refactor parse_cord19_csv.py into tool

1 files changed, 21 insertions, 0 deletions

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)
+