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2021-03-08
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   What's New in 20.11
   Release Notes 20.11 (November 2020)
   Upcoming Features
     Release Notes 21.3 (March 2021)

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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 20.11


We're delighted to announce the release of LabKey Server version 20.11.

Highlights of Version 20.11

Sample Manager

Biologics

  • Sample Management - Improved user experience for defining, naming, and importing samples, including importing samples by drag-and-drop and directly entering sample information in the user interface.

LabKey Server

  • Ontology Module - Import and manage standardized vocabularies. A new data type "Ontology Lookups" applies ontology concepts to your data.
  • Module Editor - Developers can edit module-based resources, add new resources, and edit module structure directly from the user interface.
  • Query-based Specimen Import - Automatically load specimens from a Query specified on the server.
  • NAb Assay - Improved Curve Plotting - NAb dilution data is now exported with fit parameter data, simplifying full curve plotting
  • Field Editor Export/Import - Export and import sets of fields to reuse common data columns.

Premium Resources Highlights

Release Notes

Community Highlights


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Release Notes 20.11 (November 2020)


LabKey Sample Manager


LabKey Biologics

  • Sample Management - Improved user experience for defining and importing samples, and generating sample IDs, including importing samples by drag-and-drop and directly entering sample information in the user interface.
  • Assay Data Management - Improved user experience for defining, importing and managing assay data directly in the Biologics application.
  • Sequence Validation - Improved validation of whitespaces and stop codons in nucleotide and protein sequences.

LabKey Server

Ontology

  • Ontology Module - Import and manage standardized vocabularies. A new data type "Ontology Lookup" resolves and imports ontology concepts in your data.

Assays

Data and Reporting

Electronic Data Capture (Surveys)

Targeted Mass Spectrometry (Panorama)

  • Refinements to Multi-Attribute Methods Reports - Peptide reporting shows more information of interest.
  • Small Molecule Chromatogram Libraries - Curate and export chromatogram libraries for small molecules in addition to proteomics data.
  • Performance improvements for QC metric reporting.
  • Higher resolution plots - Chromatograms and sample comparison plots leverage higher resolution displays when available. (Introduced in 20.11.1)

Abstraction/Annotation

Administration

  • User Management - Project admins can now more easily add new users to the site.

Study Specimens

  • Load External Specimens - Load specimens from an external source.
  • Query-based Specimen Import - Automatically load specimens from a Query specified on the server.
  • Upcoming changes - Beginning with release 21.3 (March 2021), Specimen tracking functionality will be removed from standard distributions of LabKey Server. Instead, we recommend using Sample Types and Sample Manager for managing specimen information. Clients who rely on the existing repository will still receive it with their subscriptions.

New Premium Resources

New Documentation Topics

Development

  • Module Editor - Developers can edit module-based resources, add new resources, and edit module structure directly from the user interface.
  • Completed migration of source code and history to GitHub. A read-only copy of the trunk code will remain available in subversion to assist in migration, but all new development will be on GitHub. (docs)
  • The developer links menu has been reorganized to better support developer needs. (docs)
  • Upgrade to the Log4j 2 API with release 20.11. A backwards-compatibility JAR will be available if you are not able to upgrade immediately. Learn more in the docs.
  • Updates to module.properties file handling

Security Updates

  • API calls like selectRows and executeSql and UI-based requests that render data grids will now return a 400 error response if the parameters have invalid values. For example, if the maxRows parameter has a non-numeric value. In the past these bogus values were ignored, and the server used the parameter's default.

Upcoming Distribution Changes

  • Beginning with version 21.3.0 (March 2021), Microsoft SQL Server (and all other non-PostgreSQL database connections) will be supported only in Premium Edition distributions. The BigIron module, which provides support for Microsoft SQL Server, Oracle, MySQL, and SAS/SHARE will move to the Starter Edition and higher distributions.
  • Starting in 21.3.0, Specimen Repository functionality will be removed from our standard distributions (Community, Starter, Professional, etc.). We will continue to support this functionality and provide it to clients who currently use it. But for future development, we strongly recommend the use of Sample Types and Sample Manager going forward.
  • Beginning in January 2021, the FCSExpress module will be removed from all distributions and is no longer supported.

Client APIs

Python API

  • Python API Release Notes
  • Python API Version 2.0 - A major release of the LabKey Python API has launched and is available for upgrade. Note that you do not need to upgrade to this new API to use LabKey Server version 20.11.
    • Before considering the timing of your upgrade, review the release notes and consider a migration plan for existing scripts. Several APIs have changed and scripts that used the 1.x version of the API may need changes.
    • Upgrade to Python 3.x - Version 2.0 of the LabKey Python client API uses Python 3.x and drops support for Python 2.x. Until you are able to update your own usage of Python, you will not want to upgrade your LabKey Python Client API.

@labkey/components package

  • @labkey/components v1.0.0: Public API docs
  • Version 1.0.0 of the @labkey/components npm package has been released.
    • This package contains some React based components, models, actions, and utility functions that will help with data access and display of LabKey schemas/tables in React applications.
    • Module developers creating LabKey pages or applications using React can find more information, installation instructions, and usage examples in the public API docs.

Upgrade


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Upcoming Features


Upcoming Features

Releases we are currently working on:

Recent Documentation Updates




Release Notes 21.3 (March 2021)


This topic is under construction for the 21.3 (March 2021) release of LabKey Server.


LabKey Sample Manager

  • Freezer management:
    • Match virtual storage to physical storage in your lab
    • Easily store and locate stored samples from anywhere in the application
    • Track locations and movements of samples
    • Check in and out, recording usage and incrementing freeze/thaw counts
    • Import sample data simultaneously with location data making it easy to migrate from another system
  • The field editor now includes checkboxes to enable deletion of multiple fields and export of subsets of fields.
  • Background Import:
    • Removal of previous size limits on data import
    • Progress reporting for asynchronous imports
    • In-app Notifications when background imports complete.
  • Create derivative samples (aliquots) in bulk
  • Trials of Sample Manager are preloaded with example data
  • New header navigation menu
  • New storage unit: Tube rack

LabKey Biologics

  • New main dashboard and master menu, available throughout the application. (docs)
  • Manage more data without leaving the application
    • Define and manage Sample Types (docs)
    • Improved Assay designer within the application (docs)
  • Easily switch applications when needed. (docs)
  • In-app Notifications when background imports are completed (docs)

Integrations

  • Use a Puppeteer web service to generate PDFs (docs)

LabKey Server

Administration

  • New menu for switching among LabKey applications. (docs)
  • Synchronous Startup option - use a command line option to ensure that all modules are upgraded, started, and initialized before any requests can be processed. (docs)

Data and Reporting

  • Field editor styling improvements and addition of field selection for partial export or group deletion of fields.
  • View fields in detailed or summary mode.

Study

  • Dataset merge (also available in 20.11.3)
  • Specimen functionality is being removed from the study module. If you need to continue using this functionality, you will need to add the specimens module when you upgrade. Contact your Account Manager with questions or concerns.
  • Changes to Dataset-level security options

Assays

  • New Assay Type Selection Interface - Simplified method for selecting a Standard assay (recommended and most common), vs. one of the Specialty assays. (docs)
  • Improved Interface for Export/Import of Assay Designs - (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 (available in 20.11). (docs)
  • Experimental ELISA multiplate and inclusion of metadata - (docs)
  • Removal of integration with FCS Express: The FCSExpress module has been removed from the core distribution and is no longer supported.

Targeted Mass Spectrometry (Panorama)

  • Instrument summary page
  • QC and Experiment folders are now linked when they have data from the same instrument
  • Reference guidesets - If a custom date range is selected for QC plots, the user can now reference the previous guideset.

Development

  • Run Reports via ETL: A new RunReportTask option for ETLs. (docs)
  • ETLs now support triggers on bulk and archive imports
  • ETL Source Filters - Specify a data filter in the ETL definition.
  • Transformation Script Syntax: "httpSessionId" has been deprecated in favor of the new ${apiKey} parameter for authentication. (docs)

Ontologies

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.
  • SIMILAR_TO support added to LabKey SQL (Postgres only) (docs)
  • Additional documentation about SQL annotations - (docs)

Issues

  • The Issues API now supports closing an issue/assigning to 'guest'

Distribution Changes

  • Beginning with version 21.3.0 (March 2021), Microsoft SQL Server (and all other non-PostgreSQL database connections) will be supported only in Premium Edition distributions. The BigIron module, which provides support for Microsoft SQL Server, Oracle, MySQL, and SAS/SHARE will move to the Starter Edition and higher distributions.
  • Starting in 21.3.0, Specimen Repository functionality will be removed from our standard distributions (Community, Starter, Professional, etc.). We will continue to support this functionality and provide it to Premium Edition clients who currently use it. For future development, we strongly recommend the use of Sample Types and Sample Manager going forward.
  • The FCSExpress module has been removed from all distributions and is no longer supported.

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.

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.

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