move scripts/ to bin/

1 files changed, 104 insertions, 0 deletions

diff --git a/bin/cord19_fatcat_enrich.py b/bin/cord19_fatcat_enrich.py
new file mode 100755
index 0000000..a911007
--- /dev/null
+++ b/bin/cord19_fatcat_enrich.py
@@ -0,0 +1,104 @@
+#!/usr/bin/env python3
+
+"""
+Takes a JSON-transformed CORD-19 *metadata* file and enriches it with fatcat
+metadata.
+"""
+
+import sys
+import json
+import argparse
+import datetime
+
+import requests
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry # pylint: disable=import-error
+
+
+def requests_retry_session(retries=10, backoff_factor=3,
+        status_forcelist=(500, 502, 504), session=None):
+    """
+    From: https://www.peterbe.com/plog/best-practice-with-retries-with-requests
+    """
+    session = session or requests.Session()
+    retry = Retry(
+        total=retries,
+        read=retries,
+        connect=retries,
+        backoff_factor=backoff_factor,
+        status_forcelist=status_forcelist,
+    )
+    adapter = HTTPAdapter(max_retries=retry)
+    session.mount('http://', adapter)
+    session.mount('https://', adapter)
+    return session
+
+
+def do_line(row, args):
+
+    pubmed_id = row.get('pubmed_id') or None
+    pmcid = row.get('pmcid') or None
+    doi = row.get('doi') or None
+    fatcat_release = None
+
+    if doi == '0.1126/science.abb7331':
+        doi = '10.1126/science.abb7331'
+
+    if not fatcat_release and pmcid:
+        resp = args.session.get('https://api.fatcat.wiki/v0/release/lookup',
+            params={
+                'pmcid': pmcid,
+                'expand': 'container,files,filesets,webcaptures',
+                'hide': 'abstracts,references',
+        })
+        if resp.status_code == 200:
+            fatcat_release = resp.json()
+    if not fatcat_release and doi:
+        resp = args.session.get('https://api.fatcat.wiki/v0/release/lookup',
+            params={
+                'doi': doi,
+                'expand': 'container,files,filesets,webcaptures',
+                'hide': 'abstracts,references',
+        })
+        if resp.status_code == 200:
+            fatcat_release = resp.json()
+    if not fatcat_release and pubmed_id:
+        resp = args.session.get('https://api.fatcat.wiki/v0/release/lookup',
+            params={
+                'pmid': pubmed_id,
+                'expand': 'container,files,filesets,webcaptures',
+                'hide': 'abstracts,references',
+        })
+        if resp.status_code == 200:
+            fatcat_release = resp.json()
+
+    obj = dict(
+        cord19_paper=row,
+    )
+    if fatcat_release:
+        obj['fatcat_release'] = fatcat_release
+        obj['release_id'] = fatcat_release['ident']
+        obj['fatcat_url'] = "https://fatcat.wiki/release/{}".format(obj['release_id'])
+    print(json.dumps(obj, sort_keys=True))
+
+def run(args):
+    for l in args.json_file:
+        l = json.loads(l)
+        do_line(l, args)
+
+def main():
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('json_file',
+        help="CORD-19 parsed JSON file",
+        type=argparse.FileType('r'))
+    subparsers = parser.add_subparsers()
+
+    args = parser.parse_args()
+    args.session = requests_retry_session()
+
+    run(args)
+
+if __name__ == '__main__':
+    main()
+