コード例 #1
0
 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   
コード例 #2
0
    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')
コード例 #3
0
 def setUp(self):
     self.p = Parser()
コード例 #4
0
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]        
コード例 #5
0
########################################################################################
#                                                                                      #
#   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)
コード例 #6
0
########################################################################################
#                                                                                      #
#   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