System Integration

  • Improved ETL Development - Develop and deploy ETLs using the web user interface. Deployment of a custom module is no longer necessary. (docs)
  • Spotfire Integration - Use data stored in LabKey Server to create Spotfire visualizations. (docs)
  • Enterprise Master Patient Index (EMPI) Integration - LabKey studies can use the Enterprise Master Patient Index to identify duplicate participant data. (docs)
  • Improved Reload - The file watcher-based reloader for studies, folders, and lists has an updated configuration UI and an expanded set of tasks that can be performed. (docs)
  • S3 Migration - New file migration options for S3 storage. (docs)
  • Amazon Redshift Data Sources - Redshift has been added as a new external data source type. (docs)
  • Medidata Rave - Support for Medidata Rave has been introduced as an initial beta release. Contact us for support options. (docs)

Instrument Data

  • QC Trend Reporting - Track various metrics and create reports including Levey-Jennings plots for assays and other data. (docs)
  • Exclude Assay Data - Exclude specific GPAT or file-based assay rows from later analysis. (docs)
  • MaxQuant Module - Load, analyze, and present MaxQuant analysis data. (docs)

Natural Language Processing

  • Configurable Terminology in NLP - Customize label displays in the abstraction UI. (docs)
  • Slimmed Distribution for NLP - A distribution of LabKey Server with a reduced feature set is available for usage with Natural Language Processing.


  • Experiments - Build and define experiments with samples. (docs)
  • Details for Related Entities - The user interface for related entities has been improved with expandable details panels. (docs)
  • Editable Grid Improvements - Insert sample details or upload assay data in a grid. (docs)
  • Bulk Import for Media - Quickly specify ingredients for recipes or batches. (docs)


  • Adjudication Audit Log - Adjudication events are now audited. (docs)

LabKey SQL

  • Common Table Expressions - Use a SQL "WITH" clause to simplify complex queries and create recursive queries. (docs)

Structured Narrative Datasets

  • Package Dependencies - Add requirement rules to super-packages. (docs)
  • Events - Events have attribute data and the API now includes save/delete/get Events. (docs) and (docs)
  • Event Triggers - Define actions to be performed when specific events occur. (docs)
  • Narrative Generation - Update and cache narratives using templates and entered data. (docs)
  • Quality Control and Security - Customize access permissions based on the QC state of SND data. (docs)
  • SND: Additional API Documentation - Enhanced API descriptions, including JSON samples. (docs)
  • SND: API Testing Framework - Test SND events with a new framework. (docs)

Panorama - Targeted Proteomics

  • Improved Pharmacokinetic Report - Pharmacokinetic (PK) calculations are provided per subgroup, replicate annotations are included, and non-IV routes of administration are supported. (docs)
  • LOD/LOQ Skyline Compatibility - Limit of Detection (LOD) is now shown in Panorama, and there is support for additional Limit of Quantitation (LOQ) configuration as defined in Skyline. (docs)


  • Moderator Review - Configure message boards to add a review step prior to posting. (docs)
  • Admin Console Changes - The option to Map Network Drives (Windows only) has been moved from the "Site Settings" to the "Files" configuration area. (docs)
  • Report PHI Columns - Administrators can generate a report of columns and their associated PHI Levels. (docs)


  • New SVN Server - The LabKey source enlistment server has moved and can now be found at (docs)
  • Node Dependency Changes - Beginning with version 1.3 of the gradlePlugins, the build process will download the versions of npm and node that are specified by the properties npmVersion and nodeVersion. Remove node_modules directories from your LabKey modules' directories before doing your first build with the 1.3 version. (docs)
  • Python API - Support for Domains APIs has been added. - (docs)
  • Documentation - New example for creating "master-detail" pages with JavaScript. (docs)

Potential Backward Compatibility Issues

  • Changes to CSRF Default Setting In 18.2, we have switched the default CSRF checking setting (affecting only new servers) to "All POST requests". We recommend that all clients run their servers with the "All POST requests" setting, ideally on production servers but at a minimum on their tests/staging servers. In the upcoming 18.3 release, we plan to force the setting (on all existing servers at upgrade time) to "All POST requests". We will retain the ability to revert back to "Admin requests" for deployments that still need to make their external modules or custom pages compatible with this setting. For release 19.1, we plan to remove the setting entirely and check CSRF tokens on every POST (except for specially annotated actions).
  • Query Details Metadata Retrieval - Lookup columns in query views are no longer treated as native to the dataset. (docs)
  • LabKey JDBC Driver - LabKey's JDBC Driver is only available with Premium Editions of LabKey starting in 18.2. (docs)
  • Removed Unimplemented Attributes in ETL.xsd - During the initial development of LabKey's ETL framework, several options were defined but not needed and have now been removed. You will no longer see the following items and will need to remove them from any ETLs in order to pass XML validation.
    • TransformType "file"
    • TransformType "streaming"
    • SourceOptionType "deleteRowsAfterSelect": Not needed; instead specify a truncate step against the source table if desired.
  • Importing Data with 'Container' Column - File-based data imports of TSV, Excel and similar file formats that include a Container or Folder column may produce errors if the value cannot be resolved in the target server. ETLs that include a Container or Folder column in the source data may produce similar behavior. To resolve these errors, remove the Container or Folder column from the source data file or SQL query.

Important Upcoming Changes

  • Windows Graphical Installer - The Windows Graphical Installer will no longer be distributed with the Community Edition starting in 18.3.
  • Create Chart View - The old chart creation tool "Create Chart View" is being removed in 18.3. Existing chart views created by users will be automatically migrated to the new implementation.
  • Timer-based Study Reload - Timer-based study reloads will be removed in 18.3. For premium edition clients, existing study reload configurations will automatically be upgraded to file watcher configurations, with no interruption of service or change in functionality anticipated. If necessary, premium edition clients will also receive individual assistance migrating existing scripts and reloads. Options for study reload continue to include file watcher-based reloading, manual reloading, and using a script to call the "checkForReload" API action. (docs)


  • Support for MySQL 8.0 - The MySQL 8.0-compatible JDBC driver requires minor changes to data source definition settings. For details see External MySQL Data Sources.
  • Tomcat 8.0.x is no longer supported - If you are using Tomcat 8.0.x, you should upgrade to 8.5.x at your earliest convenience. No configuration changes in LabKey Server are necessary as part of this upgrade. For details see Supported Technologies.
  • Connection Pool Size - We recommend reviewing the connection pool size settings on your production servers. For details, see Troubleshoot Server Installation and Configuration.
  • Web Application Firewall - Deploy an AWS Web Application Firewall (WAF) to protect LabKey instances from DDoS and Malicious Attacks. (docs)

- Denotes Premium Edition functionality.

Was this content helpful?

Log in or register an account to provide feedback

expand allcollapse all