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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.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',
}
t = get_xml(params)
print t
# edit the clustalw-multialign task
params = {
'object':'task',
'action':'update',
'workflow_id':w.id,
'task_id':t.id,
'suspend':'false',
'description':'Run a clustalw',
}
t = get_xml(params)
print t
# create the protdist task
params = {
'object':'task',
'action':'create',
'workflow_id':w.id,
'service_pid':'protdist',
}
t = get_xml(params)
print t
# edit the protdist task
params = {
'object':'task',
'action':'update',
'workflow_id':w.id,
'task_id':t.id,
'suspend':'true',
'description':'Run a protdist',
}
t = get_xml(params)
print t
# create the sequences input parameter
params = {
'object':'parameter',
'action':'create',
'workflow_id':w.id,
'stream':'input',
}
p = get_xml(params)
print p
# edit the sequences parameter
params = {
'object':'parameter',
'action':'update',
'workflow_id':w.id,
'parameter_id':p.id,
'name': 'sequences',
'prompt': 'Input sequences',
'example': """>R
AAATA
>S
AAATT
""",
'datatype_class': 'Sequence',
'biotype':'Protein'
}
p = get_xml(params)
print p
# create the format input parameter
params = {
'object':'parameter',
'action':'create',
'workflow_id':w.id,
'stream':'input',
}
p = get_xml(params)
print p
# edit the sequences parameter
params = {
'object':'parameter',
'action':'update',
'workflow_id':w.id,
'parameter_id':p.id,
'name': 'alignment_format',
'prompt': 'Alignment format',
'datatype_class': 'String'
}
p = get_xml(params)
print p
# create the matrix output parameter
params = {
'object':'parameter',
'action':'create',
'workflow_id':w.id,
'stream':'output',
}
p = get_xml(params)
print p
# edit the matrix output parameter
params = {
'object':'parameter',
'action':'update',
'workflow_id':w.id,
'parameter_id':p.id,
'name': 'matrix',
'prompt': 'Distance matrix',
'datatype_class': 'Matrix',
'datatype_superclass': 'AbstractText',
'biotype':'Protein'
}
p = get_xml(params)
print p
# create the sequences-to-clustalw link
params = {
'object':'link',
'action':'create',
'workflow_id':w.id,
}
l = get_xml(params)
print l
# edit the sequences-to-clustalw link
params = {
'object':'link',
'action':'update',
'workflow_id':w.id,
'link_id':l.id,
'from_parameter': '1',
'to_task': '1',
'to_parameter': 'infile'
}
p = get_xml(params)
print p
# create the alig_format-to-clustalw link
params = {
'object':'link',
'action':'create',
'workflow_id':w.id,
}
l = get_xml(params)
print l
# edit the alig_format-to-clustalw link
params = {
'object':'link',
'action':'update',
'workflow_id':w.id,
'link_id':l.id,
'from_parameter': '2',
'to_task': '1',
'to_parameter': 'outputformat'
}
p = get_xml(params)
print p
# create the clustalw-to-protdist link
params = {
'object':'link',
'action':'create',
'workflow_id':w.id,
}
l = get_xml(params)
print l
# edit the clustalw-to-protdist link
params = {
'object':'link',
'action':'update',
'workflow_id':w.id,
'link_id':l.id,
'from_task': '1',
'from_parameter': 'aligfile',
'to_task': '2',
'to_parameter': 'infile'
}
p = get_xml(params)
print p
# create the protdist-to-output link
params = {
'object':'link',
'action':'create',
'workflow_id':w.id,
}
l = get_xml(params)
print l
# edit the protdist-to-output link
params = {
'object':'link',
'action':'update',
'workflow_id':w.id,
'link_id':l.id,
'from_task': '2',
'from_parameter': 'outfile',
'to_parameter': '3'
}
p = get_xml(params)
print p
# get the workflow
params = {
'object':'workflow',
'action':'get',
'workflow_id':w.id
}
w = get_xml(params)
print 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,
'sequences': """>A
TTTT
>B
TATA""",
'alignment_format': 'PHYLIP',
'email': 'hmenager@pasteur.fr'}
resp = get_str(params)
print resp
|
