add script to normalize bibliovid data

bibliovid_add_abstract.py

@@ -8,7 +8,10 @@ from datetime import datetime, date
 
 pubmed = PubMed(tool="https://covid19.lis-lab.fr", email="benoit.favre@univ-amu.fr")
 
-articles = json.loads(sys.stdin.read())
+with open(sys.argv[1]) as fp:
+  articles = json.loads(fp.read())
+
+print(len(articles['results']), file=sys.stderr)
 
 def normalize(text):
   return re.sub('[^a-zA-Z]', '', text).lower()
@@ -38,13 +41,12 @@ for article in articles['results']:
     if found:
       break
   if not found:
-    print('NOT FOUND:', title)
+    print('NOT FOUND:', title, file=sys.stderr)
 
-print('TOTAL', len(articles['results']))
+print('TOTAL', len(articles['results']), file=sys.stderr)
 for key, value in stats.items():
-  print(key, value, value / len(articles['results']))
+  print(key, value, value / len(articles['results'], file=sys.stderr))
 
-with open(sys.argv[1], 'w') as fp:
-  fp.write(json.dumps(articles, indent=2))
+print(json.dumps(articles, indent=2))
 
 

bibliovid_normalize.py

+import sys, json
+
+with open(sys.argv[1]) as fp:
+  articles = json.loads(fp.read())
+
+if type(articles) == dict:
+  articles = articles['results']
+
+for article in articles:
+  article['topics'] = [article['category']['name']] + [x['name'] for x in article['specialties']]
+  article['author_list'] = article['authors']
+  article['authors'] = ', '.join([x['name'] for x in article['authors']])
+  day, month, year = article['verbose_date'].split('.')
+  article['publication_date'] = '%s-%s-%s' % (year, month, day)
+
+print(json.dumps(articles, indent=2))
+

litcovid_add_abstract.py

@@ -43,8 +43,9 @@ def fetch(articles):
     for article in root.findall('.//PubmedArticle'):
       pmid = article.findtext('.//PMID')
       if pmid in by_id:
+        found = by_id[pmid]
         abstract = ' '.join([''.join(line.itertext()) for line in article.findall('.//Abstract/AbstractText')])
-        by_id[pmid]['abstract'] = abstract
+        found['abstract'] = abstract
 
 if len(sys.argv) != 2:
   print('usage: %s <articles-json>' % sys.argv[0])

run.sh

@@ -13,19 +13,20 @@ out="$dir/data/"`date '+%Y%m%d'`
 mkdir -p "$out"
 
 # CORD-19 metadata
-curl https://ai2-semanticscholar-cord-19.s3-us-west-2.amazonaws.com/latest/metadata.csv > "$out/cord19-metadata_stage1.csv"
-python "$dir/cord19_csv2json.py" "$out/cord19-metadata_stage1.csv" > "$out/cord19-metadata.json"
+#curl https://ai2-semanticscholar-cord-19.s3-us-west-2.amazonaws.com/latest/metadata.csv > "$out/cord19-metadata_stage1.csv"
+#python "$dir/cord19_csv2json.py" "$out/cord19-metadata_stage1.csv" > "$out/cord19-metadata.json"
 
 # litcovid
-python "$dir/litcovid_scrapper.py" > "$out/litcovid_stage1.json"
-python "$dir/litcovid_add_abstract.py" "$out/litcovid_stage1.json" > "$out/litcovid.json"
+#python "$dir/litcovid_scrapper.py" > "$out/litcovid_stage1.json"
+#python "$dir/litcovid_add_abstract.py" "$out/litcovid_stage1.json" > "$out/litcovid.json"
 
 # bibliovid
-count=`curl 'https://bibliovid.org/api/v1/posts?format=json' | python -mjson.tool | grep '"count":' | grep -o '[0-9]*'`
-curl "https://bibliovid.org/api/v1/posts?format=json&offset=0&limit=$count" | python -mjson.tool > "$out/bibliovid_stage1.json"
-python "$dir/bibliovid_scrapper.py" "$out/bibliovid_stage1.json" > "$out/bibliovid_stage2.json"
-python "$dir/bibliovid_add_abstract.py" "$out/bibliovid.json" < "$out/bibliovid_stage2.json"
+#count=`curl 'https://bibliovid.org/api/v1/posts?format=json' | python -mjson.tool | grep '"count":' | grep -o '[0-9]*'`
+#curl "https://bibliovid.org/api/v1/posts?format=json&offset=0&limit=$count" | python -mjson.tool > "$out/bibliovid_stage1.json"
+#python "$dir/bibliovid_scrapper.py" "$out/bibliovid_stage1.json" > "$out/bibliovid_stage2.json"
+python "$dir/bibliovid_add_abstract.py" "$out/bibliovid_stage2.json" > "$out/bibliovid_stage3.json"
+python "$dir/bibliovid_normalize.py" "$out/bibliovid_stage3.json" > "$out/bibliovid.json"
 
 # cleanup
-rm "$out/cord19-metadata_stage*" "$out/litcovid_stage*" "$out/bibliovid_stage*"
+rm "$out/*stage*"