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########################################################################################
# #
# Author: Herve Menager, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
MOBYLEHOME = None
import os
import sys
if os.environ.has_key('MOBYLEHOME'):
MOBYLEHOME = os.environ['MOBYLEHOME']
if not MOBYLEHOME:
sys.exit('MOBYLEHOME must be defined in your environment')
if ( os.path.join( MOBYLEHOME , 'Src' ) ) not in sys.path:
sys.path.append( os.path.join( MOBYLEHOME , 'Src' ) )
import urllib, urllib2, cookielib #@UnresolvedImport
from Mobyle.ConfigManager import Config
from Workflow import Parser
if __name__ == "__main__":
cfg = Config()
url = cfg.cgi_url()+'/workflow.py'
# the cookie jar keeps the Mobyle session cookie in a warm place, so that
# all the HTTP requests connect to the same workspace
cj = cookielib.CookieJar()
opener = urllib2.build_opener(urllib2.HTTPHandler(debuglevel=1),urllib2.HTTPCookieProcessor(cj))
mp = Parser()
def get_str(params):
data = urllib.urlencode(params)
req = urllib2.Request(url, data)
handle = opener.open(req)
str = handle.read()
return str.strip('\n')
def get_xml(params):
return mp.XML(get_str(params))
# create a workflow and store its id
params = {
'object':'workflow',
'action':'create'
}
w = get_xml(params)
print w
# edit workflow properties
params = {
'object':'workflow',
'action':'update',
'workflow_id':w.id,
'description':'test workflow description',
'title':'test workflow title',
}
w = get_xml(params)
print w
# create the clustalw-multialign task
params = {
'object':'task',
'action':'create',
'workflow_id':w.id,
'service_pid':'clustalw-multialign',
'suspend':'false',
'description':'Run a clustalw',
'parameter::infile':""">A
TTTT
>B
TATA""",
'parameter::outputformat':'PHYLIP'
}
t = get_xml(params)
print t
# create the protdist task
params = {
'object':'task',
'action':'create',
'workflow_id':w.id,
'service_pid':'protdist',
'suspend':'true',
'description':'Run a protdist',
'from_task': '1',
'from_parameter': 'aligfile',
'to_task': 'self',
'to_parameter': 'infile'
}
t = get_xml(params)
print t
# get the workflow
params = {
'object':'workflow',
'action':'get',
'workflow_id':w.id
}
w = get_xml(params)
print mp.tostring(w)
# get the workflow
params = {
'object':'workflow',
'action':'get_url',
'workflow_id':w.id
}
w = get_str(params)
print "created workflow definition: %s" % w
#
# list the session workflow IDs...
params = {
'object':'workflow',
'action':'list'
}
l = get_str(params)
print "list of workflow definitions for current session: %s" % l
url = cfg.cgi_url()+'/session_job_submit.py'
params = {'workflowUrl': w}
resp = get_str(params)
print resp
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