tesk.api.ga4gh.tes package¶

Subpackages¶

tesk.api.ga4gh.tes.service_info package

Submodules¶

tesk.api.ga4gh.tes.controllers module¶

Controllers for GA4GH TES API endpoints.

tesk.api.ga4gh.tes.controllers.CancelTask(id, *args, **kwargs)[source]¶

Cancel unfinished task.

Parameters:

id – Task identifier.
*args – Variable length argument list.
**kwargs – Arbitrary keyword arguments.

Return type:

dict

tesk.api.ga4gh.tes.controllers.CreateTask(*args, **kwargs)[source]¶

Create task.

Parameters:

*args – Variable length argument list.
**kwargs – Arbitrary keyword arguments.

Return type:

dict

tesk.api.ga4gh.tes.controllers.GetServiceInfo()[source]¶

Get service info.

Return type:: dict

tesk.api.ga4gh.tes.controllers.GetTask(*args, **kwargs)[source]¶

Get info for individual task.

Parameters:

id – Task identifier.
*args – Variable length argument list.
**kwargs – Arbitrary keyword arguments.

Return type:

dict

tesk.api.ga4gh.tes.controllers.ListTasks(*args, **kwargs)[source]¶

List all available tasks.

Parameters:

*args – Variable length argument list.
**kwargs – Arbitrary keyword arguments.

Return type:

dict

tesk.api.ga4gh.tes.models module¶

Models for TES API.

class tesk.api.ga4gh.tes.models.Artifact(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)[source]¶

Bases: Enum

Artifact type.

tes = 'tes'¶

class tesk.api.ga4gh.tes.models.Organization(**data)[source]¶

Bases: BaseModel

Organization responsible for a GA4GH service.

name: str¶

url: AnyUrl¶

class tesk.api.ga4gh.tes.models.Service(**data)[source]¶

Bases: BaseModel

GA4GH service.

contactUrl: Optional[str]¶

createdAt: Optional[datetime]¶

description: Optional[str]¶

documentationUrl: Optional[AnyUrl]¶

environment: Optional[str]¶

id: str¶

name: str¶

organization: Organization¶

type: ServiceType¶

updatedAt: Optional[datetime]¶

version: str¶

class tesk.api.ga4gh.tes.models.ServiceType(**data)[source]¶

Bases: BaseModel

Type of a GA4GH service.

artifact: str¶

group: str¶

version: str¶

class tesk.api.ga4gh.tes.models.TesCancelTaskResponse(**data)[source]¶

Bases: BaseModel

CancelTaskResponse describes a response from the CancelTask endpoint.

class tesk.api.ga4gh.tes.models.TesCreateTaskResponse(**data)[source]¶

Bases: BaseModel

CreateTaskResponse describes a response from the CreateTask endpoint.

It will include the task ID that can be used to look up the status of the job.

id: str¶

class tesk.api.ga4gh.tes.models.TesExecutor(**data)[source]¶

Bases: BaseModel

An executor is a command to be run in a container.

command: List[str]¶

env: Optional[Dict[str, str]]¶

ignore_error: Optional[bool]¶

image: str¶

stderr: Optional[str]¶

stdin: Optional[str]¶

stdout: Optional[str]¶

workdir: Optional[str]¶

class tesk.api.ga4gh.tes.models.TesExecutorLog(**data)[source]¶

Bases: BaseModel

ExecutorLog describes logging information related to an Executor.

end_time: Optional[str]¶

exit_code: int¶

start_time: Optional[str]¶

stderr: Optional[str]¶

stdout: Optional[str]¶

class tesk.api.ga4gh.tes.models.TesFileType(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)[source]¶

Bases: Enum

Define if input/output element is a file or a directory.

It is not required that the user provide this value, but it is required that the server fill in the value once the information is available at run time.

DIRECTORY = 'DIRECTORY'¶

FILE = 'FILE'¶

class tesk.api.ga4gh.tes.models.TesInput(**data)[source]¶

Bases: BaseModel

Input describes Task input files.

content: Optional[str]¶

description: Optional[str]¶

name: Optional[str]¶

path: str¶

streamable: Optional[bool]¶

type: Optional[TesFileType]¶

url: Optional[str]¶

class tesk.api.ga4gh.tes.models.TesListTasksResponse(**data)[source]¶

Bases: BaseModel

ListTasksResponse describes a response from the ListTasks endpoint.

next_page_token: Optional[str]¶

tasks: List[TesTask]¶

class tesk.api.ga4gh.tes.models.TesOutput(**data)[source]¶

Bases: BaseModel

Output describes Task output files.

description: Optional[str]¶

name: Optional[str]¶

path: str¶

path_prefix: Optional[str]¶

type: Optional[TesFileType]¶

url: str¶

class tesk.api.ga4gh.tes.models.TesOutputFileLog(**data)[source]¶

Bases: BaseModel

OutputFileLog describes a single output file.

This describes file details after the task has completed successfully, for logging purposes.

path: str¶

size_bytes: str¶

url: str¶

class tesk.api.ga4gh.tes.models.TesResources(**data)[source]¶

Bases: BaseModel

Resources describes the resources requested by a task.

backend_parameters: Optional[Dict[str, str]]¶

backend_parameters_strict: Optional[bool]¶

cpu_cores: Optional[int]¶

disk_gb: Optional[float]¶

preemptible: Optional[bool]¶

ram_gb: Optional[float]¶

zones: Optional[List[str]]¶

class tesk.api.ga4gh.tes.models.TesServiceInfo(**data)[source]¶

Bases: Service

ServiceInfo describes the service that is running the TES API.

storage: Optional[List[str]]¶

tesResources_backend_parameters: Optional[List[str]]¶

type: Optional[TesServiceType]¶

class tesk.api.ga4gh.tes.models.TesServiceType(**data)[source]¶

Bases: ServiceType

Type of a TES service.

artifact: Artifact¶

class tesk.api.ga4gh.tes.models.TesState(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)[source]¶

Bases: Enum

Task state.

CANCELED = 'CANCELED'¶

CANCELING = 'CANCELING'¶

COMPLETE = 'COMPLETE'¶

EXECUTOR_ERROR = 'EXECUTOR_ERROR'¶

INITIALIZING = 'INITIALIZING'¶

PAUSED = 'PAUSED'¶

PREEMPTED = 'PREEMPTED'¶

QUEUED = 'QUEUED'¶

RUNNING = 'RUNNING'¶

SYSTEM_ERROR = 'SYSTEM_ERROR'¶

UNKNOWN = 'UNKNOWN'¶

class tesk.api.ga4gh.tes.models.TesTask(**data)[source]¶

Bases: BaseModel

Task describes a task to be run.

creation_time: Optional[str]¶

description: Optional[str]¶

executors: List[TesExecutor]¶

id: Optional[str]¶

inputs: Optional[List[TesInput]]¶

logs: Optional[List[TesTaskLog]]¶

name: Optional[str]¶

outputs: Optional[List[TesOutput]]¶

resources: Optional[TesResources]¶

state: Optional[TesState]¶

tags: Optional[Dict[str, str]]¶

volumes: Optional[List[str]]¶

class tesk.api.ga4gh.tes.models.TesTaskLog(**data)[source]¶

Bases: BaseModel

TaskLog describes logging information related to a Task.

end_time: Optional[str]¶

logs: List[TesExecutorLog]¶

metadata: Optional[Dict[str, str]]¶

outputs: List[TesOutputFileLog]¶

start_time: Optional[str]¶

system_logs: Optional[List[str]]¶

Module contents¶

TESK API GA4GH TES package.