CHANGELOG.md

Changelog

[24.12] - 2024/12/20

• [Documentation]: Developer installation documentation updated with new instructions for Java 17. See PR 1563
• [UI]: Fixed bug in AnalysisTextPreview component which prevented the loaded file size from being displayed in file preview. See PR 1560
• [Developer]: Updated to use Java 17. See PR 1538
• [Developer/UI]: Updated to React 18, Ant Design 4.24.16, and switched over to use mdxeditor markdown editor. See PR 1537
• [Developer]: Updated node (20.14.0), pnpm (9.12.3), and eslint (9.14.0). See PR 1524

[23.10.1] - 2023/12/07

• [UI]: Fixed issue where filter inputs required focus when they are opened on the project samples page. See PR 1503
• [UI]: Fixed bug preventing sorting and paging on the project members page. See PR 1504
• [Developer]: Fixed race condition where FastQC file processor would start on incomplete file by filtering out files on non complete sequencing runs. PR 1506

[23.10] - 2023/10/15

• [Developer]: Added functionality to delete sequence files from file system when a sequence run is removed. See PR 1468
• [Developer]: Added script to do initial cleanup of sequence files from file system. See PR 1469
• [UI]: Add identifier to project drop-down on project synchronization page. See PR 1474
• [Developer]: Added functionality to delete sequence files from file storage when removed from sample. See PR 1476
• [Developer]: Added override flag that determines if files should be deleted from file storage. See PR 1486
• [Developer]: Fixed flaky text in PipelinesPhylogenomicsPageIT#testPageSetup test. See PR 1490
• [ALL]: Added LDAP/ADLDAP support.
• [Developer]: Added start and ends dates to filesystem clean up script. See PR 1487

23.01.3 - 2023/05/09

• [Developer]: Fixed issue with metadata uploader removing existing data. See PR 1489

23.01.2 - 2023/04/17

• [UI]: Fixed bug that caused all metadata fields to be removed when single field was removed from a template. See PR 1482
• [Developer]: Fixed bug which allowed duplicated entries in the user_group_project table which prevented the user group from being removed. Fixed bug which was preventing analyses with html file outputs from completing. See PR 1483
• [Developer]: Fixed flaky PipelinesPhylogenomicsPageIT test. See PR 1482
• [REST]: Fixed issues with syncing between newer IRIDA (>22.09) and older IRIDA (<=20.09) by disabling requests for application/xml for some of the REST requests and only requesting data as application/json. See PR 1484.

23.01.1 - 2023/03/21

• [UI]: Fixed issue where template order was not applied when applying a linelist template. See PR 1479
• [UI]: Added select all to associated projects filter on project > samples page. See PR 1479

23.01 - 2023/02/28

• [UI/Developer]: Updated react-router to the version 6.4.3. SeePR 1405
• [Developer] Updated developer setup documentation, ignore java_pid*.hprof files, and added quality of life file gradle.properties. See PR 1415.
• [Documentation]: Updated broken links in developer documentation. See PR 1418.
• [Developer] Updated developer setup documentation, ignore java_pid*.hprof files, and added quality of life file gradle.properties
• [UI]: Refreshed global search page to use Ant Design. See PR 1409
• [UI/Developer]: Removed old notification system hack and updated to use only Ant Design notifications. See PR 1447
• [UI]: Fixed bug where the User column was named User Group on the admin User Groups page. See PR 1450
• [Developer]: Replaced Apache OLTU with Nimbusds for performing OAuth2 authentication flow during syncing and Galaxy exporting. See PR 1432
• [Developer/UI]: Performance enhancements to the metadata uploader. See PR 1445.
• [Developer/UI]: Fix for updating sample modified date when metadata is deleted. See PR 1457.
• [Developer]: Added support for cloud based storage. Currently, Microsoft Azure Blob and Amazon AWS S3 are supported. See PR 1194
• [Developer]: Updated metadata uploader to use react-router-dom Outlet. See PR 1464
• [Developer]: Deprecated "/api/projects/{projectId}/samples/bySequencerId/{seqeuncerId}" in favour of "/api/projects/{projectId}/samples/bySampleName", which accepts a json property "sampleName"
• [Developer]: Fixed bug in setting a default_sequencing_object and default_genome_assembly to NULL` for a sample when the default sequencing object or genome assembly were removed. See PR 1466
• [Developer]: Fixed bug preventing a sample with an analysis submission from being deleted. See PR 1467

22.09.7 - 2023/01/24

• [UI]: Fixed bugs on NCBI Export page preventing the NCBI submission.xml file from being properly written. See PR 1451

22.09.6 - 2022/12/21

• [UI]: Fixed bug on NCBI Export page preventing the export from occuring. See PR 1439

22.09.5 - 2022/12/14

• [Developer/UI]: Fixed bug preventing a manager of a user group from adding new members when this manager is a collaborator on one of these users projects. Also, fixed issue with a user group member added with an owner role for a group was set with a member role. See PR 1431
• [Developer/UI]: Updated synchronize new remote project page to display http errors when setting the url manually and an error is encountered. See PR 1433
• [Developer]: Added liquibase migration for renamed NCBI Instrument Models. See PR 1436
• [Developer]: Removed ABI SOLID platforms from NCBI Instrument Models. See PR 1436

22.09.4 - 2022/11/14

• [REST]: Fixed issue with project/samples api response missing samples when a sample has a default sequencing object. See PR 1413

22.09.3 - 2022/11/10

• [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 - 2022/11/04

• [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 - 2022/10/21

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

22.09 - 2022/10/07

• [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 - 2022/06/28

• [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
• [UI]: Updated the NCBI SRA Submission details page to Ant Design. See PR 1311

22.05.4 - 2022/06/16

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

22.05.3 - 2022/06/14

• [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 - 2022/06/10

• [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 - 2022/06/01

• [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 - 2022/05/30

• [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 executions due to bean wiring issue (issue #1287).

22.03.1 - 2022/04/05

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

22.03 - 2022/03/23

• [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 - 2022/02/28

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

22.01.3 - 2022/02/24

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

22.01.2 - 2022/02/24

• [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.

22.01.1 - 2022/02/04

• [REST]: Corrected behaviour of date fields in REST API to return epoch instead of textual string.

22.01 - 2022/01/28

• [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.

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