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2021-06-20
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   Release Notes 21.3 (March 2021)
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What's New in 21.3


We're delighted to announce the release of LabKey Server version 21.3.

Highlights of Version 21.3

LabKey Server

  • Ontologies Integration - Control vocabularies and semantics using ontology integration. (docs)
    • Browse the concepts in your ontologies and add concept annotations to data. (docs)
    • Use an Ontology Lookup to map entered information to preferred vocabularies. (docs)
    • Additional SQL functions and annotations. (docs)
  • Option to merge changes when importing dataset data. (Also available in 20.11.3) - (docs)
  • Dataset audit logs provide a detailed view of what data has changed - (docs)
  • New Assay Type Selection Interface - Simplified method for selecting a Standard assay (recommended and most common), vs. one of the Specialty assays. (docs)

Sample Manager

  • Freezer management has been added to Sample Manager. Key features include:
    • Match digital storage to physical storage in your lab with configurable freezers. (docs)
    • Easily store and locate samples from anywhere in the application. (docs)
    • Track locations and chain of custody of samples. (docs)
    • Check in and out, record amount used, and increment freeze/thaw counts. (docs)
    • Easily migrate from another system by importing sample data simultaneously with location data. (docs)
  • Improved sample import includes removal of previous size limits on data import, background sample imports, and in-app notifications when background imports complete. (docs | docs)

Biologics

  • A new home page highlights samples and assay data.
  • A new navigation menu has been introduced and is available throughout the application. (docs)
  • Improved user experience for creation and management of Sample Types and Assay Designs. (docs | docs)
  • In-app Notifications are provided when background imports are completed. (docs)

Premium Resources Highlights

Release Notes


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Release Notes 21.3 (March 2021)


LabKey Sample Manager

  • Freezer management has been added to Sample Manager. Key features let you:
    • Match digital storage to physical storage in your lab. (docs)
    • Easily store and locate samples. (docs)
    • Track location history and chain of custody. (docs)
    • Check samples in and out of storage, record amount used, and increment freeze/thaw counts. (docs)
    • Easily migrate from another system by importing sample data simultaneously with location data. (docs)
  • Improved sample import includes removal of previous size limits on data import, background sample imports, and in-app notifications when background imports complete. (docs | docs)
  • Derive children samples from one or more parent samples. (docs)
  • Pool multiple samples into a set of new samples. (docs)
  • Trials of Sample Manager are available preloaded with example data. Contact us to request a free trial.

LabKey Biologics

  • User experience improvements include:
    • A new home page, which highlights samples and recently added assay data. (docs)
    • A new navigation menu, conveniently available throughout the application. (docs)
  • Sample Types and Assay Designs can now be created and managed with a Biologics-based user interface. (docs | docs)
  • In-app Notifications are provided when background imports are completed. (docs)

LabKey Server

Ontology Integration

  • Ontologies Integration - Control vocabularies and semantics using ontology integration. (docs)
    • Browse the concepts in your ontologies and add concept annotations to data. (docs)
    • Use an Ontology Lookup to map entered information to preferred vocabularies. (docs)
    • Additional SQL functions and annotations. (docs)

Administration

  • New menu for switching between Sample Manager, Biologics, and LabKey Server. (docs)
  • LDAP Authentication can be configured to use any user property, not just uid or email. (docs)
  • Smart Updates - When updating datasets and lists, LabKey performs targeted changes to existing data, deleting, inserting, and updating the minimal set of records. (docs | docs)
  • Field editor improvements include:
    • A summary view of current field properties. (docs)
    • Export of subsets of fields. (docs)
    • Deletion of multiple fields. (docs)
    • Styling and layout improvements. (docs)
  • Synchronous Startup option ensures that all modules are upgraded, started, and initialized before any requests can be processed. (docs)
  • Option to support login by a name not matching an email address. (docs)
  • Data Classes can now be added to an exported folder archive. (docs)
  • Query Browser Changes - Within a schema folder, the subfolders named 'user-defined queries' and 'built-in queries' have been removed. All queries are now listed in alphabetical order. Different icons are now used to signal the difference between user-defined and built-in queries. (docs)
  • Message forums that use moderator approval prior to making a posting public now respect the email subscriptions for the folder, instead of always emailing all server admins.

Study

  • Option to merge changes when importing dataset data. Also available in 20.11.3. (docs)
  • Dataset audit logs provide a detailed view of what data has changed. (docs)
  • Specimen functionality has been removed from the study module. If you are using a Premium Edition and need to continue using this functionality, contact your Account Manager to obtain the specimen module. Do not upgrade a Community Edition if you want to continue using specimen as part of study.
  • Dataset-Level Security now correctly supports non-Editor roles. For example, those assigned the Author role are now able to insert into datasets, as intended. Study administrators should review their study security settings. (docs)

Assays

  • Terminology Change - The General assay type has been renamed as the "Standard" assay type. Instrument-specific assays have been grouped together as "Specialty" assays. (docs)
  • Improved Assay Type Selection - When designing new assays, the Standard assay type is presented first (the recommended and most common path), whereas the Specialty assays have been grouped together on a separate tab. (docs)
  • Improved Interface for Export/Import of Assay Designs - The user interface for importing a XAR file (an assay archive file) has been relocated to a separate tab. (docs)
  • Automatic Copy-to-Study Can Target "Current Folder" - Assay designs defined at the site or project level can be configured to copy assay data to the local target study upon import, rather than a fixed target study. (docs)
  • ELISA Visualization Improvements - Customize the way run results are visualized with a new plot editor. Also available in 20.7.6 (docs)
  • ELISA Assay enhancements include support for: 4-plex data format, additional curve fit options, high-throughput 384 well multiplates, import of plate metadata, and additional statistics calculations. (docs)
  • Removal of integration with FCS Express - The FCSExpress module has been removed from the core distribution and is no longer supported. Support for Flow Cytometry is provided in the LabKey Flow module. If you would like additional information, please contact us.

Targeted Mass Spectrometry (Panorama)

  • Link from Experiment data to QC folder - Panorama automatically links data in Experiment folders to the QC folder(s) that contain data from the same instrument, making it quick to see how the instrument was performing at the time of acquisition. (docs)
  • Instrument summary on replicate page - Easily see which instruments acquired the data in a Skyline document. (docs)
  • Always include guide set data in QC plots - When zooming in to view QC data for a specific date range, juxtapose the guide set data that's being used to identify outliers. (docs)
  • MxN reproducibility reports - New reporting summarizes intra- and inter-day variability for peptides within a protein to assess its reproducibility. (docs)
  • PDF and PNG plot exports - Many Panorama reports are now rendered as vector-based plots in the web browser for better clarity and offer PDF and PNG export formats. (docs | docs)
  • Reduced memory usage during import - Importing large Skyline documents uses 80% or less memory, offering much better performance and scaling. (docs)
  • Enhanced chromatogram library exports - Chromatogram libraries (.clib files) now include additional optimization and ion mobility information. (docs)

Development

  • Run R Reports via ETL - A new RunReportTask option allows ETLs to generate R Reports. (docs)
  • ETLs now support triggers on archive imports. (docs)
  • Broader trigger script availability - Trigger scripts can be run in more data import scenarios, including TSV-based imports of study datasets, and folder archive imports of most table types. (docs)
  • ETL Source Filters - Specify a data filter in the ETL definition. (docs)
  • Transformation Script Syntax: "httpSessionId" has been deprecated in favor of the new ${apiKey} parameter for authentication. (docs)

LabKey SQL

  • Ontology Functions added to LabKey SQL: Include concept, subclass, and ontology path relationships in your SQL queries. (docs)
  • Support for PostgreSQL JSON and JSONB operators and functions. (docs)
  • SIMILAR_TO support added to LabKey SQL. Supported for PostgreSQL only. (docs)
  • Additional documentation about SQL annotations is now available. (docs)
  • Queries that produce duplicate column names are now allowed via automatic alias creation. (docs)

Issues

  • The Issues API now supports closing an issue and assigning to 'guest'. (docs)

Premium Resources

Documentation


Client APIs

JavaScript API

  • The @labkey/api JavaScript package is now the only implementation available on the client. An experimental flag that had enabled use of the prior implementation has been removed. (docs)

R API

  • Rlabkey version 2.6.0 has been released. New additions include the pipeline API for getting status information and starting pipeline jobs. Available on CRAN. (docs)

Python API

  • Updated examples and documentation for use with the new version. (docs)

Distribution Changes

  • Changes to How Redshift JAR files are Distributed - The Redshift JDBC driver is now distributed inside the Redshift module, making it unnecessary to manually copy it to the CATALINA_HOME/lib directory during installation and upgrade. Before you upgrade to 21.3, you must delete the previous Redshift driver and its dependencies from CATALINA_HOME/lib to avoid conflicts. (docs)
  • Support for running under the upcoming JDK 16 release is available with use of a special flag. You cannot yet build LabKey from source with JDK 16. Learn more here: Supported Technologies
  • Microsoft SQL Server (and all other non-PostgreSQL database connections) are supported only in Premium Edition distributions. The BigIron module, which provides support for Microsoft SQL Server, Oracle, MySQL, and SAS/SHARE, has moved to Premium Edition distributions.
  • Specimen Repository functionality has been removed from all standard distributions (Community, Starter, Professional, and Enterprise). We will continue to provide and support this functionality only for Premium Edition clients who currently use it. Going forward, and for all other groups, we strongly recommend the use of Sample Types and Sample Manager.
  • The FCSExpress module has been removed from all distributions and is no longer supported. Support for flow cytometry is provided in the LabKey Flow module. If you would like additional information, please contact us.
  • The option to evaluate LabKey using a prebuilt virtual machine trial has been removed. If you are interested in evaluating LabKey, please contact us to arrange a custom demo or hosted trial of any product. You can also manually install the Community Edition for an on-premise evaluation.

Upgrade

  • Java 13 No Longer Supported - LabKey has removed support for JDK 13. Before upgrading LabKey Server, Java must be upgraded to a supported version.
  • Upgrade all LabKey Dependencies - We strongly recommend that, as part of your LabKey Server upgrade, you also upgrade all major LabKey dependencies to the latest point releases: AdoptOpenJDK 15 64-bit (x64) with HotSpot JVM, Tomcat 9.0.x, and PostgreSQL 13.x.
  • Upgrade Instructions - Follow the steps in this topic to upgrade to the latest release of LabKey Server: Upgrade LabKey

Upcoming Distribution Changes

  • Beginning with version 21.7 (July 2021), support for PostgreSQL 9.5.x will be removed. Before upgrading, PostgreSQL must be upgraded to a supported version.
  • Due to low adoption, beginning with version 21.7 (July 2021), Specialty Assays will be removed from the Community Edition. In future releases, users will need to subscribe to a Premium Edition to use ELISA, ELISpot, NAb, Luminex, and other specialized assays. The Community Edition will continue to support the customizable Standard Assay (formerly known as the General Purpose Assay, or GPAT).

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Upcoming Features


Upcoming Features

Releases we are currently working on:

Recent Documentation Updates




Release Notes 21.7 (July 2021)


This topic is under construction.


LabKey Server

Field Editor

  • Improved behavior when inferring fields that match system/reserved fields. (docs)
  • Assign PHI levels to fields in DataClasses. (docs)
  • Sample Types and Data Classes can include fields to reference files and attachments. (docs)

Lists

  • Merge option for bulk import to lists (docs)

Assays

  • Terminology Change: '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 have been removed from the Community Edition. Users will need to subscribe to a Premium Edition to use ELISA, ELISpot, NAb, Luminex, and other specialized assays. The Community Edition will continue to support the customizable Standard Assay. (docs)
  • Due to lack of use, the Protein Expression Matrix assay has been removed. Please contact us if you need assistance.

Flow Cytometry

  • See the values used to join Samples and FCSFiles in the Sample Overview page. This will help troubleshoot any linking issues. (docs)

Samples

  • Barcode generation for Samples with "UniqueID" field. (docs)
  • Tag participant and timepoint in Sample Types. todo
  • Support for Linking Samples to Study (docs)

Study

  • Integrate Samples with other Study data

File Watchers

  • Improved behavior of assay filewatchers. todo
  • Improved UI - todo
  • Additional filewatchers for Sample Types and Standard Assays. todo

Ontology

  • Filtering of Ontology lookup fields by specific concept or presence anywhere in a subtree. todo
  • Concept picker for Ontology annotated fields. todo

Compliance Module

  • Page content will be blurred when a user session has timed out or expired. (docs)

LabKey SQL

  • Addition of concat_ws to LabKey SQL. (docs)

Panorama (Targeted Mass Spectrometry)

  • Additional MxN Reproducibility Report options. (docs)
  • Pull a specific trace in a chromatogram by time point. todo

Distribution Changes

  • Support for PostgreSQL 9.5.x has been removed. Before upgrading, PostgreSQL must be upgraded to a supported version.
  • 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

  • Product selection menu is now container-specific, and can be hidden from non-admins. todo
  • RStudio version compatibility fixes. todo
  • RStudio authentication using LDAP attributes. todo
  • Improved configuration of SAML authentication. todo
  • LDAP/SSO authorization enhancements. todo

Premium Resources

Documentation

Upcoming Changes

  • Beginning with 22.1.0, our upgrade support policy will change to reflect our recently adopted annual schema versioning approach. At that point, every release will be able to upgrade servers running versions released earlier that year or any time the previous year. For details, see our LabKey Releases and Upgrade Support Policy page.

Sample Manager

  • Permissions changes to better coordinate administrator roles. todo
  • Create Aliquots of samples singly or in bulk (docs)
  • Create and manage Picklists of samples to simplify operations on groups of samples (docs)
  • Track movement of storage units within a freezer, or to another freezer. (docs)
  • Copy a Freezer definition (docs)
  • Samples and Sources can include images and other file attachments (docs)
  • Generate Barcodes with "UniqueID" field type - Generates values when samples are added to a Sample Type or when the barcode field is added to an existing sample type. (docs)
  • When inferring fields to create Sources, Sample Types, and Assay Designs, any "reserved" fields present will not be shown in the inferral, simplifying the creation process. (docs)
  • When importing data, any unrecognized fields will be ignored and a banner will be shown (docs)
  • On the main menu, "My Assigned Work" has been renamed "My Queue" (docs)

Biologics

  • Electronic Lab Notebooks added to LabKey Biologics. (docs)
  • Removal of "Experiment" mechanism from the UI. Use workflow jobs instead.
  • Create and manage Aliquots of samples (docs)
  • Parent details are included on the Overview tab for samples (docs)
  • Nucleotide and Protein Sequence values can be hidden from users who have access to read other data in the system. (docs)
  • Sample Types and Data Classes can include:
    • Marking of fields at different levels of PHI. (docs)
    • Fields to reference files and attachments. Learn more in the Sample Manager documentation here. (docs)
  • Generate barcodes for Samples with "UniqueID" field type (docs)
  • Options to create samples from more places in the application (docs)
  • Create pooled samples and/or derive new samples from one or more parents (docs)
  • Integrated workflow with job templates and personalized queues of tasks (docs)
  • Specialty Assays can now be defined and integrated, in addition to Standard Assays (docs)
  • Creation of Raw Materials in the application uses a consistent interface with other sample type creation (docs)
  • When inferring fields to define data structures, the "reserved" fields will not be shown, but are always created (docs)
  • When importing data, any unrecognized fields will be ignored; in some cases a banner will be shown (docs)

Client APIs and Development Notes

  • 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

  • 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)

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