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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