Premium Resource - Specimen functionality is a legacy feature available with Premium Editions of LabKey Server. For new installations, we recommend using Sample Manager instead. Learn more or contact LabKey.

A Standard Specimen Repository manages specimen data imported from elsewhere - to edit the data, you need to make changes in the external source and then reimport it into the repository. You cannot edit simple specimen data directly in the database.

If you are using an Advanced (External) Specimen Repository, you can also make changes externally and reimport the archive, or you can configure the repository to be editable after data is imported, enabling administrators to edit specimen data.

  • Select the Manage tab.
  • Click Change Repository Type.
  • Under Specimen Data, choose Editable.
  • Click Submit.

This allows you to edit specimen data directly within LabKey Server. For example, you could correct conflicting or missing data from the import itself, correct inconsistencies caused by time-lag between imports, or even add new specimen data.

Warning: Proceed with caution as any changes made to a repository in this way will overwrite existing data.

Edit Specimen Data

  • Open the desired individual specimen view, typically from the Specimen Data tab.
  • Hover over the row you want to edit to reveal the (Edit) icon on the left. Click it to edit that row.
  • Change fields as desired in the SpecimenDetail view:
  • Any values which cannot be edited, such as global unique ID, will be shown as read-only.
  • Click Submit to save your changes.

Fields that can be changed via this interface have entry windows, checkboxes, or pulldown option lists. Hover over the ? next to the field name for more information about the type of input accepted and purpose for any specific field.

An attempt to edit specimen data will fail if that specimen is in a request that is not in a final state.

Note: Edits to specimen data are not logged in the Admin Console Audit Log.

When you edit a SpecimenDetail row, it is processed as if you imported a specimen archive containing only that 1 row of edited data, and no previous events for the vial are considered, so there will be no conflicts with previous events. Requestability rules are still applied and QC flags can be used to catch consistency issues.

Add New Specimen Data

  • Click (Insert New Row) in the individual vial view
  • Complete the available fields on the Insert SpecimenDetail page.
    • Any fields which do not have an entry option, such as Row Id will be populated automatically.
    • Participant Id and Sequence Num are required.
  • Click Submit.

When a new record is added, it is processed in the same way as a record from an uploaded specimen archive, so requestability rules are applied and QC flags can be used to catch consistency issues.

Note: Additions to specimen repository data are not logged in the Admin Console Audit Log.

On a specimen record that an administrator has added to the repository, the Availability Reason column will contain the message "This vial's availability status was set by an administrator. Please contact an administrator for more information."

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