What happened?

On August 28, 2024, an issue in Benchling’s Weekly Validation Check caused unintentional updates to metadata fields in certain entities in specific tenants. This issue impacted Entity Link fields that reference duplicate entities, potentially causing incorrect entity links in data. Affected entities and fields have been identified.

This help article outlines the issue and provides guidance on how to resolve the incorrect metadata fields.

In this example, Protein 1 and Protein 2 are “Duplicate Pair of Entities.” 

Duplicate Entities are typically merged at the time of submission in a registration workflow, however there are a few rare scenarios where duplicates can exist in a registry:

• When an already registered entity is edited to now be flagged as a duplicate per a configured uniqueness constraint
• When 2 registered entities are duplicates that existed and were registered before a uniqueness constraint was configured/adjusted to now define those entities as duplicates
  

How do I know if I’m Impacted?

Not all customer tenants were affected by this issue. If you would like to know if any entities in Benchling were affected, please reach out to Benchling support by emailing support@benchling.com with the subject line : ‘Entity Link field Fields Inaccuracy Issue’. 

What are the options to resolve this issue?

For the affected entities, the Entity Link field will need to be updated to the correct value. This can be done by performing this task for each entity individually, but you may also perform this task via API or via the Bulk Update tool in Search.

Option 1: Bulk Updates via Search (Recommended)

If you have many entities affected, you may prefer to use Benchling’s Bulk Update tool:

1. Use the search functionality in Benchling to find the impacted entities.
2. Use the Edit tool to modify the affected fields with the correct entity link for all impacted entities at once.

Option 2: Manual Updates Per Entity 

1. Navigate to an affected entity’s Metadata tab.
2. In the “Schema” section, click the “Edit” button.
3. Update the affected field with the correct linked entity, as provided by Benchling Support.
4. Click “Save” to confirm your changes.

Option 3: Updates via API

For users familiar with Benchling’s API, the same updates can be applied programmatically:

1. Refer to the API documentation to identify the correct endpoint for entity updates.
2. Use the API to update the affected fields for the impacted entities based on the original entity values provided by Benchling Support.

What are the next steps?

1. Review the Entity List: Start by reviewing the impacted entities and fields as detailed in the notification email or given to you by Benchling Support.
2. Choose a Resolution Method: Decide whether you will update the fields manually, via the Bulk Update tool, or through the API. Follow the appropriate steps above to correct the impacted metadata fields.
3. Validate Changes: After completing the updates, confirm that the affected metadata fields reflect the correct entity links.

If any impacted Entity Link schema field is used in a Computed Field, let Benchling know by reaching out to support@benchling.com and we can assist with recomputing affected Computed Fields

We apologize for any inconvenience this may have caused. Should you have any questions, feel free to contact us for assistance by emailing support@benchling.com and including in the subject: ‘Entity Link Fields Inaccuracy Issue’.