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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  1. Administration
  2. Config Slicer Tool

Upgrading a configuration package/manifest file for compatibility with Config Slicer v3.0.x

If running Config Slicer v3.0.x against a configuration package or manifest file that was generated with a pre-3.0 version of Config Slicer, an error message displays.

Scenario 1: Out-of-Date Configuration Package

In this scenario the error message will resemble the following:

Package was generated with an older version of config slicer incompatible with the current version (3.0.2).
Please upgrade the configuration package (java -jar upgrade-config-slice.jar 'configuration_package.xml'),
verify the results, and try again. 

SOLUTION:

Upgrade the configuration package file by running upgrade-config-slice.jar against it.

  • This jar file should be located in the same directory as Config Slicer (/tools/config-slicer).

  • The upgrade script will save an upgraded copy of the configuration package file (to the same directory), which can be inspected and imported.

Example:

java -jar upgrade-config-slice.jar configuration_package.xml 

To upgrade a manifest file at the same time, simply add it to the script as a second argument:

java -jar upgrade-config-slice.jar configuration_package.xml manifest.properties 

Scenario 2: Out-of-Date Manifest File with no Corresponding Configuration Package

In this scenario the error message resembles the following:

Manifest was generated with an older version of config slicer incompatible with the current version (3.0.2). 
If you have the corresponding configuration package available the manifest can be automatically upgraded 
(java -jar upgrade-config-slice.jar configuration_package.xml 'manifest_file.properties'). Otherwise please 
regenerate the manifest with the current version of config slicer and try again. 

SOLUTION:

This upgrade process is a little more involved:

  1. Extract the list of process types from the manifest file
.

  2. Format them as parameters to Config Slicer's custom manifest generation for process types.

    For example, assuming we extracted the process types Process Type 1 and Process Type 2 in step 1, the following command would be used:

    java -jar config-slicer.jar -o custom -s localhost -u admin -p pass -pt 
    "Process Type 1" -pt "Process Type 2"
  3. Run the custom manifest generation.

  4. Take the list of analyte UDFs and ResultFile UDTs from the manifest file that was generated and add them to the old manifest file
.

  5. Add the following line of text to the top of the old manifest file:

    ConfigSlicerVersion=3.0-compatible
PreviousManaging Configurations with Config SlicerNextConfig Slicer Use Cases

Last updated 9 months ago

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