#                                                                                      #
#   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 Workflow, Task, Link, Parameter, Type, Datatype, Biotype, Parser  #@UnusedImport

print __file__

if __name__ == "__main__":
    
    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'
 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]