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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  • Script Properties
  • Run the Script
  • Examples
  • Overriding Properties

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  1. Administration
  2. LDAP Integration

Using the LDAP Checker Tool

This section explains how to use the LDAP Checker tool a script (ldap-checker.jar) that checks and reports on an LDAP configuration. Instructions for use are also provided in the README.txt file that accompanies the tool.

The ldap-checker script is included with the Clarity LIMS installation and is available at the following location:

/opt/gls/clarity/tools/ldap-checker

The ldap-checker script performs numerous checks of the LDAP configuration and reports on any incorrect items found.

Script Properties

Point the script to one or more files containing (at a minimum) the database connection properties. Alternatively, set these properties from the command line.

The script loads properties from the following sources and in the following order:

  1. Any JDBC properties files specified with -f (see the table for options).

    If multiple properties files specify the same property, the last file is used.

  2. Any Java system properties specified on the command line using

    -D<propertyName>=<propertyValue>

    Properties specified on the command line are only checked if they do not appear in the properties files.

  3. The properties table in the database.

    The properties table is only checked if the same property is not already specified in the properties file or on the command line.

After the script has the basic database connection properties, it loads further settings from the corresponding Clarity LIMS database.

The following JDBC properties are required:

  • jdbc.driverClassName

  • jdbc.url

  • jdbc.username

  • jdbc.password

Options:

-f
--files
Property files to process

-h

--help

Show usage information

-u

--users

Usernames to check

Run the Script

  1. Change to the directory containing ldap-checker tool:

    /opt/gls/clarity/tools/ldap-checker
  2. Run the script. To specify a properties file, use the following example:

    java -jar ldap-checker-<version>.jar -f database.properties 

Example Properties File

The tool includes an example database.properties file. This example shows a properties file that is specified with the -f option.

The following options are available:

  • Edit this file and use it.

  • Provide properties on the command line, using: -D.

    For example:

    -Djdbc.url=<url to properties file> 

Examples

Example 1: Using SSL

Specify and provide the path to the keystore:

java -Djavax.net.ssl.trustStore=/path/to/keystore -jar ldap-checker-<version>.jar -f database.properties 

Example 2: Checking Users

To check a set of specific users (even those that have not been provisioned), use the following script:

java -jar ldap-checker-<version>.jar -u usertocheck -f database.properties 

Overriding Properties

To override properties that are typically loaded from the properties table, use command-line system properties or one or more properties files.

Using system property ( -D options must be specified before the -jar option):

java -Djavax.net.ssl.trustStore=/path/to/keystore -Dldap.managerPass=mypassword -jar ldap-checker-<version>.jar -u usertocheck -f database.properties

Using multiple properties files:

java -jar ldap-checker-<version>.jar -u usertocheck -f database.properties custom-ldap.properties
  • In this example, Custom-ldap.properties might resemble the following:

ldap.managerDn=CN=GLS Admin,CN=Users,DC=gls,DC=lan

ldap.managerPass=mypassword
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Last updated 6 months ago

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