def add_output(self, split_id, key, value, is_path=True, **kwargs):
# Check that split id exists
if split_id not in self.output:
logging.error(
"In module %s, cannot add output of type '%s' to undeclared split with id '%s'!"
% (self.module_id, key, split_id))
raise RuntimeError(
"Splitter attempted to add output to undeclared split!")
# Check that output type hasn't already been set
if key in self.output[split_id]:
logging.error(
"In module %s, the output key '%s' is defined multiple times in same split (split_id: %s)!"
% (self.module_id, key, split_id))
raise RuntimeError(
"Output key '%s' has been defined multiple times within the same split!"
% key)
# Convert paths to GAPFiles if they haven't already been converted
if is_path and not isinstance(value, GAPFile) and value is not None:
file_id = "%s.%s.%s" % (self.module_id, split_id, key)
self.output[split_id][key] = GAPFile(file_id,
file_type=key,
path=value,
**kwargs)
# Otherwise just set the value
else:
self.output[split_id][key] = value
def __make_gap_files(self):
# Convert path strings to GAPFile objects
for path_type, paths in self.paths.items():
# More than one path of same type
if isinstance(paths, list):
for i in range(len(paths)):
file_id = "%s_%s_%s" % (self.name, path_type, i)
self.paths[path_type][i] = GAPFile(file_id,
path_type,
paths[i],
sample_name=self.name)
# One path of a given type
else:
file_id = "%s_%s_1" % (self.name, path_type)
self.paths[path_type] = GAPFile(file_id,
path_type,
paths,
sample_name=self.name)
def __init_resource_files(self):
# Parse resources listed in configs and convert to config objects
# Return dictionary of resource objects indexed by resource name
resources = {}
for resource_id, resource_data in self.config["Path"].items():
path = resource_data.pop("path")
resource_type = resource_data.pop("resource_type")
resources[resource_id] = GAPFile(resource_id, resource_type, path,
**resource_data)
return resources
def __init_resource_files(self):
# Parse resources available to docker image
# Return dictionary of resource objects indexed by resource name
resources = {}
for resource_id, resource_data in self.config.items():
path = resource_data.pop("path")
resource_type = resource_data.pop("resource_type")
resources[resource_id] = GAPFile(resource_id, resource_type, path,
**resource_data)
resources[resource_id].flag("docker")
return resources
def add_output(self, key, value, is_path=True, **kwargs):
if key in self.output:
logging.error(
"In module %s, the output key '%s' is defined multiple time!" %
(self.module_id, key))
raise RuntimeError(
"Output key '%s' has been defined multiple times!" % key)
if is_path and not isinstance(value, GAPFile) and value is not None:
# Convert paths to GAPFiles if they haven't already been converted
file_id = "%s.%s" % (self.module_id, key)
value = GAPFile(file_id, file_type=key, path=value, **kwargs)
self.output[key] = value
def generate_gapfile(self, key, value, **kwargs):
# Generate file id
file_id = "%s.%s" % (self.module_id, key)
return GAPFile(file_id, file_type=key, path=value, **kwargs)