unpaywall blobs.fatcat.wiki backfill notes

1 files changed, 59 insertions, 0 deletions

diff --git a/postgrest/backfill/backfill_grobid_unpaywall.py b/postgrest/backfill/backfill_grobid_unpaywall.py
new file mode 100755
index 0000000..58e9e3c
--- /dev/null
+++ b/postgrest/backfill/backfill_grobid_unpaywall.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+"""
+This is a "one-time" tranform helper script for GROBID backfill into
+sandcrawler minio and postgresql.
+
+This variant of backfill_grobid.py pushes into the unpaywall bucket of
+sandcrawler-minio and doesn't push anything to sandcrawler table in general.
+"""
+
+import json, os, sys, collections, io
+import base64
+import requests
+from minio import Minio
+import psycopg2
+import psycopg2.extras
+
+
+def b32_hex(s):
+    s = s.strip().split()[0].lower()
+    if s.startswith("sha1:"):
+        s = s[5:]
+    if len(s) != 32:
+        return s
+    return base64.b16encode(base64.b32decode(s.upper())).lower().decode('utf-8')
+
+def stdin_to_minio():
+    mc = Minio('localhost:9000',
+        access_key=os.environ['MINIO_ACCESS_KEY'],
+        secret_key=os.environ['MINIO_SECRET_KEY'],
+        secure=False)
+    counts = collections.Counter({'total': 0})
+    for l in sys.stdin:
+        if counts['raw_lines'] > 0 and counts['raw_lines'] % 10000 == 0:
+            print("Progress: {}...".format(counts))
+        counts['raw_lines'] += 1
+        l = l.strip()
+        if not l:
+            continue
+        row = json.loads(l)
+        if not row:
+            continue
+        sha1hex = b32_hex(row['pdf_hash'])
+        grobid_xml = row['tei_xml'].encode('utf-8')
+        grobid_xml_len = len(grobid_xml)
+        grobid_xml = io.BytesIO(grobid_xml)
+
+        key = "grobid/{}/{}/{}.tei.xml".format(
+            sha1hex[0:2],
+            sha1hex[2:4],
+            sha1hex)
+        mc.put_object("unpaywall", key, grobid_xml, grobid_xml_len,
+            content_type="application/tei+xml",
+            metadata=None)
+        counts['minio-success'] += 1
+
+    print("Done: {}".format(counts))
+
+if __name__=='__main__':
+    stdin_to_minio()