def addWriter(self, writerName, outputPath):
"""
Add to the computational scheme a new write element of the supplied type,
set its output file path and get the element's name
"""
absPath = serializer.getUnixAbsPath(outputPath)
return super(Scheme, self).addWriter(unicode(writerName), absPath)
def addWriter( self, writerName, outputPath ) :
"""
Add to the computational scheme a new write element of the supplied type,
set its output file path and get the element's name
"""
absPath = serializer.getUnixAbsPath( outputPath )
return super( Scheme, self ).addWriter( unicode( writerName ), absPath )
def __init__( self, *args ) :
argCount = len( args )
if 1 == argCount :
schemeFilePath = serializer.getUnixAbsPath( args[0] )
super( Scheme, self ).__init__( unicode( schemeFilePath ) )
elif 1 < argCount :
algorithmName = args[0]
inputData = self._serializer.bioListToString( args[1], True )
outputData = self._serializer.createTmpFileAndGetItsPath( )
if 3 == argCount :
outputData = serializer.getUnixAbsPath( args[2] )
elif 3 < argCount :
raise TypeError( 'expected 3 or less arguments' )
super( Scheme, self ).__init__( unicode( algorithmName ), unicode( inputData ), unicode( outputData ) )
else :
super( Scheme, self ).__init__( )
def __init__(self, *args):
argCount = len(args)
if 1 == argCount:
schemeFilePath = serializer.getUnixAbsPath(args[0])
super(Scheme, self).__init__(unicode(schemeFilePath))
elif 1 < argCount:
algorithmName = args[0]
inputData = self._serializer.bioListToString(args[1], True)
outputData = self._serializer.createTmpFileAndGetItsPath()
if 3 == argCount:
outputData = serializer.getUnixAbsPath(args[2])
elif 3 < argCount:
raise TypeError('expected 3 or less arguments')
super(Scheme, self).__init__(unicode(algorithmName),
unicode(inputData),
unicode(outputData))
else:
super(Scheme, self).__init__()
def launchSas( *args ) :
"""
Create and run the Single Algorithm Scheme synchronously by the Workflow Designer
"""
tempSerializer = serializer.Serializer( )
argumentCount = len( args )
if not 2 <= argumentCount <= 3 :
raise RuntimeError( 'expected 2 or 3 arguments' )
algorithmName = args[0]
outputString = unicode( '' )
if 2 == argumentCount :
outputString = tempSerializer.createTmpFileAndGetItsPath( )
elif 3 == argumentCount :
outputString = serializer.getUnixAbsPath( args[2] )
inputString = tempSerializer.bioListToString( args[1], True )
resultList = u2py_internals.Scheme.launchSas( unicode( algorithmName ), inputString, outputString )
if 2 == argumentCount :
resultList = tempSerializer.stringListToBioList( resultList )
tempSerializer.cleanUp( )
return resultList
def launchSas(*args):
"""
Create and run the Single Algorithm Scheme synchronously by the Workflow Designer
"""
tempSerializer = serializer.Serializer()
argumentCount = len(args)
if not 2 <= argumentCount <= 3:
raise RuntimeError('expected 2 or 3 arguments')
algorithmName = args[0]
outputString = unicode('')
if 2 == argumentCount:
outputString = tempSerializer.createTmpFileAndGetItsPath()
elif 3 == argumentCount:
outputString = serializer.getUnixAbsPath(args[2])
inputString = tempSerializer.bioListToString(args[1], True)
resultList = u2py_internals.Scheme.launchSas(unicode(algorithmName),
inputString, outputString)
if 2 == argumentCount:
resultList = tempSerializer.stringListToBioList(resultList)
tempSerializer.cleanUp()
return resultList
def initContext(workingDirectory):
return u2py_internals.initContext(
serializer.getUnixAbsPath(workingDirectory))
def initContext( workingDirectory ) :
return u2py_internals.initContext( serializer.getUnixAbsPath( workingDirectory ) )
