapper(endpoint_url, agent=user_agent) |
|
sparql.setQuery(query) |
|
sparql.setReturnFormat(JSON) |
|
return sparql.query().convert() |
|
|
|
|
|
results = get_results(endpoint_url, query) |
|
|
|
parsed_urls = set() |
|
|
|
wiki_wiki = wikipediaapi.Wikipedia('MyProjectName (merlin@example.com)', 'en') |
|
|
|
parsed_wikipedia = {} |
|
article_to_icd_mapping = {} |
|
sections_to_ignore = ["See also", "Explanatory notes","External links", "References", "Citations", "Cited texts", "Further reading"] |
|
|
|
for result in tqdm(results["results"]["bindings"]): |
|
if "article" not in result: |
|
continue |
|
wikipedia_url = result["article"]["value"] |
|
icd_code = result["icd10code"]["value"] |
|
qid = result["itemLabel"] |
|
entity_name = wikipedia_url.split("/")[-1] |
|
entity_name = urllib.parse.unquote(entity_name) |
|
|
|
if wikipedia_url not in parsed_urls: |
|
page = wiki_wiki.page(entity_name) |
|
if not page.exists(): |
|
continue |
|
if wikipedia_url == page.fullurl: |
|
parsed_urls.add(wikipedia_url) |
|
sections = list(filter(lambda s: s.title not in sections_to_ignore, page.sections)) |
|
sections = [{"title": s.title, "text": s.full_text()} for s in sections] |
|
article = {"title": entity_name, "icd_code": [icd_code], "sections": sections, "summary": page.summary} |
|
parsed_wikipedia[entity_name] = article |
|
else: |
|
article = parsed_wikipedia[entity_name] |
|
if icd_code not in article["icd_code"]: |
|
article["icd_code"].append(icd_code) |
|
parsed_wikipedia[entity_name] = article |
|
|
|
with open("wiki_icd_10.json", "w+") as f: |
|
json.dump(parsed_wikipedia, f) |
|
print("DONE") |
