From 328892b0e571395fbbf8a22ca8a4216c6cf71074 Mon Sep 17 00:00:00 2001
From: Bryan Newbold <bnewbold@archive.org>
Date: Fri, 3 Apr 2020 15:13:43 -0700
Subject: refactor enrich into fatcat_covid19

---
 fatcat_covid19/enrich.py | 67 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 fatcat_covid19/enrich.py

(limited to 'fatcat_covid19')

diff --git a/fatcat_covid19/enrich.py b/fatcat_covid19/enrich.py
new file mode 100644
index 0000000..245a357
--- /dev/null
+++ b/fatcat_covid19/enrich.py
@@ -0,0 +1,67 @@
+
+import sys
+import json
+import datetime
+
+from fatcat_covid19.common import requests_retry_session
+
+
+def enrich_fatcat_row(row, api_session):
+
+    cord19_paper = row.get('cord19_paper')
+    if not cord19_paper:
+        return row
+
+    pubmed_id = cord19_paper.get('pubmed_id') or None
+    pmcid = cord19_paper.get('pmcid') or None
+    doi = cord19_paper.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 = api_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 = api_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 = api_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()
+
+    if fatcat_release:
+        row['fatcat_release'] = fatcat_release
+        row['release_id'] = fatcat_release['ident']
+    print(json.dumps(row, sort_keys=True))
+
+
+def enrich_fatcat_file(json_input, json_output):
+    """
+    Takes a JSON-transformed CORD-19 *metadata* file and enriches it with
+    fatcat metadata.
+    """
+    api_session = requests_retry_session()
+    for l in json_input:
+        l = json.loads(l)
+        result = enrich_fatcat_row(l, api_session)
+        if result:
+            print(json.dumps(result, sort_keys=True), file=json_output)
-- 
cgit v1.2.3