22.09.3

If you are upgrading to release directly and skipping 22.09 please ensure that you follow the UPGRADING.md.

• [REST]: Fixed remote project syncing issues, caused by invalid refresh tokens, invalid status updates, and bad error handling of unauthorized tokens. Also fixed issue with project owners not being to able see remote settings menu or delete menu. See PR 1410

22.09.2

If you are upgrading to release directly and skipping 22.09 please ensure that you follow the UPGRADING.md.

• [UI]: Fixed bug causing associated project samples to be added to the cart with the wrong project identifier. See PR 1395
• [UI]: Fixed bug preventing the removal of locked samples within a project. See PR 1396
• [Developer/UI]: Fixed bug preventing managers from sharing project samples. See PR 1398
• [UI]: Fixed bug where a sample added to the cart from the sample detail viewer still had a Add to Cart button if the viewer was closed and relaunched. See PR 1397
• [Galaxy]: Fixed missing "deferred" state found in the Galaxy API but not in the IRIDA API for getting status of Galaxy histories. See PR 1402.
• [UI]: Fixed a bug that allowed the sharing and moving of locked samples. See PR 1403

22.09.1

If you are upgrading to release directly and skipping 22.09 please ensure that you follow the UPGRADING.md.

• [UI]: Fixed when sharing or exporting sample on the project sample page, and other minor bugs. See PR 1382

22.09

This release requires a few extra steps when deploying, please refer to UPGRADING.md.

• [Developer/UI]: Refreshed the create new user account page. See PR 1285
• [Developer/UI]: Added in typescript support to webpack build, moving forward all new frontend development will use typescript. See PR 1294 for more.
• [Developer/UI]: Removed styled-components from page header and replaced with CSS variables. See PR 1284
• [Developer/UI]: Updated eslint rule to check for object and array destructuring. See PR 1322
• [UI]: Fixed user routes for admin panel. See PR 1323
• [Developer/UI]: Added eslint-prettier-pluggin. See PR 1328
• [Developer]: Replaced Maven with Gradle for build. See PR 1300
• [Developer/UI]: Switched to pnpm from yarn for frontend dependency management. See PR 1332
• [Developer]: Switched custom exception handling to use built in Spring Boot exception handling. See PR 1319
• [UI]: Fixed issue with sorting OAuth clients table in admin panel. See PR 1342
• [UI]: Updated share samples review page to list the actual samples which will not be shared with the target project either due to the same sample identifiers or the same samples names already in the target project. See PR 1343
• [REST]: Updated synchronizing of sample data to remove sequencing objects and assemblies that no longer exist on the remote sample. See PR 1345
• [UI]: Fixed issue with filtering samples by files using a windows encoded text file causing sample name truncation. See PR 1346
• [Developer]: Fixed deleting a project with project subscriptions. See PR 1348
• [Developer]: Updated OAuth2 implementation to use Spring Security 5 OAuth2 libraries. See PR 1339
• [Developer]: Add identifier to project drop-downs. See PR 1352
• [UI]: Fixed issue with Biohansel pipeline being launched without selecting an option for a required parameter. See PR 1356
• [Developer]: Unified validate sample names into one endpoint. See PR 1353
• [Developer/UI]: Increased speed of Project Samples table export and added estimated coverage to Project Samples table and exports. See PR 1360
• [Workflow]: Start the Galaxy Data Library timeout when an upload begins rather than when it is first queued up. See PR 1337
• [Developer]: Added description and metadata to create & update project sample endpoints. See PR 1359
• [UI]: Fix issue where year is displayed incorrectly when the last day of the week for the date is in another year. See PR 1364
• [Developer]: Fix issue where large downloads silent failed due to async request timeout. See PR 1368
• [Developer]: Update to Spring Boot 2.7.3 and update various other dependencies. See PR 1369
• [Developer]: Fixed issue with disabled user accounts requesting a password reset. See PR 1373
• [Developer/UI]: Updated sample details view to use Ant Design and moved into a modal which can be launched from anywhere the sample name is listed. See PR 1370
• [UI]: Updated analysis results manage results page to not allow a project collaborator to view the save results back to a sample section. See PR 1377
• [UI]: Updated phylogenetic tree visualization on the analysis details using Ant Design and the new phylocanvas.gl. See PR 1280
• [Developer]: Added security scanning of GitHub pull-requests with CodeQL (scans for code vulnerabilities) and Grype (scans for Java package dependency vulnerabilities). See PR 1282.
• [UI]: Updated layout of the analysis view to allow for scrollable sections. SeePR 1378

22.05.5

This release fixes a few URL issues when IRIDA is not deployed to the root path. it also re-adds the ability for admin's to update users passwords.

A summary of changes are below:

• [UI]: Fixed bug preventing export of project samples table due to invalid url. PR 1331
• [UI]: Updated user account security page to allow admins to change passwords for other users. See PR 1330

22.05.4

This release fixed a few URL issues when IRIDA is not deployed to the root path.

A summary of changes are below:

• [UI]: Fixed bug preventing filter samples by file to fail on invalid url. See PR 1318

22.05.3

This release fixed an issue with the admin statistics dashboard and with group members accessing metadata within a project.

A summary of changes are below:

• [Developer]: Fix bug where users with only group access to a project couldn't view sample details or metadata. See PR 1313
• [Developer]: Fix sql order by bug on admin statistics page that was causing page not to load when ONLY_FULL_GROUP_BY enabled. See PR 1313

22.05.2

This release fixed an issue with a database migration edge case, and incorrect url generation on the login and password reset pages.

A summary of changes are below:

• [Developer/UI]: Fix flaky UI Integration tests. See PR 1313
• [Developer]: Update war build to decrease size and remove executable ability. See PR 1313
• [Developer/UI]: Fixed bug where context path was not set for login and password reset components. See PR 1313
• [Developer]: Fixed bug where duplicate project_subscriptions were added for users who had direct project membership with email subscriptions and were also a member of the project through group membership. See PR 1313

22.05.1

This release fixes an issue where 22.05 deploy was failing due to having user groups with members but not assigned to any projects. If you encountered a database migration issue for 22.05 you can skip that release and use this one instead.

A summary of changes is below:

• [UI]: Fixed bug where samples could not be removed from share page. See PR 1296 for more.
• [Developer]: Fixed bug where project_subscriptions were added for groups without projects. See PR 1296 for more.

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).