Release Notes

 2024-04-16

Version 23.11, released November 2023

  • Panorama is compatible with the Skyline 23.1 file format beginning with version 23.7.3. (learn more)

LabKey Server General Enhancements

  • The page for managing short URLs uses a standard grid, making it easier to use and faster to load. (docs)
  • Administrators can improve security by selecting a new, stronger, entropy-based password rule. Site administrators of production deployments will now see a warning if they use the "Weak" password option, which will be removed entirely in the next major release. (docs)
  • Individual fields in Lists, Datasets, Sample Types, and Data Classes, can be defined to require that every value in that column of that table must be unique. (docs)
View the full LabKey Server 23.11 release notes.

Version 23.7, released July 2023

  • Use a Calendar View to easily visualize performance and utilization of instruments over time. (docs) Also available in 23.3.6
  • Improved outlier indicators make it easier to see the severity of an issue at a glance. (docs) Also available in 23.3.6
  • Panorama will be compatible with the upcoming Skyline 23.1 file format beginning with version 23.7.3.

LabKey Server General Enhancements

  • Permissions for an existing user can be updated to match those of another user account. (docs)
  • Export a folder archive containing metadata-only by excluding all data. (docs)
  • Administrators can configure the retention time for audit log events. (docs)
View the full LabKey Server 23.7 release notes.

Version 23.3, released March 2023

  • New Panorama MAM report for early-stage post-translational modification (PTM) with improved formatting and layout. (docs)
  • New QC plots let you track the trailing mean and %CV of any QC folder metric over a specified number of runs. (docs) Also available in 22.11.6.
  • An example of using a custom run-scoped metric has been added to the documentation and examples available on PanoramaWeb. Capture and track Peptide ID Count following these steps. (example)

LabKey Server General Enhancements

  • Enhancements have been made to clarify the options of importing new data, updating existing data, and merging both update and new data in the same import. (docs)
  • Administrators are now proactively warned about "unknown modules," modules that were previous installed but no longer exist in the current deployment. Administrators are encouraged to delete these modules and their schemas. (details)
View the full LabKey Server 23.3 release notes.

Version 22.11, released November 2022

Panorama

  • Protein groups (mapping a peptide to multiple possible proteins) will be represented in Panorama folders when a Skyline document. (docs) Also available in version 22.7.2.
  • Performance and plotting improvements for QC folders with many samples. (docs)
  • Support for z+1 and z+2 ions.
  • Amino acid indices within protein sequences are based at 1 (instead of 0) for consistency with Skyline. (docs) Also available in version 22.7.2.

LabKey Server General Enhancements

  • New role available: Editor without Delete. Users with this role can read, insert, and update information but cannot delete it. (docs)
  • Lists can use definitions that are shared across multiple containers, improving the ability to use them for cross-folder data consistency. (docs)
View the full LabKey Server 22.11 release notes.

Version 22.7, released July 2022

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.

LabKey Server General Enhancements

  • Use wiki aliases to redirect legacy links when page names change. (docs)
  • 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)
View the full LabKey Server 22.7 release notes.

Version 22.3, released March 2022

Panorama

  • Configure which peptide and small molecule precursors are tracked for system suitability, 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.

Distribution Changes

Upcoming Distribution Changes

  • Beginning with LabKey Server 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 22.4 (April 2022), support for Microsoft SQL Server 2012 as the primary database for LabKey Server will be removed. Before upgrading, your database will need to be upgraded to a supported version of Microsoft SQL Server.
View the full LabKey Server 22.3 release notes.

Version 21.11, released November 2021

Panorama

  • When viewing a protein or molecule list, multiple peptides and molecules chromatograms are plotted together. (docs)
  • Monitor iRT metrics (slope, intercept, and r-squared correlation) to track system suitability. (docs)
  • Integrate Panorama with LabKey Sample Manager (docs)

Operations/Development

  • Release 21.11 of LabKey Server no longer supports Java version 14 or 15. We recommend upgrading to Java 17 for long term support. (docs)
    • Running under JDK 16 or 17 still requires use of special JVM flags. (docs)
  • Support for PostgreSQL 9.6 has been removed. Before upgrading, PostgreSQL must be upgraded to a supported version.

Upcoming Distribution Changes

View the full LabKey Server 21.11 release notes.

Version 21.7, released July 2021

Panorama

  • Reproducibility Report - Now integrated into chromatogram libraries, assess inter- and intra-day variation based on raw, normalized, or calibrated values, along with calibration curve and figures of merit data. (docs)
  • Improved navigation and summarization for calibration curve and figure of merit reporting. (docs) | (docs)
  • Pressure Traces - In QC folders, use pressure traces as sources for metrics to monitor for system suitability and identify column and other problems. (docs)

Operations/Development

  • Support for PostgreSQL 9.5.x has been removed. Before upgrading, PostgreSQL must be upgraded to a supported version.
  • Support for Apache Tomcat 8.5.x has been deprecated and will be removed in 21.8.0. Please upgrade to Tomcat 9.0.x ASAP. (docs)
  • The build has been updated to use Gradle 7, which now allows building LabKey from source with JDK 16. Running under JDK 16 still requires use of a couple special JVM flags. (docs)
View the full LabKey Server 21.7 release notes.

Version 21.3, released March 2021

Panorama

  • Link from Experiment data to QC folder - Panorama automatically links data in Experiment folders to the QC folder(s) that contain data from the same instrument, making it quick to see how the instrument was performing at the time of acquisition. (docs)
  • Instrument summary on replicate page - Easily see which instruments acquired the data in a Skyline document. (docs)
  • Always include guide set data in QC plots - When zooming in to view QC data for a specific date range, juxtapose the guide set data that's being used to identify outliers. (docs)
  • MxN reproducibility reports - New reporting summarizes intra- and inter-day variability for peptides within a protein to assess its reproducibility. (docs)
  • PDF and PNG plot exports - Many Panorama reports are now rendered as vector-based plots in the web browser for better clarity and offer PDF and PNG export formats. (docs | docs)
  • Reduced memory usage during import - Importing large Skyline documents uses 80% or less memory, offering much better performance and scaling. (docs)
  • Enhanced chromatogram library exports - Chromatogram libraries (.clib files) now include additional optimization and ion mobility information. (docs)

Operations/Development

  • Java 13 No Longer Supported - LabKey has removed support for JDK 13. Before upgrading LabKey Server, Java must 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 the latest point releases: AdoptOpenJDK 15 64-bit (x64) with HotSpot JVM, Tomcat 9.0.x, and PostgreSQL 13.x.
  • Upgrade Instructions - Follow the steps in this topic to upgrade to the latest release of LabKey Server: Upgrade Instructions
  • Support for running under the upcoming JDK 16 release is available with use of a special flag. You cannot yet build LabKey from source with JDK 16. Learn more here: docs
  • Microsoft SQL Server (and all other non-PostgreSQL database connections) are supported only in Premium Edition distributions. The BigIron module, which provides support for Microsoft SQL Server, Oracle, MySQL, and SAS/SHARE, has moved to Premium Edition distributions.
View the full LabKey Server 21.3 release notes.

Version 20.11, released November 2020

Panorama

  • Refinements to Multi-attribution Methods Reports - Peptide reporting shows more information of interest. (docs)
  • Small Molecule Chromatogram Libraries - Curate and export chromatogram libraries for small molecules in addition to proteomics data. (docs)
  • 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)

Operations/Development

  • Completed migration of LabKey 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. (docs)
  • Updates to module.properties file handling
  • Security Update: 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.
View the full LabKey Server 20.11 release notes.

Version 20.7, released July 2020

Panorama

  • Panorama QC Performance - Performance improvements when reporting on QC folders with high data volume. (docs)
  • Skyline Audit Log - Improvements to import and display of Skyline document's audit log. (docs)
  • 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.

Operations

  • 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.
  • 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, we strongly recommend you also upgrade all major LabKey dependencies to their latest point releases. (docs)
  • Upgrade Instructions - Follow the steps in this topic to upgrade to the latest release of LabKey Server: Upgrade LabKey Server
View the full LabKey Server 20.7 release notes.

Version 20.3, released March 2020

  • Month-based Version Names - A new month-based naming pattern has been adopted for LabKey Server. This March 2020 release is named 20.3; the next production release in July 2020 will be 20.7.

Panorama

  • Skyline Document Version Updates - Updates to Panorama to ensure full compatibility with changes to Skyline's file format.
  • Sample File Scoped Chromatograms - Display and provide API access to chromatogram-style data contained within Skyline documents. (docs)
  • Multi Attribute Method (MAM) reporting - To support MAM analysis, Panorama now includes a post-translational modification (PTM) report that shows the percent of peptides that included tracked PTMs across samples, as well as a Peptide ID report that shows the identified peptides with their retention times, and expected and observed masses.

Operations

  • Important Security Update - LabKey Server 20.3 includes an important security update, which has been back-ported to version 19.3.7. We strongly recommend that you upgrade your servers to at least 19.3.7 to pick up this security update.
  • AdoptOpenJDK 13 - Starting with LabKey Server 20.3.0, we recommended AdoptOpenJDK 13 for new installations and upgrades. (docs)
  • 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. (docs)
View the full LabKey Server 20.3 release notes.

Version 19.3, released November 2019

Panorama

  • Panorama Premium: Auto-enabling Metrics - Metrics are shown when relevant data is detected; these metrics are hidden when relevant data is not detected. (docs)
  • Skyline List Support - Lists defined in Skyline are imported and available in Panorama folders. (docs)
  • Isotopologue Metrics - Plot isotopologue metrics including LOD and LOQ when data is available from Skyline. (docs)
  • Total Ion Chromatogram Metric - In QC folders, track the total ion chromatogram area as a metric, scoped to the entire run. (docs)
  • Skyline Audit Log - Import the Skyline audit log into Panorama. (docs)

Version 19.2, released July 2019

Panorama

  • Zip files during upload - .raw and .d directories or raw data files (from Agilent, Waters, and Bruker instruments) are automatically zipped before upload to a Panorama files repository. (docs)
  • Premium Features for Panorama Partners: New features available exclusively to members of the Panorama Partners Program and on PanoramaWeb.org:
    • Panorama Premium: Outlier Notifications - Subscribe to email notifications for new QC folder data imports, or only when the number of outliers in a series of imports is over a threshold. (docs)
    • Panorama Premium: Configure QC Metrics - Configure which QC metrics are used for analysis. (docs)

Operations

  • MS1 Module Removed - The MS1 module has reached end of life and due to lack of usage, has been removed.
  • Internet Explorer - End of Support - LabKey no longer supports Internet Explorer. For details, see supported browsers.
  • Upgrade to Java 12 - Oracle has ended public support for Java 11, and as a result, LabKey has completely removed support for Java 11 in the 19.2.0 release. For details, see supported Java versions.
  • Upgrade Tomcat Version - If you are using Tomcat 7 or 8, be sure to update to the latest point release. LabKey Server version 19.2.0 will be incompatible with Tomcat releases prior to 7.0.76 or 8.5.12. If you are using an incompatible version, you may see JSP compilation errors. Tomcat 9 releases (beginning with 9.0.0) are compatible and will not see these errors. For details, see supported Tomcat versions.

Development

  • Source Code Migration to GitHub - Core LabKey Server modules have been migrated from SVN to GitHub, as well as the central automated test code and all of the modules from server/customModules. (docs | docs)
  • Performance improvements by caching virtual schema metadata - Database schema metadata has always been cached, but beginning with release 19.2.x, table and column metadata for user schemas (i.e., virtual schemas) is also cached per request. This improves performance when processing complex queries.

Version 19.1, released March 2019

Panorama

  • Improved Replicate Views - The replicate view of a Skyline document now highlights the annotations present in that single file, as well as showing more information about the samples being used.
  • QC Folder Optimizations - Page load times for QC folders with substantial amounts of data should be improved.
  • Import Optimizations - The time required to import a Skyline document has been reduced, by 50% or more in many cases.

Security

  • See User and Group Details Role - Allow non-administrators to see email addresses and contact information of other users as well as information about security groups. (docs)
  • Enforce CSRF Checking - All POST requests must include a CSRF token. This is no longer a configurable option. (docs)

Sample Management

  • Sample Set Updates - The sample set creation and import pages have been streamlined and standardized. Performance has been improved when importing large sample sets, as well as for query and update operations. (docs).

Administration

  • Configure Allowable External Redirects - Create a whitelist of allowable redirects to external sites. (docs)

Operations

  • Upgrade to Java 12 - We strongly recommend upgrading your server installations to Oracle OpenJDK 12 as soon as possible. 19.1.x installations will continue to run on Java 11, but site administrators will see a warning banner. Oracle has ended public support for Java 11; as a result, LabKey will completely remove support for Java 11 in the 19.2.0 release. For details see Supported Technologies.
  • Remove Support for Java 8 - Oracle ended public support for Java 8 in January 2019; as a result, LabKey Server no longer supports Java 8. For details, see Supported Technologies.

Potential Backwards Compatibility Issues

  • Remote API Date Format Change - The date format in JSON responses has been changed to include milliseconds: "yyyy-MM-dd HH:mm:ss.SSS". In previous releases the following format was used: "yyyy/MM/dd HH:mm:ss".
  • Removal of Legacy JFree Chart Views - Existing charts of these older types are rendered as JavaScript charts. No action is needed to migrate them. (docs)
  • Legacy MS2 Views - Options in the Grouping and Comparison views previously marked as "legacy" have been removed.
  • User and Group Details Access Change - Access to contact information fields in the core.Users and core.SiteUsers queries, the core.Groups query, and the getGroupPerms API now require the Administrator or "See User and Group Details" role.
  • External Redirects Change - External redirects are now restricted to the host names configured using the new Configure Allowable External Redirects administration feature. The 18.3.x experimental feature that unconditionally allowed external redirects has been removed.
  • POST Method Required for Many APIs - Many LabKey APIs and actions have been migrated to require the POST method, which has security benefits over GET. The LabKey client APIs have been adjusted to call these server APIs using POST, but code that invokes LabKey actions directly using HTTP may need to switch to POST.

Upcoming Changes

  • End of Support for IE 11 - Support for IE 11 will end in the upcoming LabKey Server 19.2.0 release, scheduled for July 2019. Please contact us for workaround options if this change strongly impacts you. (docs)

Version 18.3, released November 2018

Panorama

  • Normalized Y-axes in QC Plots - Support for normalizing Levey-Jennings and Moving Range plots using percent of mean or standard deviation as the zero point on the Y-axis. (docs)
  • Improved Figures of Merit performance - Rendering performance for the Figures of Merit report has been improved. (docs)
  • Read Chromatograms Directly from SKYD files - An experimental feature allows you to read chromatograms directly from SKYD files instead of storing them in the database. (docs)

Administration

  • Subfolder Web Part - This web part shows the subfolders of the current location; included in new collaboration folders by default. Also available in the 18.2 release. (docs)
  • Connect to Existing Amazon S3 Directories - Connect to an existing S3 directory or create a new one for each LabKey folder. (docs)
  • Improved Navigation Menu - The project menu and any custom menus you define have a more consistent interface, and each contain graphical elements signaling that they are interactive elements. You can also access the project menu from the admin console. (docs)

Reporting and Visualization

  • Scatter and Line Plot Enhancements - Specify multiple Y axes. Show all data on a single plot or display separate plots per measure. (docs | docs)

Development and APIs

  • NaN and Infinity Values - LabKey SQL supports constants NaN, INF, and -INF. (docs)

Potential Backwards Compatibility Issues

  • Changes to CSRF Setting - At 18.3 upgrade time, the CSRF checking setting on all servers will be set to "All POST requests". Site administrators will have the ability to revert back to "Admin requests" for deployments that still need to make their external modules or custom pages compatible with this setting. For release 19.1, we plan to remove the setting entirely and check CSRF tokens on every POST (except for specially annotated actions). When servers are protecting against CSRF attacks, they will require the following minimum versions: Skyline - 4.2; Skyline-daily - 4.1.1.18151; AutoQC Loader - 1.1.0.18302 (docs)

Operations

  • Support for Java 11 - We recommend upgrading your server installation to Java 11. Oracle is expected to end public support for Java 8 in January 2019, and, as a result, LabKey Server will no longer support Java 8 for the 19.1 release. For details see Supported Technologies.
  • Support for PostgreSQL 11 - PostgreSQL 11.1 and above is supported (not the initial PostgreSQL 11.0 release). For details, see Supported Technologies.
  • Remove support for PostgreSQL 9.3 - PostgreSQL 9.3 reached end-of-life in November 2018. We recommend upgrading your PostgreSQL installation to version 10 or later. For details, see Supported Technologies.
View the full LabKey Server 18.3 release notes.

Version 18.2, released July 2018

Panorama

  • Improved Pharmacokinetic Report - Pharmacokinetic (PK) calculations are provided per subgroup, replicate annotations are included, and non-IV routes of administration are supported. (docs)
  • LOD/LOQ Skyline Compatibility - Limit of Detection (LOD) is now shown in Panorama, and there is support for additional Limit of Quantitation (LOQ) configuration as defined in Skyline. (docs)

System Integration

  • Spotfire Integration - Use data stored in LabKey Server to create Spotfire visualizations. (docs)

LabKey SQL

  • Common Table Expressions - Use a SQL "WITH" clause to simplify complex queries and create recursive queries. (docs)

Development

Potential Backward Compatibility Issues

  • Changes to CSRF Default Setting In 18.2, we have switched the default CSRF checking setting (affecting only new servers) to "All POST requests". We recommend that all clients run their servers with the "All POST requests" setting, ideally on production servers but at a minimum on their tests/staging servers. In the upcoming 18.3 release, we plan to force the setting (on all existing servers at upgrade time) to "All POST requests". We will retain the ability to revert back to "Admin requests" for deployments that still need to make their external modules or custom pages compatible with this setting. For release 19.1, we plan to remove the setting entirely and check CSRF tokens on every POST (except for specially annotated actions).

Operations

  • Tomcat 8.0.x is no longer supported - If you are using Tomcat 8.0.x, you should upgrade to 8.5.x at your earliest convenience. No configuration changes in LabKey Server are necessary as part of this upgrade. For details see Supported Technologies.
  • Connection Pool Size - We recommend reviewing the connection pool size settings on your production servers. For details, see Troubleshooting.
View the full LabKey Server 18.2 release notes.

Version 18.1, released March 2018

Panorama

  • Pharmacokinetic Calculations - See the stability, longevity, and uptake of compounds of interest. (docs)
  • Figures of Merit for Quantitation Data - Summary statistics show the mean, standard deviation, and %CV for the replicates, along with lower limit of detection, quantitation, etc. (docs)

Collaboration

  • Files Table - All files under @files, @pipeline, and @filesets in a container can be managed using a new exp.Files table. Developers can use exp.Files to programmatically control all files at once. (docs)
  • Messages Default to Markdown - Markdown is a simple markup language for formatting pages from plain text, similar to LabKey's Wiki syntax. The Messages editor window includes a Markdown syntax key and message preview tab. (docs)

Security

  • New Role: See Absolute File Paths - A new site-level role allows users to see absolute file paths in the File Repository. (docs)
  • Impersonation Auditing - Audit records are created when a user starts or stops impersonating a role or group. docs)
  • API Keys - Client code can access the server using API keys. Administrators can allow users to obtain new API keys and manage when keys expire. (docs)
  • Captcha for Self Sign-up - Self-registration now includes a captcha step to prevent abuse by bots. (docs)
  • Cross-Site Request Forgery (CSRF) Protection Changes - All LabKey pages have been tested and updated to protect against CSRF. We recommend that site admins change the default CSRF protection setting to "All POST requests" to enable this increased protection. This may cause issues with custom pages that are not configured to submit CSRF tokens when doing an HTTP POST. For details see the Potential Backwards Compatibility Issues section below.

Operations

Potential Backwards Compatibility Issues

  • New Cross-Site Request Forgery Protection (CSRF) Recommendation - We recommend that administrators begin the process of converting their servers from the current default CSRF protection setting of "Admin requests" to "All POST requests". The more stringent security setting may cause issues for custom pages that submit HTTP POST requests. If you have no custom pages or forms, we recommend that you immediately change the CSRF setting for all test, staging, and production servers running 18.1. If you have custom pages and forms, we recommend that you begin testing on your test and staging servers. In a future release, LabKey Server will enforce that all HTTP POSTs include the CSRF token, at which point all custom pages will be required to be do so. For details on configuring custom pages with CSRF protection, see here.
View the full LabKey Server 18.1 release notes.