diff data_manager_monorail_index/data_manager/data_manager.py @ 3:1032e2599a5e draft

Uploaded

--- a/data_manager_monorail_index/data_manager/data_manager.py	Mon Nov 11 23:38:27 2019 -0500
+++ b/data_manager_monorail_index/data_manager/data_manager.py	Tue Nov 12 00:24:25 2019 -0500
@@ -19,11 +19,17 @@
 def main(args):
     workdir = os.path.join(os.getcwd(), 'monorail_index')
     data_manager_entry = {}
+    ref = args.url.split('/')[-1]
     if args.name is None:
-        args.name = args.url.split('/')[-1]
+        args.name = ref
     data_manager_entry['value'] = args.name.lower()
     data_manager_entry['name'] = args.name
-    data_manager_entry['path'] = args.output
+    jsonin = open(args.output).read()
+    sys.stderr.write(jsonin)
+    params = json.loads(jsonin)
+    target_directory = params['output_data'][0]['extra_files_path']
+    data_manager_entry['path'] = params['output_data'][0]['extra_files_path']
+    data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + ref + os.sep + 'gtf' + os.sep + 'exons.bed'
     data_manager_json = dict(data_tables=dict(monorail_index=data_manager_entry))
     file(args.output, 'w').write(json.dumps(data_manager_json))