Important upgrade note: LabKey has released updated versions (21.11.3 and 21.7.11) to address vulnerabilities discovered in Log4J, a popular Java logging library that LabKey Server versions 20.11 and later use. To protect your server, you should immediately upgrade to the latest patched release and/or applying the -Dlog4j2.formatMsgNoLookups=true system property. Premium edition users will find the new release on their support portal now; community users can download the new version here.

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LabKey Server

File Watchers

  • Sample Types - Import and update Sample data using a file watcher. (docs)
  • Assay Designs - Import data to a Standard assay design, including result data, run and batch properties, and plate metadata. Multi-sheet Excel files are supported, as well as TSV and CSV file formats. (docs)
  • Improved User Experience - Manually entered properties have been replaced with radio button selectors, improved tooltips.

Ontology

  • Ontology Field Filters - Filter field values to a specific concept, set of concepts, or area of the concept hierarchy. (docs)
  • Ontology Concept Picker - Improve data entry by guiding users to a specific part of the concept hierarchy. (docs)

Security and Compliance

  • Improved Browser Security - Page content will be blurred when a user session has timed out or expired. (docs)
  • Project Locking - Administrators can manually lock a project, making it inaccessible to non-administrators.(doc)
  • Project Review Workflow - Administrators can enforce regular review of project access permissions. (doc)
  • Expanded Support for PHI Fields - Assign PHI levels to fields in SampleTypes and DataClasses. (docs)
  • The project-GetContainersAction API has been updated so that it verifies that the requesting user has permissions to the given container. Available in release 21.7.5.

Study

  • Study/Sample Integration - Link samples to studies and tag participant / timepoint fields in Sample Types. (docs) | (docs)
  • Options for exporting study datasets have been renamed for clarity. (docs)

General Server Enhancements

  • Product Navigation Menu - The product navigation menu has been streamlined to focus on navigating between LabKey Server, Biologics, and Sample Manager. The menu can be hidden from non-administrators. (docs)
  • Improved Field Inference - Improved behavior when inferring fields that match system/reserved fields. When inferring fields as part of table design, any "reserved" fields present will not be shown in the preview, simplifying the creation process. (docs)
  • File and Attachment Fields - Sample Types and Data Classes can include fields to reference files and attachments. (docs)
  • Merge Option - Lists now support merging of data on bulk import. New rows are inserted, already existing rows are updated in the List. (docs)

Samples

  • Barcode Field - A new field type generates unique id values for Samples. Useful for generating and printing barcodes for samples. (docs)
  • Study/Sample Integration - Link samples to studies and tag participant / timepoint fields in Sample Types. (docs) | (docs)
  • When using Sample Manager within LabKey Server, you can link Samples to Studies from within the application. (docs)

Assays

  • Terminology Change - The phrase 'Copy to Study' has been changed to 'Link to Study', to better reflect the action of connecting assay data to a study. The behavior of this action has not changed. (docs)
  • Specialty Assays - Specialty Assays have been removed from the Community Edition. Users will need to subscribe to a Premium Edition to use ELISA, ELISpot, NAb, Luminex, Flow, and other specialized assays. The Community Edition will continue to support the customizable Standard Assay. (docs)
  • Protein Expression Assay - Due to lack of use, the Protein Expression Matrix assay has been removed. Please contact us if you need assistance.

Flow Cytometry

  • Improved Troubleshooting - See the values used to join Samples and FCSFiles in the Sample Overview page. This will help troubleshoot any linking issues. (docs)
  • Improved display of gating plots when exponential y-axis is used in FlowJo. Note that if plots were created previously, they must be recomputed (the run must be re-imported) in order to display correctly.

LabKey SQL

  • concat_ws Function - The PostgreSQL function concat_ws has been added to LabKey SQL. Supported on PostgreSQL only. (docs)

Panorama (Targeted Mass Spectrometry)

  • Reproducibility Report - Now integrated into chromatogram libraries, assess inter- and intra-day variation based on raw, normalized, or calibrated values, along with calibration curve and figures of merit data. (docs)
  • Improved navigation and summarization for calibration curve and figure of merit reporting. (docs) | (docs)
  • Pressure Traces - In QC folders, use pressure traces as sources for metrics to monitor for system suitability and identify column and other problems. (docs)

Distribution Changes

  • Support for PostgreSQL 9.5.x has been removed. Before upgrading, PostgreSQL must be upgraded to a supported version.
  • Support for Apache Tomcat 8.5.x has been deprecated and will be removed in 21.8.0. Please upgrade to Tomcat 9.0.x ASAP. Learn more here: Supported Technologies
  • The build has been updated to use Gradle 7, which now allows building LabKey from source with JDK 16. Running under JDK 16 still requires use of a couple special JVM flags. Learn more here: Supported Technologies

Premium Integrations

  • LabKey Server version 21.7 is compatible with RStudio Pro version 1.4.11.06.
  • RStudio authentication using LDAP attributes. (docs)
  • Improved setup of SAML authentication; the configuration parameter is provided for you. (docs)

Premium Resources

Documentation

Upcoming Changes

  • Beginning with 22.1.0 (January 2022), our upgrade support policy will change to reflect our recently adopted annual schema versioning approach. For details, see our LabKey Releases and Upgrade Support Policy page.

Sample Manager

  • Security Changes - Permissions have been updated to align Sample Manager and LabKey Server Premium Edition administrator roles. (docs)
  • Study/Sample Integration - Link samples to studies and assign participant / timepoint fields in Sample Types. (docs) | (docs)
  • Sample Actions - Actions, such as adding samples to a job, are available in more places throughout the application. (docs) | (docs)
  • Aliquots - Create aliquots of samples singly or in bulk. (docs)
  • Picklists - Create and manage picklists of samples to simplify operations on groups of samples. (docs)
  • Move Storage Units - Track movement of storage units within a freezer, or to another freezer. (docs)
  • Clone Freezer - Create a new freezer definition by copying an existing. (docs)
  • File and Attachment fields - Samples and Sources can include images and other file attachments. (docs)
  • Barcode/UniqueID Fields - A new field type, "UniqueID", generates system-wide unique values that can be encoded as Barcodes when samples are added to a Sample Type or when the barcode field is added to an existing sample type. (docs)
  • Improved Field Inference - When inferring fields to create Sources, Sample Types, and Assay Designs, any "reserved" fields present will not be shown in the preview, simplifying the creation process. (docs)
  • Improved Data Import - When importing data, any unrecognized fields will be ignored and a banner will be shown. (docs)
  • Workflow - On the main menu, "My Assigned Work" has been renamed "My Queue". (docs)

Biologics

  • Electronic Lab Notebooks have been added to LabKey Biologics. Link directly to data in the registry and collaboratively author/review notebooks. (docs)
  • Experiment Menu - The "Experiment" menu has been removed from the UI. Use workflow jobs instead.
  • Aliquots - Create and manage aliquots of samples. (docs)
  • Parentage/Lineage - Parent details are included on the Overview tab for samples. (docs)
  • Hide Sequence Fields - Nucleotide and Protein Sequence values can be hidden from users who otherwise have access to read data in the system. (docs)
  • PHI Fields - Marking fields with PHI levels is now supported in Sample Types and Data Classes. (docs)
  • Files and Attachment Fields - Fields to reference files and attachments are now supported. Learn more in the Sample Manager documentation here.
  • Barcode/UniqueID Fields - A new field type, "UniqueID", generates values when samples are added to a Sample Type or when the barcode field is added to an existing sample type. (docs)
  • Create Samples - The options to create samples is available from more places in the application. (docs)
  • Pool and Derive Samples - Create pooled samples and/or derive new samples from one or more parents. (docs)
  • Workflow - Workflow functionality has been added, with job templates and a personalized queues of tasks. (docs)
  • Assays - Specialty Assays can now be defined and used, in addition to Standard Assays. (docs)
  • Raw Materials - Creation of Raw Materials in the application uses a consistent interface with other sample type creation. (docs)
  • Improved Data Import - When importing data, any unrecognized fields will be ignored; in some cases a banner will be shown. (docs)

Client APIs and Development Notes

Python API

  • Updated Python Script Export - When exporting a data grid as a Python script, the generated script now targets the Python client API version 2.0.0.
  • Python API version 2.1.0 has been released, including:
    • Support for impersonate_user and stop_impersonating.
    • ServerContext.make_request supports json kwarg and the payload is now optional.
    • Support for Ontology based column filters for determining "in_subtree".
    • Learn more: (docs)

The symbol indicates a feature available in a Premium Edition of LabKey Server.

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