This topic is under construction.

Premium Editions of LabKey Server include the option to use the Sample Manager application within a project and integrate with LabKey Studies and other resources.

Sample Manager Project

Sample Manager is designed to be contained in a project on LabKey Server. This provides advantages in scoping permissions, and supports using the product selection menu.

Create a new project, selecting the folder type Sample Manager.

Using Sample Manager in a Folder

If you do not need the interconnection and permissions scoping features offered by using Sample Manager at the project level, you can use it in a folder, with two options:

Folder of "Sample Manager" Type

You can create a new folder and select the "Sample Manager" folder type. The application will launch every time you navigate to this folder, as if it were at the project level. However, you will not be able to access it through the product selection menu.

It is not possible to "promote" a folder to the project level within LabKey Server. You may use folder export and import to relocate data, but some adjustment of permissions will likely be required.

Enable "SampleManagement" Module

If you want to use Sample Manager resources in a folder, but do not want to auto-navigate to the application, you can create a folder of another type (such as Study) and then enable the "SampleManagement" module via (Admin) > Folder > Management > Folder Type.

You will not be navigated directly to the application in this folder, but can still reach it by editing the URL to replace "project-begin.view?" with "sampleManager-app.view?".

Export and Import of Sample Manager

As with other projects and folders in LabKey, you can export folder objects and data using the folder management tools.

  • Switch to the LabKey Server interface in your Sample Manager project.
    • Note that if your Sample Manager application is in a folder, you will need to use the navigation menu to reach it, then manually replace "sampleManager-app.view?#/" in the URL with "project-begin.view?".
  • Select (Admin) > Folder > Management and click the Export tab.
  • Select the folder objects you want to export; a list is below.
  • Select whether to include any PHI columns, and whether export to the pipeline root or via the browser.
  • Click Export.

Sample Manager Folder Objects

When exporting a project or folder containing Sample Manager, include these folder objects for the corresponding Sample Manager resources:

  • Experiments, Protocols, and Runs
    • Assay definitions and Data
    • Workflow jobs, tasks, templates, assignments, and files
  • Sample Types and Data Classes
    • Samples and Sample Types, including their lineage
    • Sources and Source Types, including their lineage
  • Inventory locations and items
    • Freezer configurations
    • Storage locations for samples

Sample Manager Permissions

Sample Manager, whether in a project or folder, has a few special behaviors regarding LabKey's role-based permissions. Learn more about those permissions in this topic: Security Roles Reference

The "Reader" and "Editor" roles in Sample Manager map to the corresponding container scoped roles, but the "Administrator" role in Sample Manager does not map to any container specific role.

Reader and Editor

  • When a user is granted either the "Reader" or "Editor" role, either in the LabKey Server folder permissions interface or the Sample Manager > Administration > Permissions tab, they will have that role in both interfaces.
  • Assigning a user to a role in either place, or revoking that role in either place will apply to both the Sample Manager and LabKey Server resources in that container.

Administrator

  • When a Sample Manager user is added to the "Administrators" group, they are assigned the "App Admin" role at the site level. Likewise, any "App Admin" on the site will appear in Sample Manager as an administrator.
  • Users with the "Folder Administrator" or "Project Administrator" role on a project or folder containing Sample Manager have no automatic role assignment in the application. Site Administrators are also not shown in the group of Administrators in Sample Manager.
  • Note that Folder/Project/Site Administrators do have permission to edit folder permissions in the LabKey Server interface to grant themselves "Reader" or "Editor" access. Site administrators can also add themselves to the "App Admin" role to gain Sample Manager Administrator access.

Permission Notes

  • If Sample Manager is defined in a folder, and that folder inherits permissions from a parent container, you will not be able to change Editor and Reader assignments within the application.

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