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 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')
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__)
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 PhasesMessage(Message):
response = repeated(PhaseMessage)
class Pet(Message):
sounds = repeated(String())
class IntegerList(Message):
values = repeated(Integer())
class M(dict):
items = repeated(Field(str))
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)
class SampleModelsMessage(Message):
response = repeated(String(description='Possible models for the sample'))
class StringList(Message):
values = repeated(String())
class SamplesMessage(Message):
response = repeated(SampleMessage)
class ExperimentsMessage(Message):
response = repeated(ExperimentMessage)
class MaximumYieldMessage(Message):
growth_rate = repeated(
Float32(description='Growth rates collected from the experiment'))
metabolites = MapField(
MetabolitePhasePlaneMessage,
description='Data for the metabolites collected from the experiment')
class MetabolitePhasePlaneMessage(Message):
flux = repeated(
Float32(description=
'Measurement for the metabolite collected from experiment'))
phase_planes: PhasePlanesMessage