add info on sources

README.md

@@ -19,3 +19,16 @@ Designed to be run at most once a day.
 ```
 ./run.sh
 ```
+
+Sources
+-------
+
+* litcovid: NIH-curated list of COVID-19 articles (https://www.ncbi.nlm.nih.gov/research/coronavirus/)
+Labels (8): General Information, Mechanism, Transmission, Diagnosis, Treatment, Prevention, Case Report, Epidemic Forecasting
+Note that topic labels are semi-automatically assigned.  See for details https://www.ncbi.nlm.nih.gov/research/coronavirus/faq
+
+* bibliovid: Paper categories and fine-grained analysis by experts (https://bibliovid.org/)
+Labels (7): Autres, Diagnostique, Thérapeutique, Épidémiologique, Pronostique, Recommandations, Modélisation
+Labels (19): Hépato-gastro-entérologie, Neurologie, Cardiologie et maladies métaboliques, Hématologie, Gériatrie, Infectiologie, Gynécologie Obstétrique, Dermatologie, Pédiatrie, Pneumologie, Transversale, Psychiatrie, Virologie, Anesthésie-Réanimation, Radiologie, Hygiène, Néphrologie, Confinement/Déconfinement, Immunité 
+
+* CORD-19 metadata: large set of papers metadata selected with broad queries on general coronavirus research

bibliovid_add_abstract.py

@@ -8,6 +8,10 @@ from datetime import datetime, date
 
 pubmed = PubMed(tool="https://covid19.lis-lab.fr", email="benoit.favre@univ-amu.fr")
 
+if len(sys.argv) != 3:
+  print('usage: %s <input> <output>' % sys.argv[0], file=sys.stderr)
+  sys.exit(1)
+
 with open(sys.argv[1]) as fp:
   articles = json.loads(fp.read())
 
@@ -43,7 +47,8 @@ for article in articles['results']:
   if not found:
     print('NOT FOUND:', title, file=sys.stderr)
 
-print(json.dumps(articles, indent=2))
+with open(sys.argv[2], 'w') as fp:
+  fp.write(json.dumps(articles, indent=2))
 
 print('TOTAL', len(articles['results']), file=sys.stderr)
 for key, value in stats.items():

run.sh

@@ -24,7 +24,7 @@ python "$dir/litcovid_add_abstract.py" "$out/litcovid_stage1.json" > "$out/litco
 count=`curl 'https://bibliovid.org/api/v1/posts?format=json' | python -mjson.tool | grep '"count":' | grep -o '[0-9]*'`
 curl "https://bibliovid.org/api/v1/posts?format=json&offset=0&limit=$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_add_abstract.py" "$out/bibliovid_stage2.json" "$out/bibliovid_stage3.json"
 python "$dir/bibliovid_normalize.py" "$out/bibliovid_stage3.json" > "$out/bibliovid.json"
 
 # cleanup