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2022-07-03
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LabKey Biologics Documentation

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What's New in 22.3


We're delighted to announce the release of LabKey Server version 22.3.

Highlights of Version 22.3

LabKey Server

  • The Text Choice data type provides an easy way to define a set of expected text values for a field. (docs)
  • Sample naming patterns are validated during sample type definition. Example names are visible to users creating new samples. (docs)
  • Queries can be included in published studies. (docs)
  • Ontology insert and update forms now support type ahead filtering for quick input into ontology lookup fields. (docs)

Sample Manager

  • Sample Finder: Find samples based on source and parent properties, giving users the flexibility to locate samples based on relationships and lineage details. (docs)
  • New Storage Editor and Storage Designer roles, allowing admins to assign different users the ability to manage freezer storage and manage sample and assay definitions. (docs)
  • Redesigned main dashboard featuring storage information and prioritizing what users use most. (docs)

Biologics

  • ELN Improvements:
    • Notebook entry locking and protection: Users are notified if someone else is already editing a notebook entry and prevented from accidentally overwriting their work. (docs)
    • Find notebooks easily based on a variety of filtering criteria. (docs)
  • Freezer Management for Biologics: Create a virtual match of your physical storage system, and then track sample locations, availability, freezer capacities, and more. (docs)
  • User-defined barcodes can also be included in sample definitions and search-by-barcode results. (docs)

Premium Resources

Release Notes


The symbol indicates a feature available in a Premium Edition of LabKey Server.




Release Notes 22.3 (March 2022)


This topic provides the full release notes for LabKey version 22.3 (March 2022).
Important upgrade note:

LabKey has released updated versions (22.3.2 and 21.11.10) to address the Spring MVC security vulnerability (CVE-2022-22965). In order to minimize the impact of this vulnerability, all administrators must upgrade their installations immediately.

Premium edition users will find the latest patch release on their support portal now. Community users can download the latest version here.

Learn more in this message thread:


LabKey Server

Data Types

  • The Text Choice data type lets admins define a set of expected text values for a field. (docs)
  • The field editor allows more flexibility in changing the data type of a field. (docs)

Samples

  • Sample naming patterns are validated during sample type definition. (docs)
  • See and set the value of the "genId" counter for naming patterns. (docs)
  • Sample status types and values are exported and imported with folder archives, when the sampleManagement module is present. (docs)
  • Linking samples to studies has become more flexible:
    • Use any names for fields of the "Subject/Participant" and "VisitID/VisitDate" types. (docs)
    • The subject and visit fields may be defined as properties of the sample itself, or can be defined on the parent sample. (docs)

Assays

  • Administrators can require that users enter a comment when changing the QC state of an assay run. (docs)

Flow Cytometry

  • If Samples are defined at the project level, they can be referenced from Flow subfolders without having to redefine new local copies. (docs) (Also available in version 21.11.1.)

LabKey SQL

  • Support for NULLIF() has been added. (docs)

Study

  • Queries can be included when you publish a study. (docs)

Folder and Study Archives

  • Import and reload from "study archives" is no longer supported. (A study archive is a zip file or a collection of individual files with study.xml at the root; LabKey stopped exporting study archives 10 years ago.) Use folder archives to export/import/reload studies and other LabKey objects and data. (docs)
  • The elements supported in study and dataset XML files have changed. (docs)
    • In study.xml, the "<lists>", "<queries>", "<reports>", "<views>", and "<missingValueIndicators>" elements are no longer allowed. These elements belong in the folder.xml file.
    • In datasets_manifest.xml, the "defaultDateFormat" and "defaultNumberFormat" attributes are no longer allowed. These were moved many years ago to the folder.xml file.
    • In datasets_manifest.xml, the "<categories>" element is no longer allowed. This was replaced many years ago by a separate viewCategories.xml file.
  • Categories are now exported in any folder archive; previously they were only included when exporting from study folders. (docs)

Administration

  • Linked schemas now grant the Reader role only within the source container. (docs)
  • View raw schema metadata for assistance in troubleshooting external data connections. (docs)
  • Administrators can substitute server property values into the server name shown on page headers. (docs)
  • The Project Creator role lets users without full site administrator access invoke an API to create projects. (docs)
  • Set a Content-Security-Policy for your Tomcat installation using a new filter in the bootstrap jar. (docs)
  • Show alert highlighting when the clock on the database and server differ by more than 10 seconds. (docs)

DataFinder

  • The DataFinder module has been enhanced to support partial word searching, custom publication facets and reordering of facets, and multiple data finders on a single server. Several unused publication facets have been removed. (docs) (Also available in version 21.11.4)

Panorama

  • Configure which peptide groups and small molecules are shown in plots, so that you can focus on the most relevant ones. (docs)
  • Set the default view for QC plots for providing customized and consistent views to users. (docs)
  • Improvements to Reproducibility Report: Select either light/heavy ratio or peak areas. (docs)
  • Performance of AutoQC plots has been improved.
  • Panorama is available only with Premium Editions of LabKey Server through the Panorama Partners Program.

Ontologies

  • The standard insert and update forms now support type ahead filtering for quick input into ontology lookup fields. (docs)

Premium Resources

Distribution Changes and Upgrade Notes

  • Panorama is available only with Premium Editions of LabKey Server through the Panorama Partners Program. It is no longer included in the Community Edition.
  • Mass Spectrometry Support (protein database search workflows provided by LabKey Server's MS2 module) has been removed from the Community Edition and is available only with Premium Editions of LabKey Server.
  • Redshift external datasources are now supported in all Premium Editions of LabKey Server. Previously they were only provided as an add-on or in the Professional or Enterprise Editions.
  • Rotation of labkey.log and other log files now uses naming consistent with labkey-errors.log. The most recently rotated copy of labkey.log is now named labkey.log.1 instead of labkey.log.7. (docs)
  • Our upgrade support policy now reflects annual schema versioning. You may need to perform an intermediate upgrade in order to upgrade to version 22.3. For details, see our LabKey Releases and Upgrade Support Policy page.
  • Upgrade Performance: In order to expand the long-term capacity of audit log tables, event table rowIDs have been changed from integer to bigInt. Depending on the size of your audit logs, the audit module upgrade step can take considerable time and disk space. Be patient and alert for settings like Tomcat timeouts and available disk space that may need adjustment for this one time upgrade action to complete. (details)

Backwards Compatibility Notes

  • Support for importing study archives has been removed. Use folder archives instead. Review the Folder and Study Archive section above for details about changes to elements supported in some XML metadata files.
  • If a query has a syntax error or metadata problem, LABKEY.Query.validateQuery() (and its related bindings in other client API languages) now uses a 200 HTTP status code to convey the information. Previously, it used a 400 or 500 status code, so callers may need to update their success/failure handlers accordingly.
  • LabKey no longer accepts the JSESSIONID in place of the CSRF token. All POST requests must include a CSRF token. (docs)

Upcoming Dependency Changes

  • Beginning with version 22.4 (April 2022), support for Java 16 will be removed. Before upgrading, Java will need to be upgraded to a supported version of JDK 17.
  • Beginning with version 22.6 (June 2022), support for Microsoft SQL Server 2012 as the primary database will be removed. Before upgrading, your database will need to be upgraded to a supported version of Microsoft SQL Server.

Developer Resources


Sample Manager

Sample Manager Release Notes listing features by monthly version.
  • Sample Finder: Find samples based on source and parent properties, giving users the flexibility to locate samples based on relationships and lineage details. (docs)
  • Redesigned main dashboard featuring storage information and prioritizing what users use most. (docs)
  • Updated freezer overview panel and dashboards present storage summary details. (docs)
  • Available freezer capacity is shown when navigating freezer hierarchies to store, move, and manage samples. (docs | docs)
  • Storage labels and descriptions give users more ways to identify their samples and storage units. (docs)
  • New Storage Editor and Storage Designer roles, allowing admins to assign different users the ability to manage freezer storage and manage sample and assay definitions. (docs)
    • Note that users with the "Administrator" and "Editor" role no longer have the ability to edit storage information unless they are granted one of these new storage roles.
  • Multiple permission roles can be assigned to a new user at once. (docs)
  • Sample Type Insights panel summarizes storage, status, etc. for all samples of a type. (docs)
  • Sample Status options are shown in a hover legend for easy reference. (docs)
  • When a sample is marked as "Consumed", the user will be prompted to also change it's storage status to "Discarded" (and vice versa). (docs | docs)
  • Search menu includes quick links to search by barcode or sample ID. (docs)
  • A new Text Choice data type lets admins define a set of expected text values for a field. (docs)
  • Naming patterns are validated during sample type definition, and example names are visible to users creating new samples or aliquots. (docs)
  • Editable grids include visual indication when a field offers dropdown choices. (docs)
  • Add freezer storage units in bulk. (docs)
  • User-defined barcodes can be included in Sample Type definitions as text or integer fields and are scanned when searching samples by barcode. (docs | docs)
  • If any of your Sample Types include samples with only strings of digits as names, these could have overlapped with the "rowIDs" of other samples, producing unintended results or lineages. With this release, such ambiguities will be resolved by assuming that a sample name has been provided. (docs)
  • The "Sample Count by Status" graph on the main dashboard now shows samples by type (in bars) and status (using color coding). Click through to a grid of the samples represented by each block. (docs)
  • Grids that may display multiple Sample Types, such as picklists, workflow tasks, etc. offer tabs per sample type, plus a consolidated list of all samples. This enables actions such as bulk sample editing from mixed sample-type grids. (picklists | tasks | sources)
  • Improved display of color coded sample status values. (docs)
  • Include a comment when updating storage amounts or freeze/thaw counts. (docs)
  • Workflow tasks involving assays will prepopulate a grid with the samples assigned to the job, simplifying assay data entry. (docs)

Biologics

Biologics release notes listing features by monthly version.
  • Notebook Entry Locking and Protection: Users are notified if someone else is already editing a notebook entry and prevented from accidentally overwriting their work. (docs)
  • Copy and paste from Google Sheets or Excel to add a table to a notebook. (docs)
  • Redesigned main dashboard featuring storage information. (docs)
  • Updated freezer overview panel and dashboards present storage summary details. (docs)
  • Available freezer capacity is shown when navigating freezer hierarchies to store, move, and manage samples. (docs | docs)
  • Storage labels and descriptions give users more ways to identify their samples and storage units. (docs)
  • Find notebooks easily based on a variety of filtering criteria. See your own ELN task status(es) at a glance. (docs)
  • Users will see progress feedback for background imports being processed asynchronously. (docs)
  • New Storage Editor and Storage Designer roles, allowing admins to assign different users the ability to manage freezer storage and manage sample and assay definitions. (docs)
    • Note that users with the "Administrator" and "Editor" role no longer have the ability to edit storage information unless they are granted these new storage roles.
  • Sample Type Insights panel summarizes storage, status, etc. for all samples of a type. (docs)
  • Sample Status options are shown in a hover legend for easy reference. (docs)
  • When a sample is marked as "Consumed", the user will be prompted to also change it's storage status to "Discarded" (and vice versa). (docs | docs)
  • Search menu includes quick links to search by barcode or sample ID. (docs)
  • ELN improvements:
    • Tables pasted into an ELN will be reformatted to fit the page width. Users can adjust the display before exporting or finalizing the notebook. (docs)
    • Printing to PDF includes formatting settings including portrait/landscape and fit-to-page. (docs)
    • Comments on Notebooks will send email notifications to collaborators with more detail. (docs)
  • A new Text Choice data type lets admins define a set of expected text values for a field. (docs)
  • Naming patterns are validated during sample type definition, and example names are visible to users creating new samples or aliquots. (docs)
  • User-defined barcodes can be included in Sample Type definitions as text or integer fields and are scanned when searching samples by barcode. (docs | docs)
  • Editable grids include visual indication when a field offers dropdown choices. (docs)
  • Add freezer storage units in bulk (docs)
  • If any entities are named using only digits as names, these could create ambiguities if overlapped with the "rowIDs" of other entities, producing unintended results or lineages. With this release, such ambiguities will be resolved by assuming a name has been provided. (docs)
  • Freezer Management for Biologics: Create a virtual match of your physical storage system, and then track sample locations, availability, freezer capacities, and more. (docs)
  • Samples can be gathered on user-curated picklists to assist in many bulk actions. (docs)
  • Workflow job sample lists, and other grid views containing samples of different types, offer tabs for viewing all the samples of each individual type as well as a consolidated tab showing all samples. (docs)
  • When a workflow job includes samples, tasks that import assay data will auto-populate the assigned samples. (docs)
  • Additional formatting options available for electronic lab notebooks, including special characters. (docs)

The symbol indicates a feature available in a Premium Edition of LabKey Server.

The symbols indicate an additional feature available with the Panorama Partners Program

Previous Release Notes: Version 21.11




Upcoming Features


Upcoming Features

Releases we are currently working on:

Recent Documentation Updates




Release Notes: Version 22.7 (July 2022)


Here's what we're working on for LabKey version 22.7 (July 2022).

LabKey Server

Samples and Data Classes

  • Include lookups to ancestor columns in sample grids.
  • The name of a Data Class or Sample Type can now be edited later. (docs | docs)
  • Sample Types, Source Types, and Data Classes defined in the /Shared project will also be available for use in LabKey Sample Manager and LabKey Biologics projects. (docs | docs)
  • Commas are supported, though not recommended, in Sample and Data Class entity names. (docs)

Reports

  • Export python reports in a format that Jupyter can ingest.

Study

  • Clearer interface for defining and using custom study properties. (docs)

Wikis

  • Use wiki aliases to redirect legacy links when page names change. (docs)

Issue Trackers

  • Set a default folder in which to create any related issues. (docs)

RedCap Integration

  • Duplicate multichoice field lists will only be imported once for matching key/value pairs, improving performance of reloading studies from RedCap. (docs) Also available in release 22.3.3.

Panorama

  • Improved and streamlined QC Plot user interface. (docs) These changes are also available in version 22.3.4.
    • When showing all series in a single plot, hovering over a point will highlight the selected series.
    • Points in plots are no longer shown as different shapes; all points are now circles, with excluded data shown as an open circle.
    • Streamlined interface for QC plots, including removal of the small/large option, adjusted spacing for better display, and rearrangement of the plot checkboxes and options.
  • Support for crosslinked peptides, including improvements in multi-attribute method reporting about how and where peptides are linked. (docs) Also available in version 22.3.6.
  • Show peak area or quality info in the protein sequence view.
  • Copy Panorama QC folders, including annotations, guide sets, and customized view settings, to facilitate easier publication on Panorama Public.
  • Consistency improvements in the interface for excluding/including precursors and viewing grids.
  • Include full +/- 3 standard deviation range in QC plots.

Administration

  • Administrators can configure a warning when the number of active users approaches a set limit. The option to prevent creation of new users past a given number is also available. Premium Resource Available
  • New options to clear all objects and reset default selections on the export folder/study objects page make it easier to select the desired content of a folder or study archive. (docs)

Premium Resources

Distribution Changes and Upgrade Notes

  • Administrators should ensure that none of the "example webapps" shipped with Tomcat (e.g., examples, docs, manager, and host-manager) are deployed. Deploying these on a production instance creates a security risk. If any are found (on production mode servers only), the administrators will see a warning banner, beginning with version 22.6.
  • Beginning with version 22.6 (June 2022), the Oracle JDBC driver is included with all Premium Edition distributions. Our clients no longer need to download and install this driver themselves, and will need to delete any Oracle driver in the previous location (<CATALINA_HOME>/lib) to avoid a version conflict.

Backwards Compatibility Notes

  • LabKey no longer accepts the JSESSIONID in place of the CSRF token. All POST requests must include a CSRF token. (docs)
  • The default container filter for viewing Data Class entities has been changed from "CurrentPlusProjectAndShared" to "Current", i.e. only the current container. This may result in seeing fewer entities than previously; you can restore the prior behavior using the grid customizer. (docs)

Dependency Changes

Developer Resources


Sample Manager

Sample Manager Release Notes listing features by monthly version.

  • Electronic Lab Notebooks available in Sample Manager
  • Rename Samples without losing history or lineage.
  • Export tabbed multi-tab sample grids as multi-tabbed Excel files.
  • Custom saved grid views
  • Export data from an 'edit in grid' panel - most useful in assay data
  • Save time looking for samples and create standard sample reports by saving your Sample Finder searches to access later. (docs)
  • Support for commas in Sample and Source names. (docs)
  • Administrators will see a warning when the number of users approaches the limit for your installation. (docs)
  • Updated grid menus: Sample grids now help you work smarter (not harder) by highlighting actions you can perform on samples and grouping them to make them easier to discover and use. (docs)
  • Revamped grid filtering and enhanced column header options for more intuitive sorting, searching and filtering. (docs)
  • Sort and filter based on 'lineage metadata', bringing ancestor information (Source and Parent details) into sample grids (docs)
  • Rename Source Types and Sample Types to support flexibility as your needs evolve. Names/SampleIDs of existing samples and sources will not be changed. (docs)
  • Descriptions for workflow tasks and jobs can be multi-line when you use Shift-Enter to add a newline. (docs)
  • In the Sample Finder, apply multiple filtering expressions to a given column of a parent or source type. (docs)
  • Download data import templates from more places, making it easier to import samples, sources, and assay data from files. (docs)

Biologics

Biologics release notes listing features by monthly version.

  • Export tabbed multi-tab sample grids as multi-tabbed Excel files.
  • Custom saved grid views
  • Export data from an 'edit in grid' panel - most useful in assay data
  • Biologics subfolders are now 'projects'
  • Compound Registry type added to support use of SMILES (Simplified Molecular Input Line Entry System).
  • Save time looking for samples and create standard sample reports by saving your Sample Finder queries to access later.
  • Support for commas in Sample and Bioregistry (Data Class) entity names. (docs)
  • Export a signed and human readable ELN snapshot, reliably recording your work.
  • Update existing bioregistry entries with merge option on data class file import, edit data classes including lineage, in a grid or in bulk
  • Images in ELN notebooks will load more quickly
  • ELN entries can include checkboxes
  • Bioregistry entities include a Common Name field
  • Define and edit Bioregistry entity lineage
  • Updated grid menus: Sample and registry grids now help you work smarter (not harder) by highlighting actions you can perform and grouping them to make them easier to discover and use. (docs | docs | docs)
  • Revamped grid filtering and enhanced column header options for more intuitive sorting, searching and filtering. (docs)
  • Sort and filter based on 'lineage metadata', bringing ancestor information (Source and Parent details) into sample grids. (docs)
  • Rename Data Classes and Sample Types to support flexibility as your needs evolve. Names/SampleIDs of existing samples and bioregistry entities will not be changed. (docs | docs)
  • Update Data Class members (i.e. Registry entities) via file import. (docs)
  • Descriptions for workflow tasks and jobs can be multi-line when you use Shift-Enter to add a newline. (docs)
  • Download templates from more places, making file imports easier. (docs)
  • Share freezers across multiple Biologics subfolders. (docs)
  • Manage user accounts and permissions assignments within the Biologics application. (docs)
  • Full text search will find results across Bioregistry entities, samples, notebooks, and more. (docs)
  • Use the Sample Finder to find samples based on parent properties, giving users the flexibility to locate samples based on bioregistry details and lineage details. (docs)

Client APIs and Development Notes

  • Version 1.5.0 of the LabKey Java API (labkey-client-api) has been published.
    • There is an accompanying v1.1.1 of labkey-api-jdbc, which updates the dependency version for labkey-client-api.
  • Upgrade to version 4.2.0 of R.
  • API Resources

The symbol indicates a feature available in a Premium Edition of LabKey Server.

Previous Release Notes: Version 22.3