Ejemplo n.º 1
0
 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]        
Ejemplo n.º 2
0
    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"
    
Ejemplo n.º 3
0
>B
TATA
"""
    iv2 = InputValue()
    iv2.name = 'outputformat'
    iv2.value = 'PHYLIP'

    t1.input_values = [iv,iv2]
    
    t2 = Task()
    t2.id = 2
    t2.service = 'protdist'
    t2.suspend = True
    t2.description = "Run a protdist"
    
    l = Link()
    l.from_task = t1.id
    l.to_task = t2.id
    l.from_parameter = "aligfile"
    l.to_parameter = "infile"
    
    wf.tasks = [t1, t2]
    wf.links = [l]

    mp = Parser()
    
    print mp.tostring(wf)
    
    wffile = open( '/tmp/workflow2.xml', 'w' )
    wffile.write( mp.tostring(wf)) 
    wffile.close()