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attachment:tools_1.py of Events/GCC2013/TrainingDay/API

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   1 #!/usr/bin/env python
   2 
   3 """
   4 Access a Galaxy instance and get data for Tools.
   5 
   6 (You definitely can get quite a bit of tool info currently from the API, but
   7 for the purposes of this workshop we won't fill this module out except for the
   8 upload_hda function.)
   9 
  10 Allows us to create an HDA by uploading a file.
  11 """
  12 import os
  13 import sys
  14 import pprint
  15 
  16 import setup
  17 import common
  18 
  19 # This script is from scripts/api in your galaxy installation and (unfortunately) relies
  20 #   on the requests module (available from See http://docs.python-requests.org/en/latest/)
  21 # It does most of the heavy lifting for getting a file into the API call and - for the
  22 #   purposes of the workshop - this section won't be explained in full
  23 import upload_to_history
  24 
  25 RESOURCE_URL = '/api/tools'
  26 
  27 # ----------------------------------------------------------------------------- functions
  28 def upload_hda( history_id, filepath ):
  29     """
  30     Use the upload_to_history script to upload the file at `filepath`
  31     to the history with the id `history_id`.
  32     :param history_id: the id of the history where the new HDA will be created
  33     :param filepath: the local OS path and filename of the file to upload
  34     """
  35     apikey = setup.get_apikey()
  36     # upload_to_history builds it's own url - so we only need to send in the base
  37     base_url = setup.get_base_url()
  38     return upload_to_history.upload_file( base_url, apikey, history_id, filepath )
  39 
  40 
  41 # ----------------------------------------------------------------------------- main
  42 if __name__ == '__main__':
  43     # this time two arguments:
  44     if len( sys.argv ) <= 2:
  45         print 'USAGE: hdas_1.py <history id> <filepath to upload>'
  46         sys.exit( 1 )
  47 
  48     history_id = sys.argv[1]
  49     filepath   = sys.argv[2]
  50     returned = upload_hda( history_id, filepath )
  51     pprint.pprint( returned, indent=2 )

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  • [get | view] (2013-06-24 16:01:09, 8.2 KB) [[attachment:Galaxy-Workflow-Joined_Solexa_QC.ga]]
  • [get | view] (2013-06-24 16:46:36, 14.0 KB) [[attachment:all-scripts.tar.gz]]
  • [get | view] (2013-06-24 16:01:23, 5.2 KB) [[attachment:common.py]]
  • [get | view] (2013-06-24 16:04:07, 0.9 KB) [[attachment:datasets_1.py]]
  • [get | view] (2013-06-24 16:04:15, 1.2 KB) [[attachment:datasets_2.py]]
  • [get | view] (2013-06-24 16:04:22, 3.4 KB) [[attachment:datasets_3.py]]
  • [get | view] (2013-06-24 16:04:33, 1.5 KB) [[attachment:hdas_1.py]]
  • [get | view] (2013-06-24 16:04:50, 1.7 KB) [[attachment:hdas_2.py]]
  • [get | view] (2013-06-24 16:05:07, 2.2 KB) [[attachment:hdas_3.py]]
  • [get | view] (2013-06-24 16:03:38, 0.9 KB) [[attachment:histories_1.py]]
  • [get | view] (2013-06-24 16:03:52, 2.1 KB) [[attachment:histories_2.py]]
  • [get | view] (2013-06-24 16:05:25, 2.2 KB) [[attachment:histories_3.py]]
  • [get | view] (2013-06-24 16:05:34, 3.3 KB) [[attachment:lddas_1.py]]
  • [get | view] (2013-06-24 16:05:41, 1.3 KB) [[attachment:libraries_1.py]]
  • [get | view] (2013-06-24 16:01:36, 0.8 KB) [[attachment:setup.py]]
  • [get | view] (2013-06-24 16:02:45, 1.1 KB) [[attachment:step_1.py]]
  • [get | view] (2013-06-24 16:07:15, 9.9 KB) [[attachment:step_10.py]]
  • [get | view] (2013-06-24 16:03:28, 1.4 KB) [[attachment:step_2.py]]
  • [get | view] (2013-06-24 16:06:01, 1.6 KB) [[attachment:step_3.py]]
  • [get | view] (2013-06-24 16:06:11, 1.1 KB) [[attachment:step_4.py]]
  • [get | view] (2013-06-24 16:06:20, 1.9 KB) [[attachment:step_5.py]]
  • [get | view] (2013-06-24 16:06:44, 2.5 KB) [[attachment:step_6.py]]
  • [get | view] (2013-06-24 16:06:53, 4.9 KB) [[attachment:step_7.py]]
  • [get | view] (2013-06-24 16:07:05, 5.9 KB) [[attachment:step_8.py]]
  • [get | view] (2013-06-30 13:51:46, 8.0 KB) [[attachment:step_9.py]]
  • [get | view] (2013-06-24 16:41:51, 1.8 KB) [[attachment:tools_1.py]]
  • [get | view] (2013-06-24 16:44:32, 2.0 KB) [[attachment:upload_to_history.py]]
  • [get | view] (2013-06-24 16:03:03, 1.3 KB) [[attachment:users_1.py]]
  • [get | view] (2013-06-24 16:44:44, 2.9 KB) [[attachment:workflows_1.py]]
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