BaseSpace Clarity LIMS v6.0 Release Notes
These Release Notes describe the key changes made to software components for BaseSpace Clarity LIMS since version 5.4.
When upgrading from a version prior to v5.4, review the release notes for v5.4 for a list of features and bug fixes introduced in that version.
Clarity LIMS v6 is deployable in both cloud hosted and on-premise environments.
New Features
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Technology updates—An up-to-date technical stack ensures continued reliability, improved speed and capacity, and optimized system performance. For a complete list of updates, refer to the Appendix. |
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Project level automation—Users can now write custom scripts and perform custom actions on submitted samples. These custom actions can be triggered manually from the Projects & Samples screen. |
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Performance improvements—Improvements to the overall performance of Clarity LIMS v6 and to the existing API endpoints. A complete list of enhancements is provided in the Appendix. |
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Support for on-premise customers—Clarity LIMS v6 supports on-premise deployment renewals at launch. Contact your local sales specialist for more information. |
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ICA integration—Wet lab data can now be made available to data analysis pipelines via step level scripts. |
Defect Repairs
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An Elasticsearch error is no longer generated when date-formatted text is entered in a non-date field type. |
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Resolved an issue where controls were added to more workflows than samples processed in a step. |
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An API call to the reagent lot endpoint no longer fails when the lot status is expired automatically by the Clarity LIMS system. |
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Resolved inconsistent behavior on archived controls and deleted instrument types in Manifest and XML configuration slice files. |
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The root artifact name no longer reverts to default when updates to submitted sample details are submitted via automation. |
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Executing the Processes API endpoint on projects with over 500 samples and with a project name filter no longer returns an incomplete set of data. |
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A completed workflow stage is no longer missing from the Artifacts API endpoint if the previous step was not an output step. |
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Queue screen page load performance has been optimized. |
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Users no longer experience decreased performance associated with the Queue API making too many calls. |
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Users no longer experience decreased performance when loading Previous Step queue grouping. |
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Users no longer experience decreased performance when grouping types on Ice Bucket screen. |
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Dropdown fields that do not allow custom entries and have first option set as default are no longer silently applied to various API endpoints and sample sheet upload. |
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The changeWorkflow script no longer fails when processing 1152 derived samples. |
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Naming syntax LIST option now permits a combination of letters and numbers. |
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Master step configuration can now be updated when there is a comma in the naming convention. |
Known Issues
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There are no known issues at this time. |
Additional Notes
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Clarity LIMS v4.x is no longer supported by Illumina. |
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Clarity LIMS v6 does not support Oracle database. Illumina will continue to support v5.2 for on-premise customers requiring Oracle. |
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Clarity LIMS v6 does not support the Reporting module. |
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Clarity LIMS v6 has been reviewed for log4j vulnerabilities. All potential vulnerabilities have been addressed. |
For questions or assistance, contact the Illumina Support team.
Appendix
Technical Update Details
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Elasticsearch
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6.2.4
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7.16.3
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Java
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Oracle JDK 8u202
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AdoptOpenJDK 8u292
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RabbitMQ Server
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3.6
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3.8.16
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Tomcat Application Server
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8.5.54
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9.0.54
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Grails Web Framework
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2.4.5
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4.0.10
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PostgreSQL Database
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12.4
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12.7
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Performance Details
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The overall performance of the Clarity LIMS system has been optimized on the following screens/actions: |
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Assigning samples to workflow |
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Removing samples from workflow |
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Ice Bucket screen load and loading of all grouping types |
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Adding labels to samples |
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List of API endpoints with enhanced performance is as follows. |
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POST /api/{version}/samples/batch/retrieve |
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POST /api/{version}/samples/batch/create |
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POST /api/{version}/route/artifacts |
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POST /api/{version}/artifacts/batch/update |
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POST /api/{version}/artifacts/batch/retrieve |
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PUT /api/{version}/steps/{limsid}/actions |
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GET /api/{version}/steps/{limsid}/actions |
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POST /api/{version}/steps |
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GET /api/{version}/steps/{limsid}/details |
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GET /api/{version}/queues/{protocolStepId} |
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POST /api/{version}/steps/{limsid}/advance |
