MNT: utility script to refresh UKB schema

funpack/scripts/refresh_showcase_schema.py

+#!/usr/bin/env python
+#
+# This script refreshes the UKB showcase schema files that are built into
+# FUNPACK. I run it by hand when releasing a new version of FUNPACK.
+#
+
+
+import itertools  as it
+import subprocess as sp
+import os.path    as op
+import               glob
+import               shlex
+
+
+def download_file(url, dest):
+    print(f'{url} -> {dest}')
+    cmd = f'wget -O {dest} {url}'
+    sp.run(shlex.split(cmd), stdout=sp.DEVNULL, stderr=sp.DEVNULL)
+
+
+def main():
+    basedir = op.join(op.dirname(__file__), '..', '..')
+    datadir = op.join(basedir, 'funpack', 'data')
+
+    baseurl = 'biobank.ctsu.ox.ac.uk/'
+
+    download_file(f'{baseurl}/ukb/scdown.cgi?fmt=txt&id=1',
+                  op.join(datadir, 'field.txt'))
+    download_file(f'{baseurl}/ukb/scdown.cgi?fmt=txt&id=2',
+                  op.join(datadir, 'encoding.txt'))
+
+    codings = it.chain(
+        glob.glob(op.join(datadir, 'coding',    '*.tsv')),
+        glob.glob(op.join(datadir, 'hierarchy', '*.tsv')))
+
+    for coding in codings:
+        # all files are called "coding<ID>.tsv"
+        cid = op.basename(coding)[6:-4]
+        url = f'{baseurl}/crystal/codown.cgi?id={cid}'
+        download_file(url, coding)
+
+
+if __name__ == '__main__':
+    main()