Premium Feature — Available in the Professional Edition of Sample Manager and all Premium Editions of Biologics LIMS. Also available when Sample Manager is used with a Premium Edition of LabKey Server. Learn more or contact LabKey.
Folders allow users to organize and partition sensitive data within the application, all while maintaining a shared storage environment. Data structures and resources like reagent lists can also be shared lab-wide to support consistency, while individual teams work with their own secured data.
In this video, you will see how to configure and use Folders to work with data across different teams using Sample Manager Professional.
Note that there have been many improvements to the interface and user experience for working in Folders since the making of the video, including but not limited to the change from using "Project" to using "Folder" for data partitioning containers.
Overview
Without the use of Folder organization, Sample Manager does not partition data for different teams. Permissions are granted to all data simultaneously in a single "container".When you enable Folders in the Professional Edition of Sample Manager, data can be grouped and partitioned by teams.
Home and "Sub" Folders
The home is the top level container and provides shared definitions and storage configurations. Data can be added directly in the home or to the individual "sub" folders as appropriate. Permissions are controlled independently in each folder, making it easy to partition separate team spaces.
Sample Types, Source Types, etc. are defined in the home folder to support lab-wide consistency. Administrators can create and/or edit these structures from within subfolders, but the changes will be made to the home definition and shared by all subfolders.
Storage systems like freezers are also defined in the home to match the shared physical space. Individual teams can see the details of stored samples they have permission to read, but only see space allocated to other teams as "occupied".
Reports and views of all data you have access to can be created in the home, summarizing all the data an individual user has access to.
Create shared resources like reagents in the home so that they can be shared & viewed by all folders.
Use folder permissions to partition each study from one another making it easy to operate in compliance with regulations.
Manage Folders
To manage Sample Manager Folders, open the application and select > Folders.On the Folders administration page, you'll see a listing of any existing folders, with the first selected by default. You can edit existing folder details or create a new one.
Create New Folder
Click Create a Folder to add a new folder. Enter the Folder Name and uncheck the checkbox if you wish to provide a different label.For the panels below the folder name, uncheck boxes if you want to limit the resources that are shown in your new folder. The default is that everything from the home is visible in all folders. Learn more about each section below.
When first created, only administrators can view a new folder. This can be useful when configuring the folder for a team to ensure the users only access it when ready.You can configure folder permissions immediately when you create it by clicking Update folder permissions. Later you can also reach this page by clicking the for the folder on the main menu, or from anywhere in the folder by selecting > Permissions.Note that within a folder, the Application Administrator role is not assignable; it can only be set at the top application level. On a Premium Edition of LabKey Server, you can set the Folder Administrator role to apply to this folder only, but cannot set the application-wide role.Learn about configuring permissions in this topic:
When a folder is deleted, all data contained in it will also be deleted. The administrator will see a warning detailing the folder's contents and need to confirm to proceed.
Select Data in Folder
An administrator can restrict the Source Types, Sample Types, and Assay Designs that are visible in a given folder. This can be configured during folder creation or later by editing folder settings.You'll see all the Source Types, Sample Types, and Assay Designs available in the home (top-level) project. By default, everything available will be visible in the folder, but you can uncheck boxes for types of data that will not be used in the folder. If data is present, you'll see a message about what will no longer be visible.Note that 'hiding' or deselecting a data structure here does not delete any data that may exist using it. It just simplifies dropdown menus for users. The hidden entities will not be seen, but will still be present (and lineage relationships preserved). Nor does hiding a type of data prevent it from being used in the future if these settings are edited.The folders in which a given data structure is visible can also be set while creating or editing the data structure itself in the Folders panel. For example, if the "Labs" Source is not in use for "Team B", the Folders panel might look like this:
Exclude Sample Types from Dashboard Insights
When using Folders in Sample Manager, the ability to exclude Sample Types from Dashboard Insights is moved to the Folders tab. There is a Dashboard section for each folder, including for the top level home folder.Learn more in this topic:
An administrator can limit the storage systems that are accessible from a given folder by using checkboxes in the Storage panel. For example, if you wanted to create a folder for a team that would only use a single freezer in their local lab, you could hide all other storage systems.Note that this does not delete any storage or change how samples are stored in the hidden freezers, it just simplifies the dropdown menus for users in the folder.The folder in which a given storage system is visible can also be set while creating or editing the storage definition using the Folders panel below the hierarchy. For example, if this freezer is not in use in the "Team Beta" folder, that box can be unchecked:
Work within Folders
Once one or more folders have been defined, the main menu will include the name of the current folder and a panel on the left for selecting the home or another folder. Each user will see only the folders to which they have access.To navigate, click the name of the desired folder, then the page of interest from the main menu. When you hover over a folder name, you'll see quick links to key pages for that folder:
Dashboard
Administration
When you are in the home of the application, you can add or manage data and definitions like Sample Types and Assay Designs for all the folders to be able to share.When in a folder, you will still see data for all folders you can access, but additional data added will only be available in that folder and visible only to users permitted to see that folder's contents.Note that changes like editing a Sample Type definition in a folder require permission to make those changes at the home level and they will apply to all folders.Learn about actions across folders in this topic:
All users must have Read access to the top level of the application.
Recommended: Only assign non-admin users Read access (and Storage Designer/Editor as appropriate) in the top level Home folder. Edit/add permissions will be granted in individual folders.
The Home is where all Source Types, Sample Types, Assays, Storage Systems and Templates for ELN and Workflow are defined.
Administrators can create and edit Source Types, Sample Types, Assays, Storage Systems from within folders, but all changes are made in the home definitions and apply to all folders.
Add to the Home all "shared resources" you want to be able to access in other folders, such as shared reagent lists, etc.
Folders
Team/Group/Study-based access to sources, samples, assay data, workflow & ELNs.
Within a folder, users can edit/update their folder data.
From the Home level, users can read their folder data (and all data they can access).
For data to be readable by everyone but that does not need to integrate (or inherit from) other data, create a folder that everyone has access to.
On the Folders administration page, you'll see a listing of any existing folders, with the first selected by default. You can edit existing folder details or create a new one.
For the panels below the folder name, uncheck boxes if you want to limit the resources that are shown in your new folder. The default is that everything from the home is visible in all folders. Learn more about each section below.
Note that within a folder, the Application Administrator role is not assignable; it can only be set at the top application level. On a Premium Edition of LabKey Server, you can set the Folder Administrator role to apply to this folder only, but cannot set the application-wide role.Learn about configuring permissions in this topic:
When a folder is deleted, all data contained in it will also be deleted. The administrator will see a warning detailing the folder's contents and need to confirm to proceed.
Note that 'hiding' or deselecting a data structure here does not delete any data that may exist using it. It just simplifies dropdown menus for users. The hidden entities will not be seen, but will still be present (and lineage relationships preserved). Nor does hiding a type of data prevent it from being used in the future if these settings are edited.The folders in which a given data structure is visible can also be set while creating or editing the data structure itself in the Folders panel. For example, if the "Labs" Source is not in use for "Team B", the Folders panel might look like this:
Learn more in this topic:
Note that this does not delete any storage or change how samples are stored in the hidden freezers, it just simplifies the dropdown menus for users in the folder.The folder in which a given storage system is visible can also be set while creating or editing the storage definition using the Folders panel below the hierarchy. For example, if this freezer is not in use in the "Team Beta" folder, that box can be unchecked:
When you are in the home of the application, you can add or manage data and definitions like Sample Types and Assay Designs for all the folders to be able to share.When in a folder, you will still see data for all folders you can access, but additional data added will only be available in that folder and visible only to users permitted to see that folder's contents.Note that changes like editing a Sample Type definition in a folder require permission to make those changes at the home level and they will apply to all folders.
Learn about actions across folders in this topic:
