22.05

• [ALL]: Upgraded to Spring Boot 2.6.6 which fixes CVE-2022-22965. (22.03.1)
• [Developer/UI]: Fixed Project details to be transactional to resolve scalability issue on large projects >5000 samples. (22.03.1)
• [Developer/UI]: Fixed updates in UI service classes to use @transactional annotation to fix scalability issue on large projects >5000 samples. (22.03.1)
• [Developer]: Add --no-yarn to skip the yarn build in run.sh
• [Developer]: Updated frontend dependencies: babel, eslint, postcss, and webpack
• [Database]: Updated group and user project queries to improve performance for all pages/calls that depend on project permissions.
• [UI]: Updated Create Remote Api to use Ant Design.
• [UI]: Removed old bootstrap client details/edit page and updated with a modal on the clients listing page.
• [UI]: Updated Dashboard Recent Activity to use Ant Design.
• [Developer]: Updated to Ant Design v4.19.3.
• [Developer]: Removed unused DataTables code.
• [UI]: Sorted columns for advanced charts and added labels to tiny charts on admin statistics page.
• [UI]: Fixed: Allow organism name not included in the current taxonomy.
• [Developer]: Removed prop-types as a front-end development dependency.
• [UI]: Updated User and Admin help documentation URLs.
• [Developer/UI]: Refreshed the user account page.
• [UI]: Updated message displayed to user when an invalid reference file is uploaded while launching a workflow.
• [Developer]: Updated nodejs to v16.15.0 in the pom.xml file.
• [Developer]: Updated redux API within the cart page to use Redux Toolkit.
• [All]: Added functionality for project managers to restrict metadata fields depending on the Collaborator's metadata role on the project.
• [Developer]: Removed IRIDA virtual appliance build scripts and references in documentation.
• [Workflow]: Disable the built-in SISTR and the MentaLiST pipelines by default as they are deprecated. They can be re-enabled in /etc/irida/irida.conf.
• [Workflow]: Automated pipelines which become marked as disabled will now be prevented from running, similar to out-of-date automated pipelines.
• [Developer]: Upgrade to Apache POI 5.2.2, and switched to excel-streaming-reader 3.6.1 from xlsx-streamer 2.1.0
• [UI]: Added clarification that deleting or removing genomics data will not remove the underlying data files (e.g., sequencing data) but will only make it inaccessible.
• [UI]: Updated project samples page to use Ant Design.
• [Documentation]: Updated SNVPhyl install instructions since installing bcftools_view separately is no longer needed. Fixed broken link for sequence read test data. Removed Search option since it no longer works in our documentation.
• [UI]: Fixed: Excel output file preview displaying numeric values as a whole number rather than in scientific notation.
• [UI]: Updated the sequence run page to use Ant Design.
• [UI]: Updated forgot password, account activation, and reset password pages to use Ant Design.
• [Developer/Workflow]: Fixed issue with deleting AnalysisSubmission raising null pointer execptions due to bean wiring issue (issue #1287).

22.03.1

This release predominately fixes the SpringShell vulnerability, along with some small fixes for updates taking a long time on projects with a large amount of samples.

A summary of changes is below:

• [ALL]: Upgraded to Spring Boot 2.6.6 which fixes CVE-2022-22965. (22.03.1)
• [Developer/UI]: Fixed Project details to be transactional to resolve scalability issue on large projects >5000 samples. (22.03.1)
• [Developer/UI]: Fixed updates in UI service classes to use @Transactional annotation to fix scalability issue on large projects >5000 samples. (22.03.1)

22.03

This is a predominately a performance release that addressed a major scalability issue related to increasing number of Samples in a Project. All work completed in this release was done in !1211.

A summary of changes is below:

• [All]: Fixed scalability bug in updating Project modifiedDate during handling of ProjectEvent that was increasing in
  operation time as number of Samples increased within a project.
• [UI]: Fixed load times on Project Samples page.
• [UI]: Fixed text overflow issue in Command-line Linker modal.
• [UI]: Fixed bug with Command-line Linker modal making multiple requests to the server to get the command string.
• [UI]: Fixed issue with CSV/XLSX export on linelist page from not completing on massive projects >100,000 samples.
• [UI]: Adding in batch loading to linelist page (provides feedback to user, important on large projects >5000 samples)
• [UI]: Added a progress indicator when loading samples into the linelist table.
• [UI]: Added a warning notification when selecting all samples on the project samples page.

22.01.4

• [UI]: Fixed bug preventing updating of project details. (22.01.4)

22.01.3

• [REST]: Fixed bug that was preventing syncing remote projects from versions 20.09 and older. (22.01.3)

22.01.2

• [Documentation]: Fixed issue that prevented a user from saving analysis results back to a sample and concatenating sequence files. Fixed date format in Swagger REST API documentation. (22.01.2)

22.01.1

• [REST]: Corrected behaviour of date fields in REST API to return epoch instead of textual string. (22.01.1)
• [REST]: Fixed bug where analysis output file bytes were being included in responses when only JSON should have been sent. (21.09.1)
• [All]: Updated some dependency packages to latest versions to remove any Critical|High issues as reported by Grype https://github.com/anchore/grype. (21.09.2)
• [REST]: Fixed bug prevending REST API clients from updating the collectedDate on samples.
• [Developer]: Updated antd to version 4.16.13
• [Developer/UI]: Refreshed the metadata uploader.
• [Developer/UI]: Updated to the latest release of react-router-dom v6.0.2.
• [UI]: Refactored share/move samples between projects to use a separate page.
• [UI]: Added capability to share/move samples between projects from the line list page.
• [UI]: Fixed issue with dynamic pipeline parameters with only one value not rendering.
• [Developer]: Updated to use Yarn v3 and updated browserlist to v4.19.17.
• [Developer]: Added parsing of CHROMEWEBDRIVER in ./run-tests.sh to detect and use chromedriver provided by github actions ubuntu20.04 image.
• [UI/Workflow]: Added in support for displaying html files found inside of zipped html output files.
• [Developer]: Converted the project from bare Spring to Spring Boot 2.6.3, which involved upgrading a number of dependencies.
• [Developer]: Update to react-router v6 from @reach-router.

21.09.2

• [All]: Updated some dependency packages to latest versions to remove any Critical|High issues as reported by Grype https://github.com/anchore/grype. (21.09.2)

21.09.1

• [REST]: Fixed bug where analysis output file bytes were being included in responses when only JSON should have been sent. (21.09.1)

21.09

• [Developer]: Added pipeline plugin path configuration option
• [UI]: Update of Project Activities page to use Ant Design.
• [UI]: Fixes bug where the page title on Remote IRIDA Connections page was not displaying properly.
• [UI]: Fixed bug where a remote project in UNSYNCHRONIZED state would have the Sync buttons disabled on the Project Synchronization Settings page. (21.05.1)
• [UI]: Added back Users option for managers in main navigation. (21.05.1)
• [Documentation]: Added Swagger and OpenAPI to the IRIDA REST API documentation.
• [UI]: Update of Create New Project page to use Ant Design.
• [Developer]: Updated Redux Toolkit to stable version 1.6.2
• [Workflow]: SNVPhyl has been updated to version 1.2.3 to fix an installation issue (#1018). Since this updates a pipeline you will have to upgrade the Galaxy tool suite for SNVPhyl as described in our instllation documentation. (21.05.2)
• [UI]: Fixed bug which prevented a manager on a remote project from adding/removing members and groups. (21.05.2)
• [UI]: Fixed bug which caused newly created metadata templates to no be displayed after creation. (21.05.3)
• [UI]: Fixed bug that would send many emails to users when they request a pipeline completion email. (21.05.3)
• [Developer]: Updated xlsx to version 0.17.0
• [Test]: Updated chromedriver to version 92.0.0.
• [UI]: Updated Project Single Sample Analyses Outputs pages to use Ant Design.
• [UI]: Updated Your Single Sample Analysis Outputs page to use Ant Design.
• [Developer]: Fix dependabot warning for path-parse, set resolution of path-parse to 1.0.7.
• [UI]: Fixed bug where the length of the project name was not checked on project creation.
• [UI]: Fixed bug which prevented the first created metadata template from being displayed after creation.
• [UI]: Sample modified date is now updated when sample metadata is modified.
• [Developer]: Fix dependabot warning for set-value, force using a set-value above 4.0.1
• [Developer]: Updated chromedriver to v93.0.1.
• [Database]: Updated query to improve performance for metadata in REST API and line list.
• [UI]: Fixed bug when exporting samples from project > samples page while using filter by file, all sample were exported.