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2020-07-07
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   What's New in 20.3
   Release Notes 20.3
   Upcoming Features
     Release Notes 20.7 (July 2020)

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Release Notes

Getting Started

Trial Servers

LabKey Server Documentation

LabKey Biologics Documentation

LabKey Sample Manager Documentation

Premium Resources

Community Resources




What's New in 20.3


We're delighted to announce the release of LabKey Server version 20.3.

Highlights of Version 20.3

Documentation Highlights

  • FDA MyStudies Documentation Portal - A new portal centralizes documentation for the FDA MyStudies platform.
  • Installation Documentation - The installation documentation has been improved, including separate checklists for Linux and Windows installations, Linux command examples, clarified requirements for Tomcat configuration, and more.

Premium Resources Highlights

Release Notes


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Release Notes 20.3


Sample Manager

  • LabKey Sample Manager is now available with every Premium Edition, offering easy tracking of laboratory workflows, sample lineage, and experimental data.

Assays

User Experience

  • List Designer - Create and edit Lists with an improved user interface, including: drag-and-drop reordering of fields, improved primary key selection, and responsive implementation using ReactJS.
  • Specimens and File Properties - The user interface for editing file properties and specimen fields has been similarly improved.

Provenance Module

  • Run Builder - Capture laboratory processees by linking samples and/files to a "run". For example, to define and characterize processes which have samples as inputs and result files as outputs.

Security Administration

  • Improved Authentication Administration - User authentication administration has been updated with a modern, easy-to-use interface that supports multiple configurations per authentication protocol and drag-and-drop reordering.
  • LDAP Configuration Changes - LDAP authentication is a premium feature beginning in version 20.3 (March 2020). In addition, LDAP Search configuration has been moved to the administration interface.

Reporting

  • Expanded Rlabkey Authentication - Rlabkey version 2.3.4 supports username/password authentication directly in an R script via the labkey.setDefaults() helper function.

Biologics

File Watchers

  • Prevent Domain Changes - When filewatchers are configured to update lists and datasets, set the parameter "allowDomainUpdates" to false to retain the column set of the existing list.

Panorama

  • Sample File Scoped Chromatograms - Display and provide API access to chromatogram-style data contained within Skyline documents.
  • Skyline Document Version Updates - Updates to Panorama to ensure full compatibility with changes to Skyline's file format.

Administration

Operations

  • Important Security Update - LabKey Server 20.3 includes an important security update, which has been back-ported to version 19.3.7. We strongly recommend that you upgrade your servers to at least 19.3.7 to pick up this security update.
  • Month-based Version Names - A new month-based naming pattern has been adopted for LabKey Server. This March 2020 release is named 20.3; the next production release in July 2020 will be 20.7.
  • SchemaVersion Property - Modules have a new property 'SchemaVersion' used to control the running of SQL schema upgrade scripts.
  • Changes to Names of Premium Editions - The names of the Premium Editions of LabKey Server have changed. The Professional edition is now called "Starter" and the Professional Plus edition is now called "Professional".
  • AdoptOpenJDK 13 - Starting with LabKey Server 20.3.0, AdoptOpenJDK 13 is supported for new installations and upgrades.

Upgrade

Upcoming Releases

  • Mass Spec Metadata Assay Type to be Removed - The Mass Spec Metadata assay type is scheduled to be removed from distributions beginning with release 20.7 (July 2020).
  • Java, Tomcat, and PostgreSQL Versions - Beginning with release 20.4 (April 2020), LabKey will no longer support JDK 12.x, Tomcat 7.0.x, and PostgreSQL 9.4.x. These components will need to be upgraded to versions supported by their vendors.

Documentation

  • FDA MyStudies Documentation Portal - A new portal centralizes documentation for the FDA MyStudies platform.
  • Installation Documentation - The installation documentation has been improved, including separate checklists for Linux and Windows installations, Linux command examples, clarified requirements for Tomcat configuration, and more.

New Premium Resources

Click here for a full list of premium resources available.

Maintenance Releases

  • Version 20.3.1
    • AdoptOpenJDK 14 - Starting with LabKey Server version 20.3.1, AdoptOpenJDK 14 is supported for production installations (and for developers who are compiling from source).
  • Version 20.3.7
    • LabKey wishes to thank community member Sushant Kumawat for alerting us to an important defect that we addressed in this release.

Release of Rlabkey Version 2.4.0

The update of the Rlabkey client library for R to version 2.4.0 brings several notable changes:
  • labkey.experiment.saveBatch includes the batchPropertyList parameter
  • labkey.domain.createDesign now has a labkey.domain.createIndices helper and indices parameter
  • New methods for managing projects and folders: labkey.security.getContainers, labkey.security.createContainer, labkey.security.deleteContainer, labkey.security.moveContainer

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Upcoming Features


Upcoming Features

Releases we are currently working on:

Recent Documentation Updates




Release Notes 20.7 (July 2020)


This topic is under construction for the July 2020 release of LabKey Server.

Sample Manager

  • Sample Sources (Available in 20.4) - Track both physical and biological sources of your samples. (docs)
  • Sample Timeline (Available in 20.5) - Review all events related to a specific sample in a convenient graphical timeline. (docs)
  • Search Enhancements - Filter and refine search results by type, user, date, and more. (docs)

Sample Types and Data Classes

  • The term "Sample Set" has been changed to "Sample Type" to better represent all samples that share common properties. There are no functionality changes implied by this name change. (docs)
  • Consolidation of UI pages for creating sample types (docs)
  • Data classes are now indexed for searching (docs)
  • Sample parents can be updated individually or deleted using merge during import (docs)
  • Sample timeline added to audit logging (docs)
  • Run Graph Detail Improvements - (todo)

System Integration

  • ODBC for Hosted Servers todo

Biologics

  • Expanded import options

User Interface

  • Datasets, Issues, and Query Metadata now use the same field editor UI as all other data structures. (docs, docs, and docs)
  • Add a Responsive Logo to display when browser is too narrow for ordinary logo. (docs)
  • The "Settings" tab is now the default when you open the admin console. (docs)

Specimens

  • Specimen File Watcher (docs)

Authentication

  • A SAML identity provider can be the default authenticator (docs)
  • CAS authentication supports the /logout API. (docs)

Administration

  • Cross-folder query dependency tracing (docs)
  • Removal of "Mass Spec Metadata" built in assay type

Rlabkey

  • Rlabkey version 2.4.0 The update of the Rlabkey client library for R to version 2.4.0 brings several notable changes:
    • labkey.experiment.saveBatch includes the batchPropertyList parameter
    • labkey.domain.createDesign now has a labkey.domain.createIndices helper and indices parameter
    • New methods for managing projects and folders: labkey.security.getContainers, labkey.security.createContainer, labkey.security.deleteContainer, labkey.security.moveContainer

Python API

  • The Python API now supports defining and using the following. Find documentation and examples on GitHub.
    • Conditional formatting for fields (Domain API)
    • QC states for study datasets (Query API)

Reporting

  • ODBC for Cloud Deployment of LK (todo)
  • STATA Integation - todo

Development

  • Load and update modules using the user interface and without server restart. (docs)
  • Edit module code directly through the server user interface. todo
  • JS API
    • new version numbers
    • available on Artifactory
  • Proxy Servlets (docs)
  • Python API Additions - Define and update dataset QC states; set and update conditional formats. (docs)

Operations

  • Changes to How JDBC Jars are Distributed - The JDBC jars (jtds.jar, postgresql.jar, mysql.jar) are now versioned and distributed inside the module directories like any other third-party jar, making it unnecessary to copy them to the CATALINA_HOME/lib directory during installation and upgrade. When you upgrade to 20.7, delete these JDBC jars files from CATALINA_HOME/lib to avoid conflicts.
  • When building from source, the /optionalModules and /externalModules directories are no longer used. Move all contents from these directories into /server/modules. Note that this change only applies to developers building the server from source; for production servers /externalModules can still be used for deploying modules.
  • Changes to How Proteomics Binaries are Distributed - The proteomics binaries are now downloaded automatically without further action. This download can be skipped if desired.

Premium Resources


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