Developing Splicer

These are some special instructions for developing splicer components.

Django Settings

Django and its ORM can be used outside of its webserver. The only requirements are
  • the directory containing is on the sys.path
  • environment variable DJANGO_SETTINGS_MODULE is set to the settings

Splicer components should all do this automatically using python code to add the correct directory to sys.path. This works as long as the components are run from the directory containing

import os, sys
#python magic to add the current directory to the pythonpath

# ----------------------------------------------------------
# Setup django environment
# ----------------------------------------------------------
if not os.environ.has_key('DJANGO_SETTINGS_MODULE'):
os.environ['DJANGO_SETTINGS_MODULE'] - 'settings
# ----------------------------------------------------------
# Done setting up django environment
# ----------------------------------------------------------

Running Components from the command line

Splicer Subtasks all contain main code that starts the tasks using arguments passed in. All should give you a list of required arguments if you do not pass them in. The main intention of this is to allow easier debugging on tasks.

For example ProcessPDBTask requires a pdb code followed by resolution, threshold, rfactor, and rfree. For testing purposing the properties do not need to be real values.

~/pgd/pgd $ ./pgd_splicer/ 12SB 1 2 3 4