def __populate_output_dataset_wrappers(self, param_dict, output_datasets, job_working_directory):
for name, hda in output_datasets.items():
# Write outputs to the working directory (for security purposes)
# if desired.
param_dict[name] = DatasetFilenameWrapper(hda, compute_environment=self.compute_environment, io_type="output")
output_path = str(param_dict[name])
# Conditionally create empty output:
# - may already exist (e.g. symlink output)
# - parent directory might not exist (e.g. Pulsar)
if not os.path.exists(output_path) and os.path.exists(os.path.dirname(output_path)):
open(output_path, 'w').close()
# Provide access to a path to store additional files
# TODO: move compute path logic into compute environment, move setting files_path
# logic into DatasetFilenameWrapper. Currently this sits in the middle and glues
# stuff together inconsistently with the way the rest of path rewriting works.
file_name = hda.dataset.extra_files_path_name
param_dict[name].files_path = os.path.abspath(os.path.join(job_working_directory, "working", file_name))
for out_name, output in self.tool.outputs.items():
if out_name not in param_dict and output.filters:
# Assume the reason we lack this output is because a filter
# failed to pass; for tool writing convienence, provide a
# NoneDataset
ext = getattr(output, "format", None) # populate only for output datasets (not collections)
param_dict[out_name] = NoneDataset(datatypes_registry=self.app.datatypes_registry, ext=ext)
def __populate_output_dataset_wrappers(self, param_dict, output_datasets, output_paths, job_working_directory):
output_dataset_paths = dataset_path_rewrites( output_paths )
for name, hda in output_datasets.items():
# Write outputs to the working directory (for security purposes)
# if desired.
real_path = hda.file_name
if real_path in output_dataset_paths:
dataset_path = output_dataset_paths[ real_path ]
param_dict[name] = DatasetFilenameWrapper( hda, dataset_path=dataset_path )
try:
open( dataset_path.false_path, 'w' ).close()
except EnvironmentError:
pass # May well not exist - e.g. Pulsar.
else:
param_dict[name] = DatasetFilenameWrapper( hda )
# Provide access to a path to store additional files
# TODO: path munging for cluster/dataset server relocatability
param_dict[name].files_path = os.path.abspath(os.path.join( job_working_directory, "dataset_%s_files" % (hda.dataset.id) ))
for child in hda.children:
param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child )
for out_name, output in self.tool.outputs.iteritems():
if out_name not in param_dict and output.filters:
# Assume the reason we lack this output is because a filter
# failed to pass; for tool writing convienence, provide a
# NoneDataset
ext = getattr( output, "format", None ) # populate only for output datasets (not collections)
param_dict[ out_name ] = NoneDataset( datatypes_registry=self.app.datatypes_registry, ext=ext )
def __populate_output_dataset_wrappers(self, param_dict, output_datasets, output_paths, job_working_directory):
output_dataset_paths = dataset_path_rewrites( output_paths )
for name, hda in output_datasets.items():
# Write outputs to the working directory (for security purposes)
# if desired.
real_path = hda.file_name
if real_path in output_dataset_paths:
dataset_path = output_dataset_paths[ real_path ]
param_dict[name] = DatasetFilenameWrapper( hda, dataset_path=dataset_path )
try:
open( dataset_path.false_path, 'w' ).close()
except EnvironmentError:
pass # May well not exist - e.g. Pulsar.
else:
param_dict[name] = DatasetFilenameWrapper( hda )
# Provide access to a path to store additional files
# TODO: path munging for cluster/dataset server relocatability
param_dict[name].files_path = os.path.abspath(os.path.join( job_working_directory, "dataset_%s_files" % (hda.dataset.id) ))
for child in hda.children:
param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child )
for out_name, output in self.tool.outputs.iteritems():
if out_name not in param_dict and output.filters:
# Assume the reason we lack this output is because a filter
# failed to pass; for tool writing convienence, provide a
# NoneDataset
ext = getattr( output, "format", None ) # populate only for output datasets (not collections)
param_dict[ out_name ] = NoneDataset( datatypes_registry=self.app.datatypes_registry, ext=ext )