--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_ceas_fetch_annotations.py	Wed Jan 28 05:04:46 2015 -0500
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+#
+
+import sys
+import os
+import optparse
+import urllib2
+import gzip
+
+from galaxy.util.json import from_json_string, to_json_string
+
+# Download file from specified URL and put into local subdir
+
+if __name__ == '__main__':
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('--download',dest='url',action='store',
+                      type="string",default=None,help='URL to download')
+    options,args = parser.parse_args()
+    print "options: %s" % options
+    print "args   : %s" % args
+    if len(args) != 2:
+        p.error("Need to supply JSON file name and description text")
+
+    # Read the JSON supplied from the data manager tool
+    # Results from this program will be returned via the
+    # same file
+    jsonfile = args[0]
+    params = from_json_string(open(jsonfile).read() )
+    print "%s" % params
+
+    # Extract the data from the input JSON
+    # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29
+    # for example of JSON
+    #
+    # We want the values set in the data manager XML
+    dbkey = params['param_dict']['dbkey']
+    description = params['param_dict']['description']
+    # Where to put the output file
+    # Nb we have to make this ourselves, it doesn't exist by default
+    target_dir = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_dir)
+
+    # Dictionary for returning to data manager
+    data_manager_dict = {}
+
+    # Download from URL
+    if options.url is not None:
+        print "Downloading: %s" % options.url
+        annotation_file_name = os.path.basename(options.url)
+        annotation_file_path = os.path.join(target_dir,annotation_file_name)
+        print "Annotation file name: %s" % annotation_file_name
+        print "Annotation file path: %s" % annotation_file_path
+        open(annotation_file_path,'wb').write(urllib2.urlopen(options.url).read())
+        if annotation_file_name.endswith('.gz'):
+            # Uncompress
+            uncompressed_file = annotation_file_path[:-3]
+            open(uncompressed_file,'wb').write(gzip.open(annotation_file_path,'rb').read())
+            # Remove gzipped file
+            os.remove(annotation_file_path)
+            annotation_file_name = os.path.basename(uncompressed_file)
+            annotation_file_path = uncompressed_file
+        # Update the output dictionary
+        data_manager_dict['data_tables'] = dict()
+        data_manager_dict['data_tables']['ceas_annotations'] = {
+            'dbkey': dbkey,
+            'name': description,
+            'value': annotation_file_name,
+        }
+    else:
+        raise NotImplementedError("Non-download options not implemented")
+
+    #save info to json file
+    open(jsonfile,'wb').write(to_json_string(data_manager_dict))
+