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| # pip install sparqlwrapper | |
| # https://rdflib.github.io/sparqlwrapper/ | |
| 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]) | |
| # TODO adjust user agent; see https://w.wiki/CX6 | |
| 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") |