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Benchling APIProtein

Get bulk-create-and-register-proteins-and-components task results

Beta

Get the results of a completed bulk-create-and-register-proteins-and-components task.

This endpoint returns an identifier for the output dataset, plus an optional pre-signed URL to download the errors file if any inputs failed validation.

Task IDs for this endpoint remain queryable for 14 days after the job is created. After that TTL expires, this endpoint returns 404. Retrieve the dataset ID and any errors file URL you need before the task ID expires.

Partial Success: A job can complete with both successful and failed inputs. Always check errorsFileUrl even when datasetId is present, since some inputs may have been rejected while others were created successfully.

Behavior:

  • Returns 400 unless the task has a COMPLETED status. While a task is running you can poll the GET /tasks/bulk-create-and-register-proteins-and-components/{task_id} endpoint first and only call this endpoint once status == "COMPLETED". If the status becomes FAILED, this endpoint will always return 400.
  • If the task is in a COMPLETED status, returns parameters you can use to fetch output and error data. See the descriptions of the output parameters for more detail.

Authentication

AuthorizationBearer

Bearer authentication of the form Bearer <token>, where token is your auth token.

Path parameters

task_idstringRequired

Headers

EARLY-ACCESSstringOptional

Set to true to access beta operations via /api/v3.

Response

Task results
taskIdstring
datasetIdstringOptional

If no proteins were registered, this parameter is absent. Otherwise, datasetId identifies a Dataset object with the results data.

Use this id with the Datasets API to look up the dataset and fetch its rows. This dataset will be the same one displayed in the Benchling UI and referenced in emails about this task.

Dataset Columns

  • The results dataset will have an input column giving the index of the input protein data associated to this results row.
  • It will have a protein column giving the api id of the protein that was registered for that input.
  • It will have a {label}_aa and optionally a {label}_dna column for each domain label in the format. The DNA column will only be present if the job registered DNA sequence entities for that format.
  • It will have similar {label}_dna and {label}_aa columns for chains that it registered.
  • It will also have {label1}_{label2}_pair_dna and {label1}_{label2}_pair_aa columns for any registered DNA and AA pairs.
errorsFileUrlstringOptionalformat: "uri"

If all inputs were registered successfully, this parameter is absent. Otherwise, it’s a pre-signed S3 URL for downloading the errors CSV.

This CSV will have an Input # column giving the index of the input to the job associated with one particular protein that failed to be registered. The Error Message column gives a description of the error.

This file may also contain additional columns for any sequence data that the job attempted to use when it failed to register this particular protein. Those columns will follow the same naming scheme as described above for the Dataset output.

Errors

400
Bulk Create and Register Proteins and Components Results Get Request Bad Request Error
403
Bulk Create and Register Proteins and Components Results Get Request Forbidden Error
404
Bulk Create and Register Proteins and Components Results Get Request Not Found Error
429
Bulk Create and Register Proteins and Components Results Get Request Too Many Requests Error
500
Bulk Create and Register Proteins and Components Results Get Request Internal Server Error