class ModelRequestMessage(Message):
sample_ids = repeated(Int(description='Sample IDs'))
model_id = String(description='Model ID (f.e. iJO1366)')
phase_id = Int(description='Phase ID')
map = String(description='Name of map to show')
method = String(description='Simulation method to run')
with_fluxes = Bool(description='Add flux information to the response')
objective = String(description='Reaction ID to be set as objective')
class PhasePlaneMessage(Message):
objective_upper_bound = repeated(
Float32(description='Upper bound for theoretical yield objective'))
objective_lower_bound = repeated(
Float32(description='Lower bound for theoretical yield objective'))
objective = repeated(Float32(description='Theoretical objective values'))
objective_id = String(description='Objective reaction ID')
class QueryResponse(Message):
class Meta:
description = 'Information about pets'
ids = repeated(Field(Pet, description='Bunch of pets'))
pet = Field(Pet, description='The other pet')
repeat = repeated(String(description='Bunch of strings'))
class ParameterMessage(Message):
in_ = String(json_name='in') # TODO: enum
description: str
required: bool
name: str
type: str
items: SchemaMessage
schema: SchemaMessage
class ModelMessage(Message):
model_id = String(
description=
'The saved model ID which can be used for retrieving cached information'
)
fluxes = map_(
Float32()) # TODO: fix not implemented while trying to add description
growth_rate = Float32(description='Growth rate for this simulation')
model: JSONValue
class ErrorResponse(Message):
status = Int32()
description = String()
# TODO Repeat(String)
path = String()
# TODO helper for raising errors
def raise_(self):
if self.status == 501:
raise NotImplemented_()
# if self.status == 500:
# raise ServerError(self.message or '')
# if self.status == 404:
# raise NotFound(self.message or '')
raise RuntimeError('HTTP status {}: {}'.format(self.status,
self.description))
class MeasurementMessage(Message):
type = String(
description=
'The subject of the measurement, e.g. "compound", "protein" or "reaction"'
)
id = Int(
description=
'identifier associated with the measured subject, e.g. metabolite identifier'
)
name = String(description='In case of metabolite, human-readable name')
db_name = String(
description=
'In case of xref data, the miriam name of the database, e.g. uniprot')
mode = String(
description='Quantification mode, e.g. "relative" or "quantitative"')
measurements = repeated(
Float32(description='Measurements taken during the experiment'))
units = MapField(str, description='Units in which measurements are taken')
rate = String(description='Rate')
class SchemaMessage(Schema):
ref = String(json_name='$ref')
type: str # TODO: enum
description: str
items = Field('venom.rpc.reflect.openapi.SchemaMessage')
properties = MapField('venom.rpc.reflect.openapi.SchemaMessage')
additional_properties = Field('venom.rpc.reflect.openapi.SchemaMessage')
async def test_magic_request_message_auto_unpack(self):
def func(self, value: str) -> StringValue:
return StringValue(value)
inspect = magic_normalize(func, auto_generate_request=True)
self.assertEqual(inspect.response, StringValue)
self.assertEqual(inspect.request.__meta__.name, 'FuncRequest')
self.assertEqual(fields(inspect.request), (
String(name='value'),
))
# TODO StringValue() should be equal to StringValue('')
self.assertEqual(await inspect.invokable(None, inspect.request()), StringValue(''))
self.assertEqual(await inspect.invokable(None, inspect.request('foo')), StringValue('foo'))
def test_stub_rpc_response_repeat_auto(self):
class GreeterStub(Stub):
@rpc(auto=True)
def get_greetings(self) -> List[str]:
raise NotImplementedError
self.assertEqual(GreeterStub.get_greetings.response.__meta__.name,
'GetGreetingsResponse')
self.assertEqual(tuple(fields(GreeterStub.get_greetings.response)),
(repeated(String(), name='values')))
self.assertEqual(GreeterStub.greet.response, StringValue)
self.assertEqual(GreeterStub.greet.name, 'get_greetings')
def test_stub_rpc_request_repeat_auto(self):
class GreeterStub(Stub):
@rpc(auto=True)
def greet_many(self, names: List[str]) -> str:
raise NotImplementedError
self.assertEqual(GreeterStub.greet_many.request.__meta__.name,
'GreetManyRequest')
self.assertEqual(tuple(fields(GreeterStub.greet_many.request)),
(repeated(String(), name='names'), ))
self.assertEqual(GreeterStub.greet_many.response, StringValue)
self.assertEqual(GreeterStub.greet_many.name, 'greet_many')
def test_stub_rpc_request_auto(self):
class GreeterStub(Stub):
@rpc(auto=True)
def greet(self, name: str, shout: bool = False) -> str:
raise NotImplementedError
self.assertEqual(GreeterStub.greet.request.__meta__.name,
'GreetRequest')
self.assertEqual(tuple(fields(GreeterStub.greet.request)), (
String(name='name'),
Bool(name='shout'),
))
self.assertEqual(GreeterStub.greet.response, StringValue)
self.assertEqual(GreeterStub.greet.name, 'greet')
def test_message_type_hints(self):
class Pet(Message):
sounds: List[str]
size: float
speed: int
age: int
self.assertIsInstance(Pet.__fields__, OrderedDict)
self.assertEqual(('sounds', 'size', 'speed', 'age'),
tuple(Pet.__fields__.keys()))
self.assertEqual(
{
'sounds': repeated(String(), name='sounds'),
'size': Field(float, name='size'),
'speed': Field(int, name='speed'),
'age': Field(int, name='age')
}, Pet.__fields__)
def test_field_string(self):
self.assertEqual(String(), Field(str))
class Pet(Message):
id = Int()
name = String()
tag = String()
class FooInner(Message):
i = String()
class Pet(Message):
class Meta:
description = 'Very important object'
pet_id = String(description='Pet ID to query')
class Pet(Message):
sound = String()
class Pet(Message):
sounds = repeated(String())
class HelloRequest(Message):
name = String()
class ExperimentMessage(Message):
id = Int(description='Experiment ID')
name = String(description='Experiment name')
class ExperimentsRequestMessage(Message):
taxon_code = String(
descripton=
'Species five-letter mnemonic short_code that must be associated with at least one '
'sample belonging to the experiment')
class HelloResponse(Message):
message = String()
class SampleModelsMessage(Message):
response = repeated(String(description='Possible models for the sample'))
class PhaseMessage(Message):
id = Int(description='Phase ID')
name = String(description='Phase name')
class MetaboliteMediumMessage(Message):
id = Int(description='Metabolite ID')
name = String(description='Metabolite human-readable name')
concentration = Float32(description='Concentration in medium')
class HelloRequest(Message):
name = String()
shout = Bool()
class Foo(Message):
string = String()
class SampleMessage(Message):
id = repeated(Int(description='Sample IDs'))
name = String(description='Sample name')
organism = String(description='Organism short code')
class SampleInfoMessage(Message):
genotype_changes = repeated(
String(description='Gnomic strings for genotype changes'))
measurements = repeated(MeasurementMessage)
medium = repeated(MetaboliteMediumMessage)
