move and tweak scripts

2 files changed, 7 insertions, 23 deletions

diff --git a/scripts/who_enrich.py b/scripts/cord19_fatcat_enrich.py
index b445927..5d3a554 100755
--- a/scripts/who_enrich.py
+++ b/scripts/cord19_fatcat_enrich.py
@@ -1,17 +1,8 @@
 #!/usr/bin/env python3
 
 """
-This script takes a "Paper" MAG TSV file which has been joined with (at most) a
-single "PaperExtendedAttributes", parses it into JSON, and does fatcat fetches
-to "enrich" the output. Outputs a single JSON object per line with attributes:
-
-    mag_id
-    mag_paper
-    release_id
-    fatcat_release
-
-Input columns:
-
+Takes a JSON-transformed CORD-19 *metadata* file and enriches it with fatcat
+metadata.
 """
 
 import sys
@@ -50,6 +41,9 @@ def do_line(row, args):
     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={
@@ -79,7 +73,7 @@ def do_line(row, args):
             fatcat_release = resp.json()
 
     obj = dict(
-        who_paper=row,
+        cord19_paper=row,
     )
     if fatcat_release:
         obj['fatcat_release'] = fatcat_release
@@ -96,7 +90,7 @@ def main():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument('json_file',
-        help="WHO/S2 parsed JSON file",
+        help="CORD-19 parsed JSON file",
         type=argparse.FileType('r'))
     subparsers = parser.add_subparsers()
 
diff --git a/scripts/deliver_file2disk.py b/scripts/deliver_file2disk.py
index d661acc..9ec234a 100755
--- a/scripts/deliver_file2disk.py
+++ b/scripts/deliver_file2disk.py
@@ -10,16 +10,6 @@ Behavior:
     - try downloading from any archive.org or web.archive.org URLs
     - verify SHA-1
     - write out to disk
-
-TODO:
-x blob_path(sha1hex) -> returns relative/local path file would be saved to
-x filter_files(files) -> list of files to try
-- fetch_release(release) -> tries to download PDF bytes
-- fetch_file(file) -> returns bytes of fetched file
-- fetch_content(url) -> tries to download PDF bytes
-
-LATER:
-- GRBOID XML as well, from minio?
 """
 
 # XXX: some broken MRO thing going on in here due to python3 object wrangling