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Illumina Connected Software
For the complete documentation index, see llms.txt. This page is also available as Markdown.

System Settings

The System Settings screen allows for viewing and managing of certain operations: Clarity LIMS system configurations, log files export and whitelisting, that are previously possible only through using SSH command or CLI scripts.

System Settings screen

To access the System Settings screen, the SystemSettings:action permission is required. Without this permission, the System Settings is not visible.

By default, only the administrator role has the SystemSettings:action permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.

Access the SystemSettings Screen

In Clarity LIMS, select System Settings on the top right menu bar to access the screen. Use this screen to do the create and manage the following:

Applications Properties

Applications Properties allows for management of Clarity LIMS system configuration that is stored in the database.

You may view, create, modify, delete application properties.

Create an Application Property

To create a custom application property, complete the following steps:

  1. On the system settings screen, select the Application Properties tab, then select Create Property.

  2. Type a name for the property.

    NOTE: The name of property must be unique.

  3. [Optional] Enter additional details about the property, such as the value, default value and description.

  4. Select Save. The new property displays in the Application Properties list.

View and Modify Application Properties

You can select multiple properties and modify its associated property value at the same time.

To view, or modify, Application properties, complete the following steps:

  1. On the system settings screen, select the Application Properties tab.

  2. In the Properties list, select the property. The Property Details area displays the details for the selected property.

    • Select Select All to include all properties to be shown in Property Details area.

    NOTE: Use the Search box to filter through the list of application properties.

  3. To modify property value, edit as required. In the Property Details area, enter the values for the selected properties.

    Default value of selected properties is read-only and cannot be edited.

  4. To restore default value of the property, select Restore Defaults.

  5. Select Save.

  6. To unselect all the currently selected properties, select Cancel.

View and Delete an Application Property

To view, or delete an application property, complete the following steps:

  1. On the system settings screen, select the Application Properties tab.

  2. In the Properties list, select the property.

  3. To delete the property, select Delete.

    NOTE: Only custom application properties can be deleted.

Banner allows for management of custom announcement in Clarity LIMS. This banner shows up at the top of Clarity LMS page for all users when configured.

Create, Modify a Banner

To create a banner message, complete the following steps:

  1. On the system settings screen, select the Banner tab.

  2. Type your message in the Message field.

    NOTE: Text box is kept at the limit of 250 characters. New lines will not be displayed in the actual banner.

  3. Select Save. The banner message displays at the top of Clarity LMS page.

Delete a Banner

  1. On the system settings screen, select the Banner tab.

  2. Delete the message.

  3. Select Save.

Export Logs

You can use Export Logs to retrieve the following log file generated by the various Clarity LIMS services for debugging purposes.

  • Automation Worker

  • Tomcat UI

  • Tomcat API

  • Elasticsearch

  • HTTPD Access Log

  • Search Indexer

Export Logs is available only on Illumina Hosted environments. To export log files for On-premise environment, see Clarity LIMS Log Files.

To Export Logs:

  1. On the system settings screen, select the Export Logs tab.

  2. Select the log to be exported.

  3. Select Export.

Global Tokens

Global Tokens setting allows you to create and manage a list of user-defined tokens to be used in automations.

The following list of tokens is provided by default and cannot be deleted:

  • {java}

Create a Global Token

To create a global token, complete the following steps:

  1. On the system settings screen, select Global Tokens tab, then select Create Global Token.

  2. Type a name for the global token and enter value.

  3. Select Save. The new global token is added to the Tokens list.It is now available to be displayed on Configuration Automation screen under Global Tokens.

NOTE: Global tokens used in the Step's automation do not get exported together with the workflow by Config Slicer Tool. You must manually created these tokens after importing the exported workflow slice into the system.

View and Modify a Global Token

To view, or modify, a global token, complete the following steps:

  1. On the system settings screen, select Global Tokens tab.

  2. In the Tokens list, select the token. The Global Token Details area displays the details for the selected token.

  3. To modify token value, edit as required in the Global Token Details area.

  4. Select Save.

View and Delete a Global Token

NOTE: Only custom tokens can be deleted.

To view, or delete a global token, complete the following steps:

  1. On the system settings screen, select the Global Tokens tab.

  2. In the Tokens list, select the Token.

  3. To delete the token, select Delete.

IP Whitelisting

IP Whitelisting allows you to request for access to specific ports from the whitelisted IP.

IP whitelisting is available only on Illumina Hosted environments.

You can request for access to the following three access types:

  • Clarity Access Type: Port 80, 443

  • SSH Access Type: Port 22

  • Database Access Type: Port 5432

NOTE: For Database Access Type request, PostgreSQL config file (pg_hba.conf) need to be updated to allow the access to the database, in addition to submitting an IP whitelisting request. Contact Illumina Support Team to request for the read-only access credentials.

Request for New IP Whitelisting

  1. On the system settings screen, select IP Whitelisting tab, then select Add IP To List.

  2. In IP Details area, complete the required fields:

    • Type an IP address for the field. You can whitelist multiple PI addresses by separating them with a comma.

      NOTE: Only IPv4 address is supported. Local addresses (10.0.0.0 to 10.255.255.255, 172.16.0.0 to 172.31.255.255, 192.168.0.0 to 192.168.255.255) cannot be requested.

    • Select the appropriate access type from drop-down list. At least one of the three access type must be selected.

  3. Select Request. The new IP whitelisting request is added to the record table in IP Requests area.

By default, when a new IP request is added, the status is Requesting.

Copy IP Addresses

You can populate IP addresses to IP Details form using the copy functionality.

To copy IP addresses from IP requests record table:

  1. In IP Requests area, select the IP addresses.

  2. Select Copy. Selected IP addresses are auto-populated onto the IP Details form.

An IP whitelisting request will takes less than 30min to complete on the server. If there are other pending IP requests in the server (eg, N number of requesting), the time to complete the new request should be less than (N + 1) * 15 * 2 minutes.

Example

1 new IP whitelist request on a system with 5 pending IP whitelist requests will take less than 180 minutes to complete.

IP Whitelisting Status

The status of an IP whitelisting may be Requesting, Active, Failed, Delisting, Delist Failed or Archived. You can view and manage the list of IP requests records in IP Requests area.

The following table provides an overview of each IP request status:

Status
Description

Requesting

Request to whitelist IP address is being processed. All new request is defaulted to this status.

Request Failed

IP request to whitelist IP address has failed. Contact Illumina Support with Reference ID provided in Failure column for further assistance.

Active

IP address is whitelisted and access to port is enabled.

Delisting

Request to delist IP address is being processed.

Delist Failed

Request to delist IP address has failed and port continues to be accessible. Contact Illumina Support with Reference ID provided in Failure column for further assistance.

Archived

IP address is removed from whitelisted list and can no longer access to port.

NOTE: IP addresses with Failed status will be removed from IP Request table after 30 days.

Delist Whitelisted IP Addresses

  1. In IP Requests area, select the IP addresses with Active or Delisted Failed status.

  2. Select Delist.

Roles and Permissions management

Roles and Permissions management that allows you to create, modify, and delete roles and the associated permissions to a role.

Create a Role

To create a role, complete the following steps:

  1. On the system settings screen, select Roles and Permissions tab, then select Create Role.

  2. Type a name for the role.

  3. [Optional] Select the permission allowed from the Assigned Permissions drop-down list.

  4. Select Save. The new role displays in the Roles list.

View and Modify Role and Permissions

To view, or modify, a role and its associated permissions, complete the following steps:

  1. On the system settings screen, select Roles and Permissions tab.

  2. In the Roles list, select the role. The Role Details area displays the details for the selected role.

  3. To modify role values, edit as required in the Role Details area.

  4. Select Save.

View and Delete Role and Permissions

NOTE: Roles cannot be deleted if they are assigned to users. To view the roles that are currently assigned to a user, go to User Management Configuration Screen.

  1. On the system settings screen, select Roles and Permissions tab.

  2. In the Roles list, select the role.

  3. To delete the role, select Delete.

SSH Request

SSH Request that allows you to request for SSH access via user public key.

SSH Request is available only on Illumina Hosted environments.

Request for New SSH Access

  1. On the system settings screen, select SSH Access tab, then select SSH Access.

  2. In SSH Details area, complete the required fields:

    • Select the username from drop-down list.

      NOTE: The username must satisfy the following Linux requirements:

      • Maximum of 32 characters.

      • Contains only alphanumerics, underscores, hyphens and periods. Note - Cannot consist of only numbers.

      • Does not start with a hyphen character.

      • Last character may be a dollar character.

    • Enter SSH public key of the user.

      NOTE: SSH public key provided must follow SSH-RSA public key format.

  3. Select Request. The new SSH access request is added to the record table in SSH Listings area.

By default, when a new SSH request is added, the status is Requesting.

SSH Request Status

The status of SSH Request may be Requesting, Active, Request Failed, or Archived. You can view and manage the list of SSH request records in SSH Listings area.

The following table provides an overview of each SSH request status:

Status
Description

Requesting

Request to enable SSH access is being processed. All new request is defaulted to this status.

Request Failed

Request to enable SSH access has failed. Contact Illumina Support with Reference ID provided in Failure column for further assistance.

Active

Request to enable SSH access is successful. Access is valid for 180 days, from date of request.

Archived

Validity of access has expired. SSH access for user is removed.

NOTE: SSH access with Request Failed and Archived status will be removed from SSH listing table after 30 days.

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