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2022-12-08
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What's New in 22.11


We're delighted to announce the release of LabKey Server version 22.11.

Highlights of Version 22.11

LabKey Server

  • Analyze LabKey data using JMP statistical analysis software via an ODBC connection. (docs)
  • Query dependency reports now include any Lookups to and from the given query, list, or table. (docs)
  • Choose whether file and attachment fields will download or be viewed in the browser when links are clicked. (docs)
  • Use Ancestors in sample naming patterns, making it possible to create common name stems based on the history of a sample. (docs)
  • New role available: Editor without Delete. Users with this role can read, insert, and update information but cannot delete it. (docs)

Sample Manager

  • Sample Finder: Reporting: Create sample reports based on lineage, sources, and assay data results. (docs | video)
  • Easily capture Amendments to signed Notebooks when a discrepancy is detected to ensure the highest quality entries and data capture, tracking the events for integrity. (docs)
  • Aliquots can have fields that are not inherited from the parent sample. Administrators can control which parent sample fields are inherited and which can be set independently for the sample and aliquot. (docs)

Biologics

  • Searchable, filterable, standardized user-defined fields on workflow enable teams to create structured requests for work, define important billing codes for projects and eliminate the need for untracked email communication. (docs)
  • Each event in the history of a sample can now be viewed with ease on the Sample Timeline. (docs)
  • Manage user permissions and review assignments by group. (docs)

Premium Resources

Release Notes


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




Release Notes: 22.11 (November 2022)


Here are the full release notes for version 22.11 (November 2022).

LabKey Server

Query

  • Query dependency report includes any lookups to and from the given query, list, or table. (docs)
  • Various query performance improvements based on findings from analysis with DataDog.

Lists

  • Improvements in the behavior of cross-folder lists to support sharing across containers.

Authentication

  • Control the page size used for LDAP Synchronization. (docs) Also available in version 22.7.2.

Samples and Data Classes

  • Use Sample and Data Class ancestors in naming patterns, making it possible to create common name stems based on the history of a sample. (docs)
  • Data Class and Sample Type grids can now be filtered by "Current folder, project, and shared project". (docs)

Studies

  • Editors can access a read-only view of dataset properties and review the import history via a Details link above dataset grids. (docs)

Panorama

  • Protein groups (mapping a peptide to multiple possible proteins) will be represented in Panorama folders when a Skyline document. (docs) Also available in version 22.7.2.
  • Performance and plotting improvements for QC folders with many samples.
  • Support for z+1 and z+2 ions.
  • Amino acid indices within protein sequences are based at 1 (instead of 0) for consistency with Skyline. (docs) Also available in version 22.7.2.

Integrations

Administration

  • New role available: Editor without Delete. Users with this role can read, insert, and update information but cannot delete it. (docs)
  • URLs no longer end with question marks when there are no parameters. See below for steps developers may need to take if they were relying on this question mark in building custom URLs.
  • Missing value indicator tables can be accessed via the schema browser. (docs)
  • Choose whether file and attachment fields will download or be viewed in the browser when links are clicked. (docs)
  • During startup, administrators will be proactively warned of mismatches between schema XML and database schemas. Mismatches may indicate scripts that have not been run or other issues to be addressed. These warnings will not halt startup, but should be reviewed and any inconsistency corrected. (more detail)
  • Administrators can download a report of usage statistics and exceptions. (docs)

Premium Resources

Distribution Changes and Upgrade Notes

  • LabKey has been updated to use Spring Framework 5.3.22. Developers can read about potential backwards compatibility issues below.
  • The Microsoft SQL Server JDBC driver is now strongly recommended. Support for the jTDS driver will be removed in 23.3.0. (docs)

Database Compatibility Notes

  • PostgreSQL 10.x has reached end of life and is no longer maintained by the PostgreSQL team. PostgreSQL 10.x installations should be upgraded to a current PostgreSQL version as soon as possible. Support for PostgreSQL 10.x will be removed in LabKey Server 22.12. (docs)
  • LabKey Server now supports recently released PostgreSQL 15.x. (docs)
  • LabKey Server now supports recently released Microsoft SQL Server 2022. (docs)

Developer Resources


Sample Manager

The Sample Manager Release Notes list features by monthly version.

  • Add samples to multiple freezer storage locations in a single step. (docs)
  • Improvements in the Storage Dashboard to show all samples in storage and recent batches added by date. (docs)
  • View all assay results for samples in a tabbed grid displaying multiple sample types. (docs)
  • ELN improvements to make editing and printing easier with a table of contents highlighting all notebook entries and fixed width entry layout. (docs)
  • New role available: Workflow Editor, granting the ability to create and edit workflow jobs and picklists. (docs)
  • Notebook review can be assigned to a user group, supporting team workload balancing. (docs)
  • Use sample ancestors in naming patterns, making it possible to create common name stems based on the history of a sample. (docs)
  • Additional entry points to Sample Finder. Select a source or parent and open all related samples in the Sample Finder. (docs | docs)
  • New role available: Editor without Delete. Users with this role can read, insert, and update information but cannot delete it. (docs)
  • Group management allowing permissions to be managed at the group level instead of always individually. (docs | docs)
  • With the Professional Edition, use assay results as a filter in the sample finder helping you find samples based on characteristics like cell viability. (docs)
  • Assay run properties can be edited in bulk. (docs)
  • Searchable, filterable, standardized user-defined fields on workflow enable teams to create structured requests for work, define important billing codes for projects and eliminate the need for untracked email communication. (docs)
  • Storage grids and sample search results now show multiple tabs for different sample types. With this improvement, you can better understand and work with samples from anywhere in the application. (docs | docs | docs)
  • The leftmost column of sample data, typically the Sample ID, is always shown as you examine wide datasets, making it easy to remember what sample's data you were looking at. (docs)
  • By prohibiting sample deletion when they are referenced in an ELN, Sample Manager helps you further protect the integrity of your data. (docs)
  • Easily capture amendments to signed Notebooks when a discrepancy is detected to ensure the highest quality entries and data capture, tracking the events for integrity. (docs)
  • When exploring a Sample of interest, you can easily find and review any associated notebooks. (docs)
  • Aliquots can have fields that are not inherited from the parent sample. Administrators can control which parent sample fields are inherited and which can be set independently for the sample and aliquot. (docs)
  • Drag within editable grids to quickly populate fields with matching strings or number sequences. (docs)
  • When exporting a multi-tabbed grid to Excel, see sample counts and which view will be used for each tab. (docs)

Biologics

The Biologics release notes list features by monthly version.

  • Add samples to multiple freezer storage locations in a single step. (docs)
  • Improvements in the Storage Dashboard to show all samples in storage and recent batches added by date.
  • View all assay results for samples in a tabbed grid displaying multiple sample types.
  • ELN improvements to make editing and printing easier with a table of contents highlighting all notebook entries and fixed width entry layout.
  • Notebook review can be assigned to a user group, supporting team workload balancing.
  • New role available: Workflow Editor, granting the ability to edit workflow jobs.
  • Documentation added describing how to add an AnnotationType, such as for recording Protease Cleavage Site.
  • Use sample ancestors in naming patterns, making it possible to create common name stems based on the history of a sample. (docs)
  • Additional entry points to Sample Finder. Select a registry entity or parent and open all related samples in the Sample Finder.
  • Consistency improvements in the audit log and storage experience.
  • New role available: Editor without Delete. Users with this role can read, insert, and update information but cannot delete it. (docs)
  • Use assay results as a filter in the sample finder helping you find samples based on characteristics like cell viability. (docs)
  • Group management allowing permissions to be managed at the group level instead of always individually.
  • Bulk editing of assay run properties.
  • Data grids may be partially populated when submitting assay data; previously if the first row was null, other values would be ignored.
  • Electronic Lab Notebooks from any project can be submitted from the home project.
  • Tables in Notebooks will be fully rendered in PDF printouts.
  • Improved interface for creating and managing Projects in Biologics.
  • Searchable, filterable, standardized user-defined fields on workflow enable teams to create structured requests for work, define important billing codes for projects and eliminate the need for untracked email communication. (docs)
  • Storage grids and sample search results now show multiple tabs for different sample types. With this improvement, you can better understand and work with samples from anywhere in the application. (docs | docs | docs)
  • The leftmost column of data grids, typically the Entity ID, is always shown as you examine wide datasets, making it easy to remember which row you were looking at. (docs)
  • Send sample information directly to BarTender for easier printing and managing of sample labels. (docs)
  • By prohibiting deletion of entities, media, samples, assay runs, etc. when they are referenced in an ELN, LabKey Biologics helps you further protect the integrity of your data. (docs | docs)
  • Easily capture Amendments to signed Notebooks when a discrepancy is detected to ensure the highest quality entries and data capture, tracking the events for integrity. (docs)
  • When exploring a Registry Entity, Sample, or Media of interest, you can easily find and review any associated Notebooks from a panel on the Overview tab. (docs | docs | docs)
  • Before you had to dig through the audit tables to piece together the event history of a sample but now each sample's history can be easily viewed in an understandable way on the Timeline. (docs)
  • Aliquoting of media batches and raw materials is now supported, allowing you to determine their final storage quantities and register them as such. (docs | docs)
  • Aliquots can have fields that are not inherited from the parent sample. Administrators can control which parent sample fields are inherited and which can be set independently for the sample and aliquot. (docs)
  • Drag within editable grids to quickly populate fields with matching strings or incrementing integers. (docs)
  • When exporting a multi-tabbed grid to Excel, see the count and which view will be used for each tab. (docs)
  • Use the Sample Finder to find based on any ancestor entity from the Bioregistry. The lineage backbone tracks existing entity relationships relevant to samples. (docs)
  • Search for data across projects in Biologics. (docs)

Client APIs and Development Notes

  • Version 4.0.0 of the Java remote API and version 2.2.0 of the LabKey JDBC driver have been released. (details)
  • New Storage API available in Java, JavaScript, Python, and R for programmatically creating and updating freezers. (docs)
  • LabKey has been updated to use Spring Framework 5.3.22. This version of Spring now treats HTTP requests with overlapping GET and POST parameters as if there are multiple values. For integer parameters, this fails to parse as it's treated as a delimited concatenation of the duplicate values. For string parameters, you get the concatenated version. Developers with code passing such duplicate parameters will need to delete either the GET or POST version of the parameter from the request.
  • URLs no longer end with question marks when there are no parameters. If developers have code using simple string concatenation of parameters (i.e. expecting this question mark) they may need to update their code to use the more reliable addParameter() method. Through the 22.11 release, it will be possible to 'restore' the trailing question mark temporarily while developers update their code.
  • Module developers can include query metadata to apply to all sample types in a container by supplying it in a queries/samples/AllSampleTypes.query.xml file. (docs)
  • The Gradle build no longer supports a manually maintained jars.txt as a way to document library dependencies. To ensure that the credits page in the Admin Console is accurate for your module, use the Gradle dependency declaration that automatically includes it in the listing. (docs)
  • New Premium Resource for Developers:

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

Previous Release Notes: Version 22.7




Upcoming Features


Upcoming Features

Releases we are currently working on:

Recent Documentation Updates