Clarity LIMS
Illumina Connected Software
Clarity LIMS v6.3 & Lablink v2.5
Clarity LIMS v6.3 & Lablink v2.5
  • Release Notes Clarity LIMS v6.3
    • Release Notes Clarity LIMS v6.3.1
    • Release Notes Clarity LIMS v6.3.0
  • Technical Overview
    • Technical Requirements
  • Installation
    • Installation Procedure
    • Guide to Secret Management
    • Install/Upgrade Secret Management for Integration Modules
    • Change the Clarity LIMS Hostname
    • Update Server Passwords and Database Connection Details
  • On-Premise Deployments
    • Pre-installation Requirements
      • Install a Purchased SSL/TLS Certificate
      • Configure Your HashiCorp Vault
    • On Premise to On Premise Upgrade Procedures
    • On Premise to On Premise In-place Upgrade Procedures
    • On Premise to Hosted Upgrade Procedures
    • Hosted to On Premise Upgrade Procedures
  • Administration
    • Database Cleanup Procedure
    • Backup and Restore Procedure
    • Receiving and Decrypting Cloud Backup Data
    • LDAP Integration
      • Using the LDAP Checker Tool
    • Illumina Connected Software Platform Integration
    • Clarity LIMS Log Files
    • Customize the Term Used for Projects
    • Enforcing Unique Sample Names Within a Project
    • Container Name Uniqueness
    • Configure Electronic Signatures
    • Creating Enrypted Passwords
    • Config Slicer Tool
      • Managing Configurations with Config Slicer
      • Upgrading a configuration package/manifest file for compatibility with Config Slicer v3.0.x
      • Config Slicer Use Cases
      • Troubleshooting Config Slicer
    • Audit Trail
      • Enabling, Validating and Disabling Audit Trail
    • System Settings
    • Automation Worker Nodes
      • Troubleshooting Automation Worker
  • Clarity LIMS v6.3 Reference Guide
    • Dashboards
      • Overview Dashboard
      • Projects Dashboard
    • Projects and Samples
      • Projects
      • Samples Accessioning
        • Sample List for Batch Import
        • Guidelines and Tips for Batch Sample Import
      • Assign and Process Samples
    • Lab View
      • Requeue and Rework Samples
      • Storing Sample Aliquots for Later Use
      • Modifying Completed Step Details
      • Alert Notifications
    • Configuration
      • Lab Work
        • Steps and Master Steps
          • Step Milestones
          • Derived Sample Naming Convention Tokens
        • Protocols
        • Workflows
      • Consumables
        • Reagents
          • Reagent Kit Lot Manifest for Batch Import
        • Controls
        • Instruments
        • Labels
        • Containers
      • Custom Fields
      • User Management
        • Manage User Access
        • User Roles
        • Configured Role-Based Permissions
        • User and Profile Page
      • Automations
        • Automation Trigger Configuration
        • Copy Custom Fields from Step Input to Output
        • Template Files Associated With Automations
    • Automated Quality Control
      • Configure a QC System
    • Search
      • Basic Search
      • Advanced Search
    • Genealogy View
    • System Performance
      • Queue Performance and Usability
      • Demultiplexing API Endpoint Performance
    • Terms and Definitions
  • LabLink v2.5 Reference Guide
    • Project
      • Email Notifications for Notes
    • Resource Materials & Contact Us
    • Users
    • Configuration
    • Publishing Files and Progress
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  • Update Operating System User Passwords
  • Update Clarity LIMS User Passwords
  • Update Database Connection Details

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  1. Installation

Update Server Passwords and Database Connection Details

This document describes the steps required to update the Clarity LIMS application configuration.

Two levels of user passwords are created in the Clarity LIMS system: one at the operating system level and one at the Clarity LIMS level.

Following are details on the user passwords, instructions for changing them, and instructions for updating Clarity LIMS with the new database connection details.

The following steps are only required if the passwords for glsftp and/or apiuser have been changed.

Update Operating System User Passwords

The user passwords created at the operating system level are for the glsai, glsjboss, and glsftp users.

  • glsai and glsjboss users:

    • These users have no configuration associated with them.

    • You may change their passwords at any time.

  • glsftp user:

    • After installation of Clarity LIMS, you can change this password. However, you must also update it in the file/vault secret store, using the Secret Management Util tool.

To change the glsftp password after installing Clarity LIMS, using SecretUtil:

  1. Change the glsftp user's password on the server.

  2. Log in to the server as the root user.

  3. Stop Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh stop
  4. Go to /opt/gls/clarity/tools/secretutil.

  5. Update the password in the secret store.

    • For vault-based secret storage, use either the Vault command line interface (CLI) or Vault user interface (UI) to update the password.

    • For file-based secret storage, use Secret Management Util to update the password as follows:

      $ java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -u="new-password" app.ftp.password
  6. Start Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh start

Update Clarity LIMS User Passwords

The user passwords created at the Clarity LIMS level are for the admin, facility, and apiuser users.

  • admin and facility users:

    • These users have no configuration associated with them.

    • You may change their passwords at any time.

  • apiuser user:

    • After installation of Clarity LIMS, you can change this password. However, you must also update it in the file/vault secret store, using the Secret Management Util.

To change the apiuser password after installing Clarity LIMS:

  1. Check for any remote Automation Workers, and take note of their locations in your network. You will need to restart these after changing the password.

  2. Log in to the server as the root user.

  3. Stop Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh stop
  4. Go to /opt/gls/clarity/tools/secretutil.

  5. Update the password in the secret store

    • For vault-based secret storage, use either the Vault command line interface (CLI) or Vault user interface (UI) to update the password.

    • For file-based secret storage, use Secret Management Util to update the password as follows:

      $ java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=integration -u="new-password" "apiusers/apiuser"
  6. Start Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh start

Update Database Connection Details

In some circumstances (such as security breaches/compromises), the database connection details (eg, database password) are updated, which prevents Clarity LIMS from connecting to the database. You can correct this issue by updating Clarity LIMS with the new database connection details as follows.

  1. Check for any remote Automation Workers.

  2. Update the existing tenant with the new details.

  3. Restart any Automation Workers.

To update database connection details:

  1. Check for any remote Automation Workers, and take note of their locations in your network.

  2. Log in to the server as the root user.

  3. Stop Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh stop
  4. Go to /opt/gls/clarity/tools/secretutil.

  5. Update existing tenant with new details.

    • For vault-based secret storage, use either the Vault CLI or Vault UI to update the password.

    • For file-based secret storage, use the Secret Management Util to update the database password as the root user.

    $ java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -u="db-password" db.<db-name>.password
  6. Start Clarity LIMS using the following command:

    /opt/gls/clarity/bin/run_clarity.sh start
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Last updated 9 months ago

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