# generated by datamodel-codegen:
# filename: https://raw.githubusercontent.com/ga4gh/task-execution-schemas/develop/openapi/task_execution_service.openapi.yaml
# timestamp: 2022-09-28T18:20:32+00:00
# Not available in Python 3.6...
# from __future__ import annotations
from datetime import datetime
from enum import Enum
from typing import Dict, List, Optional
from pydantic import AnyUrl, BaseModel, Field
class TesCancelTaskResponse(BaseModel):
pass
class TesCreateTaskResponse(BaseModel):
id: str = Field(..., description="Task identifier assigned by the server.")
[docs]
class TesExecutor(BaseModel):
image: str = Field(
...,
description="Name of the container image. The string will be passed as the image\nargument to the containerization run command. Examples:\n - `ubuntu`\n - `quay.io/aptible/ubuntu`\n - `gcr.io/my-org/my-image`\n - `myregistryhost:5000/fedora/httpd:version1.0`",
example="ubuntu:20.04",
)
command: List[str] = Field(
...,
description='A sequence of program arguments to execute, where the first argument\nis the program to execute (i.e. argv). Example:\n```\n{\n "command" : ["/bin/md5", "/data/file1"]\n}\n```',
example=["/bin/md5", "/data/file1"],
)
workdir: Optional[str] = Field(
None,
description="The working directory that the command will be executed in.\nIf not defined, the system will default to the directory set by\nthe container image.",
example="/data/",
)
stdin: Optional[str] = Field(
None,
description='Path inside the container to a file which will be piped\nto the executor\'s stdin. This must be an absolute path. This mechanism\ncould be used in conjunction with the input declaration to process\na data file using a tool that expects STDIN.\n\nFor example, to get the MD5 sum of a file by reading it into the STDIN\n```\n{\n "command" : ["/bin/md5"],\n "stdin" : "/data/file1"\n}\n```',
example="/data/file1",
)
stdout: Optional[str] = Field(
None,
description='Path inside the container to a file where the executor\'s\nstdout will be written to. Must be an absolute path. Example:\n```\n{\n "stdout" : "/tmp/stdout.log"\n}\n```',
example="/tmp/stdout.log",
)
stderr: Optional[str] = Field(
None,
description='Path inside the container to a file where the executor\'s\nstderr will be written to. Must be an absolute path. Example:\n```\n{\n "stderr" : "/tmp/stderr.log"\n}\n```',
example="/tmp/stderr.log",
)
env: Optional[Dict[str, str]] = Field(
None,
description='Enviromental variables to set within the container. Example:\n```\n{\n "env" : {\n "ENV_CONFIG_PATH" : "/data/config.file",\n "BLASTDB" : "/data/GRC38",\n "HMMERDB" : "/data/hmmer"\n }\n}\n```',
example={"BLASTDB": "/data/GRC38", "HMMERDB": "/data/hmmer"},
)
class TesExecutorLog(BaseModel):
start_time: Optional[str] = Field(
None,
description="Time the executor started, in RFC 3339 format.",
example="2020-10-02T10:00:00-05:00",
)
end_time: Optional[str] = Field(
None,
description="Time the executor ended, in RFC 3339 format.",
example="2020-10-02T11:00:00-05:00",
)
stdout: Optional[str] = Field(
None,
description="Stdout content.\n\nThis is meant for convenience. No guarantees are made about the content.\nImplementations may chose different approaches: only the head, only the tail,\na URL reference only, etc.\n\nIn order to capture the full stdout client should set Executor.stdout\nto a container file path, and use Task.outputs to upload that file\nto permanent storage.",
)
stderr: Optional[str] = Field(
None,
description="Stderr content.\n\nThis is meant for convenience. No guarantees are made about the content.\nImplementations may chose different approaches: only the head, only the tail,\na URL reference only, etc.\n\nIn order to capture the full stderr client should set Executor.stderr\nto a container file path, and use Task.outputs to upload that file\nto permanent storage.",
)
exit_code: int = Field(..., description="Exit code.")
class TesFileType(Enum):
FILE = "FILE"
DIRECTORY = "DIRECTORY"
class TesInput(BaseModel):
name: Optional[str] = None
description: Optional[str] = None
url: Optional[str] = Field(
None,
description='REQUIRED, unless "content" is set.\n\nURL in long term storage, for example:\n - s3://my-object-store/file1\n - gs://my-bucket/file2\n - file:///path/to/my/file\n - /path/to/my/file',
example="s3://my-object-store/file1",
)
path: str = Field(
...,
description="Path of the file inside the container.\nMust be an absolute path.",
example="/data/file1",
)
type: TesFileType
content: Optional[str] = Field(
None,
description='File content literal.\n\nImplementations should support a minimum of 128 KiB in this field\nand may define their own maximum.\n\nUTF-8 encoded\n\nIf content is not empty, "url" must be ignored.',
)
class TesOutput(BaseModel):
name: Optional[str] = Field(None, description="User-provided name of output file")
description: Optional[str] = Field(
None,
description="Optional users provided description field, can be used for documentation.",
)
url: str = Field(
...,
description="URL for the file to be copied by the TES server after the task is complete.\nFor Example:\n - `s3://my-object-store/file1`\n - `gs://my-bucket/file2`\n - `file:///path/to/my/file`",
)
path: str = Field(
...,
description="Path of the file inside the container.\nMust be an absolute path.",
)
type: TesFileType
class TesOutputFileLog(BaseModel):
url: str = Field(
..., description="URL of the file in storage, e.g. s3://bucket/file.txt"
)
path: str = Field(
...,
description="Path of the file inside the container. Must be an absolute path.",
)
size_bytes: str = Field(
...,
description="Size of the file in bytes. Note, this is currently coded as a string\nbecause official JSON doesn't support int64 numbers.",
example=["1024"],
)
[docs]
class TesResources(BaseModel):
cpu_cores: Optional[int] = Field(
None, description="Requested number of CPUs", example=4
)
preemptible: Optional[bool] = Field(
None,
description="Define if the task is allowed to run on preemptible compute instances,\nfor example, AWS Spot. This option may have no effect when utilized\non some backends that don't have the concept of preemptible jobs.",
example=False,
)
ram_gb: Optional[float] = Field(
None, description="Requested RAM required in gigabytes (GB)", example=8
)
disk_gb: Optional[float] = Field(
None, description="Requested disk size in gigabytes (GB)", example=40
)
zones: Optional[List[str]] = Field(
None,
description="Request that the task be run in these compute zones. How this string\nis utilized will be dependent on the backend system. For example, a\nsystem based on a cluster queueing system may use this string to define\npriorty queue to which the job is assigned.",
example="us-west-1",
)
backend_parameters: Optional[Dict[str, str]] = Field(
None,
description='Key/value pairs for backend configuration.\nServiceInfo shall return a list of keys that a backend supports.\nKeys are case insensitive.\nIt is expected that clients pass all runtime or hardware requirement key/values\nthat are not mapped to existing tesResources properties to backend_parameters.\nBackends shall log system warnings if a key is passed that is unsupported.\nBackends shall not store or return unsupported keys if included in a task.\nIf backend_parameters_strict equals true,\nbackends should fail the task if any key/values are unsupported, otherwise,\nbackends should attempt to run the task\nIntended uses include VM size selection, coprocessor configuration, etc.\nExample:\n```\n{\n "backend_parameters" : {\n "VmSize" : "Standard_D64_v3"\n }\n}\n```',
example={"VmSize": "Standard_D64_v3"},
)
backend_parameters_strict: Optional[bool] = Field(
False,
description="If set to true, backends should fail the task if any backend_parameters \nkey/values are unsupported, otherwise, backends should attempt to run the task",
example=False,
)
class Artifact(str, Enum):
tes = "tes"
class ServiceType(BaseModel):
group: str = Field(
...,
description="Namespace in reverse domain name format. Use `org.ga4gh` for implementations compliant with official GA4GH specifications. For services with custom APIs not standardized by GA4GH, or implementations diverging from official GA4GH specifications, use a different namespace (e.g. your organization's reverse domain name).",
example="org.ga4gh",
)
artifact: str = Field(
...,
description="Name of the API or GA4GH specification implemented. Official GA4GH types should be assigned as part of standards approval process. Custom artifacts are supported.",
example="beacon",
)
version: str = Field(
...,
description="Version of the API or specification. GA4GH specifications use semantic versioning.",
example="1.0.0",
)
class Organization(BaseModel):
name: str = Field(
...,
description="Name of the organization responsible for the service",
example="My organization",
)
url: AnyUrl = Field(
...,
description="URL of the website of the organization (RFC 3986 format)",
example="https://example.com",
)
class Service(BaseModel):
id: str = Field(
...,
description="Unique ID of this service. Reverse domain name notation is recommended, though not required. The identifier should attempt to be globally unique so it can be used in downstream aggregator services e.g. Service Registry.",
example="org.ga4gh.myservice",
)
name: str = Field(
...,
description="Name of this service. Should be human readable.",
example="My project",
)
type: ServiceType
description: Optional[str] = Field(
None,
description="Description of the service. Should be human readable and provide information about the service.",
example="This service provides...",
)
organization: Organization = Field(
..., description="Organization providing the service"
)
contactUrl: Optional[AnyUrl] = Field(
None,
description="URL of the contact for the provider of this service, e.g. a link to a contact form (RFC 3986 format), or an email (RFC 2368 format).",
example="mailto:support@example.com",
)
documentationUrl: Optional[AnyUrl] = Field(
None,
description="URL of the documentation of this service (RFC 3986 format). This should help someone learn how to use your service, including any specifics required to access data, e.g. authentication.",
example="https://docs.myservice.example.com",
)
createdAt: Optional[datetime] = Field(
None,
description="Timestamp describing when the service was first deployed and available (RFC 3339 format)",
example="2019-06-04T12:58:19Z",
)
updatedAt: Optional[datetime] = Field(
None,
description="Timestamp describing when the service was last updated (RFC 3339 format)",
example="2019-06-04T12:58:19Z",
)
environment: Optional[str] = Field(
None,
description="Environment the service is running in. Use this to distinguish between production, development and testing/staging deployments. Suggested values are prod, test, dev, staging. However this is advised and not enforced.",
example="test",
)
version: str = Field(
...,
description="Version of the service being described. Semantic versioning is recommended, but other identifiers, such as dates or commit hashes, are also allowed. The version should be changed whenever the service is updated.",
example="1.0.0",
)
[docs]
class TesState(Enum):
UNKNOWN = "UNKNOWN"
QUEUED = "QUEUED"
INITIALIZING = "INITIALIZING"
RUNNING = "RUNNING"
PAUSED = "PAUSED"
COMPLETE = "COMPLETE"
EXECUTOR_ERROR = "EXECUTOR_ERROR"
SYSTEM_ERROR = "SYSTEM_ERROR"
CANCELED = "CANCELED"
class TesTaskLog(BaseModel):
logs: List[TesExecutorLog] = Field(..., description="Logs for each executor")
metadata: Optional[Dict[str, str]] = Field(
None,
description="Arbitrary logging metadata included by the implementation.",
example={"host": "worker-001", "slurmm_id": 123456},
)
start_time: Optional[str] = Field(
None,
description="When the task started, in RFC 3339 format.",
example="2020-10-02T10:00:00-05:00",
)
end_time: Optional[str] = Field(
None,
description="When the task ended, in RFC 3339 format.",
example="2020-10-02T11:00:00-05:00",
)
outputs: List[TesOutputFileLog] = Field(
...,
description="Information about all output files. Directory outputs are\nflattened into separate items.",
)
system_logs: Optional[List[str]] = Field(
None,
description="System logs are any logs the system decides are relevant,\nwhich are not tied directly to an Executor process.\nContent is implementation specific: format, size, etc.\n\nSystem logs may be collected here to provide convenient access.\n\nFor example, the system may include the name of the host\nwhere the task is executing, an error message that caused\na SYSTEM_ERROR state (e.g. disk is full), etc.\n\nSystem logs are only included in the FULL task view.",
)
class TesServiceType(ServiceType):
artifact: Artifact = Field(..., example="tes")
class TesServiceInfo(Service):
storage: Optional[List[str]] = Field(
None,
description="Lists some, but not necessarily all, storage locations supported\nby the service.",
example=[
"file:///path/to/local/funnel-storage",
"s3://ohsu-compbio-funnel/storage",
],
)
tesResources_backend_parameters: Optional[List[str]] = Field(
None,
description="Lists all tesResources.backend_parameters keys supported \nby the service",
example=["VmSize"],
)
type: TesServiceType
[docs]
class TesTask(BaseModel):
id: Optional[str] = Field(
None,
description="Task identifier assigned by the server.",
example="job-0012345",
)
state: Optional[TesState] = None
name: Optional[str] = Field(None, description="User-provided task name.")
description: Optional[str] = Field(
None,
description="Optional user-provided description of task for documentation purposes.",
)
inputs: Optional[List[TesInput]] = Field(
None,
description="Input files that will be used by the task. Inputs will be downloaded\nand mounted into the executor container as defined by the task request\ndocument.",
example=[{"url": "s3://my-object-store/file1", "path": "/data/file1"}],
)
outputs: Optional[List[TesOutput]] = Field(
None,
description="Output files.\nOutputs will be uploaded from the executor container to long-term storage.",
example=[
{
"path": "/data/outfile",
"url": "s3://my-object-store/outfile-1",
"type": "FILE",
}
],
)
resources: Optional[TesResources] = None
executors: List[TesExecutor] = Field(
...,
description="An array of executors to be run. Each of the executors will run one\nat a time sequentially. Each executor is a different command that\nwill be run, and each can utilize a different docker image. But each of\nthe executors will see the same mapped inputs and volumes that are declared\nin the parent CreateTask message.\n\nExecution stops on the first error.",
)
volumes: Optional[List[str]] = Field(
None,
description="Volumes are directories which may be used to share data between\nExecutors. Volumes are initialized as empty directories by the\nsystem when the task starts and are mounted at the same path\nin each Executor.\n\nFor example, given a volume defined at `/vol/A`,\nexecutor 1 may write a file to `/vol/A/exec1.out.txt`, then\nexecutor 2 may read from that file.\n\n(Essentially, this translates to a `docker run -v` flag where\nthe container path is the same for each executor).",
example=["/vol/A/"],
)
tags: Optional[Dict[str, str]] = Field(
None,
description='A key-value map of arbitrary tags. These can be used to store meta-data\nand annotations about a task. Example:\n```\n{\n "tags" : {\n "WORKFLOW_ID" : "cwl-01234",\n "PROJECT_GROUP" : "alice-lab"\n }\n}\n```',
example={"WORKFLOW_ID": "cwl-01234", "PROJECT_GROUP": "alice-lab"},
)
logs: Optional[List[TesTaskLog]] = Field(
None,
description="Task logging information.\nNormally, this will contain only one entry, but in the case where\na task fails and is retried, an entry will be appended to this list.",
)
creation_time: Optional[str] = Field(
None,
description="Date + time the task was created, in RFC 3339 format.\nThis is set by the system, not the client.",
example="2020-10-02T10:00:00-05:00",
)
class TesListTasksResponse(BaseModel):
tasks: List[TesTask] = Field(
...,
description="List of tasks. These tasks will be based on the original submitted\ntask document, but with other fields, such as the job state and\nlogging info, added/changed as the job progresses.",
)
next_page_token: Optional[str] = Field(
None,
description="Token used to return the next page of results. This value can be used\nin the `page_token` field of the next ListTasks request.",
)