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Benchling_Read_Object

Node​

Node Description​

Reads Benchling data specified by input Benchling ID string.

Executes Benchling API call(s) based on user-defined function and upload results to data lake

Passes Benchling ID to user-defined function for retrieving Benchling API data. The user-defined function returns one or more DataFrames, which are uploaded as tables into the Ganymede data lake.

Node Attributes​

  • input_string_id
    • Benchling API ID, specified on node
  • 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; has form xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
  • benchling_client_secret: Client_Secret; has form cs_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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 input parameter. This node should be used in conjunction with the Input_Param 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 Benchling entry could be accessed 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