def ascwl(self, global_step_outputs=False):
"""Serialize graph to CWL workflow.
:param global_step_outputs: Make all step outputs global.
"""
workflow = Workflow()
input_index = 1
steps = {}
def _source_name(key):
"""Find source name for a node."""
if self.G.in_degree(key) == 0:
return None
assert self.G.in_degree(key) == 1
tool_key, node = list(self.G.pred[key].items())[0]
return '{0}/{1}'.format(steps[tool_key], node['id'])
def _relative_default(client, default):
"""Evolve ``File`` path."""
if isinstance(default, File):
path = (client.workflow_path / default.path).resolve()
return attr.evolve(default, path=path)
return default
for tool_index, (key, node) in enumerate(self._tool_nodes, 1):
_, path = key
tool = node['tool']
step_id = 'step_{0}'.format(tool_index)
steps[key] = step_id
ins = {
edge_id: _source_name(target_id)
for target_id, _, edge_id in self.G.in_edges(key, data='id')
}
outs = [
edge_id for _, _, edge_id in self.G.out_edges(key, data='id')
]
for input_ in tool.inputs:
input_mapping = ins.get(input_.id)
if input_mapping is None:
input_id = 'input_{0}'.format(input_index)
workflow.inputs.append(
InputParameter(
id=input_id,
type=input_.type,
default=_relative_default(self.client,
input_.default),
))
input_index += 1
ins[input_.id] = input_id
workflow.add_step(
run=self.client.path / path,
id=step_id,
in_=ins,
out=outs,
)
output_keys = (key for _, key in self.G.out_edges(steps.keys())
) if global_step_outputs else self._output_keys
for index, key in enumerate(output_keys):
output_id = 'output_{0}'.format(index)
workflow.outputs.append(
WorkflowOutputParameter(
id=output_id,
type='File',
outputSource=_source_name(key),
))
return workflow
def ascwl(
self,
input_paths=None,
output_paths=None,
outputs=None,
use_latest=True,
):
"""Serialize graph to CWL workflow.
:param global_step_outputs: Make all step outputs global.
"""
if output_paths is None:
output_paths = {
node.path
for node in outputs if _safe_path(node.path)
}
workflow = Workflow()
processes = set()
stack = []
output_keys = {(node.commit, node.path) for node in outputs}
nodes = {(node.commit, node.path): node for node in self.nodes}
def connect_file_to_directory(node):
"""Return step connecting file to a directory."""
process = attr.evolve(
LINK_CWL,
inputs={
'input_directory': 'Directory',
'filename': {
'type':
'string',
'default':
str(Path(node.path).relative_to(node.parent.path)),
},
})
process_run = ProcessRun(
commit=node.commit,
client=node.client,
path=None,
process=process,
inputs={
node.parent.path:
Usage(
entity=node.parent,
role='input_directory',
),
},
outputs={
node.path: 'output_file',
},
)
for generated in process_run.generated:
nodes[(generated.commit, generated.path)] = generated
return process_run
for node in self.nodes:
if (node.commit, node.path) not in output_keys:
continue
process_run = None
if isinstance(node, Entity) and not hasattr(node, 'activity'):
process_run = connect_file_to_directory(node)
stack.append(process_run)
processes.add(process_run)
else:
assert hasattr(node, 'activity'), node
assert isinstance(node.activity, ProcessRun)
plan = node.activity.association.plan
latest = self.latest(plan)
if use_latest and latest:
plan = nodes[(latest, plan.path)]
process_run = plan.activity
if process_run not in processes:
stack.append(process_run)
processes.add(process_run)
while stack:
action = stack.pop()
if not hasattr(action, 'inputs'):
continue
for path, dependency in action.inputs.items():
# Do not follow defined input paths.
if input_paths and path in input_paths:
continue
node = nodes.get((dependency.commit, dependency.path),
dependency)
if isinstance(node, Generation):
process_run = node.activity
elif isinstance(node, Collection) and node.parent:
raise NotImplementedError('Can not connect subdirectory')
elif isinstance(node, Entity) and node.parent:
process_run = connect_file_to_directory(node)
else:
process_run = None
# Skip existing commits
if process_run and isinstance(process_run, ProcessRun):
plan = process_run.association.plan
latest = self.latest(plan)
if process_run.path and use_latest and latest:
plan = nodes[(latest, plan.path)]
process_run = plan.activity
if process_run not in processes:
stack.append(process_run)
processes.add(process_run)
steps = {
tool: 'step_{0}'.format(tool_index)
for tool_index, tool in enumerate(processes, 1)
}
def _source_name(commit, path):
"""Find source name for a node."""
try:
process_run = nodes[(commit, path)].activity
output_id = process_run.outputs[path]
return '{0}/{1}'.format(steps[process_run], output_id)
except (KeyError, AttributeError):
pass
def _relative_default(client, default):
"""Evolve ``File`` or ``Directory`` path."""
if isinstance(default, PATH_TYPES):
path = (client.workflow_path / default.path).resolve()
return attr.evolve(default, path=path)
return default
input_index = 1
for action, step_id in steps.items():
tool = action.process
ins = {}
for path, dependency in action.inputs.items():
alias = _source_name(dependency.commit, path)
if alias:
ins[dependency.role] = alias
outs = list(set(action.outputs.values()))
for generated in action.generated:
if generated.entity.path not in output_paths:
output_paths.add(generated.entity.path)
outputs.add(generated.entity)
for input_ in tool.inputs:
input_mapping = ins.get(input_.id)
if input_mapping is None:
input_id = 'input_{0}'.format(input_index)
workflow.inputs.append(
InputParameter(
id=input_id,
type=input_.type,
default=_relative_default(self.client,
input_.default),
))
input_index += 1
ins[input_.id] = input_id
workflow.add_step(
run=self.client.path / action.path if action.path else tool,
id=step_id,
in_=ins,
out=outs,
)
for index, node in enumerate(
(node for node in outputs if node.path in output_paths)):
commit, path = node.commit, node.path
id_ = 'output_{0}'.format(index)
process_run = nodes[(commit, path)].activity
if process_run.process is None or process_run.path is None:
continue
output_id = process_run.outputs[path]
type_ = next(output for output in process_run.process.outputs
if output.id == output_id).type
type_ = type_ if type_ == 'Directory' else 'File'
output_source = _source_name(commit, path)
if output_source is None:
continue
workflow.outputs.append(
WorkflowOutputParameter(
id=id_,
type=type_,
outputSource=output_source,
))
return workflow
def ascwl(
self,
input_paths=None,
output_paths=None,
outputs=None,
use_latest=True,
):
"""Serialize graph to CWL workflow.
:param global_step_outputs: Make all step outputs global.
"""
if output_paths is None:
output_paths = {
node.path
for node in outputs if _safe_path(node.path)
}
workflow = Workflow()
processes = set()
stack = []
output_keys = {(node.commit, node.path) for node in outputs}
nodes = {(node.commit, node.path): node for node in self.nodes}
for node in self.nodes:
if (node.commit, node.path) not in output_keys:
continue
process_run = None
if isinstance(node, ProcessRun):
process_run = node
elif isinstance(node.activity, ProcessRun):
process_run = node.activity
if process_run:
latest = self.latest(process_run)
if use_latest and latest:
process_run = nodes[(latest, process_run.path)]
if process_run not in processes:
stack.append(process_run)
processes.add(process_run)
while stack:
action = stack.pop()
if not hasattr(action, 'inputs'):
continue
for path, dependency in action.inputs.items():
# Do not follow defined input paths.
if input_paths and path in input_paths:
continue
try:
process_run = nodes[(dependency.commit,
dependency.path)].activity
except AttributeError:
continue
# Skip existing commits
if process_run and isinstance(process_run, ProcessRun):
latest = self.latest(process_run)
if use_latest and latest:
process_run = nodes[(latest, process_run.path)]
if process_run not in processes:
stack.append(process_run)
processes.add(process_run)
steps = {
tool: 'step_{0}'.format(tool_index)
for tool_index, tool in enumerate(processes, 1)
}
def _source_name(commit, path):
"""Find source name for a node."""
try:
process_run = nodes[(commit, path)].activity
output_id = process_run.outputs[path]
return '{0}/{1}'.format(steps[process_run], output_id)
except (KeyError, AttributeError):
pass
def _relative_default(client, default):
"""Evolve ``File`` or ``Directory`` path."""
if isinstance(default, PATH_TYPES):
path = (client.workflow_path / default.path).resolve()
return attr.evolve(default, path=path)
return default
input_index = 1
for action, step_id in steps.items():
tool = action.process
ins = {}
for path, dependency in action.inputs.items():
alias = _source_name(dependency.commit, path)
if alias:
ins[dependency.role] = alias
outs = list(set(action.outputs.values()))
for generated in action.generated:
if generated.entity.path not in output_paths:
output_paths.add(generated.entity.path)
outputs.add(generated.entity)
for input_ in tool.inputs:
input_mapping = ins.get(input_.id)
if input_mapping is None:
input_id = 'input_{0}'.format(input_index)
workflow.inputs.append(
InputParameter(
id=input_id,
type=input_.type,
default=_relative_default(self.client,
input_.default),
))
input_index += 1
ins[input_.id] = input_id
workflow.add_step(
run=self.client.path / action.path,
id=step_id,
in_=ins,
out=outs,
)
for index, node in enumerate(
(node for node in outputs if node.path in output_paths)):
commit, path = node.commit, node.path
id_ = 'output_{0}'.format(index)
process_run = nodes[(commit, path)].activity
if process_run.process is None:
continue
output_id = process_run.outputs[path]
type_ = next(output for output in process_run.process.outputs
if output.id == output_id).type
type_ = type_ if type_ == 'Directory' else 'File'
output_source = _source_name(commit, path)
if output_source is None:
continue
workflow.outputs.append(
WorkflowOutputParameter(
id=id_,
type=type_,
outputSource=output_source,
))
return workflow
