After signing into Clarity LIMS, you can update some of the details associated with your profile, including your password, email address, and profile photo.

Update User Profile

1. In Clarity LIMS, at the right of the menu bar, select your username and then select Profile.

2. The Profile page opens, displaying the details associated with your user profile.

3. On this page, you can:

   • Change your password.

   • Change your email address.

   • Upload an image to associate with your profile.

Reset a forgotten password

1. On the Sign In screen, click the Forgot your password link.

2. In the Reset Your Password screen, enter your username or email address and click Submit.

This section describes two tasks that Clarity LIMS administrators are often required to perform:

• Temporarily prevent a user from logging in by archiving the user.

• Email a link to a user that allows them to reset their Clarity LIMS password.

Archive a User

1. On the main menu, select Configuration.

2. Select User Management.

3. Select the Users tab to see a list of all current active and archived users in the system, categorized by role.

4. Select the user to archive.

   The details for the selected user display in the User Details area on the right. The Status slider displays the current status of the user.

5. Select Archived to temporarily archive the user.

6. Select Save.

By default, every new user created in Clarity LIMS is an active user and can sign in to Clarity LIMS with their username and password.

Reset a User Password

1. On the main menu, select Configuration.

2. Select User Management.

3. Select the Users tab to see a list of all current active and archived users in the system.

4. Select the user whose password is to be reset.

   The details for the selected user display in the User Details area on the right.

5. Select Login and Password and select Reset password.

   This sends the user a link that allows them to reset their password.

   NOTE: The new password must satisfy the following requirements:

   • Contain at least 12 characters

   • Contain at least one special character (# $ % ? ! @, etc.)

   • Contain at least one number

   • Contain at least one lowercase letter

   • Contain at least one uppercase letter

The Send login instructions option sends the user the following information:

• The URL for the login screen.

• Instructions on how to set their login password.

• This email is sent automatically when a new user is created, but you may occasionally need to resend it.

Clarity LIMS users are assigned roles. These roles control permissions and the ability to:

• Access certain Clarity LIMS features.

• Perform certain actions.

• Sign in to the Clarity LIMS interfaces.

In a typical LIMS lab environment, there are four primary user roles:

• #system-administrator-and-facility-administrator

• #researcher

• #collaborator

The following sections describe the default permissions of the four primary user roles. Some user role permissions are configurable (see Configured Role-Based Permissions).

System Administrator and Facility Administrator

By default, both the System Administrator and Facility Administrator user roles have access to:

• All configuration areas of the Clarity LIMS web interface, allowing them to:

  • Add and configure workflows, protocols, and steps.

  • Add consumables—reagents, controls, instruments, reagent labels, containers.

  • Add and configure custom fields.

  • Add and configure automations.

• Supervisory and lab management functions in the Clarity LIMS web interface, allowing them to:

  • Review escalations.

  • Remove samples from workflows.

  • Move samples into the next step in a workflow.

  • Access the Overview and Projects dashboards.

• User management, allowing them to:

  • Create, modify, and delete user accounts.

  • Modify user roles and permissions.

  • Approve access requests from external collaborators.

Researcher

The Researcher role is typically assigned to the laboratory scientist. By default, individuals who are assigned this user role are able to:

• Log in to Clarity LIMS.

• Access Lab View.

• Manage and work with samples contained in all projects in the system.

• Edit their own user profiles—ie, they can change their own passwords and other profile information.

• Access three Consumables configuration areas: Reagents, Controls, and Instruments, and do the following.

  • View reagent kits and add new reagent lots to those kits (researchers cannot create reagent kits).

  • View controls.

  • View instrument types and add new instruments to those instrument types (researchers cannot create instrument types).

  • Reactivate expired (archived) instruments by resetting the expiration date.

Collaborator

The Collaborator role is assigned to external collaborators who interact with Clarity LIMS using the LabLink Interface.

The Collaborator role is supported in v5.3 and later. It is not supported in v5.0.x to v5.2.x.

An external person can request a user ID through LabLink. By default, when the request is approved by an administrator, the collaborator is able to:

• Sign in to LabLink.

• Create, view, and delete projects. (Collaborators are automatically given full permissions to projects they create.)

• Submit samples to projects, and delete samples from projects.

By default, collaborators do not have access to the main Clarity LIMS web interface.

User Management Configuration Screen

• Users are the individuals who have access to the Clarity LIMS interface. Because each step in Clarity LIMS is associated with a user, you can make use of user profiles to track the work moving through your lab. While users are associated with the steps they perform as part of a project, they are not directly associated with that project—unless they are assigned as the project client.

• Clients are directly associated with projects in Clarity LIMS. When you create a project, you must associate it with a client. Clients differ from users in that they are not able to log in and access the Clarity LIMS web interface. They are typically external collaborators or customers who submit samples to the lab.

• Accounts must be directly associated with projects, users, and clients that are created in Clarity LIMS.

  NOTE: Viewing user/client/account details, and adding, modifying, and deleting users/clients/accounts are role-based permissions. For more information, see Configured Role-Based Permissions.

Add and Manage Users and Clients

This section describes how to add and manage users and clients in Clarity LIMS.

When creating users, keep the following in mind:

• The username must be unique among active users in the system. This is validated when you save the user details.

• If the username is already associated with an existing user, an error message displays and you are not be able to save the new user profile.

• All users must provide their email address and reset their password upon upgrading their software to v5.4 (or later).

Add a User

1. From User Management, select the Users tab.

2. Select inside the Role field to display a drop-down list of roles:

   • Select the role to assign to this user.

   • To remove a role from this field, select the X to the left of the role name.

3. [Optional] Enter a title, phone number, and fax number for the user.

4. Select Save.

   An invitation email is automatically sent to the user. This email includes the login screen URL and information on how to set the login password. You may resend the login instructions email at any time (see #modify-user-details).

   The user displays in the Users list.

5. [Optional] By default, the status of a new user is set to Active, which means that they can log in to Clarity LIMS. To temporarily prevent a user from logging in, change this setting by selecting Archived. (See also Manage User Access)

Modify User Details

1. From User Management, select the Users tab.

2. Select the user to modify.

3. In the User Details area, modify the details as required. If you change the username, a password reset email is sent automatically to the user.

4. Select Login and Password to access the following options:

   • Send login instructions—Choose this option to re-send the user the login screen URL and information on how to set their login password.

   • Reset password—Choose this option to send the user a link that allows them to reset their login password (see Manage User Access).

5. Select Save.

Delete a User

1. From User Management, select the Users tab.

2. Select the user to delete.

3. In the User Details area, select Delete.

When deleting users, keep the following in mind:

• You cannot delete a user if that user has logged in to Clarity LIMS.

• You cannot delete a user if that user is associated with a project (eg, the user is the project client).

• Deleting a user removes them from Clarity LIMS. You may instead prefer to archive the user or temporarily remove their access to the system. For details, see Manage User Access.

Add and Modify Clients

When adding new clients, each client must be a unique entry in the LIMS.

To add a client:

1. From User Management, select the Clients tab.

2. Select New Client.

3. In the Client Details area, complete the following required information:

   • Enter the first name and last name of the client.

   • Select inside the Account field and select the client account from the drop-down list.

   • Enter the client email address.

4. [Optional] Enter client title, phone number, and fax number.

5. Select Save.

   The user displays in the Clients list, under their account name.

Delete a Clients

A client cannot be deleted if that client is associated with a project.

1. From User Management, select the Clients tab.

2. Select the client to delete.

3. In the Client Details area, select Delete.

Add and Manage Accounts

Accounts are the organizations with which a facility conducts business. In the Clarity LIMS Projects and Samples screen, select the existing account from the Account drop-down list to associate projects and samples with it.

To create a new account, type directly into the Account field.

For Clarity LIMS v6.2 and later, you can also create a new account through the Accounts section of the User Management tab that is under Configuration.

Add a New Account

1. From Configuration, select the User Management tab.

2. Select the Accounts tab.

3. In the Account Details area, select New Account.

4. Type a name for the account and complete any other applicable fields (eg, Billing Address).

5. Select Save.

Modify Account Details

1. From Configuration, select the User Management tab.

2. Select the Accounts tab.

3. In the Accounts list, select the account that you want to modify.

4. In the Account Details area, update the fields that need to be modified.

5. Select Save.

Delete an Account

1. From Configuration, select the User Management tab.

2. Select the Accounts tab.

3. In the Accounts list, select the account that you want to delete.

4. Select Delete.

   You cannot delete an account that is associated with a user or project.

Manage the permissions of the System Administrator, Facility Administrator, Researcher, and Collaborator user roles to restrict or allow the following actions:

• Sign in to Clarity LIMS.

• Sign in to the API.

• View and interact with certain features of the interface.

• Perform certain actions in the interface.

• View and restrict any actions in the interface. [Clarity LIMS v6.1 and above]

NOTE: You can use System Settings to configure role-based permission in Clarity LIMS v6.3. For details, see .

Command-line Permissions Tool

Role-based permissions are controlled through the permissions-tool.jar tool, at /opt/gls/clarity/tools/permissions/.

For assistance with running the command-line permissions tool, contact the Illumina Support team.

Functionality includes the following commands:

• —List all roles in the system.

• —List names and descriptions of all permissions in the system.

• —Create a role.

• —List permissions assigned to each role in the system.

• —List permissions assigned to a specific role.

• —Assign a permission to a role.

• —Remove a permission from a role.

NOTE: The permissions-tool.jar tool function names and property names are case-sensitive. If you type the incorrect case, your command or property cannot be understood.

There can be a delay (up to 20 minutes) before changes to some API-related permissions take effect.

Supported Commands

listRoles

List all user roles in the system:

describeRole

Show permissions for a specific role:

createRole

Create a role:

showSummary

Show assigned permissions for all roles:

listPermissions

List names and descriptions of all permissions:

assignPermission

Assign a permission to a role (the example assigns permission to create controls):

[Clarity LIMS v6.1 and above] Assign a permission to a role (the example assigns read-only permission to a role):

removePermission

Remove a permission from a role (the example removes permission to create controls):

Usage

Options

Supported Permissions

The sections below list LIMS permissions and actions, and the user roles to which each permission/action is assigned by default.

By default, System Administrators and Facility Administrators have all permissions listed.

Permission: AdministerLabLink

The default role with AdministerLabLink permission is Administrator. This permission is added to the existing System Administrator & Facility Administrator roles.

The Collaborator role is based on the existing Collaborator role in LabLink v1.0.

Note: The existing Researcher role does not have the new permission and behaves similarly to the LabLink Collaborator role.

Permission: ClarityLogin

Default roles with this permission: Administrator, Researcher

Permission: APILogin

Permission: Project

Permission: Sample

Permission: Controls

Default roles with these permissions: Administrator

Permission: ReagentKit

Default roles with these permissions: Administrator

Permission: Role

Default roles with these permissions: Administrator

Permission: Read-Only [Clarity LIMS v6.1 and above]

Default roles with this permission: Not applicable. You can assign this permission to any role.

Permission: User

Default roles with these permissions: Administrator

In the LIMS user interface, the term 'contact' has been replaced with 'client.' However, the API still uses the permission Contact.

All users with ClarityLogin permission can view and edit their own user details (except for assigning/removing roles).

Permission: Contact

Default roles with these permissions: Administrator

In the LIMS user interface, the term 'contact' has been replaced with 'client.' However, the API still uses the permission Contact.

Users with ClarityLogin permission can view and edit their own client and user details.

Clients can edit their own details (except for assigning/removing roles) without having update permission.

Permission: Process

Default roles with these permissions: Administrator

In the LIMS user interface, the term 'process' has been replaced with 'master step.' However, the API still uses the permission Process.

Permission: OverviewDashboard

Default roles with this permission: Administrator

Permission: Configuration

Default roles with this permission: Administrator

Permission: ReQueueSample

Default roles with this permission: Administrator, Researcher, Collaborator

Permission: SampleWorkflowAssignment

Default roles with this permission: Administrator, Researcher, Collaborator

Permission: RemoveSampleFromWorkflow

Default roles with this permission: Administrator

Permission: MoveToNextStep

Default roles with this permission: Administrator

Permission: SampleRework

Default roles with this permission: Administrator

Permission: ReviewEscalatedSamples

Default roles with this permission: Administrator

Permission: ESignatureSigning

Default roles with this permission: Administrator

Permission: CanEditCompletedSteps (LIMS v5.1 and Later)

Default roles with this permission: None

Modifications are limited to what is available on the Record Details screen for the step.

Details such as sample placement or routing cannot be modified.

Only steps completed after upgrading to LIMS v5.1 can be edited. Steps completed in v5.0 or earlier cannot be edited.

Steps that were executed using the Process API cannot be edited.