These Release Notes describe the key changes made to software components for Clarity LIMS v6.2.
Published: Aug 30, 2023
Last Updated: Aug 30, 2023
Latest Patch: 6.2.0
These Release Notes describe the key changes made to software components for Clarity LIMS v6.2.
Clarity LIMS v6.2 is deployable in both cloud hosted and on-premise environments.
The operating system (OS) changes from CentOS7 to Oracle Linux v8.8.
Lab account management that allows you to create, update, and delete accounts in Clarity LIMS.
You can now set and update account custom field values. These configured fields are available in the new Account management screen when you view, create, or update an account.
A red dot alert that displays when a required field without a default value is added to Clarity LIMS. This alert shows up LabLink next to the Configuration menu, the drop-down list in the Custom Fields menu, and next to Custom Fields in the Configuration tab.
Configure client custom fields in LabLink through the Custom Fields Configuration page after they have been created through the Custom Fields Configuration Page in Clarity LIMS. The Users page in LabLink shows the configured custom fields when creating, editing, viewing, and reviewing a user.
The Queue View page performance has been optimized.
Reviewed and addressed potential vulnerabilities for cross site scripting (XSS).
Fixed a bug where the upload of the sample submission spreadsheet with leading or trailing spaces in any of the header tags (eg, </TABLE HEADER>) resulted in import errors.
Fixed a bug where the LIMS ID (Process) in the Record Details step disappeared when you select No preset.
Fixed a bug where the custom term for Projects did not propagate to LabLink.
Fixed a bug where samples were not placed correctly when you drag and drop from the plate GUI. This bug happened when a step was configured to have samples ordered by Column and placed by Row in the placement stage.
Fixed a bug where false errors occured when the Config-slicer tool was used to import automation template files. In this update, the Config-slicer tool ignores any differences in the automation file XML tag, but logs a reminder in the configslicer-issues.log file. The file lists the different automation names that the users should check against so that the automation files for those names are uploaded properly. The file also shows warnings or errors logged.
Fixed a bug where the Config-slicer command-line interface (CLI) tool showed false negative reports with control types and reagent kits when the values were empty during the import or validation of the slice.
Fixed a bug that affected the UI for the File Attachment Method for the Demultiplexing step in Master Step and Step during the Configuration stage.
Updated UI and API application logs so that they contain only useful log information.
There is a bulk indexing error due to the memory space limitation for search-indexer when the indexing batch size is too large.
There can be additional or missing search results when using Date Received of a sample as one of the search criteria in Advanced Search when the client and server are in different time zones.
Multiple accounts that share the same email address only receive a reset password email for one of the accounts when a reset password request is made using Email information.
Clarity LIMS v6.2 supports both Python2 and Python3 versions. However, there is no symbolic link created for /usr/bin/python to Python2 and there will not be a default link. Scripts have to be updated specifically to either Python2 or Python3.
Published: July 30, 2024
Last Updated: June 07, 2024
Latest Patch: 6.2.1
These Release Notes describe the key changes made to software components for Clarity LIMS v6.2.1. The Clarity LIMS v6.2.1 patch release supersedes v6.2.0. It is intended for customers on or migrating to Clarity LIMS v6.2.0.
This release resolves customer-reported issues related to the following functions:
Search-indexer performance
Basic search failure when searching with multiple custom fields in the system
Necessary handling of controls for a configured step
There are no new features added with this release.
Fixed a bug where the search-indexer did not quickly consume messages from the queue. This issue caused 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 the basic search failed when searching with large numbers of custom fields in the system.
Fixed a bug where details about the step failed to show 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 a step cannot be started when controls and samples are in the standard step and the Enable QC flag is set to Yes.
There can be additional or missing search results when using Date Received of a sample as one of the search criteria in Advanced Search when the client and server are in different time zones.
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.
Users with the Read-Only permission do not have access to Advanced Search.
{ProjectName} in the {ProjectName} token appears as duplicated when there is more than one sample in a step.
On the Place Samples 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. This placement order change only happens when samples are transferred from more than one source container. If the Sample View List table is sorted by a specific column, the order of the listed samples is ignored when they are placed in a destination plate.
The config slicer tool will takes longer time (~8 times) to import a config slice into instance with Clarity LIMS v6.2 when compared to earlier versions (v6.1 and below).
Customers connecting remotely to PostgreSQL database need to make sure that their JDBC driver is compatible with the PostgreSQL version used.
For on-premise deployments, Clarity LIMS v6.2.1 is qualified to run with the following server OS versions:
Oracle Linux v8.8 and v8.9 (64-bit)
RedHat Enterprise Linux v8.8 and v8.9 (64-bit)
Security vulnerabilities in PostgreSQL 15.x have been addressed. PostgreSQL 15.2–15.6 is at a low risk of security vulnerabilities for customers on Clarity LIMS v6.2.1.
PostgreSQL 15.2 and 15.6 are now qualified to run in Clarity LIMS v6.2.1.