LabKey Sample Manager
- Sample Sources - Track the sources and provenance of your samples, such as organism or lab of origin.
- Sample Timeline - Capture all events related to a specific sample in a convenient graphical timeline for auditing purposes and chain of custody tracking. Timeline information can be exported to Excel, TSV, and CSV formats.
- Search Enhancements - Filter and refine search results by type, user, date, and more.
Sample Types and Data Classes
- Terminology Change - The term "Sample Set" has been changed to "Sample Type". There are no functionality changes implied by this name change.
- Event/Timeline Auditing - Sample timeline events, such as editing a sample or adding it to a job, are added to the audit log.
- Lineage Editing - Sample parents can be updated individually or deleted using merge during import.
- Data Class Search - Data classes are now indexed for full-text searching.
- Improved Sample Type Creation - The wizard for creating sample types has been consolidated into one page, instead of the previous two pages.
- Run/Parentage Graph Improvements - Experiment runs can be rendered using a new React-based graph. Click elements in the graph to change focus and see details.
- Plotly Dash - Administrators can configure a proxy servlet to provide integration with Plotly Dash and other external web applications.
- ODBC on Cloud Hosted Servers - Connect Tableau and other analysis tools to cloud hosted LabKey Servers using ODBC.
- ODBC Setup Guidance - An in-server dashboard provides easy access to the correct port, server, and TLS certificate to use when configuring an ODBC connection
- Panorama QC Performance - Performance improvements when reporting on QC folders with high data volume.
- Skyline Audit Log - Improvements to import and display of Skyline document's audit log.
- Crosslinked-Peptides - Support for Skyline's new handling of cross-linked peptides.
- Multi Attribute Method (MAM) Folder Type - Panorama includes a new folder type intended for groups doing MAM analysis, making key reports easily available.
User Interface / User Experience
- Expanded Query Dependency Reporting - Trace query dependencies that reside in different folders.
- Mass Spec Metadata - The "Mass Spec Metadata" built in assay type has been removed.
- Rlabkey version 2.4.0 The update of the Rlabkey client library contains the following improvements:
- 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
- Client Library Changes - Client libraries have a new versioning system, to support a release schedule decoupled from LabKey Server. To download client libraries distributions, see the topic API Resources.
- JS API - The JS API has been re-implemented using TypeScript, and is now distributed as an official NPM package release with version 1.0.0.
- Conditional Formats - Both the Python API and the R API now support conditional formats and QC states for datasets:
- Define conditional formatting for fields.
- Define QC states, and set QC states on study dataset data.
- Module Loading Load file-based modules on a production server directly through the user interface without restart.
- Module Editing Edit module-based resources including SQL queries and R reports using the server user interface on a development server.
- Proxy Servlets - Configure Proxy Servlets to act as reverse proxies for external web applications.
- 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 jar files from CATALINA_HOME/lib to avoid conflicts.
- Changes to Source Directory Structure - 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.
- Coming soon: Upgrade to Python 3.x: Version 2.0 of the LabKey Python client API will use Python 3.x and drop 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. Learn more in the labkey-api-python documentation on GitHub.
- Java, Tomcat, and PostgreSQL Versions - LabKey has removed support for JDK 12.x, Tomcat 7.0.x, and PostgreSQL 9.4.x. Before upgrading LabKey Server, these components will need to be upgraded to a supported version.
- Upgrade all LabKey Dependencies - We strongly recommend that, as part of your LabKey Server upgrade, you also upgrade all major LabKey dependencies to their latest point releases, these include: Java, Tomcat, and your database server.
- Upgrade Instructions - Follow the steps in this topic to upgrade to the latest release of LabKey Server: Manual Upgrade Checklist for Linux and OSX
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