Upload scrape_icd_9.py

scrape_icd_9.py

@@ -0,0 +1,76 @@
+# 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 ?icd9code WHERE {
+  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE]". }
+  {
+    SELECT DISTINCT ?item ?article ?icd9code WHERE {
+        ?item p:P1692 ?statement0.
+        ?statement0 (ps:P1692) _:anyValueP1692.
+        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:P1692 ?icd9code.
+      }
+    }
+}
+"""
+
+
+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["icd9code"]["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_9.json", "w+") as f:
+    json.dump(parsed_wikipedia, f)
+print("DONE")