Clarity LIMS v6.3 & Lablink v2.5
Illumina Connected Software

Release Notes Clarity LIMS v6.3.0

Published:July 30, 2024

Last Update: Oct 30, 2024

Latest Release: v6.3.0

These release notes describe the key changes made to software components for Clarity LIMS v6.3.

Clarity LIMS v6.3 is deployable in both cloud hosted and on-premise environments.

New Features

  • System Settings allows the following features

    • You can now use Applications Properties setting to view, set and update the database property field value in the system. There is also option to create and delete custom application properties.

    • You can now use Banner setting to create, update and delete custom announcement in Clarity LIMS and LabLink. This banner shows up at the top of page when configured.

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

    • Roles and Permissions management that allows you to create, modify, and delete roles.

    • You can now use Export Logs to retrieve specific log file generated by the various Clarity LIMS services for debugging purposes. This feature is however, not available to on-premise environments.

    • IP Whitelisting allows you to request for whitelisting of IP. This feature is not available to on-premise environments.

    • SSH Request that allows you to request for SSH access via user public key. This feature is not available to on-premise environments.

  • Illumina Connected Software Platform (ICP) Integration allows user name and password authentication against ICS to govern access to Clarity LIMS and Lablink. SAML SSO login is also supported via these services. This feature is available as part of Clarity LIMS Enterprise Software for hosted instances.

  • You can now update account information of LDAP - or ICP provisioned Clarity LIMS users via API or Configuration > User Management screen.

  • Illumina Connected Software Platform (ICP) Integration allows user name and password authentication against ICS to govern access to Clarity LIMS and Lablink. SAML SSO login is also supported via these services. This feature is available as part of Clarity LIMS Enterprise Software for hosted instances.

  • You can now update account information of LDAP - or ICP provisioned Clarity LIMS users via API or Configuration > User Management screen.

  • Support bulk import of reagent kit lots via a reagent kit lot list file.

  • New Advanced Search endpoints:

    • allow you to retrieve a list of user created advanced search saved queries.

    • output the advanced search result of the specified saved query into a CSV file.

  • Advanced search improvements:

    • Advanced search screen now shows the indexing status of the root entity when selected.

    • Display columns selected using the column drawer is now saved in a Saved query.

  • You can now perform both basic and advanced search as the full re-indexing process progresses. Data will be indexed from the latest to the oldest records.

  • Clarity LIMS are upgraded to utilise dynamic widths, allowing UI components to elongate or shorten according to the screen resolution. The following UI pages are, however, not included in this upgrade:

    • Dashboards - Overview, Projects

    • Profile

    • Configuration - Reagents, Controls

  • Performance improvements—Improvements to the overall performance of the existing API endpoints. A complete list of enhancements is provided in the Appendix.

  • Details of the technician who completed the step can be retrieved using GET /api/{version}/steps/{limsid} endpoint.

  • You can now view version number of LabLink on LabLink login screen.

  • You can now configure display of Submitting Lab Name field in Request A New User ID page of LabLink. This field is hidden on UI by default and can be modified via lablink.requestuser.submittinglabname in Application Properties.

Defect Repairs

  • Includes a security improvement that updates spring-security from 5.7.8 to 5.8.12.

Bug Fixes

  • Fixed a bug in Automation Worker where the 21st line of an EPP output is missing when the EPP has more than 20 lines of output upon completion.

  • Fixed a bug where {ProjectName} token appears as duplicated when there is more than one sample in a step.

  • Fixed a bug where users with the Read-Only permission do not have access to Advanced Search.

  • Fixed a bug where un-assigning of a sample using POST /api/{version}/route/artifacts did not correspondingly remove the sample from the ice bucket of a step.

  • Fixed a bug where updating project's priority using PUT /api/{version}/projects/{limsid} caused an error and removed the project's priority.

  • Fixed a bug where non-empty container can be deleted when user tries to delete a non-empty onTheFly container using the Container UI internal API DELETE /api/containers via an API tool.

  • Fixed a bug where search indexer is not consuming messages from queue as quickly, causing data in the system to be non searchable.

  • Fixed a bug where the bulk indexing for a project, container, step, and file failed due to a limitation in memory space for search-indexer. This bug occurred when the indexing batch size was too large. Indexing bulk size can now be modified with an attribute in /opt/gls/clarity/search-indexer/conf/search-index-config.properties.

  • Fixed a bug where basic search failed when searching with large numbers of UDFs in the system.

  • Fixed a bug where details about the step failed to be shown when selecting the LIMS ID link for steps in the Advanced Search results.

  • Fixed a bug where controls and samples must be added in a certain order for the configured step. This issue caused an error that prevented the configured protocol step from starting.

  • Fixed a bug where step cannot be started in API when controls and samples are in standard step with Enable QC flag set to Yes.

  • Fixed a bug where on the Placement screen, the sample well position in the source container takes precedence in the placement order of the destination plate when placing samples from the Sample View List table.

  • Fixed a bug where on the Placement screen, the sample well position in the source container takes precedence in the placement order of the destination plate when placing samples from the Sample View List table.

  • Fixed a bug where username is encoded to HTML when it contains special characters.

  • The root artifact name is updated when updates to submitted sample details are submitted.

  • An archived user can no longer electronically sign work in the Record Details screen when the e-Signature feature is enabled.

  • Fixed a bug where in-place upgrade does not remove the previous unpacked Tomcat webapp.

  • Fixed a bug where LabLink was not checking for CollaborationsLogin:action permission when a user logs in.

  • Fixed a bug where LabLink was not checking for CollaborationsLogin:action permission when a user logs in.

Known Issues

  • In Add Label screen, the label will starts at the well position at which user drops in when transferring the equivalent number of labels to samples in the output container at the first instance.

  • If the client and server are in different time zones, there can be additional or missing search results when using Date Received of a sample as one of the search criteria in Advanced Search.

  • Multiple accounts that share an email address only receive a reset password email for one of the accounts when a reset password request is made using Email information.

  • The step milestone screen will becomes unresponsive when the request header/URL size is larger than the defaults capacity limit configured in either Apache HTTPD or Tomcat application server.

  • If there are changes made to the existing LDAP integration settings, restarting of Tomcat service will be required to provide the user access.

  • The config slicer tool will takes longer time (~8 times) to import a config slice into instance with Clarity LIMS v6.2 or v6.3 when compared to earlier versions (v6.1 and below).

  • Clarity page will need to be refresh after applying browser zoom in/out for proper display. This is mainly due to a limitation on ExtJS in which, the width that components take are only set when the page is refreshed.

  • Value used in basic search is the case-sensitive for the following fields:

    • LIMSID

    • workflow

  • SSH request made through System setting, do not allow period (.) as part of the provided username. This is due to the Regular Expression used to validate the provided username for Linux user creation.

Additional Notes

  • The following API endpoints relating to processes have been deprecated in Clarity LIMS v6.3.0 and will be removed in the next major release:

    • POST /api/{version}/processes/

    • GET /api/{version}/processes/

    • GET /api/{version}/processes/{processId}

    • PUT /api/{version}/processes/{processId}

  • The following API endpoints relating to UDT will be deprecated and removed in the next major release:

    • PUT /{version}/configuration/udts/{udtid}

    • GET /{version}/configuration/udts

    • GET /{version}/configuration/udts/{udtid}

    • POST /{version}/configuration/udts

Appendix

Performance Details

List of API endpoints with enhanced performance is as follows.

  • PUT clarity/api/work/{id}

  • PUT clarity/api/work/{id}

  • POST clarity/api/ice-bucket/checkout/{id}

  • POST /api/{version}/artifacts/batch/update

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