Prerequisites
The Computation ID can only be accessed from the Computation Object.
A typical use case is to use
Both methods will have the Computation ID in the Response that can be used in Computations API for further tracking and getting results.
Computation Object
id string
Computational id
created float64
Computation create time
name string
Display name of the Computation
run_time integer
Total run time in seconds
cloud_workstation boolean
Indicates whether this Computation is a cloud workstation
state enum
initializing , running , finalizing , completed
end_status enum
stopped , failed , succeeded
has_results boolean
Indicates whether the Computation has results
parameters array (Optional)
Run parameters
name string
Parameter name
value string
Parameter value
data_assets array<dictionary> (Optional)
Attached Data Assets
id string
Attached Data Asset ID
mount string
Attached Data Asset mount
processes array<dictionary> (Optional)
Pipeline processes information
name string
Pipeline process name (as it appears in the main.nf)
capsule_id string
ID of the Capsule executed in the process
version boolean
Capsule version in case it's Released
public boolean
Indicates the Capsule is a Code Ocean App
parameters array<dictionary>
Run Parameters
name string
Parameter Label
param_name string
Parameter Name
value string
Parameter Value
Get Computation
GET https://{domain}/api/v1/computations/{computation_id}
This API allows for the retrieval of information from a Computational run.
Path Parameters
Scope
Request Example Bash
Copy curl https://{domain}/api/v1/computations/c229ed13-ec06-43d0-abd9-4d481af3f5e3 \
-u "cop_d23dasd312"
Copy computation = client . computations . get_computation (computation_id = "8f174aed-64ce-43eb-9c16-64d25da84bda" ) Get Result File Download URL
GET https://{domain}/api/v1/computations/{computation_id}/results/download_url
This API allows for the generation of a URL to download a result file from a Computation.
Query Parameters
Path Parameters
Scope
Copy curl https://{domain}/api/v1/computations/9390055d-7884-4997-8dfc-88bf7445b617/results/download_url?path=GSM12345_R1_fastqc.html \
-u "cop_d23dasd312" Request Example Python SDK
Copy url = client . computations . get_result_file_download_url (
computation_id = "8f174aed-64ce-43eb-9c16-64d25da84bda" ,
path = "GSM12345_R1_fastqc.html" ,
) Response Delete Computation
DELETE https://{domain}/api/v1/computations/{computation_id}
This API allows for the deletion of a Computational run. If it is running, the Computation will stop.
Path Parameters
Scope
Request Example Bash
Copy curl -X DELETE https://{domain}/api/v1/computations/c229ed13-ec06-43d0-abd9-4d481af3f5e3 \
-u "cop_d23dasd312"
Copy client . computations . delete_computation (computation_id = "8f174aed-64ce-43eb-9c16-64d25da84bda" ) Run Capsule
POST https://{domain}/api/v1/computations
This API allows for the running of Capsules/Pipelines with Data Assets and Ordered or Named Parameters.
Prerequisite
Before using this API call, you may need AWS Cloud Credentials configured as Secrets or an Assumable Role, if you are using Data Assets from Cloud Resources.
Request Body
Scope
Copy curl -X POST https://{domain}/api/v1/computations \
-u "cop_d23dasd312" \
-H "Content-Type: application/json" \
--data-raw "{
" capsule_id ": " 4bc97533-6eb4-48ac-966f-648548a756d2 "
}" Request Example Python SDK
Copy from codeocean . computation import RunParams
run_params = RunParams (capsule_id = "4bc97533-6eb4-48ac-966f-648548a756d2" )
computation = client . computations . run_capsule (run_params) Run Capsule with Data Assets and Ordered Parameters
Copy curl -X POST "https://codeocean.[my-domain].com/api/v1/computations" \
--header "Content-Type: application/json" \
-u "cop_d23dasd312" \
--data-raw "{
" capsule_id ":" eb082456-d031-4a42-80b0-f209b8728927 ",
" data_assets " : [
{
" id ": " eeefcc52-b445-4e3c-80c5-0e65526cd712 ",
" mount ": " Reference "
}
],
" parameters ": [
" 75 "," 1 "," HS25 "," SingleEnded ","",""," 1 ","","","","","",""," False "," False "
]
}"
Copy from codeocean . computation import RunParams , DataAssetsRunParam
data_assets = [
DataAssetsRunParam (id = "1az0c240-1a9z-192b-pa4c-22bac5ffa17b" ,
mount = "Reference" )
]
run_params = RunParams (capsule_id = "4bc97533-6eb4-48ac-966f-648548a756d2" ,
data_assets = data_assets,
parameters = [
"75" , "1" , "HS25" , "SingleEnded"
]
)
computation = client . computations . run_capsule (run_params) Run Capsule with Data Assets and Named Parameters
Copy curl -X POST "https://codeocean.[my-domain].com/api/v1/computations" \
--header "Content-Type: application/json" \
-u "cop_d23dasd312" \
--data-raw "{
" capsule_id ":" 4c4cd610-83bf-4a9b-9dfb-3faf6c29d11b ",
" data_assets " : [
{
" id ": " 9c5cf74f-196b-4ed1-868c-8cf95c1f7182 ",
" mount ": " Reference "
}
],
" named_parameters ": [
{
" param_name ": " NumberOfThreads ",
" value ": " 1 "
},
{
" param_name ":" NumberOfFiles ",
" value ": " 10 "
}
]
}"
Copy from codeocean import CodeOcean
from codeocean . computation import RunParams , DataAssetsRunParam , NamedRunParam
data_assets = [
DataAssetsRunParam (id = "1az0c240-1a9z-192b-pa4c-22bac5ffa17b" ,
mount = "Reference" )
]
named_parameters = [
NamedRunParam (param_name = "NumThreads" ,value = "2" )
]
run_params = RunParams (
capsule_id = "4bc97533-6eb4-48ac-966f-648548a756d2" ,
data_assets = data_assets,
named_parameter = named_parameters
)
computation = client . computations . run_capsule (run_params) Run Pipeline
Copy curl -X POST "https://codeocean.[my-domain].com/api/v1/computations" \
--header "Content-Type: application/json" \
-u "cop_d23dasd312" \
--data-raw "{
" pipeline_id ": " 4bc97533-6eb4-48ac-966f-648548a756d2 "
}" Request Example Python SDK
Copy from codeocean . computation import RunParams , PipelineProcessParams
run_params = RunParams (
pipeline_id = "4bc97533-6eb4-48ac-966f-648548a756d2"
)
computation = client . computations . run_capsule (run_params) Run Pipeline with Data Assets and Ordered Capsules
Copy curl -X POST "https://codeocean.[my-domain].com/api/v1/computations" \
--header "Content-Type: application/json" \
-u "cop_d23dasd312" \
--data-raw '{
"pipeline_id":"e7a77780-b8ae-439e-89ac-fac2549da91b",
"data_assets" : [
{
"id": "eeefcc52-b445-4e3c-80c5-0e65526cd712",
"mount": "Reference"
}
]
}'
Copy from codeocean.computation import RunParams, DataAssetsRunParam, PipelineProcessParams
data_assets = [
DataAssetsRunParam(id = "1az0c240-1a9z-192b-pa4c-22bac5ffa17b" ,
mount = "Reference" )
]
processes = [
PipelineProcessParams(
name = "capsule_star_alignment_1" ,
parameters = [
"1" , "_R1_fastq.gz" , "R2_fastq.gz"
]
)
]
run_params = RunParams (
capsule_id = "4bc97533-6eb4-48ac-966f-648548a756d2" ,
data_assets = data_assets,
processes = processes
)
computation = client.computations.run_capsule ( run_params ) Run Pipeline with Data Asset and Named Capsules
Copy curl -X POST "https://codeocean.[my-domain].com/api/v1/computations" \
--header "Content-Type: application/json" \
-u "cop_d23dasd312" \
--data-raw "{
" pipeline_id ":" 4c4cd610-83bf-4a9b-9dfb-3faf6c29d11b ",
" data_assets " : [
{
" id ": " eeefcc52-b445-4e3c-80c5-0e65526cd712 ",
" mount ": " Reference "
}
]
}"
Copy from codeocean.computation import (
RunParams,
DataAssetsRunParam,
PipelineProcessParams,
NamedRunParam
)
data_assets = [
DataAssetsRunParam(id = "1az0c240-1a9z-192b-pa4c-22bac5ffa17b" ,
mount = "Reference" )
]
processes = [
PipelineProcessParams(
name = "capsule_bwa_alignment_5" ,
named_parameters = [
NamedRunParam(param_name = "NumThreads" ,value = "2" )
]
]
run_params = RunParams (
capsule_id = "4bc97533-6eb4-48ac-966f-648548a756d2" ,
data_assets = data_assets,
processes = processes
)
computation = client.computations.run_capsule ( run_params ) Run Pipeline with Data Assets and Ordered + Named Capsules
Copy curl -X POST "https://codeocean.[my-domain].com/api/v1/computations" \
--header "Content-Type: application/json" \
-u "cop_d23dasd312" \
--data-raw "{
" pipeline_id ":" cd4ef788-b404-4406-8bda-76b5e41a7b8d ",
" data_assets " : [
{
" id ": " eeefcc52-b445-4e3c-80c5-0e65526cd712 ",
" mount ": " Reference "
}
]
}" Request Example Python SDK
Copy from codeocean . computation import (
RunParams ,
DataAssetsRunParam ,
PipelineProcessParams ,
NamedRunParam
)
data_assets = [
DataAssetsRunParam (id = "1az0c240-1a9z-192b-pa4c-22bac5ffa17b" ,
mount = "Reference" )
]
processes = [
PipelineProcessParams (
name = "capsule_bwa_alignment_5" ,
named_parameters = [
NamedRunParam (param_name = "NumThreads" ,value = "2" )
],
PipelineProcessParams (
name = "capsule_star_alignment_1" ,
parameters = [
"1" , "_R1_fastq.gz" , "R2_fastq.gz"
]
]
run_params = RunParams (
capsule_id = "4bc97533-6eb4-48ac-966f-648548a756d2" ,
data_assets = data_assets,
processes = processes
)
computation = client.computations. run_capsule (run_params) 