Table of Contents

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2018-12-11
Documentation Home
   What's New in 18.3
     What's New in 18.3
   Release Notes 18.3
     Feature Changes: 18.3
   Upcoming Features in 19.1
     Release Notes 19.1

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LabKey Server Documentation

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What's New in 18.3


We're delighted to announce the release of LabKey Server version 18.3.

Feature Highlights of Version 18.3

See the full Release Notes 18.3




What's New in 18.3


We're delighted to announce the release of LabKey Server version 18.3.

Feature Highlights of Version 18.3

See the full Release Notes 18.3




Release Notes 18.3


R Integration

  • Integrate with RStudio Pro - Use RStudio Pro to view, edit, and export LabKey Server data. (docs)
  • RStudio Data Browser - View data from the LabKey schemas within RStudio or RStudio Pro. (docs)
  • Docker-based R Engines (Experimental Feature) - Connect the server to a Docker-based R engine. (docs)
  • Per-Project R Engines - Configure multiple R engines. Individual projects can choose alternative R engines other than the site default engine. (docs)
  • Sandboxed R Engines - Declare an R engine as sandboxed to isolate it for security purposes. (docs)
  • Rlabkey Helper Functions - Two new functions have been added to the Rlabkey package: labkey.transform.getRunPropertyValue and labkey.transform.readRunPropertiesFile. Use these helper functions within an assay's R transform script to load the run data and properties. Available in Rlabkey version 2.2.4. (docs | docs)
  • Rlabkey: Set and Get Module Properties - New Rlabkey functions, setModuleProperty and setModuleProperty, allow developers to set and get a module property for a specific LabKey Server project. Available in Rlabkey version 2.2.4. (docs)

Administration

  • Antivirus Scanning - Automatically scan uploaded files for viruses using ClamAV. (docs)
  • Analyst and Trusted Analyst Roles - New site-wide roles provide different levels of access for developers writing R scripts and other code. Analysts can write code that runs on the server under their own user account. Trusted Analysts can write code to be run by other users, including custom SQL queries. (docs)
  • Platform Developer Role - A new site-wide role allows trusted users to write and deploy code. Platform developers can create and edit code and queries in folders where they have edit permission. The Platform Developer role replaces and provides the same permissions that the "Site Developers" group previously provided. (docs)
  • LDAP User/Group Synchronization - Synchronize LabKey Server user accounts with an external LDAP system. (docs)
  • Export Diagnostic Information - Download diagnostics to assist LabKey Client Services in resolving problems you encounter. (docs)
  • Connect to Existing Amazon S3 Directories - Connect to an existing S3 directory or create a new one for each LabKey folder. (docs)
  • Custom HTML Header - Add an HTML header to your site for a more custom look. Also available in 18.2. (docs)
  • Diagnostic Logs - Easily bundle and download server logs for diagnostic purposes. (docs)
  • Improved Navigation Menu - The project menu and any custom menus you define have a more consistent interface, and each contain graphical elements signaling that they are interactive elements. You can also access the project menu from the admin console. (docs)
  • Subfolder Web Part - This web part shows the subfolders of the current location; included in new collaboration folders by default. Also available in the 18.2 release. (docs)

LabKey Server Trial Instances

  • Biologics Trial Servers Available - Create a web-based server instance to explore LabKey Biologics. (docs)
  • Virtual Machine Trial Servers - Download a virtual machine image of LabKey Server for on-premise evaluation. (docs | download)

Biologics

  • Experiment Framework - Manage experiments, associated samples and assay data. Add and remove samples from an existing experiment. View the assay data linked to samples in an experiment. (docs)
  • Lineage Grid - View sample lineage in a grid format. (docs)
  • Import Constructs from GenBank Files - Import Constructs using the GenBank file format (.gb, .genbank). (docs)
  • Custom Views - Administrators can define and expose multiple views on Biologics grid data, allowing end users to select from the list of views.
  • Tutorials - Use these tutorials as a guided tour of LabKey Biologics:

Reporting and Visualization

  • Scatter and Line Plot Enhancements - Specify multiple Y axes. Show all data on a single plot or display separate plots per measure. (docs | docs)
  • Time Chart Enhancements - Hide the trend line or the data points on a time chart. (docs)
  • Add Charts to Participant Views - Include visualizations in participant views within a study. (docs)
  • QC Trend Report Options - In addition to Levey-Jennings plots, apply Moving Range and Cumulative Sum plots to GPAT and file-based assay data. (docs)

Electronic Data Capture (Survey)

  • Date & Time Question Type - An additional question type combining a date picker and time selector has been added. (docs)

Document Abstraction and Annotation

  • Document Abstraction: Multiple Result Set Review - Reviewers can now simultaneously see all abstracted results for a given document and select among differing value assignments. (docs)
  • Transfer Results between Servers - Batches of abstraction/annotation results can be encrypted and transferred between servers. (docs)

Adjudication

  • Adjudication Improvements - Compare determinations regarding HIV-1 and HIV-2 infection separately and raise alerts to infection monitors when there is consensus about a positive diagnosis for any strain. (docs)

Panorama

  • Panorama: Normalized Y-axes in QC Plots - Support for normalizing Levey-Jennings and Moving Range plots using percent of mean or standard deviation as the zero point on the Y-axis. (docs)
  • Improved Figures of Merit performance - Rendering performance for the Figures of Merit report has been improved. (docs)
  • Read Chromatograms Directly from SKYD files - An experimental feature allows you to read chromatograms directly from SKYD files instead of storing them in the database. (docs)

Development and APIs

  • Improvements to Experiment.saveBatch - The Experiment.saveBatch action has been modified to support non-assay backed runs. This allows developers to import assay data not associated with a particular assay design. In earlier versions of the API, identifying a specific assay design was required. This change has been incorporated into both the JavaScript API and the R package Rlabkey. (JS docs | R docs)
  • Modal Dialogs in JS API - A new JavaScript function in the LabKey.Utils API displays modal dialogs on the page that can have dynamic content. (docs)
  • Display PNG Images in Grids - Use a displayColumnFactory to override the display properties of a column to display images and thumbnails. (docs)
  • NaN and Infinity Values - LabKey SQL supports constants NaN, INF, and -INF. (docs)
  • Domain APIs - The Python and R APIs have been updated to allow for the inference, creation, and update of dataset and list schemas. Also available in 18.2. (Python docs | R docs)

Potential Backwards Compatibility Issues

  • Transition to Jackson Serialization - XStream serialization of pipeline jobs has been replaced with Jackson serialization. Modules that currently depend on XStream should transition to Jackson. XStream serialization has also been removed from the API. While it is always recommended to let running pipeline jobs complete prior to upgrading the server, this is especially true for the 18.3 upgrade as any jobs in progress cannot be restarted automatically. (docs)
  • Redshift Driver Upgrade - If you are using Redshift with LabKey, download the latest JDBC 4.2 driver and replace the existing driver in your Tomcat lib directory. (docs)
  • Changes to CSRF Setting - At 18.3 upgrade time, the CSRF checking setting on all servers will be set to "All POST requests". Site administrators will have 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). (docs)
  • ETL Functionality Shipping with Premium Editions - The ETL module is no longer be distributed with the Community Edition. This functionality is now included with Premium Editions of LabKey Server. (docs)

Operations

  • Support for Java 11 - We recommend upgrading your server installation to Java 11. Oracle is expected to end public support for Java 8 in January 2019, and, as a result, LabKey Server will no longer support Java 8 for the 19.1 release. For details see Supported Technologies.
  • Support for PostgreSQL 11 - PostgreSQL 11.1 and above is supported (not the initial PostgreSQL 11.0 release). For details, see Supported Technologies.
  • Remove support for PostgreSQL 9.3 - PostgreSQL 9.3 reached end-of-life in November 2018. We recommend upgrading your PostgreSQL installation to version 10 or later. For details, see Supported Technologies.

Extract-Transform-Load (ETLs)

  • ETL Definition Editor Enhancements - Define a new ETL using an existing one as a template. Autocomplete while entering XML. (docs)

Premium Resources

Premium Resources Available - Expanded documentation and code examples are available with premium editions of LabKey Server, including




Feature Changes: 18.3


This topic is provided to help administrators and developers migrate specific features to the 18.3 release.

Extract-Transform-Load (ETL)

The ETL module has been removed from the Community Edition and the functionality has migrated to the dataintegration module, available with all Premium Editions. Premium clients will not experience any change in functionality or interruption in service.

The announcement made on the Developer Forum about this change can be found here.

Developers with premium clients who have enlisted in the version control project and will be using ETLs in 18.3 and beyond will need to take the following steps in order to continue to use the premium 'dataintegration' module from Git. (Learn more about working with Git modules here).

  1. To obtain access, you will need to provide your LabKey Account Manager with the username of your GitHub account if you have not already done so.
  2. Clone the dataintegration module into your optionalModules directory.
  3. Sync your svn enlistment to remove the old svn module.
  4. Add a line like this to your settings.gradle file:
include ":server:optionalModules:dataintegration"
  1. Execute these two commands in this order to ensure that you clear out the old copy and are solely building and running the module from Git:
gradlew cleanBuild
gradlew deployApp

Create Chart View

The deprecated chart creation tool will be removed in 18.3 and existing chart views created by users will be automatically migrated to the updated implementation.

Premium subscribers have access to a variety of LabKey features outside of the community edition as well as professional support. Learn more about LabKey Premium Editions.

Windows Installer Decommission

The LabKey Server Windows-only Graphical Installer will be decommissioned as part of the 18.3 release in November 2018. Moving forward, virtual machine images will be provided with each release as an alternate method for evaluating LabKey Server on-premise. We encourage new users looking to evaluate LabKey Server to take advantage of the cloud-hosted trial version of LabKey Server.

Documentation will be provided with the 18.3 release to help ensure a smooth transition for teams currently using the graphical installer to update their LabKey Server installations.




Upcoming Features in 19.1


Upcoming Features

Some features we are currently working on for the 19.1 release of LabKey Server:

Recent Documentation Updates

Click the links below to see the most recent changes to the LabKey Server documentation.




Release Notes 19.1


This topic is under construction.
  • Enforce CSRF checking on all POST requests (This is no longer a configurable option.)
  • QC Trend report workflow improvements
  • PERL API updates
  • Antivirus scanning for cloud-based file repositories
  • ETL definitions included in folder export/import: (docs)
  • Docs: Java Module Tutorial
  • Docs: Configuring IntelliJ for XML File Editing

Biologics

  • Include "unknowns" in bulk registration of Mixtures and Batches. Also available in 18.3. (docs)
  • Bulk Upload Ingredients and Raw Materials. Also available in 18.3.
  • Attach files to Experiments. Also available in 18.3.
  • Display saved LabKey charts within Biologics