Commit 0cfaa334 authored by aknecht2's avatar aknecht2
Browse files

Removed all instances of prefix in workflow_module. Fixed setup_job_params to...

Removed all instances of prefix in workflow_module.  Fixed setup_job_params to correctly index files from the master_files list.
parent 4af598a8
......@@ -170,17 +170,16 @@ class WorkflowModule(object):
job_names.append(job_dict.keys()[0])
return job_names
def add_jobs(self, dax, master_jobs, master_files, prefix, markers, inputs, additional_inputs, outputs):
def add_jobs(self, dax, master_jobs, master_files, markers, inputs, additional_inputs, outputs):
"""
dax -- The pegasus dax object from workflow
master_jobs -- A dictionary that maps jobname -> Job object
master_files -- A dicitonary that maps filename -> File object
prefix -- Used to prefix file and jobnames
markers -- Dictionary for splitting within module
inputs -- Dictionary of input_file name -> master_files index OR input argument name -> value
additional_files -- dictionary of additional_file name -> master_files index
"""
valid, msg = self._check_params(master_files, prefix, markers, inputs, additional_inputs, outputs)
valid, msg = self._check_params(master_files, markers, inputs, additional_inputs, outputs)
if valid:
self._traverse_jobs(dax, master_jobs, master_files, markers, inputs, additional_inputs, outputs)
else:
......@@ -205,7 +204,7 @@ class WorkflowModule(object):
"""
valid_markers, msg = self._check_input_markers(markers)
if valid_markers:
required_inputs, required_additional_inputs, required_outputs = self._load_required_params(markers, prefix = prefix, master_files = master_files)
required_inputs, required_additional_inputs, required_outputs = self._load_required_params(master_files, markers)
valid_inputs, input_msg = self._check_required_params(master_files, required_inputs, inputs, "inputs")
valid_additional, additional_msg = self._check_required_params(master_files, required_additional_inputs, additional_inputs, "additional_inputs")
valid_outputs, outputs_msg = self._check_required_params(master_files, required_outputs, outputs, "outputs")
......@@ -363,13 +362,9 @@ class WorkflowModule(object):
param_name = job_dict.keys()[0]
param = job_dict[param_name]
if param["type"] in chipathlon.conf.argument_types["file"]:
full_name = self._get_full_name(prefix, markers, param_name)
# If file is an output file, add to master_files
if param_type == "outputs":
master_files[full_name] = File(full_name)
param_list.append({
"name": full_name if full_name in master_files else param_dict[param_name],
"file": master_files[full_name] if full_name in master_files else master_files[param_dict[param_name]],
"name": param_dict[param_name],
"file": master_files[param_dict[param_name]],
"type": param["type"]
})
else:
......
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