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cwl_engine management of arrays of inputs about wfexs-backend HOT 2 CLOSED

jmfernandez commented on August 18, 2024

cwl_engine management of arrays of inputs

from wfexs-backend.

Comments (2)

lrodrin commented on August 18, 2024

added cases to manage arrays of files and strings in executionInputs:

WfExS-backend/wfexs_backend/cwl_engine.py

Lines 516 to 566 in 92d8dd1

 def executionInputs(self, matInputs: List[MaterializedInput], cwlInputs): 

 """ 

  Setting execution inputs needed to execute the workflow 

  """ 

 if len(matInputs) == 0: # Is list of materialized inputs empty? 

 raise WorkflowEngineException("FATAL ERROR: Execution with no inputs") 

 if len(cwlInputs) == 0: # Is list of declared inputs empty? 

 raise WorkflowEngineException("FATAL ERROR: Workflow with no declared inputs") 

 execInputs = dict() 

 for matInput in matInputs: 

 if isinstance(matInput, MaterializedInput): # input is a MaterializedInput 

 # numberOfInputs = len(matInput.values) # number of inputs inside a MaterializedInput 

 for input_value in matInput.values: 

 name = matInput.name 

 value_type = cwlInputs.get(name, {}).get('type') 

 if value_type is None: 

 raise WorkflowEngineException("ERROR: input {} not available in workflow".format(name)) 

 value = input_value 

 if isinstance(value, MaterializedContent): # value of an input contains MaterializedContent 

 if value.kind in (ContentKind.Directory, ContentKind.File): 

 if not os.path.exists(value.local): 

 self.logger.warning("Input {} is not materialized".format(name)) 

 value_local = value.local 

 if isinstance(value_type, dict): 

 # MaterializedContent is a List of File and cwlInputs value_type is a dict 

 classType = value_type['items'] 

 execInputs.setdefault(name, []).append({"class": classType, "location": value_local}) 

 elif isinstance(value_type, list): 

 # MaterializedContent is a List of File and cwlInputs value_type is a list 

 classType = value_type[1]['items'] 

 execInputs.setdefault(name, []).append({"class": classType, "location": value_local}) 

 else: # MaterializedContent is a File 

 classType = value_type 

 execInputs[name] = {"class": classType, "location": value_local} 

 else: 

 raise WorkflowEngineException( 

 "ERROR: Input {} has values of type {} this code does not know how to handle".format( 

 name, value.kind)) 

 else: 

 if isinstance(value_type, list): # argument is a list 

 if isinstance(value_type[1], dict) and value_type[1]['type'] == "array": 

 execInputs.setdefault(name, []).append(value) 

 else: 

 execInputs[name] = value # TODO add more value types 

 else: 

 execInputs[name] = value 

 return execInputs

from wfexs-backend.

jmfernandez commented on August 18, 2024

Fixed along several commits. The issue arose when some input or output has more than one possible type. These cases are quite common in CWL, so it needed several refinements. Commits d3363a1 , 2062e81 , bc0da5f , 3a75c97 , 0f4c029 led to the proper handling of this use case

from wfexs-backend.

cwl_engine management of arrays of inputs about wfexs-backend HOT 2 CLOSED

Comments (2)

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	def executionInputs(self, matInputs: List[MaterializedInput], cwlInputs):
	"""
	Setting execution inputs needed to execute the workflow
	"""
	if len(matInputs) == 0: # Is list of materialized inputs empty?
	raise WorkflowEngineException("FATAL ERROR: Execution with no inputs")

	if len(cwlInputs) == 0: # Is list of declared inputs empty?
	raise WorkflowEngineException("FATAL ERROR: Workflow with no declared inputs")

	execInputs = dict()
	for matInput in matInputs:
	if isinstance(matInput, MaterializedInput): # input is a MaterializedInput
	# numberOfInputs = len(matInput.values) # number of inputs inside a MaterializedInput
	for input_value in matInput.values:
	name = matInput.name
	value_type = cwlInputs.get(name, {}).get('type')
	if value_type is None:
	raise WorkflowEngineException("ERROR: input {} not available in workflow".format(name))

	value = input_value
	if isinstance(value, MaterializedContent): # value of an input contains MaterializedContent
	if value.kind in (ContentKind.Directory, ContentKind.File):
	if not os.path.exists(value.local):
	self.logger.warning("Input {} is not materialized".format(name))
	value_local = value.local
	if isinstance(value_type, dict):
	# MaterializedContent is a List of File and cwlInputs value_type is a dict
	classType = value_type['items']
	execInputs.setdefault(name, []).append({"class": classType, "location": value_local})
	elif isinstance(value_type, list):
	# MaterializedContent is a List of File and cwlInputs value_type is a list
	classType = value_type[1]['items']
	execInputs.setdefault(name, []).append({"class": classType, "location": value_local})
	else: # MaterializedContent is a File
	classType = value_type
	execInputs[name] = {"class": classType, "location": value_local}
	else:
	raise WorkflowEngineException(
	"ERROR: Input {} has values of type {} this code does not know how to handle".format(
	name, value.kind))
	else:
	if isinstance(value_type, list): # argument is a list
	if isinstance(value_type[1], dict) and value_type[1]['type'] == "array":
	execInputs.setdefault(name, []).append(value)
	else:
	execInputs[name] = value # TODO add more value types
	else:
	execInputs[name] = value

	return execInputs