def collect_outputs(self, output_directory):
assert self._outputs_dict is None
outputs_dict = {}
if not output_directory:
# TODO: rather than creating a directory just use
# Galaxy paths if they are available in this
# configuration.
output_directory = tempfile.mkdtemp()
for output in get_outputs(self._runnable):
output_id = output.get_id()
dataset = self.get_dataset_metadata(output)
destination = self.download_output_to(output, output_directory)
if dataset["file_ext"] == "expression.json":
with open(destination, "r") as f:
dict_value = json.load(f)
else:
dict_value = {
"path": destination,
"class": "File",
}
outputs_dict[output_id] = dict_value
self._outputs_dict = outputs_dict
def collect_outputs(self, output_directory):
assert self._outputs_dict is None
outputs_dict = {}
if not output_directory:
# TODO: rather than creating a directory just use
# Galaxy paths if they are available in this
# configuration.
output_directory = tempfile.mkdtemp()
for output in get_outputs(self._runnable):
output_id = output.get_id()
dataset = self.get_dataset_metadata(output)
destination = self.download_output_to(output, output_directory)
if dataset["file_ext"] == "expression.json":
with open(destination, "r") as f:
dict_value = json.load(f)
else:
dict_value = {
"path": destination,
"class": "File",
}
outputs_dict[output_id] = dict_value
self._outputs_dict = outputs_dict
def test_outputs():
outputs = get_outputs(for_path(A_CWL_TOOL))
assert len(outputs) == 1
output_id = outputs[0].get_id()
assert output_id == "output_file"
def collect_outputs(self, ctx, output_directory):
assert self._outputs_dict is None, "collect_outputs pre-condition violated"
outputs_dict = {}
if not output_directory:
# TODO: rather than creating a directory just use
# Galaxy paths if they are available in this
# configuration.
output_directory = tempfile.mkdtemp()
def get_dataset(dataset_details, filename=None):
parent_basename = dataset_details.get("cwl_file_name")
if not parent_basename:
parent_basename = dataset_details.get("name")
file_ext = dataset_details["file_ext"]
if file_ext == "directory":
# TODO: rename output_directory to outputs_directory because we can have output directories
# and this is confusing...
the_output_directory = os.path.join(output_directory, parent_basename)
safe_makedirs(the_output_directory)
destination = self.download_output_to(dataset_details, the_output_directory, filename=filename)
else:
destination = self.download_output_to(dataset_details, output_directory, filename=filename)
if filename is None:
basename = parent_basename
else:
basename = os.path.basename(filename)
return {"path": destination, "basename": basename}
ctx.vlog("collecting outputs to directory %s" % output_directory)
for runnable_output in get_outputs(self._runnable):
output_id = runnable_output.get_id()
output_dict_value = None
if self._runnable.type in [RunnableType.cwl_workflow, RunnableType.cwl_tool]:
galaxy_output = self.to_galaxy_output(runnable_output)
cwl_output = output_to_cwl_json(
galaxy_output,
self._get_metadata,
get_dataset,
self._get_extra_files,
pseduo_location=True,
)
output_dict_value = cwl_output
else:
# TODO: deprecate this route for finding workflow outputs,
# it is a brittle and bad approach...
output_dataset_id = self.output_dataset_id(runnable_output)
dataset = self._get_metadata("dataset", output_dataset_id)
dataset_dict = get_dataset(dataset)
ctx.vlog("populated destination [%s]" % dataset_dict["path"])
if dataset["file_ext"] == "expression.json":
with open(dataset_dict["path"], "r") as f:
output_dict_value = json.load(f)
else:
output_dict_value = output_properties(**dataset_dict)
outputs_dict[output_id] = output_dict_value
self._outputs_dict = outputs_dict
ctx.vlog("collected outputs [%s]" % self._outputs_dict)
def collect_outputs(self, ctx, output_directory):
assert self._outputs_dict is None, "collect_outputs pre-condition violated"
outputs_dict = {}
if not output_directory:
# TODO: rather than creating a directory just use
# Galaxy paths if they are available in this
# configuration.
output_directory = tempfile.mkdtemp()
def get_dataset(dataset_details, filename=None):
parent_basename = dataset_details.get("cwl_file_name")
if not parent_basename:
parent_basename = dataset_details.get("name")
file_ext = dataset_details["file_ext"]
if file_ext == "directory":
# TODO: rename output_directory to outputs_directory because we can have output directories
# and this is confusing...
the_output_directory = os.path.join(output_directory, parent_basename)
safe_makedirs(the_output_directory)
destination = self.download_output_to(dataset_details, the_output_directory, filename=filename)
else:
destination = self.download_output_to(dataset_details, output_directory, filename=filename)
if filename is None:
basename = parent_basename
else:
basename = os.path.basename(filename)
return {"path": destination, "basename": basename}
ctx.vlog("collecting outputs to directory %s" % output_directory)
for runnable_output in get_outputs(self._runnable):
output_id = runnable_output.get_id()
if not output_id:
ctx.vlog("Workflow output identified without an ID (label), skipping")
continue
output_dict_value = None
if self._runnable.type in [RunnableType.cwl_workflow, RunnableType.cwl_tool]:
galaxy_output = self.to_galaxy_output(runnable_output)
cwl_output = output_to_cwl_json(
galaxy_output,
self._get_metadata,
get_dataset,
self._get_extra_files,
pseduo_location=True,
)
output_dict_value = cwl_output
else:
# TODO: deprecate this route for finding workflow outputs,
# it is a brittle and bad approach...
output_dataset_id = self.output_dataset_id(runnable_output)
dataset = self._get_metadata("dataset", output_dataset_id)
dataset_dict = get_dataset(dataset)
ctx.vlog("populated destination [%s]" % dataset_dict["path"])
if dataset["file_ext"] == "expression.json":
with open(dataset_dict["path"], "r") as f:
output_dict_value = json.load(f)
else:
output_dict_value = output_properties(**dataset_dict)
outputs_dict[output_id] = output_dict_value
self._outputs_dict = outputs_dict
ctx.vlog("collected outputs [%s]" % self._outputs_dict)
def collect_outputs(self, ctx, output_directory):
assert self._outputs_dict is None, "collect_outputs pre-condition violated"
outputs_dict = {}
if not output_directory:
# TODO: rather than creating a directory just use
# Galaxy paths if they are available in this
# configuration.
output_directory = tempfile.mkdtemp()
def get_dataset(dataset_details, filename=None):
parent_basename = dataset_details.get("cwl_file_name")
if not parent_basename:
parent_basename = dataset_details.get("name")
file_ext = dataset_details["file_ext"]
if file_ext == "directory":
# TODO: rename output_directory to outputs_directory because we can have output directories
# and this is confusing...
the_output_directory = os.path.join(output_directory, parent_basename)
safe_makedirs(the_output_directory)
destination = self.download_output_to(dataset_details, the_output_directory, filename=filename)
else:
destination = self.download_output_to(dataset_details, output_directory, filename=filename)
if filename is None:
basename = parent_basename
else:
basename = os.path.basename(filename)
return {"path": destination, "basename": basename}
ctx.vlog("collecting outputs to directory %s" % output_directory)
for runnable_output in get_outputs(self._runnable, gi=self._user_gi):
output_id = runnable_output.get_id()
if not output_id:
ctx.vlog("Workflow output identified without an ID (label), skipping")
continue
output_dict_value = None
is_cwl = self._runnable.type in [RunnableType.cwl_workflow, RunnableType.cwl_tool]
output_src = self.output_src(runnable_output)
if not is_cwl and output_src["src"] == "hda":
output_dataset_id = output_src["id"]
dataset = self._get_metadata("dataset", output_dataset_id)
dataset_dict = get_dataset(dataset)
ctx.vlog("populated destination [%s]" % dataset_dict["path"])
if dataset["file_ext"] == "expression.json":
with open(dataset_dict["path"], "r") as f:
output_dict_value = json.load(f)
else:
output_dict_value = output_properties(**dataset_dict)
else:
output_dataset_id = output_src["id"]
galaxy_output = self.to_galaxy_output(runnable_output)
cwl_output = output_to_cwl_json(
galaxy_output,
self._get_metadata,
get_dataset,
self._get_extra_files,
pseduo_location=True,
)
if is_cwl:
output_dict_value = cwl_output
else:
def attach_file_properties(collection, cwl_output):
elements = collection["elements"]
assert len(elements) == len(cwl_output)
for element, cwl_output_element in zip(elements, cwl_output):
element["_output_object"] = cwl_output_element
if isinstance(cwl_output_element, list):
assert "elements" in element["object"]
attach_file_properties(element["object"], cwl_output_element)
output_metadata = self._get_metadata("dataset_collection", output_dataset_id)
attach_file_properties(output_metadata, cwl_output)
output_dict_value = output_metadata
outputs_dict[output_id] = output_dict_value
self._outputs_dict = outputs_dict
ctx.vlog("collected outputs [%s]" % self._outputs_dict)
def test_outputs():
outputs = get_outputs(for_path(A_CWL_WORKFLOW))
assert len(outputs) == 1
output_id = outputs[0].get_id()
assert output_id == "count_output"
def test_outputs():
outputs = get_outputs(for_path(A_CWL_WORKFLOW))
assert len(outputs) == 1
output_id = outputs[0].get_id()
assert output_id == "count_output"
def collect_outputs(self, ctx, output_directory):
outputs_dict = {}
# TODO: rather than creating a directory just use
# Galaxy paths if they are available in this
# configuration.
output_directory = output_directory or tempfile.mkdtemp()
def get_dataset(dataset_details, filename=None):
parent_basename = dataset_details.get("cwl_file_name") or dataset_details.get("name")
file_ext = dataset_details["file_ext"]
if file_ext == "directory":
# TODO: rename output_directory to outputs_directory because we can have output directories
# and this is confusing...
the_output_directory = os.path.join(output_directory, parent_basename)
safe_makedirs(the_output_directory)
destination = self.download_output_to(ctx, dataset_details, the_output_directory, filename=filename)
else:
destination = self.download_output_to(ctx, dataset_details, output_directory, filename=filename)
if filename is None:
basename = parent_basename
else:
basename = os.path.basename(filename)
return {"path": destination, "basename": basename}
ctx.vlog("collecting outputs to directory %s" % output_directory)
for runnable_output in get_outputs(self._runnable, gi=self._user_gi):
output_id = runnable_output.get_id()
if not output_id:
ctx.vlog("Workflow output identified without an ID (label), skipping")
continue
output_dict_value = None
is_cwl = self._runnable.type in [RunnableType.cwl_workflow, RunnableType.cwl_tool]
output_src = self.output_src(runnable_output)
output_dataset_id = output_src["id"]
galaxy_output = self.to_galaxy_output(runnable_output)
try:
cwl_output = output_to_cwl_json(
galaxy_output,
self._get_metadata,
get_dataset,
self._get_extra_files,
pseduo_location=True,
)
except AssertionError:
# In galaxy-tool-util < 21.05 output_to_cwl_json will raise an AssertionError when the output state is not OK
# Remove with new galaxy-tool-util release.
continue
if is_cwl or output_src["src"] == "hda":
output_dict_value = cwl_output
else:
def attach_file_properties(collection, cwl_output):
elements = collection["elements"]
assert len(elements) == len(cwl_output)
for element, cwl_output_element in zip(elements, cwl_output):
element["_output_object"] = cwl_output_element
if isinstance(cwl_output_element, list):
assert "elements" in element["object"]
attach_file_properties(element["object"], cwl_output_element)
output_metadata = self._get_metadata("dataset_collection", output_dataset_id)
attach_file_properties(output_metadata, cwl_output)
output_dict_value = output_metadata
outputs_dict[output_id] = output_dict_value
self._outputs_dict = outputs_dict
ctx.vlog("collected outputs [%s]" % self._outputs_dict)