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 in a Project
Sample Manager is designed to be contained in a project
on LabKey Server. This provides advantages in scoping permissions specific to sample management actions. Create a new project, selecting the folder type Sample Manager
Using Sample Manager in a Folder
Depending on where the Sample Types, Assays, and study data you hope to integrate with are housed, you can also use Sample Manager in a folder, with two options. In both cases, you will be able to use the product selection
menu to switch between Sample Manager and the traditional LabKey Server interface.
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.
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, uses a subset of LabKey's role-based permissions. The "Reader", "Editor", "Folder Administrator", and "Project Administrator" roles all map to the corresponding container-scoped roles. Learn more about those permissions in this topic: Security Roles Reference
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.
In the stand-alone Sample Manager application, a single "Administrator" role is provided that maps to the site role "App Admin". This also means that any "App Admin" on the site will appear in Sample Manager as an Administrator.
When using Sample Manager within LabKey Server, administrator permissions work differently. Users with the "Folder Administrator" or "Project Administrator" role on the project or folder containing Sample Manager have those roles carry into the application. These roles may also be assigned from within the application (by users with sufficient permission). The difference between these two roles in Sample Manager is that a Project Administrator can add new user accounts, but a Folder Administrator cannot. Both admin roles can assign the various roles to existing users and perform other administrative tasks. As in any LabKey Server Installation, "Site Admin" and "App Admin" roles are assigned at the site level and grant administrative permission to Sample Manager, but are not shown in the Administrator listing therein.
- 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.