dgbowl_schemas.tomato.payload_0_2 package

class dgbowl_schemas.tomato.payload_0_2.Payload(*, version: Literal['0.2'], tomato: Tomato = None, sample: Sample, method: Sequence[Method])

Bases: BaseModel

version: Literal['0.2']

tomato: Tomato: Additional configuration options for tomato.

sample: Sample: Specification of the experimental sample.

method: Sequence[Method]: A sequence of the experimental methods.

classmethod extract_samplefile(values): If samplefile is provided in values, parse the file as sample.

classmethod extract_methodfile(values): If methodfile is provided in values, parse the file as method.

update()

Submodules

dgbowl_schemas.tomato.payload_0_2.method module

class dgbowl_schemas.tomato.payload_0_2.method.Method(*, device: str, technique: str, **extra_data: Any)

Bases: BaseModel

The Method schema is completely device- and technique- dependent, with extra arguments required by each technique defined by each device driver.

device: str: tag of the device within a tomato pipeline

technique: str: name of the technique, must be listed in the capabilities of the device

dgbowl_schemas.tomato.payload_0_2.sample module

class dgbowl_schemas.tomato.payload_0_2.sample.Sample(*, name: str, **extra_data: Any)

Bases: BaseModel

Additional attributes for each Sample may be required, depending on the Method type.

name: str: sample name for matching with tomato pipelines

dgbowl_schemas.tomato.payload_0_2.tomato module

class dgbowl_schemas.tomato.payload_0_2.tomato.Tomato(*, unlock_when_done: bool = False, verbosity: Literal['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] = 'WARNING', output: Output = None, snapshot: Snapshot | None = None)

Bases: BaseModel

Specification of job configuration for tomato.

class Output(*, path: str = None, prefix: str = None)

Bases: BaseModel

Provide the path and prefix for the final FAIR-data archive of the job.

path: str

prefix: str

class Snapshot(*, path: str = None, prefix: str = None, frequency: int = 3600)

Bases: BaseModel

Provide the frequency, path and prefix to configure the snapshotting functionality of tomato.

path: str

prefix: str

frequency: int

unlock_when_done: bool: set pipeline as ready when job finishes successfully

verbosity: Literal['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']

output: Output: Options for final FAIR data output.

snapshot: Snapshot | None: Options for periodic snapshotting.