diff retrieve_meta.py @ 0:36e37b29c1b0 draft default tip

"planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/retrieve_meta.py	Mon Dec 20 10:15:18 2021 +0000
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+
+import yaml
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('galaxy_json')
+    parser.add_argument(
+        '-o', '--ofile',
+        required=True
+    )
+    parser.add_argument(
+        '--format', choices=['yaml', 'tab'], default='yaml'
+    )
+    args = parser.parse_args()
+
+    galaxy_collection_info = json.load(open(args.galaxy_json))
+    annotation_info = next(iter(galaxy_collection_info.values()))['elements']
+    selected_ids = {i['name'] for i in annotation_info}
+    package_meta_file = os.path.join(
+        os.path.dirname(annotation_info[0]['filename']),
+        'meta.yml'
+    )
+    meta = yaml.safe_load(open(package_meta_file))
+    meta['records'] = [
+        rec for rec in meta['records'] if rec['id'] in selected_ids
+    ]
+
+    with open(args.ofile, 'w') as fo:
+        if args.format == 'yaml':
+            yaml.dump(
+                meta, fo, allow_unicode=False, default_flow_style=False
+            )
+        else:
+            print('Annotation\tVersion', file=fo)
+            for record in meta['records']:
+                print(record['name'], record['version'], sep='\t', file=fo)