Add glob functionality for attachments.

Author: DailyDreaming

test/test_client_util.py

@@ -0,0 +1,31 @@
+from __future__ import absolute_import
+
+import unittest
+import os
+import logging
+import subprocess
+
+from wes_client.util import expand_globs
+
+logging.basicConfig(level=logging.INFO)
+
+
+class IntegrationTest(unittest.TestCase):
+    def setUp(self):
+        dirname, filename = os.path.split(os.path.abspath(__file__))
+        self.testdata_dir = dirname + 'data'
+
+    def tearDown(self):
+        unittest.TestCase.tearDown(self)
+
+    def test_expand_globs(self):
+        """Asserts that wes_client.expand_globs() sees the same files in the cwd as 'ls'."""
+        files = subprocess.check_output(['ls', '-1', '.']).decode('utf-8').split('\n')
+        if '' in files:
+            files.remove('')
+        glob_files = expand_globs('*')
+        assert set(files) == glob_files
+
+
+if __name__ == '__main__':
+    unittest.main()  # run all tests

wes_client/util.py

@@ -1,5 +1,6 @@
 import os
 import json
+import glob
 import requests
 import urllib
 import logging
@@ -90,6 +91,13 @@ def fixpaths(d):
     visit(input_dict, fixpaths)
 
 
+def expand_globs(attachments):
+    expanded_list = []
+    for filepath in attachments:
+        expanded_list += glob.glob(filepath)
+    return set(expanded_list)
+
+
 def wes_reponse(postresult):
     if postresult.status_code != 200:
         logging.error("%s", json.loads(postresult.text))

wes_client/wes_client_main.py

@@ -8,7 +8,7 @@
 import logging
 import requests
 from requests.exceptions import InvalidSchema, MissingSchema
-from wes_client.util import modify_jsonyaml_paths, WESClient
+from wes_client.util import modify_jsonyaml_paths, expand_globs, WESClient
 
 
 def main(argv=sys.argv[1:]):
@@ -87,6 +87,7 @@ def main(argv=sys.argv[1:]):
         logging.basicConfig(level=logging.INFO)
 
     args.attachments = args.attachments if not args.attachments else args.attachments.split(',')
+    args.attachments = list(expand_globs(args.attachments))
     r = client.run(args.workflow_url, args.job_order, args.attachments)
 
     if args.wait: