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2022-08-10
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   Release Notes: Version 22.7 (July 2022)
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     Release Notes 22.11 (November 2022)

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LabKey ELN Documentation

LabKey Biologics Documentation

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What's New in 22.7


We're delighted to announce the release of LabKey Server version 22.7.

Highlights of Version 22.7

LabKey Server

  • Import Python reports from Jupyter Notebook for generating and sharing live LabKey data reports. (docs)
  • Sample Types and Data Classes are easier to use with improved editing of table names and ids. (docs)
  • Include ancestor metadata in grids for a more complete picture of your samples. (docs)
  • Administrators will find it easier to export folders with options to clear all objects and reset default selections. (docs)

Sample Manager

  • Electronic Lab Notebooks: Use a data-aware ELN to record and track your Sample Manager work. (docs)
  • Save time looking for samples and create standard reports by saving your Sample Finder searches to access later. (docs)
  • Revamped grid filtering for more intuitive sorting, searching and filtering. (docs)

Biologics

  • New Compound Bioregistry type supports Simplified Molecular Input Line Entry System (SMILES) strings, their associated 2D structures, and calculated physical properties. (docs)
  • Electronic Lab Notebook (ELN) Improvements:
    • Export a signed and human-readable ELN snapshot, reliably recording your work. (docs)
    • Entries can include checkboxes for tracking tasks. (docs)
    • Images added to ELN notebooks will be automatically stored as attachments, for increased efficiency. (docs)
  • Bioregistry entities can now be updated via file import, edited in the UI, and include a "Common Name" for ease of use. (docs)

Premium Resources

Release Notes


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




Release Notes: Version 22.7 (July 2022)


Here are the full release notes for LabKey version 22.7 (July 2022).

LabKey Server

Samples and Data Classes

  • Include ancestor metadata in grids for a more complete picture of your samples. (docs)
  • The name of a Data Class or Sample Type can now be changed. (docs | docs)
  • The name of a Sample can now be changed, provided it remains unique. (docs)
  • Commas are supported in Sample and Data Class entity names. (docs)
  • Sample Types, Source Types, and Data Classes defined in the Shared project are available for use in LabKey Sample Manager and LabKey Biologics projects. (docs | docs)

LabKey SQL

  • The functions is_distinct_from(a,b) and is_not_distinct_from(a,b) have been added; they treat nulls as ordinary values. (docs)

Reports

  • Import python reports from Jupyter Notebook for generating and sharing live LabKey data reports. (docs)

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 multi-choice 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

  • Protein Sequence Coverage maps provide a heatmap style view of peptide intensity and confidence scores. (docs)
  • Include annotations, guide sets, and customized view settings when you export or copy a Panorama QC folder. (docs)
  • Consistency improvements in the interface for excluding/including precursors and viewing grids. (docs)
  • Option to split precursor and transition series on chromatogram plots. (docs)
  • Quick links make it easier to subscribe to per-folder outlier email notifications. (docs)
  • 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 highlights 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.
    • Always include full +/- 3 standard deviation range in QC plots.
  • 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.
  • The Panorama Release Notes on PanoramaWeb list features by version.

Administration

  • Administrators can configure a warning when the number of active users approaches a set limit. The option to prevent the 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)
  • Export query validation results to assist in resolving issues. (docs)
  • All field designers now display lookup table references as clickable links to provide easy navigation for viewing and editing their values. (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. Beginning with version 22.6, if any are found on a production-mode server, administrators will see a warning banner. (docs)
  • 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. (docs)
  • The Microsoft SQL Server JDBC driver is now supported. In a future release, support for the jTDS driver will be removed. (docs | docs)

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

The Sample Manager Release Notes list features by monthly version.
  • Our user-friendly ELN (Electronic Lab Notebook) is designed to help scientists efficiently document their experiments and collaborate. This data-connected ELN is seamlessly integrated with other laboratory data in the application, including lab samples, assay data and other registered data. (docs) Available in the Professional Edition of Sample Manager and with the Enterprise Edition of LabKey Server.
  • Make manifest creation and reporting easier by exporting sample types across tabs into a multi-tabbed spreadsheet. (docs)
  • All users can now create their own named custom views of grids for optimal viewing of the data they care about. Administrators can customize the default view for everyone. (docs)
    • Create a custom view of your data by rearranging, hiding or showing columns, adding filters or sorting data. (docs)
    • With saved custom views, you can view your data in multiple ways depending on what’s useful to you or needed for standardized, exportable reports and downstream analysis. (docs)
    • Customized views of the audit log can be added to give additional insight. (docs)
  • Export data from an 'edit in grid' panel, particularly useful in assay data imports for partially populating a data 'template'. (docs | docs)
  • Newly surfaced Picklists allow individuals and teams to create sharable sample lists for easy shipping manifest creation and capturing a daily work list of samples. (docs)
  • Updated main dashboard providing quick access to notebooks in the Professional Edition of Sample Manager. (docs)
  • Samples can now be renamed in the case of a mistake; all changes are recorded in the audit log and sample ID uniqueness is still required. (docs)
  • The column header row is 'pinned' so that it remains visible as you scroll through your data. (docs)
  • Deleting samples from the system entirely when necessary is now available from more places, including the Samples tab for a Source. (docs)
  • 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 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. (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

The Biologics release notes list features by monthly version.
  • Make manifest creation and reporting easier by exporting sample types across tabs into a multi-tabbed spreadsheet. (docs)
  • Export data from an 'edit in grid' panel, particularly useful in assay data imports for partially populating a data 'template'. (docs | docs)
  • Biologics subfolders are now called 'Projects'; the ability to categorize notebooks now uses the term 'tags' instead of 'projects'. (docs | docs)
  • Newly surfaced Picklists allow individuals and teams to create sharable sample lists for easy shipping manifest creation and capturing a daily work list of samples. (docs)
  • Updated main dashboard, providing quick access to notebooks and associated tasks. (docs)
  • Custom properties in notebooks are now an 'experimental feature'. You must enable them if you wish to continue using them. (docs)
  • All users can now create their own named custom views of grids for optimal viewing of the data they care about. Administrators can customize the default view for everyone. (docs)
    • Create a custom view of your data by rearranging, hiding or showing columns, adding filters or sorting data.
    • With saved custom views, you can view your data in multiple ways depending on what’s useful to you or needed for standardized, exportable reports and downstream analysis.
    • Customized views of the audit log can be added to give additional insight.
  • Samples can now be renamed in the case of a mistake; all changes are recorded in the audit log and sample ID uniqueness is still required. (docs)
  • The column header row is 'pinned' so that it remains visible as you scroll through your data. (docs)
  • Deleting samples from the system entirely when necessary is now available from more places in the application, including Picklists. (docs)
  • New Compound Bioregistry type supports Simplified Molecular Input Line Entry System (SMILES) strings, their associated 2D structures, and calculated physical properties. (docs)
  • Export a signed and human-readable ELN snapshot, reliably recording your work. (docs)
  • Update existing bioregistry entries with merge option on data class file import, edit data classes including lineage, in a grid or in bulk. (docs)
  • Define and edit Bioregistry entity lineage. (docs)
  • Support for commas in Sample and Bioregistry (Data Class) entity names. (docs)
  • Images added to ELN notebooks will be automatically stored as attachments, for increased efficiency. (docs)
  • ELN entries can include checkboxes for tracking tasks. (docs)
  • Bioregistry entities include a "Common Name" field. (docs)
  • Updated grid menus: Sample and registry grids now help you work smarter 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

  • We have moved our Artifactory server from artifactory.labkey.com to labkey.jfrog.io. Learn more about this migration and steps you may need to take in this announcement on our public support forum.
  • Version 2.0.0 of the LabKey Java API (labkey-client-api) has been published. LabKey Java API v2.0.0 requires Java 17. LabKey Java API v1.5.2 is available if support for Java 8 - 16 is needed. (artifactory)
  • Version 2.0.0 of the LabKey JDBC driver has been released and will be included in all future Professional and Enterprise distributions. LabKey JDBC driver v2.0.0 requires Java 17. LabKey JDBC driver v1.1.2 is available if support for Java 8 - 16 is needed.
  • Upgrade to version 4.2.0 of R.
  • WebDAV support has been added to the Python API (docs)
  • API Resources: Links to current API resources including documentation and distributions.

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

Previous Release Notes: Version 22.3




Upcoming Features


Upcoming Features

Releases we are currently working on:

Recent Documentation Updates




Release Notes 22.11 (November 2022)


Here are the full release notes for LabKey version 22.7 (July 2022).

LabKey Server

Samples and Data Classes

Panorama

  • Protein grouping
  • 1 based instead of 0 based sequences

Distribution Changes and Upgrade Notes

  • The Microsoft SQL Server JDBC driver is now supported. In a future release, support for the jTDS driver will be removed. (docs)

Developer Resources


Sample Manager

The Sample Manager Release Notes list features by monthly version.


Biologics

The Biologics release notes list features by monthly version.


Client APIs and Development Notes


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

Previous Release Notes: Version 22.7