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openapi: 3.2.0
info:
title: Seven Bridges Tasks API
version: unknown
description: 'Operations tagged Tasks across 2 of this provider''s published API definitions: seven-bridges-cgc-openapi.json, seven-bridges-platform-openapi.json. Each path carries the servers of the definition it was published in.'
servers:
- url: https://cgc-api.sbgenomics.com/v2
- url: https://api.sbgenomics.com/v2
security:
- {}
tags:
- name: Tasks
paths:
/v2/tasks:
post:
summary: Create a new draft task
description: /tasks
operationId: create-a-new-task
responses:
'200':
description: '200'
content:
application/json:
examples:
Result:
value: '{}'
schema:
type: object
properties: {}
'400':
description: '400'
content:
application/json:
examples:
Result:
value: '{}'
schema:
type: object
properties: {}
deprecated: false
tags:
- Tasks
get:
summary: List tasks you can access (primary method)
description: /tasks
operationId: list-tasks-you-can-access
responses:
'200':
description: '200'
content:
application/json:
examples:
Result:
value: '{}'
schema:
type: object
properties: {}
'400':
description: '400'
content:
application/json:
examples:
Result:
value: '{}'
schema:
type: object
properties: {}
deprecated: false
tags:
- Tasks
servers:
- url: https://cgc-api.sbgenomics.com/v2
/tasks/{task_id}:
patch:
summary: Modify a task
description: /tasks/{task_id}
operationId: modify-a-task
responses:
'200':
description: '200'
content:
application/json:
examples:
Result:
value: '{}'
schema:
type: object
properties: {}
'400':
description: '400'
content:
application/json:
examples:
Result:
value: '{}'
schema:
type: object
properties: {}
deprecated: false
tags:
- Tasks
delete:
summary: Delete a task
description: This call deletes the specified task. The task is referred to by its ID, which you can obtain by making the call to [list all tasks you can access](ref:list-tasks-you-can-access).
operationId: delete-a-task
parameters:
- name: X-SBG-Auth-Token
in: header
description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
required: true
schema:
type: string
- name: task_id
in: path
description: The ID of the task you are deleting. See the section on [specifying tasks](ref:section-tasks) for details.
schema:
type: string
required: true
deprecated: false
x-readme:
code-samples:
- language: python
code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\ntask = api.tasks.get(id='723c949a-789c-12b3-45b6-b2dd0d8d0021')\n\n# send DELETE request to SB API\ntask.delete()"
samples-languages:
- python
tags:
- Tasks
get:
summary: Get details of a task
description: 'This call returns details of the specified task. The task is referred to by its ID, which you can obtain by making the call to [list all tasks you can access](ref:list-tasks-you-can-access).
The task details include its creator, its start and end time, the number of jobs completed in it, and its input and output files. You can also see the status of the task.'
operationId: get-details-of-a-task
parameters:
- name: X-SBG-Auth-Token
in: header
description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
required: true
schema:
type: string
- name: task_id
in: path
description: The ID of the task you are querying.
schema:
type: string
required: true
- name: fields
in: query
description: Selector specifying a subset of fields to include in the response.
schema:
type: array
items:
type: string
responses:
'200':
description: '200'
content:
application/json:
examples:
Regular task response body:
value: "{\n \"href\": \"https://api.sbgenomics.com/v2/tasks/bd5e95d9-12b3-789c-45b6-34d8696571a9\",\n \"id\": \"bd5e95d9-12b3-789c-45b6-34d8696571a9\",\n \"name\": \"grep run - 11-26-15 14:14:14\",\n \"status\": \"COMPLETED\",\n \"project\": \"RFranklin/test\",\n \"use_interruptible_instances\": false,\n \"execution_settings\": {\n \"instance_type\": \"c4.2xlarge;ebs-gp2;2000\",\n \"max_parallel_instances\": 1\n },\n \"app\": \"rfranklin/my-project/grep/5\",\n \"type\": \"v2\",\n \"batch\": false,\n \"created_by\": \"RFranklin\",\n \"executed_by\": \"RFranklin\",\n \"start_time\": \"2015-11-26T14:14:14Z\",\n \"end_time\": \"2015-11-26T14:20:30Z\",\n \"execution_status\": {\n \"steps_completed\": 19,\n \"system_limit\": false,\n \"account_limit\": false,\n \"instance_init\": false,\n \"steps_total\": 19,\n \"message\": \"Completed\",\n \"duration\": 0,\n \"queued_duration\": 0,\n \"running_duration\": 0,\n \"execution_duration\": 0\n },\n \"price\": {\n \"currency\": \"USD\",\n \"amount\": \"0.23\",\n \"breakdown\": {\n \"storage\": \"0.00\",\n \"computation\": \"0.23\"\n }\n },\n \"origin_id\": \"723c949a-789c-12b3-45b6-b2dd0d8d0021\",\n \"inputs\": {\n \"file_to_search\": {\n \"class\": \"File\",\n \"path\": \"567890abc9b0307bc0414164\",\n \"name\": \"test-text.txt\"\n },\n \"lines_of_context\": 2,\n \"pattern_to_find\": \"word\"\n },\n \"outputs\": {\n \"pattern_found\": {\n \"path\": \"567890abc1e5339df0414123\",\n \"name\": \"output.txt\",\n \"class\": \"File\"\n }\n }\n}"
Batch task response body:
value: "{\n \"href\": \"https://api.sbgenomics.com/v2/tasks/a547a1c4-45c3-441e-857e-caf2a2df96ad\",\n \"id\": \"a547a1c4-45c3-441e-857e-caf2a2df96ad\",\n \"name\": \"wes run - 09-12-15 11:24:33\",\n \"status\": \"ABORTED\",\n \"project\": \"RFranklin/batch-test\",\n \"app\": \"RFranklin/batch-test/whole-exome-sequencing-gatk-2-3-9-lite/2\",\n \"type\": \"v2\",\n \"created_by\": \"RFranklin\",\n \"executed_by\": \"RFranklin\",\n \"start_time\": \"2016-04-05T12:18:14Z\",\n \"end_time\": \"2016-04-07T11:04:42Z\",\n \"batch\": true,\n \"batch_input\": \"FASTQ\",\n \"batch_by\": {\n \"type\": \"CRITERIA\",\n \"criteria\": [\n \"metadata.sample_id\",\n \"metadata.library_id\"\n ]\n },\n \"execution_status\": {\n \"duration\": '123456789',\n \"running_duration\": '120453636',\n \"queued_duration\": '3456789',\n \"message\": \"Batch tasks list initialization.\",\n \"queued\": 0,\n \"running\": 0,\n \"completed\": 0,\n \"failed\": 0,\n \"aborted\": 0,\n \"execution_duration\": 0,\n \"system_limit\": false,\n \"account_limit\": false\n },\n \"price\": {\n \"currency\": \"USD\",\n \"amount\": \"0.00\",\n },\n \"origin_id\": \"e1b28692-d911-4f2f-9afe-fd0213a64e41\",\n \"inputs\": {\n \"Known_SNPs\": [\n {\n \"class\": \"File\",\n \"path\": \"5702cd5a60b27cfe6e8c13bf\",\n \"name\": \"dbsnp_137.b37.vcf\"\n }\n ],\n <snip>\n }\n}"
schema:
type: object
properties:
href:
type: string
example: https://api.sbgenomics.com/v2/tasks/bd5e95d9-12b3-789c-45b6-34d8696571a9
id:
type: string
example: bd5e95d9-12b3-789c-45b6-34d8696571a9
name:
type: string
example: grep run - 11-26-15 14:14:14
status:
type: string
example: COMPLETED
project:
type: string
example: RFranklin/test
use_interruptible_instances:
type: boolean
example: false
default: true
execution_settings:
type: object
properties:
instance_type:
type: string
example: c4.2xlarge;ebs-gp2;2000
max_parallel_instances:
type: integer
example: 1
default: 0
app:
type: string
example: rfranklin/my-project/grep/5
type:
type: string
example: v2
batch:
type: boolean
example: false
default: true
created_by:
type: string
example: RFranklin
executed_by:
type: string
example: RFranklin
start_time:
type: string
example: '2015-11-26T14:14:14Z'
end_time:
type: string
example: '2015-11-26T14:20:30Z'
execution_status:
type: object
properties:
steps_completed:
type: integer
example: 19
default: 0
system_limit:
type: boolean
example: false
default: true
account_limit:
type: boolean
example: false
default: true
instance_init:
type: boolean
example: false
default: true
steps_total:
type: integer
example: 19
default: 0
message:
type: string
example: Completed
duration:
type: integer
example: 0
default: 0
queued_duration:
type: integer
example: 0
default: 0
running_duration:
type: integer
example: 0
default: 0
execution_duration:
type: integer
example: 0
default: 0
price:
type: object
properties:
currency:
type: string
example: USD
amount:
type: string
example: '0.23'
breakdown:
type: object
properties:
storage:
type: string
example: '0.00'
computation:
type: string
example: '0.23'
origin_id:
type: string
example: 723c949a-789c-12b3-45b6-b2dd0d8d0021
inputs:
type: object
properties:
file_to_search:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 567890abc9b0307bc0414164
name:
type: string
example: test-text.txt
lines_of_context:
type: integer
example: 2
default: 0
pattern_to_find:
type: string
example: word
outputs:
type: object
properties:
pattern_found:
type: object
properties:
path:
type: string
example: 567890abc1e5339df0414123
name:
type: string
example: output.txt
class:
type: string
example: File
deprecated: false
x-readme:
code-samples:
- language: python
code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send GET request to SB API for all task fields\ntask = api.tasks.get(id='bd5e95d9-12b3-789c-45b6-34d8696571a9')\n\nprint(task.name, task.id, task.status, task.description, task.app)\nprint(task.inputs)\nprint(task.outputs)"
samples-languages:
- python
tags:
- Tasks
servers:
- url: https://cgc-api.sbgenomics.com/v2
/tasks/{task_id}/inputs:
get:
summary: Get task inputs
description: This call returns just the inputs provided to the specified task. The task is referred to by its ID, which you can obtain by making the call to [list all tasks you can access](ref:list-tasks-you-can-access).
operationId: get-task-inputs
parameters:
- name: X-SBG-Auth-Token
in: header
description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
required: true
schema:
type: string
- name: task_id
in: path
description: The ID of the task you are querying.
schema:
type: string
required: true
- name: fields
in: query
description: Selector specifying a subset of fields to include in the response.
schema:
type: array
items:
type: string
responses:
'200':
description: '200'
content:
application/json:
examples:
Result:
value: "{\n \"Known_SNPs\": [\n {\n \"class\": \"File\",\n \"path\": \"567890abc9b0307bc0414164\",\n \"name\": \"dbsnp_137.b37.vcf\"\n }\n ],\n \"Known_Indels\": [\n {\n \"class\": \"File\",\n \"path\": \"567890abc1e5339df0414123\",\n \"name\": \"1000G_phase1.indels.b37.vcf\"\n },\n {\n \"class\": \"File\",\n \"path\": \"567890abc4f3066bc3750174\",\n \"name\": \"Mills_and_1000G_gold_standard.indels.b37.sites.vcf\"\n }\n ],\n \"input_file\": {\n \"class\": \"File\",\n \"path\": \"56796c27e4c8c560b46ab03c\",\n \"name\": \"3d1b628fa0d554d5fefb71444511dcbb.bam\"\n },\n \"Target_BED\": {\n \"class\": \"File\",\n \"path\": \"567890abc8a5639cc6722063\",\n \"name\": \"exome_targets.b37.bed\"\n },\n \"Reference\": {\n \"class\": \"File\",\n \"path\": \"567890abc3d8130ea4047731\",\n \"name\": \"GRCh37-lite.fa\"\n },\n \"snpEff_databse\": {\n \"class\": \"File\",\n \"path\": \"567890abc8a5136ec6127063\",\n \"name\": \"snpEff_v3_3_GRCh37.71.zip\"\n },\n \"memory_per_job\": 8000\n}"
schema:
type: object
properties:
Known_SNPs:
type: array
items:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 567890abc9b0307bc0414164
name:
type: string
example: dbsnp_137.b37.vcf
Known_Indels:
type: array
items:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 567890abc1e5339df0414123
name:
type: string
example: 1000G_phase1.indels.b37.vcf
input_file:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 56796c27e4c8c560b46ab03c
name:
type: string
example: 3d1b628fa0d554d5fefb71444511dcbb.bam
Target_BED:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 567890abc8a5639cc6722063
name:
type: string
example: exome_targets.b37.bed
Reference:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 567890abc3d8130ea4047731
name:
type: string
example: GRCh37-lite.fa
snpEff_databse:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 567890abc8a5136ec6127063
name:
type: string
example: snpEff_v3_3_GRCh37.71.zip
memory_per_job:
type: integer
example: 8000
default: 0
deprecated: false
x-readme:
code-samples:
- language: python
code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\n# send GET request to SB API for all task fields\ntask = api.tasks.get(id='723c949a-789c-12b3-45b6-b2dd0d8d0021')\n\nprint(task.inputs)"
samples-languages:
- python
tags:
- Tasks
patch:
summary: Modify task inputs
description: This call enables you to modify the inputs provided to the specified task. The task is referred to by its ID, which you can obtain by making the call to [list all tasks you can access](ref:list-tasks-you-can-access).
operationId: modify-task-inputs
parameters:
- name: X-SBG-Auth-Token
in: header
description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
required: true
schema:
type: string
- name: fields
in: query
description: Selector specifying a subset of fields to include in the response.
schema:
type: array
items:
type: string
- name: task_id
in: path
description: The ID of the task you are querying
schema:
type: string
required: true
requestBody:
content:
application/json:
schema:
type: object
properties:
RAW_BODY:
type: array
description: In the body of the request, you should enter some or all of the key-value pairs contained in the input object for the task. See the section on [specifying task inputs](doc:the-api#section-inputs) for information on creating task input objects. In the example request, make sure to replace `{input_id}` with the actual ID of the input you are modifying.
items:
properties:
'{input_id}':
type: object
properties:
class:
type: string
description: Input value type. If this is a file, the value is `File`.
default: File
path:
type: string
description: File ID for file inputs.
name:
type: string
description: Name of the file for file inputs.
type: object
responses:
'200':
description: '200'
content:
application/json:
examples:
Result:
value: "{\n \"dispersion_threshold\": null,\n \"cuffdiff_zip\": {\n \"class\": \"File\",\n \"path\": \"567890abc9b0307bc0414164\",\n \"name\": \"new-file-name.vcf\"\n },\n \"density_threshold\": null,\n \"thresholds_off\": null\n}\n"
schema:
type: object
properties:
dispersion_threshold: {}
cuffdiff_zip:
type: object
properties:
class:
type: string
example: File
path:
type: string
example: 567890abc9b0307bc0414164
name:
type: string
example: new-file-name.vcf
density_threshold: {}
thresholds_off: {}
deprecated: false
x-readme:
code-samples:
- language: python
code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\ntask = api.tasks.get(id='48f79ccf-12b3-45b6-789c-b1e8d88dabcd')\n\ntask.inputs['cuffdiff_zip'] = api.files.get(id='567890abc9b0307bc0414164')\n\n# send PATCH request to SB API, same as changing any other field\ntask.save()\n\nprint(task.inputs)"
samples-languages:
- python
tags:
- Tasks
servers:
- url: https://api.sbgenomics.com/v2
/tasks/{task_id}/actions/abort:
post:
summary: Abort a task
description: This call aborts the specified task. Only tasks whose status is `"RUNNING"` or `"QUEUED"` may be aborted.
operationId: abort-a-task
parameters:
- name: X-SBG-Auth-Token
in: header
description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token).
required: true
schema:
type: string
- name: task_id
in: path
description: The ID of the task you are acting on.
schema:
type: string
required: true
- name: fields
in: query
description: Selector specifying a subset of fields to include in the response.
schema:
type: array
items:
type: string
responses:
'200':
description: '200'
content:
application/json:
examples:
Result:
value: "{\n \"href\": \"https://api.sbgenomics.com/v2/tasks/bd5e95d9-12b3-789c-45b6-34d8696571a9\",\n \"id\": \"bd5e95d9-12b3-789c-45b6-34d8696571a9\",\n \"name\": \"Workflow run - 11-15-15 15:56:11\",\n \"status\": \"Active\",\n \"project\": \"RFranklin/my-project\",\n \"use_interruptible_instances\": false,\n \"app\": \"RFranklin/my-project/workflow/1\",\n \"created_by\": \"RFranklin\",\n \"executed_by\": \"Kate\",\n \"start_time\": \"2015-11-15T15:56:11Z\",\n \"inputs\": {\n \"my_hardcoded_string\": {\n \"schema\": [\n \"null\",\n \"string\"\n ],\n \"value\": null,\n \"errors\": null,\n \"files\": null,\n \"missing_files\": null\n }\n }\n}"
schema:
type: object
properties:
href:
type: string
example: https://api.sbgenomics.com/v2/tasks/bd5e95d9-12b3-789c-45b6-34d8696571a9
id:
type: string
example: bd5e95d9-12b3-789c-45b6-34d8696571a9
name:
type: string
example: Workflow run - 11-15-15 15:56:11
status:
type: string
example: Active
project:
type: string
example: RFranklin/my-project
use_interruptible_instances:
type: boolean
example: false
default: true
app:
type: string
example: RFranklin/my-project/workflow/1
created_by:
type: string
example: RFranklin
executed_by:
type: string
example: Kate
start_time:
type: string
example: '2015-11-15T15:56:11Z'
inputs:
type: object
properties:
my_hardcoded_string:
type: object
properties:
schema:
type: array
items:
type: string
example: 'null'
value: {}
errors: {}
files: {}
missing_files: {}
deprecated: false
x-readme:
code-samples:
- language: python
code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n token='3210a98c1db9318fa9d9273156740f74')\n\ntask = api.tasks.get(id='bd5e95d9-12b3-789c-45b6-34d8696571a9')\n\n# send POST request to SB API\ntask.abort()\n\nprint(task.status)"
samples-languages:
- python
tags:
- Tasks
servers:
- url: https://api.sbgenomics.com/v2
/tasks:
post:
summary: Create a new draft task
description: 'This call creates a new task. You can create either a single task or a batch task by using the app''s default batching, override batching, or disable batching completely.
A **parent task** is a task that specifies criteria by which to batch its inputs into a series of further sub-tasks, called **child tasks**.
See the documentation on [batching tasks](doc:about-batch-analyses) for more details on batching criteria.'
operationId: create-a-new-task
parameters:
- name: fields
in: query
description: Selector specifying a subset of fields to include in the response.
schema:
type: array
items:
type: string
- name: action
in: query
description: If set to "run", the task will be run immediately upon creation.
schema:
type: string
- name: X-SBG-Auth-Token
in: header
description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
required: true
schema:
type: string
requestBody:
content:
application/json:
schema:
type: object
required:
- project
- app
properties:
project:
type: string
description: The [short name](the-api#section-project-short-names) of the project that you want to create the task in.
app:
type: string
description: The specification of the app that you want to run. Recall that apps are specified by their projects, in the form `{project_owner}/{project}/{app_name}`
name:
type: string
description: The name of the task
description:
type: string
description: An optional description of the task
execution_settings:
type: object
description: Detailed task execution parameters.
properties:
instance_type:
type: string
description: 'Possible value is the specific instance type, e.g. `"instance_type": "c4.2xlarge;ebs-gp2;2000"`.'
max_parallel_instances:
type: integer
description: 'Maximum number of instances running at the same time. Takes any integer value equal to or greater than 1, e.g. `"max_parallel_instances": 2`.'
format: int32
use_memoization:
type: boolean
description: Set to `false` by default. Set to `true` to enable [memoization](doc:about-memoization).
use_elastic_disk:
type: boolean
description: Set to `true` to enable [Elastic Disk](page:elastic-disk).
inputs:
type: array
description: See the section on [specifying task inputs](doc:the-api#section-inputs) for information on creating task input objects.
items:
properties:
'{input_id}':
type:
# --- truncated at 32 KB (65 KB total) ---
# Full source: https://raw.githubusercontent.com/api-evangelist/seven-bridges/refs/heads/main/openapi/seven-bridges-tasks-api-openapi.yml