Release Notes: 23.3 (March 2023)

2024-03-29

Here are the full release notes for version 23.3 (March 2023).

LabKey Server

Data Import

  • Enhancements have been made to clarify the options of importing new data, updating existing data, and merging both update and new data in the same import. (docs)

Folder Archives

  • File browser settings are included in folder archives. (docs)
  • Custom study security settings are included in folder archives. (docs)

Electronic Data Capture

  • REDCap integration now supports loading of data into a default study visit, supporting situations where there the REDCap study is either not longitudinal or only defines a single visit. (docs | docs) Also available in 22.11.5.
  • REDCap reloading of studies with very wide datasets including many lookups can suppress the creation of those lookups in order to be kept under the column width limit. (docs) Also available in 22.11.5.

File Watchers

  • The "Import Samples from Data File" file watcher task lets you select whether to offers merge, update, and append the incoming data. An "auditBehavior" parameter is also now available. (docs)

Samples and Data Classes

  • Built-in default system fields are shown in the field editor and can be enabled and disabled to control what users see. (docs)
  • Samples can have expiration dates, making it possible to track expiring inventories. (docs)
  • See also new sample management features available with LabKey Sample Manager and Biologics LIMS.

Integrations

  • Integration with Power BI Desktop using an ODBC connection. (docs)
  • Integration with AWS Glue. (docs)
    • Data managed by LabKey is pulled from AWS Glue and Spotfire via their built-in Postgres JDBC drivers.
  • New "Auto" and "Local" Data Exchange options for easier and more secure configurations of RServe. (docs)
  • Updated interface for connecting from external analytics tools. (docs) Also available in 22.11.4.
  • The Ruminex R package is no longer supported or used in Luminex transform scripts. (docs)

Panorama

  • New Panorama MAM report for early-stage post-translational modification (PTM) with improved formatting and layout. (docs)
  • New QC plots let you track the trailing mean and %CV of any QC folder metric over a specified number of runs. (docs) Also available in 22.11.6.

Compliance

  • PHI access control and compliance logging have been improved to provide better consistency and flexibility. For example, LabKey SQL queries using PIVOT, OUTER JOINs, and expression columns are now permitted with compliance logging enabled. (docs)

Message Boards

  • Enable moderator review for all new threads started by an Author or Message Board Contributor. (docs)

Administration

  • The path to the full-text search index can include substitution parameters such as the version or database name. Also available in 22.11.1. (docs)
  • Administrators are now proactively warned about "unknown modules," modules that were previous installed but no longer exist in the current deployment. Administrators are encouraged to delete these modules and their schemas. (details)
    • As an example, the contents of a module named "internal" were moved to other modules. This module will now be reported as "unknown" and can safely be deleted from the module details page. (docs)
  • Administrators are also notified if they attempt to upgrade a server having one or more modules whose existing schema no longer supports upgrading to the new version. In this case, the entire upgrade will be prohibited to prevent schema corruption. Administrators who upgrade regularly and delete "unknown modules" & their schemas should never encounter this situation. (docs)
  • In the event of a connection to a data source failing at startup, the administrator will have the option to retry the failed connection later without always having to restart LabKey Server. (docs)

Distribution Changes and Upgrade Notes

  • Luminex assay integration is now supported on Premium Editions using SQL Server. (docs)
  • Support for PostgreSQL 10.x has been removed. (docs)
  • Support for the jTDS driver has be removed. All Microsoft SQL Server data sources must be configured to use the Microsoft SQL Server JDBC driver (included in all premium edition distributions). (docs | docs)
  • RStudio is changing its name to Posit. The LabKey interface will be updated to reflect this rebranding and any necessary changes in a future release. (learn more)
Note: All users are encouraged to upgrade regularly to the current release in order to take advantage of all improvements and fixes. Our hotfix support policy is to only support fixes to the current major release and one previous release. Contact your Account Manager if you have questions. (docs)

Potential Backwards Compatibility Issues

  • Developers extending AbstractAssayProvider should review a possible issue below.
  • Changes to the exp.materials and inventory tables will add additional reserved fields and ensure future development in important areas.
    • Users who have coincidentally using field names that become "reserved" for system purposes may need to make changes prior to upgrading to version 23.3 or 23.4. These are not commonly used names, so issues are unlikely to impact many users.
    • For example, when we add the new column inventory.item.initialVolume, if you have been using a custom field by this name, any of its data will be deleted.
    • In 23.3, we added the exp.material.materialExpDate field to support expiration dates for all samples. If you happen to have a field by that name, you should rename it prior to upgrading to avoid loss of data in that field.
    • In Biologics version 23.3, the built in "expirationDate" field on Raw Materials and Batches will be renamed "MaterialExpDate". This change will be transparent to users as the new fields will still be labelled "Expiration Date".
  • Stricter HTML parsing has been introduced in 23.3.3 when validating HTML-based Wiki pages. Bad HTML will show the message: "An exception occurred while generating the HTML. Please correct this content."
    • For example, the new parser requires quotes around element attributes and now rejects previously tolerated HTML such as:
      <div style=display:block; margin-top:10px></div>
    • Quotes are now required, as shown here:
      <div style="display:block; margin-top:10px"></div>
    • The HTML can be fixed manually, or in many cases, can be automatically corrected by switching to the Visual tab in the Wiki editor and saving.

Documentation

  • Best Practices for System Security
  • Improved PIVOT query performance, documentation, and examples. (docs)
  • Documentation and examples of using lineage SQL to query the ancestors or descendants of objects. (docs)
  • Videos can be embedded in wiki syntax pages. (docs)

Premium Resources


Sample Manager

The Sample Manager Release Notes list features by monthly version.
  • Samples can have expiration dates, making it possible to track expiring inventories. (docs)
    • If your samples already have expiration dates, contact your Account Manager for help migrating to the new fields.
  • Administrators can see the which version of Sample Manager they are running. (docs)
  • ELN Improvements:
    • The panel of details and table of contents for the ELN is now collapsible. (docs)
    • Easily copy links to attachments. (docs)
  • Clearly capture why any data is deleted with user comments upon deletion. (docs | docs)
  • Data update (or merge) via file has moved to the "Edit" menu of a grid. Importing from file on the "Add" menu is only for adding new data rows. (docs | docs | docs)
  • Use grid customization after finding samples by ID or barcode, making it easier to use samples of interest. (docs)
  • Electronic Lab Notebooks now include a full review and signing event history in the exported PDF, with a consistent footer and entries beginning on a new page. (docs)
  • Projects in the Professional Edition of Sample Manager are more usable and flexible.
    • Data structures like Sample Types, Source Types, Assay Designs, and Storage Systems must always be created in the top level home project. (docs)
  • Lookup views allow you to customize what users will see when selecting a value for a lookup field. (Available when Sample Manager is used with a Premium Edition of LabKey Server.) (docs)
  • Storage management has been generalized to clearly support non-freezer types of sample storage. (docs)
  • Samples will be added to storage in the order they appear in the selection grid. (docs)
  • Curate multiple BarTender label templates, so that users can easily select the appropriate format when printing. (docs)
  • Electronic Lab Notebook enhancements:
    • To submit a notebook for review, or to approve a notebook, the user must provide an email and password during the first signing event to verify their identity. (docs | docs)
    • Set the font-size and other editing updates. (docs)
    • Sort Notebooks by "Last Modified". (docs)
    • Find all ELNs created from a given template. (docs)
  • An updated main menu making it easier to access resources across projects. (docs)
  • Easily update Assay Run-level fields in bulk instead of one run at a time. (docs)
  • The Professional Edition supports multiple Sample Manager Projects. (docs)
  • Improved interface for assay design and data import. (docs | docs)
  • From assay results, select sample ID to examine derivatives of those samples in Sample Finder. (docs)

Biologics

The Biologics release notes list features by monthly version.
  • Samples can now have expiration dates, making it possible to track expiring inventories. (docs)
  • ELN Improvements:
    • The panel of details and table of contents for the ELN is now collapsible. (docs)
    • Easily copy links to attachments. (docs)
  • Administrators may delete projects from within the application. (docs)
  • User profile details will be shown when a username is clicked from grids. (docs)
  • Administrators can see the which version of Biologics LIMS they are running. (docs)
  • Clearly capture why any data is deleted with user comments upon deletion. (docs | docs | docs)
  • Data update (or merge) via file has moved to the "Edit" menu of a grid. Importing from file on the "Add" menu is only for adding new data rows. (docs)
  • Use grid customization after finding samples by ID or barcode, making it easier to use samples of interest. (docs)
  • Electronic Lab Notebooks now include a full review and signing event history in the exported PDF, with a consistent footer and entries beginning on the second page of the PDF. (docs)
  • Projects in Biologics are more usable and flexible.
    • Data structures like Sample Types, Registry Source Types, Assay Designs, and Storage Systems must always be created in the top level home project. (docs)
  • Protein Sequences can be reclassified and reannotated in cases where the original classification was incorrect or the system has evolved. (docs)
  • Lookup views allow you to customize what users will see when selecting a value for a lookup field. (docs)
    • Users of the Enterprise Edition may want to use this feature to enhance details shown to users in the "Raw Materials Used" dropdown for creating media batches. (docs)
  • Storage management has been generalized to clearly support non-freezer types of sample storage. (docs)
  • Samples will be added to storage in the order they appear in the selection grid. (docs)
  • Curate multiple BarTender label templates, so that users can easily select the appropriate format when printing. (docs)
  • Electronic Lab Notebook enhancements:
    • To submit a notebook for review, or to approve a notebook, the user must provide an email and password during the first signing event to verify their identity. (docs | docs)
    • Set the font-size and other editing updates. (docs)
    • Sort Notebooks by "Last Modified". (docs)
    • References to assay batches can be included in ELNs. (docs)
    • Find all ELNs created from a given template. (docs)
  • An updated main menu making it easier to access resources across Projects. (docs)
  • Heatmap and card views of the bioregistry, sample types, and assays have been removed.
  • The term "Registry Source Types" is now used for categories of entity in the Bioregistry. (docs)
  • Buttons for creating and managing entities, samples, and assays are more consistently named.
  • Improved interface for assay design and data import. (docs | docs)
  • From assay results, select sample ID to examine derivatives of those samples in Sample Finder. (docs)

Client APIs and Development Notes

  • API and session keys are now generated without an "apikey|" or "session|" prefix. Previously generated keys that include these prefixes will continue to be accepted until they expire or are revoked. (docs | docs)
  • Developers extending AbstractAssayProvider who are also overriding the deleteProtocol method should be aware that the method signature has been changed. Overriding code needs to be updated to accept a nullable String as the third parameter. (details)

The symbol indicates a feature available in a Premium Edition of LabKey Server, Sample Manager, or Biologics LIMS.

Previous Release Notes: Version 22.11