Pipeline API

Prerequisites

• Token with Pipeline scope

• The Pipeline ID to pass to the API call

You can find the Pipelines ID on the metadata page

Run Pipeline

POST https://{domain}/api/v1/computations

This API allows for the running of capsules or pipelines.

Path Parameters

Name	Type	Description
POST*		/computations/

Headers

Name	Type	Description
-u*		Authorize with Code Ocean API Secret: -u $API_SECRET : This is setting the "Authorization Basic" base64string header
-H		Set this to: Content - Type: application/json
--data-raw		JSON data with new or updated permissions

Request Body

Name	Type	Description
capsule_id	string	the identification of the capsule

200: OK

400: Bad Request invalid request body

401: Unauthorized

403: Forbidden

404: Not Found

429: Too Many Requests

500: Internal Server Error

Response Description

• created - string

  • the data asset creation time in seconds from unix epoch

• has_results - boolean

  • if any results are available

• id - string

  • the computation internal id

• name - array

  • name of the run

• run_time - integer

  • unknown

• state - initializing

  • unknown

Request Example Bash

curl --location --request POST 'https://codeocean.com/api/v1/computations' \
--header 'Content-Type: application/json' \
-u \'${API_SECRET}:\' \
--data-raw '{
"pipeline_id": "4bc97533-6eb4-48ac-966f-648548a756d2"
}'

Request Example Python

import os, requests 


headers = {
  "Content-Type": "application/json"
}


json_data = {
  "pipeline_id": "4bc97533-6eb4-48ac-966f-648548a756d2"
} 


response = requests.put('https://codeocean.com/api/v1/data_assets/d36665a7-ef59-4b8e-a799-bee7f83ee317', 
headers=headers, json=json_data, auth=("'" + os.getenv('API_SECRET', ''), "'"), 
)

Response

{
  "created": 1689689613,
  "has_results": false,
  "id": "9af23fd6-2957-40bf-b691-16190056c94e",
  "name": "Run 9689613",
  "run_time": 0,
  "state": "initializing"
}

Run Pipeline with Data Assets

POST https://{domain}/api/v1/computations

This API allows for running of capsules or pipelines.

Path Parameters

Name	Type	Description
POST*		/computations/ Your VPC domain

Headers

Name	Type	Description
-u*		Authorize with Code Ocean API Secret: -u $API_SECRET : This is setting the "Authorization Basic" base64string header
-H*		Set this to: Content - Type: application/json
--data-raw*		JSON data with new or updated permissions

Request Body

Name	Type	Description
capsule_id*	string	the identification of the data asset to be used in computational run the id of the capsule/pipeline to run
data_assets*	string
id*	string	the identification of the data asset to be used in computational run
mount*	string	the name of the folder you wish to mount this dataset into position

200: OK

{
  "id": string - the computation internal id,
  "created": float64 - computation creation time,
  "name": string - the display name of the computation,
  "run_time": int - the total run time in seconds,

  "parameters": [
    {
      "name": string parameter name,
      "value": string parameter value
    },
    {
      "name": string parameter name,
      "value": string parameter value
    }
  ],
  "result_size": float64 - result size,
  "state": string - initializing,running,finalizing, completed
}

400: Bad Request invalid request body

401: Unauthorized

403: Forbidden

404: Not Found

429: Too Many Requests

500: Internal Server Error

Request Example Bash

curl -H "Content-Type: application/json" -u ${API_SECRET}: -X POST https://codeocean.com/api/v1/computations --data-raw '{
"pipeline_id":"4bc97533-6eb4-48ac-966f-648548a756d2",
"data_assets": [
    {
        "id": "bf8cf993-a583-495c-bebd-2f38f81d1ea1", 
        "mount": "Alignment"
    }
]

Request Example Python

import os, requests 


headers = {
  "Content-Type": "application/json"
}
 
json_data = {
  "pipeline_id": "4bc97533-6eb4-48ac-966f-648548a756d2",
  "data_assets": [
      {
        "id": "bf8cf993-a583-495c-bebd-2f38f81d1ea1",
        "mount": "Alignment"
      }
  ]
}
 
response = requests.post('https://codeocean.com/api/v1/computations', headers=headers, 
json=json_data, 
auth=(os.getenv('API_SECRET', ''), ''), 
)

Response

{
  "created": 1689691505,
  "has_results": false,
  "id": "94994ace-cd3d-4e38-9c5c-9aed12a5169d",
  "name": "Run 9691505",
  "run_time": 1,
  "state": "initializing"
}

Run Pipeline with Data Assets & Parameters

POST https://{domain}/api/v1/computations

This API allows for the running of Capsules/Pipelines with Data Assets and Named parameters.

Prerequisite

Before using this API call, you should have AWS Cloud Credentials configured as Secrets or an Assumable Role.

Path Parameters

Name	Type	Description
POST*		/computations/

Headers

Name	Type	Description
-u:*		Authorize with Code Ocean API Secret: -u $API_SECRET :
-H:*		Set this to: Content - Type: application/json
--data-raw:		JSON data with capsule/pipeline information

Request Body

Name	Type	Description
capsule_id*	string	identification of the capsule if both capsule_id and pipeline_id are used, only the capsule id wll be used
pipeline_id	string	identification of the pipeline
data_assets*	array
ID*	string	identification of the data asset to be used in the computational run
Mount*	string	name of the folder to mount the dataset into position
processes	string
name*	string	pipeline process name as it appears in the main.nf script
parameters	string	parameters expected by the capsule

200: OK

400: Bad Request

401: Unauthorized

403: Forbidden

404: Not Found

429: Too Many Requests

500: Internal Server Error

Ordered Parameters

Request Example Bash

curl --location --request POST 'https://codeocean.com/api/v1/computations' \
--header 'Content-Type: application/json' \
-u \'${API_SECRET}:\' \
--data-raw '{
 "pipeline_id":"e7a77780-b8ae-439e-89ac-fac2549da91b",
 "data_assets" : [
       {
           "id": "eeefcc52-b445-4e3c-80c5-0e65526cd712",
           "mount": "Reference"
       }
   ],
 "processes": [
       {
           "name": "capsule_art_simulation_illumina_1",
           "parameters": [
               "75","1","HS25","SingleEnded","","","1","","","","","","","False","False"
           ]      
       }
   ]
}'

Request Example Python

import os, requests

headers = {
 "Content-Type": "application/json"
}
json_data = {
 "pipeline_id":"e7a77780-b8ae-439e-89ac-fac2549da91b",
 "data_assets" : [
       {
           "id": "eeefcc52-b445-4e3c-80c5-0e65526cd712",
           "mount": "Reference"
       }
   ],
 "processes": [
       {
           "name": "capsule_art_simulation_illumina_1",
           "parameters": [
               "75","1","HS25","SingleEnded","","","1","","","","","","","False","False"
           ]      
       }
   ]
}
response = requests.post('https://codeocean.com/api/v1/computations', headers=headers,
json=json_data,auth=(os.getenv('API_SECRET', ''), ''),)

Response

{
    "created":1701872878,
    "Data_assets":
    [
        {
            "Id":"eeefcc52-b445-4e3c-80c5-0e65526cd712",
            "mount":"Reference"
        }
    ],
    "Has_results":false,
    "Id":"3e4041e3-1970-4bc8-9d55-56887d4c5375",
    "name":"Run With Parameters 1872878",
    "Run_time":1,
    "state":"initializing"
}

Named Parameters

Request Example Bash

curl --location --request POST 'https://codeocean.com/api/v1/computations' \
--header 'Content-Type: application/json' \
-u \'${API_SECRET}:\' \
--data-raw '{
 "pipeline_id":"4c4cd610-83bf-4a9b-9dfb-3faf6c29d11b",
 "data_assets": [
    {
        "id": "eeefcc52-b445-4e3c-80c5-0e65526cd712", 
        "mount": "Reference"
    }
],
 "processes": [
       {
           "name": "capsule_np_create_folders_test_1",
           "named_parameters": [
               {
                   "param_name": "NumFiles",
                   "value": "10"
               }
           ]
       }
   ]
}'

Request Example Python

import os, requests

headers = {
 "Content-Type": "application/json"
}
json_data = {
 "pipeline_id":"4c4cd610-83bf-4a9b-9dfb-3faf6c29d11b",
 "data_assets": [
    {
        "id": "eeefcc52-b445-4e3c-80c5-0e65526cd712", 
        "mount": "Reference"
    }
],
 "processes": [
       {
           "name": "capsule_np_create_folders_test_1",
           "named_parameters": [
               {
                   "param_name": "NumFiles",
                   "value": "10"
               }
           ]
       }
   ]
}
response = requests.post('https://codeocean.com/api/v1/computations', headers=headers,
json=json_data,auth=(os.getenv('API_SECRET', ''), ''),)

Response

{
    "created":1701872878,
    "Data_assets":
        [
            {
                "Id":"9c5cf74f-196b-4ed1-868c-8cf95c1f7182",
                "mount":"Reference"
            }
    ],
    "Has_results":false,
    "Id":"3e4041e3-1970-4bc8-9d55-56887d4c5375",
    "name":"Run With Parameters 1872878",
    "Run_time":1,
    "state":"initializing"
}

Ordered & Named Parameters

Request Example Bash

curl --location --request POST 'https://codeocean.com/api/v1/computations' \
--header 'Content-Type: application/json' \
-u \'${API_SECRET}:\' \
--data-raw '{
 "pipeline_id":"cd4ef788-b404-4406-8bda-76b5e41a7b8d",
 "data_assets": [
        {
            "id": "eeefcc52-b445-4e3c-80c5-0e65526cd712", 
            "mount": "Reference"
    }
],
 "processes": [
       {
           "name": "capsule_np_create_files_test_3",
           "named_parameters": [
               {
                   "param_name": "NumFiles",
                   "value": "10"
               }
           ]
       },
       {
           "name": "capsule_art_simulation_illumina_1",
           "parameters": [
               "75","1","HS25","SingleEnded","","","1","","","","","","","False","False"
           ]      
       }
   ]
}'

Request Example Python

import os, requests

headers = {
 "Content-Type": "application/json"
}

json_data = {
"pipeline_id":"cd4ef788-b404-4406-8bda-76b5e41a7b8d",
"data_assets" : [
       {
           "id": "eeefcc52-b445-4e3c-80c5-0e65526cd712",
           "mount": "Reference"
       }
   ],
 "processes": [
       {
           "name": "capsule_np_create_files_test_3",
           "named_parameters": [
               {
                   "param_name": "NumFiles",
                   "value": "10"
               }
           ]
       },
       {
           "name": "capsule_art_simulation_illumina_1",
           "parameters": [
           "75","1","HS25","SingleEnded","","","1","","","","","","","False","False"
           ]      
       }
   ]
}
response = requests.post('https://codeocean.com/api/v1/computations', headers=headers,
json=json_data,auth=(os.getenv('API_SECRET', ''), ''),)

Response

{
    "created":1701872878,
    "Data_assets":
    [
        {
            "Id":"eeefcc52-b445-4e3c-80c5-0e65526cd712",
            "mount":"Reference"
        }
    ],
    "Has_results":false,
    "Id":"3e4041e3-1970-4bc8-9d55-56887d4c5375",
    "name":"Run With Parameters 1872878",
    "Run_time":1,
    "state":"initializing"
}

Run Version of Pipeline

Request Example Bash

curl --location --request POST 'https://codeocean.com/api/v1/computations' \
--header 'Content-Type: application/json' \
-u \'${API_SECRET}:\' \
--data-raw '{
"pipeline_id": "4bc97533-6eb4-48ac-966f-648548a756d2",
"version": 1
}'

Request Example Python

import os, requests 


headers = {
  "Content-Type": "application/json"
} 


json_data = {
  "pipeline_id": "4bc97533-6eb4-48ac-966f-648548a756d2",
  "version": 1
}
 
response = requests.post('https://codeocean.com/api/v1/computations', headers=headers, json=json_data, auth=("'" + os.getenv('API_SECRET', ''), "'"), 
)

Response

{
  "created": 1689689613,
  "has_results": false,
  "id": "9af23fd6-2957-40bf-b691-16190056c94e",
  "name": "Run 9689613",
  "run_time": 0,
  "state": "initializing"
}