def parseService(self):
"""
initializes the self.service and self.servicePID properties corresponding to the service url
uses self.programUrl or self.workflowUrl
"""
if hasattr(self,'programUrl'):
self.service = parseService(self.programUrl)
self.servicePID = registry.programsByUrl[self.programUrl].pid
elif hasattr(self,'workflowUrl'):
mp = Parser()
self.service = mp.parse(self.workflowUrl)
self.service.url = self.workflowUrl
self.servicePID = registry.workflowsByUrl[ self.workflowUrl ].pid
l2 = Link()
l2.to_task = t1.id
l2.from_parameter = "2"
l2.to_parameter = "outputformat"
l3 = Link()
l3.from_task = t1.id
l3.to_task = t2.id
l3.from_parameter = "aligfile"
l3.to_parameter = "infile"
l4 = Link()
l4.from_task = t2.id
l4.from_parameter = "outfile"
l4.to_parameter = "3"
wf.tasks = [t1, t2]
wf.links = [l1, l2, l3, l4]
wf.parameters = [input, output_format, output]
mp = Parser()
print mp.tostring(wf)
wffile = open( '/tmp/workflow.xml', 'w' )
wffile.write( mp.tostring(wf))
wffile.close()
print mp.parse('/tmp/workflow.xml')
def setUp(self):
self.p = Parser()
class WorkflowTest(unittest.TestCase):
"""Tests the functionalities of Workflow"""
def setUp(self):
self.p = Parser()
def tearDown(self):
pass
def testSimpleCreate(self):
wf = Workflow()
wffile = tempfile.NamedTemporaryFile( prefix='mobyle_workflow' )
path = wffile.name
wffile.write( self.p.tostring(wf))
wffile.flush()
wf = self.p.parse(path)
self.assertTrue(isinstance(wf, Workflow))
wffile.close()
def testCreation(self):
wf = Workflow()
wf.name = 'toto'
wf.version = '1.1'
wf.title = 'test workflow'
wf.description = 'this workflow is a test one'
t1 = Task()
t1.id = 1
t1.service = 'clustalw-multialign'
t1.suspend = False
t1.description = "Run a clustalw"
t2 = Task()
t2.id = 2
t2.service = 'protdist'
t2.suspend = True
t2.description = "Run a protdist"
input = Parameter()
input.id = '1'
input.name = 'sequences'
input.prompt = 'Input sequences'
input.type = Type()
input.type.datatype = Datatype()
input.type.datatype.class_name = "Sequence"
input.type.biotypes = [Biotype("Protein")]
output_format = Parameter()
output_format.id = '2'
output_format.name = 'alignment_format'
output_format.prompt = 'Alignment format'
output_format.type = Type()
output_format.type.datatype = Datatype()
output_format.type.datatype.class_name = "String"
output = Parameter()
output.id = '3'
output.isout = True
output.name = 'matrix'
output.prompt = 'Distance matrix'
output.type = Type()
output.type.datatype = Datatype()
output.type.datatype.class_name = "Matrix"
output.type.datatype.superclass_name = "AbstractText"
output.type.biotypes = [Biotype("Protein")]
l1 = Link()
l1.to_task = t1.id
l1.from_parameter = "1"
l1.to_parameter = "infile"
l2 = Link()
l2.to_task = t1.id
l2.from_parameter = "2"
l2.to_parameter = "outputformat"
l3 = Link()
l3.from_task = t1.id
l3.to_task = t2.id
l3.from_parameter = "aligfile"
l3.to_parameter = "infile"
l4 = Link()
l4.from_task = t2.id
l4.from_parameter = "outfile"
l4.to_parameter = "3"
wf.tasks = [t1, t2]
wf.links = [l1, l2, l3, l4]
wf.parameters = [input, output_format, output]
########################################################################################
# #
# Author: Herve Menager, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
from Mobyle.Workflow import Parser
from Mobyle.WorkflowJob import WorkflowJob
if __name__ == "__main__":
mp = Parser()
#wf = mp.parse('/tmp/workflow.xml') # 1st example
wf = mp.parse('/tmp/workflow2.xml') # 2nd example
class SessionFake(object):
def getKey(self):
return "workflowjobdemotestmodule"
wf.owner = SessionFake()
parameters = {'sequences': """>A
TTTT
>B
TATA""",
'alignment_format': 'PHYLIP'}
wj = WorkflowJob(workflow=wf,email='*****@*****.**')
print wj.id
#for key, value in parameters.items(): # set values for 1st example
# wj.set_value(key, value)
########################################################################################
# #
# Author: Herve Menager, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
from Mobyle.Workflow import Parser
if __name__ == "__main__":
mp = Parser()
wf = mp.parse("/tmp/workflow.xml")
class SessionFake(object):
def getKey(self):
return "workflowjobdemotestmodule"
wf.owner = SessionFake()
parameters = {
"sequences": """>A
TTTT
>B
TATA""",
"alignment_format": "PHYLIP",
"email": "*****@*****.**",
}
import Mobyle.JobFacade