How to resolve Registry Validation errors triggered by Benchling bug fix

  • Updated


On November 4, 2023, you may have received a Registry validation email regarding entities that failed validation checks due to changes made by Benchling Support. An example screenshot of this notification is attached below.

Screenshot 2023-11-06 at 3.10.26 PM.png


Root Cause

These validation errors are appearing for any schemas that has ever had a non-Entity link schema field that was converted to an Entity link field at any point in the past.

If an existing non-Entity link field is changed to an Entity link field, the existing data in that field should have been updated to link to an Entity, and display a validation error if a corresponding Entity cannot be found. This error was not being thrown previously, allowing now-Entity link fields to store non-Entity data.

Our team had recently fixed this issue in order to ensure that all Entity link fields are properly linked to Entities, and properly trigger validation errors if not. However, this fix also retroactively triggered errors for any invalid Entity link fields across all existing schemas. These retroactively triggered errors are the validation errors referenced in the unexpected email referenced above.

Though the email indicates that these entities were modified by Benchling Support, no edits were actually made to these entities by the Benchling Support account. These errors appear this way because these errors were automatically triggered.


Finding Affected Entities

Affected entities can be found in 3 different ways:

  1. Through the notification email
    • Access individual affected entities by clicking on the value in the Entity Name column in the validation failure notification email
  2. Using the Search tool
    • Find multiple affected entities at once by using the following filter in the Search tool:
      • Under "Entity Validation", "Failure Reason" set to "Invalid entity link"
        Screenshot 2023-11-06 at 3.35.19 PM.png
  3. Through Feature Settings
    • Within the Registry settings, navigate to the Entity schemas page. On your list of Entity schemas, there is a Validation Failures column, with a value showing the amount of entities using that schema that have active validation errors.
      Screenshot 2023-11-06 at 3.42.26 PM.png
    • You can click on this value to view all possible validation failure types and the number of entities that are currently failing validation for each type. Clicking on the value for each failure type will bring up the Search view from above, filtered to that specific Entity schema. Please note that this issue specifically refers to the "Invalid entity link" failure type.

Resolution Steps

If possible, we encourage your team to review these errors and ensure that Entity links are being saved appropriately. For individual entities, these updates can be made in the Metadata tab of individual entities; for multiple entities, the Search tool can be utilized to make changes to schema fields for entities using the same schema in bulk using the "Edit Property" tool.
However, we acknowledge that there may be a very large number of affected entities, and your team may simply want to suppress these errors in bulk. If this is the case, there are three options for overriding these failures in bulk:
  1. On the Entity Metadata tab
    • In the toolbar, click on the "..." ("More") button, which will bring down a menu of additional options. In this menu, click "Override validation checks".
      Screenshot 2023-11-06 at 4.10.30 PM.png 
  2. Using the Search tool
    • First, generate a search of all affected Entities using the Search tool steps outlined above.
    • Next, select all the entities that should have their validation errors overridden, click the "More" button in the toolbar, then select "Override validation checks".
      Screenshot 2023-11-06 at 4.04.41 PM.png
  3. Through Feature Settings
    • On the Validation Failures tab for an affected schema, select the checkbox next to the desired Failure Type ("Invalid Entity Link") then click the "Override validation checks" button.
      Screenshot 2023-11-06 at 4.07.14 PM.png
Please note that overriding a validation check is an auditable event, and will appear in the audit log for that entity with a timestamp and the information of the user who performed the override.

Was this article helpful?

Have more questions? Submit a request