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sapporo-wes-spec-2.0.0.yml
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components:
schemas:
Body_create_token_token_post:
properties:
password:
description: The password for authentication.
title: Password
type: string
username:
description: The username for authentication.
title: Username
type: string
required:
- username
- password
title: Body_create_token_token_post
type: object
Body_run_workflow_runs_post:
properties:
tags:
anyOf:
- type: string
- type: 'null'
title: Tags
workflow_attachment:
items:
format: binary
type: string
title: Workflow Attachment
type: array
workflow_attachment_obj:
anyOf:
- type: string
- type: 'null'
description: 'Extension specific to sapporo-wes-2.0.0: e.g., [{ "file_name":
"path/to/file", "file_url": "https://example.com/path/to/file" }]'
title: Workflow Attachment Obj
workflow_engine:
description: Optional in original WES 1.1.0, but required in sapporo-wes-2.0.0.
title: Workflow Engine
type: string
workflow_engine_parameters:
anyOf:
- type: string
- type: 'null'
title: Workflow Engine Parameters
workflow_engine_version:
anyOf:
- type: string
- type: 'null'
title: Workflow Engine Version
workflow_params:
anyOf:
- type: string
- type: 'null'
title: Workflow Params
workflow_type:
description: Optional in original WES 1.1.0, but required in sapporo-wes-2.0.0.
title: Workflow Type
type: string
workflow_type_version:
anyOf:
- type: string
- type: 'null'
title: Workflow Type Version
workflow_url:
anyOf:
- type: string
- type: 'null'
title: Workflow Url
required:
- workflow_type
- workflow_engine
title: Body_run_workflow_runs_post
type: object
DefaultWorkflowEngineParameter:
description: A message that allows one to describe default parameters for a
workflow engine.
properties:
default_value:
anyOf:
- type: string
- type: 'null'
description: The stringified version of the default parameter. e.g. "2.45".
title: Default Value
name:
anyOf:
- type: string
- type: 'null'
description: The name of the parameter
title: Name
type:
anyOf:
- type: string
- type: 'null'
description: Describes the type of the parameter, e.g. float.
title: Type
title: DefaultWorkflowEngineParameter
type: object
ErrorResponse:
description: An object that can optionally include information about the error.
properties:
msg:
description: A detailed error message.
title: Msg
type: string
status_code:
description: The integer representing the HTTP status code (e.g. 200, 404).
title: Status Code
type: integer
required:
- msg
- status_code
title: ErrorResponse
type: object
ExecutableWorkflows:
description: '**sapporo-wes-2.0.0 extension:** Schema for executable_workflows.json.
List of workflows that can be executed in this service.'
properties:
workflows:
description: List of executable workflows. Each workflow is a URL to the
workflow file.
items:
type: string
title: Workflows
type: array
required:
- workflows
title: ExecutableWorkflows
type: object
FileObject:
description: '**sapporo-wes-2.0.0 extension:** File object used in Workflow
Attachment and Output files, etc.'
properties:
file_name:
description: File name. It is a relative path from the certain directory.
That is, if the file is ./some_dir/some_file, this field is 'some_dir/some_file'.
title: File Name
type: string
file_url:
description: Download URL of the file.
title: File Url
type: string
required:
- file_name
- file_url
title: FileObject
type: object
HTTPValidationError:
properties:
detail:
items:
$ref: '#/components/schemas/ValidationError'
title: Detail
type: array
title: HTTPValidationError
type: object
Log:
description: Log and other info
properties:
cmd:
anyOf:
- items:
type: string
type: array
- type: 'null'
description: The command line that was executed
title: Cmd
end_time:
anyOf:
- type: string
- type: 'null'
description: When the command stopped executing (completed, failed, or cancelled),
in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
title: End Time
exit_code:
anyOf:
- type: integer
- type: 'null'
description: Exit code of the program
title: Exit Code
name:
anyOf:
- type: string
- type: 'null'
description: The task or workflow name
title: Name
start_time:
anyOf:
- type: string
- type: 'null'
description: When the command started executing, in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
title: Start Time
stderr:
anyOf:
- type: string
- type: 'null'
description: A URL to retrieve standard error logs of the workflow run or
task. This URL may change between status requests, or may not be available
until the task or workflow has finished execution. Should be available
using the same credentials used to access the WES endpoint.
title: Stderr
stdout:
anyOf:
- type: string
- type: 'null'
description: A URL to retrieve standard output logs of the workflow run
or task. This URL may change between status requests, or may not be available
until the task or workflow has finished execution. Should be available
using the same credentials used to access the WES endpoint.
title: Stdout
system_logs:
anyOf:
- items:
type: string
type: array
- type: 'null'
description: 'System logs are any logs the system decides are relevant,
which are not tied directly to a workflow.
Content is implementation specific: format, size, etc.
System logs may be collected here to provide convenient access.
For example, the system may include an error message that caused
a SYSTEM_ERROR state (e.g. disk is full), etc.'
title: System Logs
title: Log
type: object
MeResponse:
properties:
username:
title: Username
type: string
required:
- username
title: MeResponse
type: object
Organization:
description: Organization providing the service.
properties:
name:
description: Name of the organization responsible for the service.
examples:
- My organization
title: Name
type: string
url:
description: URL of the website of the organization (RFC 3986 format).
examples:
- https://example.com
format: uri
maxLength: 2083
minLength: 1
title: Url
type: string
required:
- name
- url
title: Organization
type: object
RunId:
properties:
run_id:
description: workflow run ID
title: Run Id
type: string
required:
- run_id
title: RunId
type: object
RunListResponse:
description: 'The service will return a RunListResponse when receiving a successful
RunListRequest. DEPRECIATION WARNING: The use of `RunStatus` as the schema
for `runs` array items will not be permitted from the next major version of
the specification (2.0.0) onwards. We encourage implementers to use `RunSummary`
instead.
'
properties:
next_page_token:
anyOf:
- type: string
- type: 'null'
description: A token which may be supplied as `page_token` in workflow run
list request to get the next page of results. An empty string indicates
there are no more items to return.
title: Next Page Token
runs:
anyOf:
- items:
anyOf:
- $ref: '#/components/schemas/RunStatus'
- $ref: '#/components/schemas/RunSummary'
type: array
- type: 'null'
description: A list of workflow runs that the service has executed or is
executing. The list is filtered to only include runs that the caller has
permission to see.
title: Runs
title: RunListResponse
type: object
RunLog:
properties:
outputs:
anyOf:
- items:
$ref: '#/components/schemas/FileObject'
type: array
- type: 'null'
description: 'The outputs from the workflow run.
**sapporo-wes-2.0.0 extension:**
- original wes-1.1.0: Optional[Dict[str, Any]]
- sapporo-wes-2.0.0: Optional[List[FileObject]]
'
title: Outputs
request:
anyOf:
- $ref: '#/components/schemas/RunRequest'
- type: 'null'
run_id:
anyOf:
- type: string
- type: 'null'
description: workflow run ID
title: Run Id
run_log:
anyOf:
- $ref: '#/components/schemas/Log'
- type: 'null'
state:
anyOf:
- $ref: '#/components/schemas/State'
- type: 'null'
task_logs:
anyOf:
- items:
anyOf:
- $ref: '#/components/schemas/Log'
- $ref: '#/components/schemas/TaskLog'
type: array
- type: 'null'
description: The logs, and other key info like timing and exit code, for
each step in the workflow run. This field is deprecated and the `task_logs_url`
should be used to retrieve a paginated list of steps from the workflow
run. This field will be removed in the next major version of the specification
(2.0.0)
title: Task Logs
task_logs_url:
anyOf:
- type: string
- type: 'null'
description: A reference to the complete url which may be used to obtain
a paginated list of task logs for this workflow
title: Task Logs Url
title: RunLog
type: object
RunRequest:
description: "To execute a workflow, send a run request including all the details\
\ needed to begin downloading\nand executing a given workflow.\nIf workflow_engine\
\ and workflow_engine_version are not provided, servers can use the most recent\
\ workflow_engine_version of workflow_engine that WES instance uses to process\
\ the request if \nsupports for the requested workflow_type."
properties:
tags:
anyOf:
- additionalProperties:
type: string
type: object
- type: 'null'
title: Tags
workflow_engine:
anyOf:
- type: string
- type: 'null'
description: The workflow engine, must be one supported by this WES instance.
Required if workflow_engine_version is provided.
title: Workflow Engine
workflow_engine_parameters:
anyOf:
- additionalProperties:
type: string
type: object
- type: 'null'
title: Workflow Engine Parameters
workflow_engine_version:
anyOf:
- type: string
- type: 'null'
description: The workflow engine version, must be one supported by this
WES instance. If workflow_engine is provided, but workflow_engine_version
is not, servers can make no assumptions with regard to the engine version
the WES instance uses to process the request if that WES instance supports
multiple versions of the requested engine.
title: Workflow Engine Version
workflow_params:
description: 'REQUIRED
The workflow run parameterizations (JSON encoded), including input and
output file locations'
title: Workflow Params
type: object
workflow_type:
description: 'REQUIRED
The workflow descriptor type, must be "CWL" or "WDL" currently (or another
alternative supported by this WES instance)'
title: Workflow Type
type: string
workflow_type_version:
description: 'REQUIRED
The workflow descriptor type version, must be one supported by this WES
instance'
title: Workflow Type Version
type: string
workflow_url:
description: 'REQUIRED
The workflow CWL or WDL document. When `workflow_attachments` is used
to attach files, the `workflow_url` may be a relative path to one of the
attachments.'
title: Workflow Url
type: string
required:
- workflow_params
- workflow_type
- workflow_type_version
- workflow_url
title: RunRequest
type: object
RunStatus:
description: State information of a workflow run
properties:
run_id:
title: Run Id
type: string
state:
anyOf:
- $ref: '#/components/schemas/State'
- type: 'null'
description: "State can take any of the following values:\n\n + UNKNOWN:\
\ The state of the task is unknown. This provides a safe default for messages\
\ where this field is missing, for example, so that a missing field does\
\ not accidentally imply that the state is QUEUED.\n\n + QUEUED: The\
\ task is queued.\n\n + INITIALIZING: The task has been assigned to a\
\ worker and is currently preparing to run. For example, the worker may\
\ be turning on, downloading input files, etc.\n\n + RUNNING: The task\
\ is running. Input files are downloaded and the first Executor has been\
\ started.\n\n + PAUSED: The task is paused. An implementation may have\
\ the ability to pause a task, but this is not required.\n\n + COMPLETE:\
\ The task has completed running. Executors have exited without error\n\
\ and output files have been successfully uploaded.\n\n + EXECUTOR_ERROR:\
\ The task encountered an error in one of the Executor processes. Generally,\n\
this means that an Executor exited with a non-zero exit code.\n\n + SYSTEM_ERROR:\
\ The task was stopped due to a system error, but not from an Executor,\n\
for example an upload failed due to network issues, the worker's ran out\
\ of disk space, etc.\n\n + CANCELED: The task was canceled by the user.\n\
\n + CANCELING: The task was canceled by the user, and is in the process\
\ of stopping.\n\n + PREEMPTED: The task is stopped (preempted) by the\
\ system. The reasons for this would be tied to\nthe specific system running\
\ the job. Generally, this means that the system reclaimed the compute\
\ capacity for reallocation.\n"
required:
- run_id
title: RunStatus
type: object
RunSummary:
description: Small description of a workflow run
properties:
end_time:
anyOf:
- type: string
- type: 'null'
description: When the run stopped executing (completed, failed, or cancelled),
in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
title: End Time
run_id:
title: Run Id
type: string
start_time:
anyOf:
- type: string
- type: 'null'
description: When the run started executing, in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
title: Start Time
state:
anyOf:
- $ref: '#/components/schemas/State'
- type: 'null'
description: "State can take any of the following values:\n\n + UNKNOWN:\
\ The state of the task is unknown. This provides a safe default for messages\
\ where this field is missing, for example, so that a missing field does\
\ not accidentally imply that the state is QUEUED.\n\n + QUEUED: The\
\ task is queued.\n\n + INITIALIZING: The task has been assigned to a\
\ worker and is currently preparing to run. For example, the worker may\
\ be turning on, downloading input files, etc.\n\n + RUNNING: The task\
\ is running. Input files are downloaded and the first Executor has been\
\ started.\n\n + PAUSED: The task is paused. An implementation may have\
\ the ability to pause a task, but this is not required.\n\n + COMPLETE:\
\ The task has completed running. Executors have exited without error\n\
\ and output files have been successfully uploaded.\n\n + EXECUTOR_ERROR:\
\ The task encountered an error in one of the Executor processes. Generally,\n\
this means that an Executor exited with a non-zero exit code.\n\n + SYSTEM_ERROR:\
\ The task was stopped due to a system error, but not from an Executor,\n\
for example an upload failed due to network issues, the worker's ran out\
\ of disk space, etc.\n\n + CANCELED: The task was canceled by the user.\n\
\n + CANCELING: The task was canceled by the user, and is in the process\
\ of stopping.\n\n + PREEMPTED: The task is stopped (preempted) by the\
\ system. The reasons for this would be tied to\nthe specific system running\
\ the job. Generally, this means that the system reclaimed the compute\
\ capacity for reallocation.\n"
tags:
additionalProperties:
type: string
description: Arbitrary key/value tags added by the client during run creation
title: Tags
type: object
required:
- run_id
- tags
title: RunSummary
type: object
ServiceInfo:
description: GA4GH service.
properties:
auth_instructions_url:
description: A web page URL with human-readable instructions on how to get
an authorization token for use with a specific WES endpoint.
format: uri
maxLength: 2083
minLength: 1
title: Auth Instructions Url
type: string
contactUrl:
anyOf:
- format: uri
maxLength: 2083
minLength: 1
type: string
- type: 'null'
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).
examples:
- mailto:[email protected]
title: Contacturl
createdAt:
anyOf:
- type: string
- type: 'null'
description: Timestamp describing when the service was first deployed and
available (RFC 3339 format).
examples:
- '2019-06-04T12:58:19Z'
title: Createdat
default_workflow_engine_parameters:
additionalProperties:
items:
$ref: '#/components/schemas/DefaultWorkflowEngineParameter'
type: array
description: 'Each workflow engine can present additional parameters that
can be sent to the workflow engine. This message will list the default
values, and their types for each workflow engine.
**sapporo-wes-2.0.0 extension:**
- original wes-1.1.0: List[DefaultWorkflowEngineParameter]
- sapporo-wes-2.0.0: Dict[str, List[DefaultWorkflowEngineParameter]]
'
title: Default Workflow Engine Parameters
type: object
description:
anyOf:
- type: string
- type: 'null'
description: Description of the service. Should be human readable and provide
information about the service.
examples:
- This service provides...
title: Description
documentationUrl:
anyOf:
- format: uri
maxLength: 2083
minLength: 1
type: string
- type: 'null'
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.
examples:
- https://docs.myservice.example.com
title: Documentationurl
environment:
anyOf:
- type: string
- type: 'null'
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.
examples:
- test
title: Environment
id:
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.
examples:
- org.ga4gh.myservice
title: Id
type: string
name:
description: Name of this service. Should be human readable.
examples:
- My project
title: Name
type: string
organization:
$ref: '#/components/schemas/Organization'
supported_filesystem_protocols:
description: The filesystem protocols supported by this service, currently
these may include common protocols using the terms 'http', 'https', 'sftp',
's3', 'gs', 'file', or 'synapse', but others are possible and the terms
beyond these core protocols are currently not fixed. This section reports
those protocols (either common or not) supported by this WES service.
items:
type: string
title: Supported Filesystem Protocols
type: array
supported_wes_versions:
description: The version(s) of the WES schema supported by this service
items:
type: string
title: Supported Wes Versions
type: array
system_state_counts:
additionalProperties:
type: integer
title: System State Counts
type: object
tags:
additionalProperties:
type: string
description: A message containing useful information about the running service,
including supported versions and default settings.
title: Tags
type: object
type:
allOf:
- $ref: '#/components/schemas/ServiceType'
description: GA4GH service.
updatedAt:
anyOf:
- type: string
- type: 'null'
description: Timestamp describing when the service was last updated (RFC
3339 format).
examples:
- '2019-06-04T12:58:19Z'
title: Updatedat
version:
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.
examples:
- 1.0.0
title: Version
type: string
workflow_engine_versions:
additionalProperties:
$ref: '#/components/schemas/WorkflowEngineVersion'
title: Workflow Engine Versions
type: object
workflow_type_versions:
additionalProperties:
$ref: '#/components/schemas/WorkflowTypeVersion'
title: Workflow Type Versions
type: object
required:
- id
- name
- type
- organization
- version
- workflow_type_versions
- supported_wes_versions
- supported_filesystem_protocols
- workflow_engine_versions
- default_workflow_engine_parameters
- system_state_counts
- auth_instructions_url
- tags
title: ServiceInfo
type: object
ServiceType:
description: Type of a GA4GH service.
properties:
artifact:
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.
examples:
- beacon
title: Artifact
type: string
group:
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).
examples:
- org.ga4gh
title: Group
type: string
version:
description: Version of the API or specification. GA4GH specifications use
semantic versioning.
examples:
- 1.0.0
title: Version
type: string
required:
- group
- artifact
- version
title: ServiceType
type: object
State:
enum:
- UNKNOWN
- QUEUED
- INITIALIZING
- RUNNING
- PAUSED
- COMPLETE
- EXECUTOR_ERROR
- SYSTEM_ERROR
- CANCELED
- CANCELING
- PREEMPTED
- DELETED
- DELETING
title: State
type: string
TaskListResponse:
description: The service will return a TaskListResponse when receiving a successful
TaskListRequest.
properties:
next_page_token:
anyOf:
- type: string
- type: 'null'
description: A token which may be supplied as `page_token` in workflow run
task list request to get the next page of results. An empty string indicates
there are no more items to return.
title: Next Page Token
task_logs:
anyOf:
- items:
$ref: '#/components/schemas/TaskLog'
type: array
- type: 'null'
description: The logs, and other key info like timing and exit code, for
each step in the workflow run.
title: Task Logs
title: TaskListResponse
type: object
TaskLog:
description: Runtime information for a given task
properties:
cmd:
anyOf:
- items:
type: string
type: array
- type: 'null'
description: The command line that was executed
title: Cmd
end_time:
anyOf:
- type: string
- type: 'null'
description: When the command stopped executing (completed, failed, or cancelled),
in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
title: End Time
exit_code:
anyOf:
- type: integer
- type: 'null'
description: Exit code of the program
title: Exit Code
id:
description: A unique identifier which may be used to reference the task
title: Id
type: string
name:
description: The task or workflow name
title: Name
type: string
start_time:
anyOf:
- type: string
- type: 'null'
description: When the command started executing, in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
title: Start Time
stderr:
anyOf:
- type: string
- type: 'null'
description: A URL to retrieve standard error logs of the workflow run or
task. This URL may change between status requests, or may not be available
until the task or workflow has finished execution. Should be available
using the same credentials used to access the WES endpoint.
title: Stderr
stdout:
anyOf:
- type: string
- type: 'null'
description: A URL to retrieve standard output logs of the workflow run
or task. This URL may change between status requests, or may not be available
until the task or workflow has finished execution. Should be available
using the same credentials used to access the WES endpoint.
title: Stdout
system_logs:
anyOf:
- items:
type: string
type: array
- type: 'null'
description: 'System logs are any logs the system decides are relevant,
which are not tied directly to a task.
Content is implementation specific: format, size, etc.
System logs may be collected here to provide convenient access.
For example, the system may include the name of the host
where the task is executing, an error message that caused
a SYSTEM_ERROR state (e.g. disk is full), etc.'
title: System Logs
tes_uri:
anyOf:
- type: string
- type: 'null'
description: An optional URL pointing to an extended task definition defined
by a [TES api](https://github.com/ga4gh/task-execution-schemas)
title: Tes Uri
required:
- name
- id
title: TaskLog
type: object
TokenResponse:
properties:
access_token:
title: Access Token
type: string
token_type:
default: bearer
title: Token Type
type: string
required:
- access_token
title: TokenResponse
type: object
ValidationError:
properties:
loc:
items:
anyOf:
- type: string
- type: integer
title: Location
type: array
msg:
title: Message
type: string
type:
title: Error Type
type: string
required:
- loc
- msg
- type
title: ValidationError
type: object
WorkflowEngineVersion:
description: Available workflow engine versions supported by a given instance
of the service.
properties:
workflow_engine_version:
anyOf:
- items:
type: string
type: array
- type: 'null'
default: []
description: An array of one or more acceptable engines versions for the
`workflow_engine`
title: Workflow Engine Version
title: WorkflowEngineVersion
type: object
WorkflowTypeVersion:
description: Available workflow types supported by a given instance of the service.
properties:
workflow_type_version:
anyOf:
- items:
type: string
type: array
- type: 'null'
default: []
description: an array of one or more acceptable types for the `workflow_type`
title: Workflow Type Version
title: WorkflowTypeVersion
type: object
info:
contact:
name: Sapporo-WES Project Team
url: https://github.com/sapporo-wes/sapporo-service/issues
description: '*Run standard workflows on workflow execution platforms in a platform-agnostic
way.*
## Executive Summary
The Workflow Execution Service (WES) API provides a standard way for users to
submit workflow requests to workflow execution systems and monitor their execution.
This API lets users run a single workflow (currently [**CWL**](https://www.commonwl.org/)
or [**WDL**](http://www.openwdl.org/) formatted workflows, with other types potentially
supported in the future) on multiple different platforms, clouds, and environments.
Key features of the API:
- Request that a workflow be run.
- Pass parameters to that workflow (e.g., input files, command-line arguments).
- Get information about running workflows (e.g., status, errors, output file locations).
- Cancel a running workflow.
## Sapporo-WES Extensions
`sapporo-wes-2.0.0` extends the original WES API to provide enhanced functionality
and support for additional features. This document describes the WES API and details
the specific endpoints, request formats, and responses, aimed at developers of
WES-compatible services and clients.
'
license:
identifier: Apache-2.0
name: Apache 2.0
url: https://github.com/sapporo-wes/sapporo-service/blob/main/LICENSE
title: GA4GH Workflow Execution Service API specification extended for the Sapporo
version: 2.0.0
openapi: 3.1.0
paths:
/executable-workflows:
get:
description: '**sapporo-wes-2.0.0 extension:**
Return the list of workflows that can be executed in this service.
If `workflows: []`, it indicates that there are no restrictions, and any workflow
can be executed.
If `workflows` contains workflow urls, only those workflows can be executed.'
operationId: list_executable_wfs_executable_workflows_get
responses:
'200':
content:
application/json: