Release Notes 21.7 (July 2021)

Documentation

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 and Review - Administrators can manually lock a project, making it inaccessible to non-administrators. Configure an expiration workflow to enforce review project security. (doc)
  • Expanded Support for PHI Fields - Assign PHI levels to fields in SampleTypes and DataClasses. (docs)

Study

  • Study/Sample Integration - Link samples to studies and tag participant / timepoint fields in Sample Types. (docs) | (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)

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)

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 - Additional report options have been added. Also the pathway for accessing this report has been changed. (docs)
  • Pressure Traces - Define custom metrics based on pressure traces in a chromatogram. (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


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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