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Benchling_Read

Node​

Node Description​

Reads Benchling data specified by Benchling run tag.

Passes Benchling run tag to user-defined function and uploads tabular output from user-defined function to Ganymede data lake.

This node is used in conjunction with BenchlingTag; adding BenchlingTag to a Flow enables a Benchling run tag to be specified in the Flow input box. The user-defined function uses the Benchling ID associated with the run tag to retrieve data and process data into table(s), which are uploaded to the Ganymede data lake.

Node Attributes​

  • output_table_results

Notes​

Usage requires configuration of a Benchling application in the relevant Benchling tenant.

Prior to usage, the secrets below must be configured in your Ganymede environment. More information on acquiring these credentials can be found here.

  • benchling_url: URL for Benchling tenant; has form https://<tenant>.benchling.com
  • benchling_app_client_id: Client_ID
  • benchling_client_secret: Client_Secret

Secrets can be configured by clicking on your username in the upper-right hand of the Ganymede application, then selecting Environment Settings and navigating to the Secrets tab. If you need assistance, please don't hesitate to reach out to Ganymede.

In the execute function, returning NodeReturn(tables_to_upload={'results': df}) would render the DataFrame df in the Flow Editor if Table Head visualization is enabled.

User-Defined Python​

Reads Benchling data based on run tag. This node should be used in conjunction with the Benchling_Tag node.

Parameters​

  • benchling_context : BenchlingContext
    • Benchling context variable, which stores Benchling connection information
  • ganymede_context : GanymedeContext
    • Ganymede context variable, which stores flow run metadata

Returns​

NodeReturn Object containing data to store in data lake and/or file storage

Notes​

This template shows how a target plate could be pulled via the Benchling object Documentation for the Benchling API can be found here: https://benchling.com/api/reference

benchling_context is an object of class BenchlingContext, consisting of

  • conn: Benchling connection
  • run_tag: Benchling ID associated with run tag
  • display_tag: Displayed value of Benchling run tag