refactor parse_cord19_csv.py into tool

3 files changed, 55 insertions, 39 deletions

diff --git a/bin/parse_cord19_csv.py b/bin/parse_cord19_csv.py
deleted file mode 100755
index dbc6cc5..0000000
--- a/bin/parse_cord19_csv.py
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env python3
-
-"""
-Trivial helper to transform the CORD-19 CSV file to JSON, and rename a couple
-of the column keys.
-"""
-
-import sys
-import csv
-import json
-
-CSVFILE = sys.argv[1]
-
-with open(CSVFILE, newline='') as csvfile:
-    reader = csv.DictReader(csvfile)
-    for row in reader:
-        row = dict(row)
-        row['mag_id'] = row.pop('Microsoft Academic Paper ID')
-        row['who_covidence_id'] = row.pop('WHO #Covidence').replace('#', '')
-        obj = dict(cord19_paper=row)
-        print(json.dumps(obj, sort_keys=True))
diff --git a/covid19_tool.py b/covid19_tool.py
index b9bea44..345aa6e 100755
--- a/covid19_tool.py
+++ b/covid19_tool.py
@@ -9,6 +9,7 @@ Licensed the same as code under fatcat_covid19/
 import sys
 import argparse
 
+from fatcat_covid19.parse import parse_cord19_file
 from fatcat_covid19.enrich import enrich_fatcat_file
 from fatcat_covid19.derivatives import enrich_derivatives_file
 from fatcat_covid19.transform import transform_es_file
@@ -22,21 +23,18 @@ def main():
     )
     subparsers = parser.add_subparsers()
 
-    sub_webface = subparsers.add_parser('webface',
-        help="run flask web interface")
-    sub_webface.set_defaults(
-        action='webface',
+    sub_parse_cord = subparsers.add_parser('parse-cord19',
+        help="parse a CORD-19 CSV file into JSON")
+    sub_parse_cord.set_defaults(
+        action='parse-cord19',
     )
-    sub_webface.add_argument('--debug',
-        action='store_true',
-        help="enable debugging interface (note: not for everything)")
-    sub_webface.add_argument('--host',
-        default="127.0.0.1",
-        help="listen on this host/IP")
-    sub_webface.add_argument('--port',
-        type=int,
-        default=9119,
-        help="listen on this port")
+    sub_parse_cord.add_argument('csv_path',
+        help="input CSV file path",
+        type=str)
+    sub_parse_cord.add_argument('--json-output',
+        help="file to write to",
+        type=argparse.FileType('w'),
+        default=sys.stdout)
 
     sub_enrich_fatcat = subparsers.add_parser('enrich-fatcat',
         help="lookup fatcat releases from JSON metadata")
@@ -80,12 +78,26 @@ def main():
         type=argparse.FileType('w'),
         default=sys.stdout)
 
+    sub_webface = subparsers.add_parser('webface',
+        help="run flask web interface")
+    sub_webface.set_defaults(
+        action='webface',
+    )
+    sub_webface.add_argument('--debug',
+        action='store_true',
+        help="enable debugging interface (note: not for everything)")
+    sub_webface.add_argument('--host',
+        default="127.0.0.1",
+        help="listen on this host/IP")
+    sub_webface.add_argument('--port',
+        type=int,
+        default=9119,
+        help="listen on this port")
+
     args = parser.parse_args()
 
-    if args.action == 'webface':
-        # don't import until we use app; otherwise sentry exception reporting happens
-        from fatcat_covid19.webface import app
-        app.run(debug=args.debug, host=args.host, port=args.port)
+    if args.action == 'parse-cord19':
+        parse_cord19_file(args.csv_path, args.json_output)
     elif args.action == 'enrich-fatcat':
         enrich_fatcat_file(args.json_file, args.json_output)
     elif args.action == 'enrich-derivatives':
@@ -93,6 +105,10 @@ def main():
             args.base_dir)
     elif args.action == 'transform-es':
         transform_es_file(args.json_file, args.json_output)
+    elif args.action == 'webface':
+        # don't import until we use app; otherwise sentry exception reporting happens
+        from fatcat_covid19.webface import app
+        app.run(debug=args.debug, host=args.host, port=args.port)
     else:
         print("tell me what to do!")
         sys.exit(-1)
diff --git a/fatcat_covid19/parse.py b/fatcat_covid19/parse.py
new file mode 100644
index 0000000..ce2bf26
--- /dev/null
+++ b/fatcat_covid19/parse.py
@@ -0,0 +1,21 @@
+
+import sys
+import csv
+import json
+
+
+def parse_cord19_file(csv_path, json_output):
+    """
+    Trivial helper to transform the CORD-19 CSV file to JSON, and rename a
+    couple of the column keys.
+    """
+
+    with open(csv_path, newline='') as csvfile:
+        reader = csv.DictReader(csvfile)
+        for row in reader:
+            row = dict(row)
+            row['mag_id'] = row.pop('Microsoft Academic Paper ID')
+            row['who_covidence_id'] = row.pop('WHO #Covidence').replace('#', '')
+            obj = dict(cord19_paper=row)
+            print(json.dumps(obj, sort_keys=True), file=json_output)
+