def get_postprocessing_stack(username, stack_id):
"""
Fetches the Postprocessing Stack with the given ID and username from the postprocessing server
:param stack_id: The ID of the stack to fetch
:param username: The username of the user who owns this stack
:raises NotFoundError: if the requested postprocessing stack is not found
:raises UnavailableError: if the Postprocessing service is not reachable
:return: Instance of :class:`server.gen.phenopipe_r_pb2.PostprocessingStack`
"""
r_stub = phenopipe_r_pb2_grpc.PhenopipeRStub(get_r_channel())
try:
response = r_stub.GetPostprocessingStack(
phenopipe_r_pb2.GetPostprocessingStackRequest(stack_id=stack_id,
author=username))
return response.stack
except grpc.RpcError as e:
if e.code() == grpc.StatusCode.NOT_FOUND:
raise NotFoundError(e.details(), "PostprocessingStack")
elif e.code() == grpc.StatusCode.UNAVAILABLE:
raise UnavailableError("Postprocessing Service")
raise # TODO other error options?
def upload_stack(stack):
"""
Uploads the given Postprocessing Stack to the Postprocessing server via GRPC
:param stack: Instance of :class:`server.gen.phenopipe_r_pb2.PostprocessingStack`
:return: The ID of the uploaded stack
"""
r_stub = phenopipe_r_pb2_grpc.PhenopipeRStub(get_r_channel())
try:
scripts = []
for index, script in enumerate(stack.scripts):
scripts.append(phenopipe_r_pb2.PostprocessingScript(name=script.name, description=script.description,
index=index, file=script.file))
stack = phenopipe_r_pb2.PostprocessingStack(name=stack.name, description=stack.description,
author=stack.author, scripts=scripts)
response = r_stub.UploadPostprocessingStack(
phenopipe_r_pb2.UploadPostprocessingStackRequest(stack=stack)
)
stack_id = response.stack_id
print(stack_id)
return stack_id
except grpc.RpcError as e:
if e.code() == grpc.StatusCode.UNAVAILABLE:
raise UnavailableError("Postprocessing Service")
elif e.code() == grpc.StatusCode.ALREADY_EXISTS:
raise PostprocessingStackAlreadyExistsError(e.details(), e.initial_metadata()[0][1],
e.initial_metadata()[1][1])
def get_postprocessing_stacks(username):
"""
Fetches all available Postprocessing Stacks from the postprocessing server
:raises UnavailableError: if the Postprocessing service is not reachable
:return: List of instances of :class:`server.gen.phenopipe_r_pb2.PostprocessingStack`
"""
r_stub = phenopipe_r_pb2_grpc.PhenopipeRStub(get_r_channel())
try:
response = r_stub.GetPostprocessingStacks(
phenopipe_r_pb2.GetPostprocessingStacksRequest(author=username))
stacks = response.stacks
return stacks
except grpc.RpcError as e:
if e.code() == grpc.StatusCode.UNAVAILABLE:
raise UnavailableError("Postprocessing Service")
raise # TODO other error options?