Issue Summary
Key Definitions:
Structured table - Structured objects in Benchling such as Registration tables, Inventory tables, and Result tables allow data to be submitted in Benchling and preserved in the warehouse. Data submitted through structured tables can also be updated by modifying and re-submitting the data.
Entry Editor Locking - A feature that was shipped as part of Notebook Live Editing which prevented an entry from being edited by multiple users at a time, see this help article or more information.
What happened?
Benchling introduced an issue during the implementation of Entry Editor Locking which allowed for duplicate data to be submitted under very specific and rare conditions. Starting from when Notebook Live Editing was enabled on a tenant, duplicate data submissions could occur if a user sent multiple submission events from a structured table by repeatedly clicking the “Submit” button in rapid succession.
The specific conditions for data duplication and the anticipated impact for each structured table are listed below.
| Required Conditions for Data Duplication via Structured Tables | |
| 1 | Use a structured table in a Notebook entry to submit data. |
| 2 | When submitting data, click the Submit button on the structured table two or more times in rapid succession before data is fully committed. |
| Structured Table Type | Impact |
| Registration table | Duplicate* entities would be visible in the Registry, Global Search, API, and Warehouse. Duplication would not be visible in the Notebook entry. Note: Duplication of entities for Registry schemas configured with uniqueness constraints would be considered rare because these constraints prevent the creation of non-unique entities. Any duplicates created would be flagged for validation failures. |
| Result table | Duplicate* assay results would be visible on the entity’s Result tab, Global Search, API, and Warehouse. Duplication would not be visible in the Notebook entry. In addition Computed Fields taking the mean of results against an entity or other calculated averages such as Insights dashboards will be skewed by this. |
| Inventory table | Duplicate* objects would be visible from the entity’s Inventory tab, the Inventory application, Global Search, API, and Warehouse. Duplication would not be visible in the Notebook entry. |
| Plate creation table | |
| Box creation table | |
| Mixture prep table | Duplicate* objects would be visible in the Registry, Global Search, API, and Warehouse. Duplication would not be visible in the Notebook entry. |
| Workflows task table | Duplicate* objects would be visible in the Workflows Manager, Global Search, API, and Warehouse. Duplication would not be visible in the Workflow Task Group. |
| Workflows output table |
*Duplicate data that was created as a result of this issue would have unique identifiers in your Benchling environment (e.g. Duplicate instances of registered entities would have unique Registry IDs; duplicate instances of Inventory objects would have unique barcodes; duplicate instances of Results would have unique Result IDs)
What does this mean for you?
For non-validated tenants this issue could have impacted data submitted through structured tables between April 2022 and August 2, 2024.
For validated/GxP tenants this issue could have impacted data submitted through structured tables between June 17, 2022 and August 23, 2024.
Duplicate data can be viewed in your data warehouse. In some cases, duplicate data can appear in the associated application for that structured table (e.g. Duplicate entities will appear in the Registry). Duplicate data submissions will not be visible in the affected Notebook entries. Audit events will appear duplicated in the affected entry and structured table audit logs, only.
What happens next?
For all non-GxP clients, Benchling has developed a solution and rolled out the fix on Friday, August 2nd at 9AM PT. The fix will prevent erroneous duplicate data submissions in structured tables from being possible in Benchling moving forward. Additionally, Benchling has identified cases where duplicate data was submitted via structured tables as a result of this bug. Benchling recommends reviewing all impacted data with your compliance team and can provide a list of impacted tables in Notebook entries for you. If duplicates are a non-issue, leave data as-is. However, if duplicates need to be addressed, consider following the recommendations listed below for resolving the duplicate data events across different table types.
Benchling may proactively reach out to impacted customers to ensure they are aware of the issue and can escalate concerns if appropriate.
For GxP clients, Benchling released Patch 2024.2.5 to Validated Cloud Production environments on August 23, 2024.
| Structured Table Type | Recommended Resolution** |
| Registration table | Archive or merge duplicate entities. |
| Result table | Archive duplicate results via the API. |
| Inventory table | Archive duplicate Inventory objects. |
| Plate creation table | |
| Box creation table | |
| Mixture prep table | Archive or merge duplicate entities. |
| Workflows task table | Archive duplicate data via the Workflows Manager. |
| Workflows output table |
**If you determine that duplicates should be preserved in Benchling, no additional action is required.
FAQs
Does this impact my data in any way?
While duplicates were generated in select circumstances as a result of this issue, Benchling recommends assessing the level of impact for your data with your compliance team. Benchling inherently has systems in place like uniqueness constraints to protect data integrity, so this was not a widespread issue.
Can Benchling provide me with a list of impacted data?
Yes, Benchling can provide you with a list of impacted entries and tables. Please reach out to support@benchling.com with the subject line “Duplicate table submission issue”, if you would like a list of affected entries and tables provided.
Does this issue appear when updating data in structured tables?
Yes, this issue could have also occurred when updating data in structured tables. Benchling can provide a list of impacted tables in Notebook entries for you.
Could duplicate data also be submitted if making API calls?
No, this issue was specific to the Benchling web app and did not impact the Benchling API.