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Changes

21.05 to 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.

21.01 to 21.05

  • [UI]: Fixed bug which was preventing a user from viewing more than 5 rows of a tabular result file. (21.01.1)
  • [Developer]: Fixed webpack not outputting css bundle files.
  • [UI]: Updated to latest release of Ant Design (v4.12.3).
  • [Developer]: Fixed the advanced visualisation viewer for Phylogeny Tree with metadata.
  • [REST]: Added ownership option when copying sample to project in REST API (21.01.2)
  • [UI]: Update to the pipeline launch process.
  • [UI]: Fixed bug where filter menu was missing from the Analsyis Outputs Table.
  • [Developer/REST/UI]: Added announcements bell icon to main nav bar, added priority announcements modal at login, and refreshed user announcements page.
  • [UI]: Fixed bug where samples not rendering on project samples page when the config setting ngsarchive.linker.available is set to false.
  • [Developer]: Updated to Webpack v5 and Yarn v2.
  • [UI]: Updated create metadata template.
  • [Developer]: Updated to Yarn v2.4.1.
  • [Developer]: Cleaned up compile warnings related to deprecated methods in Spring, JSON parsing, and Galaxy connectivity.
  • [UI] Updated And Design to v4.15.0.
  • [Database]: Removed sample_metadata_entry table which should have been dropped in 21.01 release. (21.01.3)
  • [REST]: Added endpoint to request a full project's sample metadata at the same time.
  • [Developer]: Chromedriver updated to 90.
  • [Developer]: Updated lodash to v4.17.21 to fix security vulnerability.
  • [UI/REST]: Improved querying performance of metadata for line list and REST API.
  • [UI]: Complete upgrade of project settings to use Ant Design.
  • [Developer]: Removing many unnecessary files from the .war file build to reduce build size.
  • [UI]: Fixed issue where analyses page was not displaying for some IRIDA instances due to deprecated analysis states in their audit tables.

20.09 to 21.01

  • [UI]: Fixed bug where sequencing runs could not be deleted on sequencing runs details page. (20.09.1)
  • [Developer]: Updated the session Cart and provided a service for accessing it.
  • [Developer]: Fixed SISTR viewer so plugin and built-in pipelines can use it (20.09.1)
  • [UI]: Added two additional fields to SISTR viewer describing the number of alleles found (20.09.1)
  • [UI]: Fixed bug where users could not see or connect to Remote APIs (20.09.2)
  • [UI]: Fixed bug on project page where incorrect link to Remote API was displayed. (20.09.2)
  • [REST]: Added handling for synchronizing data from older IRIDA instances. It was failing for APIs without assembly functionality added in 20.09. (20.09.2)
  • [Developer]: Updated deprecated runWorkflow blend4j call to invokeWorkflow and switched to using jar for blend4j
  • [Developer]: Removed resolve-url-loader from front end dependencies.
  • [UI]: Fixed bug on users listing page where if a user has never logged into the system there last login date showed Dec 31 1969,
  • [Documentation]: Corrected window.PAGE to window.TL in docs on how to make custom login pages.
  • [Developer]: Removed UI dependency for bootstrap-sass.
  • [Developer]: Updated to React v17.0.1, Babel v7.12.1, and Ant Design v4.7.3.
  • [UI]: Updated FastQC page to use Ant Design.
  • [Documentation]: Added documentation for sequence file fastqc page.
  • [UI]: Updated Project Reference File page to use Ant Design.
  • [Developer]: Removed invalid javax.interceptor-api Maven artifact. It was no longer needed for the project and was causing build failures. Existing 20.09.2 installations do not need to be upgraded, this change only affects building IRIDA from source. (20.09.3)
  • [Developer]: Changed to using GitHub Actions for integration tests.
  • [Developer]: Switched to Chromedriver 86 to match Github Actions chrome version.
  • [UI]: Updated Project Reference File page to display progress of uploads.
  • [UI]: Added functionality for users to synchronize fast5 data from remote APIs.
  • [Developer]: Added smtp port and password configuration options
  • [UI]: Added usage statistics to admin panel.
  • [UI]: Updated analysis results page to show loading indicator when retrieving output file data.
  • [UI]: Updated sample details sidebar with sample files and simpler API for use on more pages, and moved it out into a modal.
  • [Developer]: Updated ini to version 1.3.7 to fix security vulnerability.
  • [Developer]: Update jest to version 26.6.3 to fix security vulnerability.
  • [UI]: New main navigation bar using Ant Design.
  • [UI]: Fixed bug where a user could not click the Sync Now button for a remote project if the status was set to Unauthorized. (20.09.4)
  • [UI]: Fixed issue with project samples table not displaying Created Date and Modified Date for samples. (20.09.4)
  • [Developer]: Updated database structure for sample metadata to improve performance and auditability. See https://irida.corefacility.ca/documentation/administrator/upgrades/#sample-metadata-audit-record-updates for more details.
  • [Documentation]: Moved IRIDA documentation to new repository at https://github.com/phac-nml/irida-documentation/. Pages can be viewed at https://phac-nml.github.io/irida-documentation/.
  • [Developer]: Updated axios to version 0.21.1
  • [UI]: Fixed broken CSS bundle links in project settings pages. (20.09.5)
  • [UI]: Added html viewer for analysis output files.
  • [REST]: Added new REST endpoint that can generate a deep hashcode of a project. This will be used for speeding up project synchronization when there are no changes to a project. Instead of checking for changes remotely, the client can check for changes only to the hash. If there are hash changes, then they can do their full sync.
  • [UI]: Added option for project managers to check for changes using the hash above, or to force a full project sync on the project remote settings page.
  • [Developer/REST/UI]: Updated announcements with a new title and priority fields.
  • [UI]: Added option for user to only receive an email upon pipeline failure.
  • [Developer]: Updated frontend-maven-plugin.
  • [UI]: Fixed issue with trying to copy a large number of samples between projects.
  • [Developer]: Chromedriver updated to 88

20.05 to 20.09

  • [UI]: Updated project user groups to use Ant Design.
  • [UI/Developer]: Removed most dependency for momentjs (only on project samples filters).
  • [Developer]: Removed deprecated Long constructor.
  • [Developer]: Updated webpack-dev-server to fix security vulnerability caused by websocket-extensions 0.1.3.
  • [UI]: Update project metadata templates listing page to use Ant Design.
  • [UI/Developer]: Removed SASS compilation step from front end build. Everything is done using postcss now.
  • [Developer]: Bumped node version to 12.18.0.
  • [UI]: Fixed bug when creating/modifying a metadata template the user could not search for a field. (20.05.1)
  • [UI]: Fixed bug where managers could not load Users listing page. (20.05.1)
  • [UI]: Added functionality for users to synchronize assembly data from remote APIs.
  • [Developer]: Updated chromedriver to version latest.
  • [UI]: Removed gravatar and replaced with user icon.
  • [Developer]: Removed webpack-dev-server.
  • [UI]: Fixed issue where analysis results pages would hang after running with remote synchronized data. (20.05.2)
  • [Developer]: Updated chromedriver to version latest. (20.05.2)
  • [Developer]: Updated frontend dependencies (babel, fontawesome, and ant-icons)
  • [UI]: Updated NCBI Exports listing pages to use Ant Design Tables.
  • [UI/Developer]: Removed irida.cart.js (an older angularjs service for the cart).
  • [UI]: Fixed issue #637 where metadata toggles were not displaying in the "on" position properly on loading the advanced phylogenic viewer.
  • [UI]: Removed unused front end dependencies (angular-boostrap-lightbox and lodash.keys).
  • [Developer/UI]: Removed irida angular app. Individual components load themselves now.
  • [Developer/UI]: Updated to Ant Design v4.4.2.
  • [UI]: Updated importing numbers through excel file. IRIDA will now check for excel formatted numeric cells and keep the formatting. (20.05.3);
  • [UI]: Updated sample details metadata so that long values will be broken up over multiple lines. (20.05.3);
  • [Developer]: Updated babel-env to fix a security vulnerability caused by dependency elleptic
  • [UI]: Updated UI for creating a sample within a project.
  • [REST]: Removed broken XML serialization config from REST API classes. It was breaking content negotiation for some tools as it sometimes tried to return XML when it couldn't.
  • [UI]: Added Create New Project button to the Projects listing page.
  • [UI]: Fixed bug where import bulk metadata button was displayed on linelist page for project collaborators. (20.05.04)
  • [UI]: Fixed bug where add member to project button was displayed on project members page for project collaborators. (20.05.04)
  • [Developer]: Added optional method getAnalysisViewer for IridaPlugin to allow external applications to use IRIDA's built in analysis visualizations (such as the phylogenetic tree viewer).
  • [REST]: Fixed issue with double slashes sometimes getting added in OAuth2 redirect URI causing auth flow to fail.
  • [Workflow]: Updated the SNVPhyl pipeline to version 1.2.2.
  • [Developer]: Updated the Galaxy Docker instance to Galaxy 20.05.
  • [Workflow]: Updated the tools Shovill, Prokka, and Quast in the Assembly and Annotation pipeline. These updates mean the issue with out-of-date tbl2asn is now fixed and the value of SHOVILL_RAM will now be set automatically by Galaxy based on assigned resources to the tool.
  • [Workflow]: Updated the tools Shovill, Prokka, and Quast in the Assembly and Annotation Collection pipeline. Also moved tool Bundle collections from the IRIDA Toolshed to the Galaxy Main Toolshed.
  • [Workflow]: Removed dependency of IRIDA on the IRIDA Toolshed (https://irida.corefacility.ca/galaxy-shed). This means that all tools for IRIDA pipelines are now available on the main Galaxy toolshed and that IRIDA is compatible with newer versions of Galaxy (20.XX+).
  • [UI]: Created admin panel for simplifying administrator tasks (Users, Clients, Remote IRIDA Connections, Sequencing Runs, NCBI Exports, and Announcements).
  • [REST]: Updated REST API to handle errors when copying existing samples more gracefully.
  • [UI]: Updated the analysis results page to auto update the progress of an analysis.
  • [UI]: Updated the analyses table to auto update the progress of the displayed analyses.
  • [UI]: Updated Remote API Connection details page to use full Ant Design and updated Oauth.
  • [UI]: Updated Create Remote Synchronized Project page to use Ant Design and updated Oauth.
  • [UI]: Updated Remote Project Synchronization Settings page to use Ant Design and updated oauth.

20.01 to 20.05

  • [UI/Developer]: Removed webpack progress.
  • [UI]: Updated clients listing table to use ant.design tables.
  • [UI]: Sending email to sync user when a remote project's token expires.
  • [UI]: Fixed bug that prevented server side filtering for analysis name on analyses table. (20.01.01)
  • [UI]: Updated admin announcements table and creation to use ant.design.
  • [UI]: Fixed bug that preventing using the ngs-linker script with >= 330 samples.
  • [UI]: Updated breadcrumbs to have cleaner look and feel and include the actual project and sample names.
  • [UI/Developer]: Updated to react 16.13.0.
  • [Developer]: Added Apache 2.0 licence information to package.json.
  • [UI]: Fixed UI bugs preventing users from selecting single-end input files for analysis pipelines. (20.01.2)
  • [UI]: Icon cleanup preparing for upgrade to Ant Design v4.
  • [UI/Developer]: Remove husky because running into issues with prettier formatting on staged files..
  • [API/Developer]: Changed the SequencingRun type to allow a user-defined sequencerType instead of it being hardcoded to MiSeq.
  • [Developer]: Updated maven jetty plugin to version 9.4.24.v20191120.
  • [UI]: Updated Remote API Listing page to use Ant Design.
  • [UI]: Updated Administrator Users page to use Ant Design.
  • [UI]: Removed DataTables from overrepresented sequence file and run files page.
  • [REST]: Added a REST API endpoint to read assemblies for samples.
  • [UI]: Added selection for linker script to get assemblies in project/samples page.
  • [Developer]: bower completely removed.
  • [UI/Developer]: Updated analysis results page with Ant Design and React.
  • [UI]: Assemblies can now be uploaded through the sample files page. See more in our upgrade notes at https://irida.corefacility.ca/documentation/administrator/upgrades/#2005.
  • [UI/Developer]: Updated to Prettier 2.0.2
  • [UI/Developer]: Updated to eslint-plugin-react-hooks to 3.0.0.
  • [UI/Developer]: Removed angular-ui-bootstrap as a global dependency (still required on several pages).
  • [UI/Developer]: New login page with developer ability to override template.
  • [UI/Developer]: Added excel file viewer to analysis outputs view.
  • [UI]: Added selection to export assemblies to Galaxy.
  • [UI]: Updated Project > Members page to remove DataDables and use Ant Design.
  • [UI/Developer]: Added image file viewer to analysis outputs view.
  • [UI]: Moved project > details into the project > settings panel.
  • [UI]: Updated Project navigation to use Ant Design menu.
  • [UI/Developer]: Updated to JQuery v3.5.1 to fix security vulnerability.
  • [UI]: Fixed bug preventing the upload of *.fastqc.gz on Mac computers.
  • [UI]: Update Groups page to remove DataTables and use Ant Design.
  • [UI]: Update Groups details page to use Ant Design and remove DataTables.
  • [UI]: Fixed bug preventing display of execution tools for first file if a provenance for another file had been viewed.
  • [Documentation]: Updated Getting Started docs to include IRIDA log in info and an updated install-libs.sh run command.
  • [Developer/UI]: Upgraded to FastQC 0.11.9.
  • [UI]: Added FAST5 format support. FAST5 support is in beta and is subject to change. See more in our upgrade notes at https://irida.corefacility.ca/documentation/administrator/upgrades/#2005.
  • [UI]: Updated user groups to use Ant Design.
  • [UI]: Fixed bug preventing advanced visualization view page load.
  • [UI/Developer]: Updated analysis urls to work with a context path.
  • [UI]: Outputs and Tree view now span the full width of the page.
  • [Processing]: Fixed bug where analyses wouldn't run if project didn't have analysis priority.

19.09 to 20.01

  • [UI]: Fixed default server language. It was accidentally set to 'fr' for release. (19.09.1)
  • [Developer]: Upgraded development Java version to Java 11 (LTS).
  • [UI]: Fixed default server language. It was accidentally set to 'fr' for release. (19.09.1)
  • [UI/Developer]: Updated ant.design and ag-grid to fix issue with horizontal scrolling in firefox.
  • [UI]: Fixed issue where links to pipelines on the cart page displayed incorrectly.
  • [UI]: Updated project and global analyses listing pages to use Ant Design tables.
  • [UI]: Updated sequencing runs table to use Ant Design tables.
  • [UI/Developer]: Minor package updates for babel, eslint and ant.design.
  • [API]: Fixed concatenating .fastq.gz files from the user interface.
  • [UI]: Fixed bug where Let the Pipeline Run button failed to empty the cart and redirect the user to the projects page.
  • [UI/Developer]: Removed marked and angular-marked as bower dependencies.
  • [UI]: Fixed issue where grant types, and refresh token validity would not populate correctly on client edit form.
  • [UI]: Fixed issue where hidden portions of client edit and creation form would not toggle correctly.
  • [UI]: Fixed issue with browser auto-filling password fields on the user edit page.
  • [UI]: Fixed issue where user role would reset if server validation failed on user create page.
  • [UI]: Fixed bug where the "Automatically create collection" could not be unchecked when exporting to Galaxy.
  • [UI/Developer]: Removed marked, angular-marked, select2, angular-bootstrap and ng-file-upload as bower dependencies.
  • [REST/Developer]: added the /api/version route to the REST API that returns the full version string.
  • [UI]: Fixed issue where issue where cart is not rendering to the full height of the page. (19.09.2)
  • [UI]: Updated and simplified associated project page.
  • [UI/Developer]: Removed old bootstrap customization files that are not used.
  • [Developer]: Upgraded Spring to 5.2.2.RELEASE, Spring Security to 5.2.1.RELEASE, Spring Security Oauth2 to 2.3.6.RELEASE, Hibernate to 5.4.7.Final, and Spring Data JPA to 2.2.0.RELEASE.
  • [UI/REST]: Removed API login controller, instead web login controller is used.
  • [UI/REST]: Added configurable redirect location to client details. This must be added to all authorization_code clients. This includes clients set up for synchronizing IRIDA data and Galaxy importer clients. See upgrade instructions at https://irida.corefacility.ca/documentation/administrator/upgrades/#2001.
  • [Developer]: Added back minification config to production webpack config.
  • [UI/Developer]: Updated to latest (3.26.0) release of ant.design.
  • [Developer]: Fixed url for downloading multiple analysis outputs as well as for viewing the user analysis outputs page.
  • [Documentation]: Removed broken NCBI link and added info to conact NCBI about NCBI SRA exports.
  • [UI/Developer]: Lazy load line list export utilities.
  • [Developer]: Update to Chromedriver 79.0.0 for Travis CI.
  • [UI/Developer]: Standardized JavaScript internationalization through webpack. See i18n documentation for more information.
  • [UI/Developer]: Update version of yarn, babel dependencies.
  • [Developer]: Sample filter input has underscores escaped so that proper samples are returned.
  • [UI/Developer]: Updated to the latest release of ag-grid (v22.1.1).
  • [UI/Developer]: Updated how url's are created to allow for the addition of the context path.
  • [Admin]: Fixed handling of file extensions of compressed sequence files uploaded to NCBI SRA.
  • [Documentation]: Updated links and references from the old IRIDA MiSeq Uploader to the new IRIDA Uploader as the old uploader will not be supported when python 2 reaches end of life.
  • [UI]: Add analyses queued and running counts to analyses listing pages, cart page, and pipeline launch page.
  • [UI/Developer]: Force angular to use only version 1.7.9 to avoid security vulnerability.
  • [UI/Developer]: Updated to V5 of styled-components.
  • [UI/Developer]: Update version of babel and eslint.
  • [Documentation]: Fixed documentation link for developer authorization/oauth docs.
  • [Documentation]: Added info about upgrading to Tomcat 8.
  • [Documentation]: Added notice to upgrading guide about mysql 5.5 hibernate dialect.
  • [UI]: Fixed page title for users list page.

19.05 to 19.09

  • [UI/Developer]: Removed datatables-bootstrap3-plugin to remove dependency on outdated jquery.
  • [UI/Developer]: Removed ImmutableJS from the Line List Page.
  • [UI/Developer]: Moved the path of compiled JavaScript and CSS to src/main/webapp.
  • [REST/Developer]: REST API applications can now select which role to add users to a project.
  • [UI/Developer]: Cleaned up some of the redux set up on the linelist page.
  • [UI/Developer]: Removed loading Bootstrap through bower and moved it into the webpack build.
  • [UI/Developer]: Removed loading angularjs through bower and moved it into the webpack build.
  • [UI/Developer]: Fixed bug where importing an metadata excel worksheet with numbers as column headers would fail.
  • [UI/Developer]: Updated axios to fix vulnerability.
  • [Workflow]: Fixing bug so that fastq files uploaded to Galaxy will be "fastqsanger" when uncompressed and "fastqsanger.gz" when compressed.
  • [UI/Developer]: Updated fstream to fix vulnerability.
  • [Developer]: Update pom file to reflect active IRIDA developers.
  • [UI]: Fixed bug where a new metadata template could not be created. (19.05.1)
  • [UI/Developer]: Updated to latest react-redux to use new hooks API.
  • [UI]: Updated session expiration modal.
  • [UI]: Removed momentjs from being loaded on every page.
  • [UI]: Removed livestampjs as a project dependency.
  • [REST]: Changed the URL suffix to analysis output files to be a numerical id instead of a hash key. Files with a . in the name were having issues resolving. No change in rels so applications should work as usual.
  • [UI]: Removed noty as a bower dependency.
  • [Developer]: Removed unnecessary exists call in updateFields method which was causing some hibernate caching issues.
  • [UI]: Removed noty as yarn dependency, only using ant.design notifications.
  • [UI/Developer]: Removed datatables as a bower dependency.
  • [UI/Developer]: Removed unused dependencies from bower (angular-bootstrap-switch, animate.css, angular-datatables, angular-daterangepicker-enhanced, lodash, clipboard, and jszip)
  • [UI]: Removed lighthouse modals from the sequence files page. Loading full images. Removed dependency angular-bootstrap-lightbox from bower.
  • [Documentation]: Fixed shed-tools command to include install subcommand for installing Galaxy tools.
  • [UI/Developer]: Updated to lodash v4.17.13 to fix security issue.
  • [Developer]: Updated UI testing to allow using an external selenium webdriver.
  • [Developer]: Update eslint config to use babel-parser.
  • [Admin/Documentation]: Added a Troubleshooting guide for troubleshooting common problems with IRIDA Pipelines/Galaxy.
  • [Developer]: Split ProjectSettingsController into smaller functional controllers and moved them to a .settings subpackage.
  • [UI/Developer]: Allowing any analysis pipeline to be run automatically on data upload. See https://irida.corefacility.ca/documentation/user/user/project/#automated-pipelines for more details.
  • [Documentation]: Added link to Galaxy Export (Import) tool documentation.
  • [REST API]: Fixed allowing uploading data to non UPLOADING state sequencing runs. Now when a sequencing run is in a COMPLETE or ERROR state, a BAD_REQUEST http response will be returned.
  • [Developer]: Internationalization features of Spring now being used properly. An interceptor was previously set up, but wasn't being taken advantage of in the UI. Currently only English is available, but could be added by developers as needed.
  • [Developer]: Updates to front-end packages: antd@3.19.8 -> antd@3.21.4, @babel/polyfill -> core-js/stable & regenerator-runtime/runtime, as well as some minor updates to webpack dependencies.
  • [Developer]: Updated to node v12.8.1.
  • [Developer]: Updated eslint to fix security vulnerability.
  • [Admin]: Added NCBI Upload FTP option to disable/enable passive mode for FTP ncbi.upload.ftp.passive.

19.01 to 19.05

  • [Documentation]: Added the CalVer updates to the documentation getting started guide.
  • [Documentation]: Added note with link to NGS Linker installation documentation to Command-line Linker modal
  • [UI/Developer]: Updated to lodash v4.17.11 to fix security issue. (19.01.1)
  • [UI/Developer]: Updated yarn to (1.13.0) and node to (11.10.0).
  • [UI]: Added ability for user to select if they would like to receive an email upon pipeline completion.
  • [UI/Developer]: Added expose loader to load external dependencies through the vendor bundle.
  • [UI/Developer]: Updated jquery to v3.3.1 to fix security issue.
  • [UI/Developer]: Updated bootstrap dependencies and cleaned up dependencies by running yarn install --flat and resolving dependencies.
  • [UI]: Fixed typo when loading data in Advanced Phylogenomic Visualization page.
  • [Admin]: Added message to add irida.db.profile param for Tomcat in docs and upgrading guide.
  • [UI/Developer]: Added code splitting to webpack bundles.
  • [UI/Developer]: Added checkbox to Create a New Project page for user to lock sample modification when a project is created from samples in the cart.
  • [UI/Developer]: Minor JavaScript code cleanup.
  • [Developer]: Updated spring security to 4.0.4.RELEASE.
  • [Admin]: Made analysis task pool size configurable with irida.workflow.analysis.threads. (19.01.2)
  • [REST]: Fixes issue where the Sample collection date was synchronized incorrectly, leading to the synced date up to one day off from the original date. (19.01.2)
  • [UI]: Fixed bug where uploading a metadata file with a . in the header row would cause an error. (19.01.2)
  • [UI]: Updated icons for datatables sorting and metadata importer.
  • [UI]: Fixed bug where users could not update their email subscriptions to projects. (19.01.2)
  • [UI/Developer]: Fixed issue where search for member to add to group resulted in no results found when search term contained capital letters.
  • [Documentation]: Added information on fixing ONLY_FULL_GROUP_BY sql error to the administrator faq docs.
  • [UI]: User on a remote project with a project role of manager has the ability to assign user groups to the project.
  • [UI]: Fixed bug preventing associated projects from being loaded into the project samples table. (19.01.3)
  • [Developer]: Moved FastQC results out of database to filesystem for a big reduction in database size and performance. See https://irida.corefacility.ca/documentation/administrator/upgrades/#1905 for more information.
  • [UI]: Added hard wrap on sample name on sample details page.
  • [UI]: New dedicated cart page.
  • [UI]: Exporting to Galaxy now runs through the new cart interface. Export to Galaxy through the Project Samples page has been deprecated.
  • [Developer]: Updated Travis CI dist to xenial.
  • [Developer]: Falling back to mysql for TravisCI testing. MariaDB currently having install issues.
  • [Developer]: Updated chromedriver in pom.xml and packages.json to newer versions to work better with newest chrome version.
  • [UI]: Removed .xlsx files from being previewed in the pipeline results page.
  • [UI/Developer]: Fixed issue with deleting a user group if it is linked to any projects.
  • [UI]: Fixes issue where importing an excel file that contained "Created Date" and "Modified Date" created metadata fields with those labels.
  • [REST]: Updated http status code returned (400 Bad Request) when uploading files to the wrong type of run
  • [UI/Developer]: Updated to jquery v3.4.0 to fix security issue.
  • [Database]: Fixed issue where FastQC description was being stored with an invalidly formatted version in the database.
  • [UI]: Fixed bug causing issues with saving Line List templates.
  • [UI]: Fixed bug when selecting all samples on the project samples page would not add them to cart.
  • [Developer]: Updated to latest version of NodeJS LTS (12.13.0) and Yarn (v1.19.1).

0.22.0 to 19.01

  • [Admin]: Updated versioning to a CalVer scheme of YY.0M.MICRO. New feature releases will have the appropriate the year and month fields, where bugfixes will increment the MICRO field.
  • [Database]: Fixed an issue where metadata entries derived from pipelines were not updating the associated analysis submission and ignorning blank entries. (0.23.5)
  • [Developer]: Added classes .jar maven export in build process.
  • [UI]: Added the sample coverage to the table exported from the project samples page.
  • [UI/Workflow]: Added option to disable workflows/analysis types from display in IRIDA using irida.workflow.types.disabled. (0.22.1)
  • [Developer]: Added wait when NCBI Uploader fails before retrying. (0.22.1)
  • [UI]: Users can now download in batch their user-generated, shared with project and automated project single sample analysis output files by selecting the files they wish to download from tables on the /analysis/user/analysis-outputs, /projects/<id>/analyses/shared-outputs, and /projects/<id>/analyses/automated-outputs pages, respectively.
  • [UI]: Added configurable warning for analysis results and metadata pages. Set the text for this warning with irida.analysis.warning. This can be used to communicate that results of analyses may be preliminary.
  • [Admin]: Added new profiles to allow IRIDA web server to run in a clustered fashion. See documentation at https://irida.corefacility.ca/documentation/administrator/web/#multi-web-server-configuration
  • [UI]: Fixed bug where all moved samples were locked. (0.22.2)
  • [UI/Developer]: Updated to lodash v4.17.10 to fix security issue. (0.22.2)
  • [UI]: Fixed bug where project samples page would freeze if there where numerous QC Issues. (0.22.3)
  • [UI]: Fixed error where synchronizing sequence files could lead to truncated files without generating an error. (0.22.3)
  • [UI]: Adding NCBI SRA accession to sample metadata when uploading data to NCBI.
  • [Developer]: Updated FastQC to 0.11.7.
  • [UI]: Fixed bug in sample edit page that didn't allow users to clear a field in the sample.
  • [Workflow]: Updated the AssemblyAnnotation pipeline to v0.5 and the AssemblyAnnotationCollection pipeline to v0.4. Both pipelines now use Shovill for assembly and QUAST for assembly quality assessment in addition to Prokka for annotation.
  • [API]: Fixed REST endpoint mapping for current user and user projects.
  • [Workflow]: Fixed issue where duplicate filenames were found after running Galaxy workflow in newer Galaxy versions. (0.22.4)
  • [Developer]: Added unused import checking to checkstyle config. The mvn site build will throw an error if unused imports are present.
  • [Developer/Workflow]: Added the ability build pipelines into independent JAR files to be loaded in IRIDA as a plugin (after placing in /etc/irida/plugins). Please see https://github.com/phac-nml/irida-plugin-example and https://irida.corefacility.ca/documentation/developer/tools/pipelines/ for more details.
  • [Developer]: Added additional FTP settings for NCBI uploads: ncbi.upload.controlKeepAliveTimeout, and ncbi.upload.controlKeepAliveReplyTimeoutMilliseconds.
  • [Developer]: Fixed issue with some settings in /etc/irida/irida.conf not being detected properly.
  • [Developer]: Added ability to adjust jdbc.pool.maxWait through an environment variable DB_MAX_WAIT_MILLIS for fixing timeout issues for tests.
  • [Developer]: Split Galaxy testing into galaxy_testing and galaxy_pipeline_testing to reduce the time it takes for all Galaxy tests to complete.
  • [Developer]: Fixed up test cases for genome assemblies and simplified saving to database.
  • [Sync]: Project sync date will be updated at start of sync job to stop quickly repeating errored syncs.
  • [UI]: IRIDA will now remove local samples when a synchronized remote sample is removed at its source.
  • [UI]: New project line list page with inline editing.
  • [Developer]: Updated Node, Yarn, and front-end webpack packages.
  • [Workflow]: Fixed Shovill Galaxy tool revision for SISTR and Assembly/Annotation pipelines.
  • [Developer]: Update to ag-grid-community v.19.1.2.
  • [Documentation]: Changed references from GitLab to GitHub in docs.
  • [UI]: Removed angular-resource, angular-messages, angular-sanitize, angular-animate, angular-datatables, ng-table and angular-drag-and-drop-lists.
  • [REST]: Added method to greatly increase speed of listing samples in a project. This was becoming an issue for projects with metadata and >5k samples.
  • [Developer]: Added pull request and issue templates for github.
  • [Developer]: Update Docker Galaxy container to Galaxy 18.09.
  • [Administration]: Updated method for automatically installing tools in Galaxy to use Ephemeris.
  • [Developer]: Updated to version 20.0.0 of ag-grid UI component.
  • [UI]: Add link back to sample for analysis input files on the Analsysis Details Page.
  • [UI]: Fixes issue where attempting to select all samples with a filter applied selected all samples in project.
  • [UI]: Fixed issue with exporting samples to galaxy through project/samples page failing.

0.21.0 to 0.22.0

  • [UI]: Fixed bug where .xls file could not be uploaded through the file picker on the metadata upload page. (0.21.1)
  • [Workflow]: Added version 0.1.9 of the MentaLiST pipeline, which includes a fix for downloading cgMLST schemes and a distance matrix output.
  • [UI]: Fixed bug where concatenate files was POSTing to incorrect URL. (0.21.2)
  • [UI]: Fixed bug where SVG files could not be exported through the advanced visualization page. (0.21.2)
  • [UI]: Fixed bug where users could not share more than nine samples. (0.21.2)
  • [UI]: Moved the position of the notification system to top center.
  • [Workflow]: Added version 2.0.0 of a pipeline for running bio_hansel (version 2.0.0)
  • [Workflow]: Added version 0.3 of a pipeline for running SISTR which now makes use of Shovill for genome assembly.
  • [Workflow]: Updated SISTR pipeline to store the following additional fields in the metadata table: serogroup, O antigen, H1, H2, and alleles matching genome.
  • [UI]: Users can save analysis results to samples after pipeline is done in "Share Results" tab.
  • [UI]: Fixed bug where edit groups page would throw a server exception. (0.21.3)
  • [UI]: Hiding user page project list for non-admins.
  • [Workflow]: Fixed bug where auto updating metadata from analysis submission failed for non-admin user. (0.21.4)
  • [UI]: Fixed bug where admin dropdown menu was hidden behind sequencing run sub navigation.
  • [Developer]: Moved file processing chain outside of SequencingObjectService. It now runs as a scheduled task. This will help balance the processing load in multi-server deployments.
  • [UI]: Ensuring ROLE_SEQUENCER users get "Access Denied" for any attempted UI interactions.
  • [Developer]: Updated yarn to the current version.
  • [UI/Workflow]: Pipeline analysis output files are rendered in the same order as they appear in the pipeline irida_workflow.xml in the <outputs> XML element.
  • [Developer]: Can now specify which chromedriver to use in UI testing with -Dwebdriver.chrome.driver=/PATH/TO/chromedriver.
  • [UI]: Fixes slow Sample cart. Quicker saving of large selections of samples to cart (POST /cart/add/samples) and loading of existing cart Samples (GET /cart).

0.20.0 to 0.21.0

  • [Workflow]: Added version 0.1 of a pipeline for running MentaLiST (version 0.1.3).
  • [Workflow]: Added version 0.1 of a pipeline for running Mash against the refseq database refseq_masher.
  • [UI]: Fixed bug where user could not cancel the upload of a sequence file on the Sample Files page.
  • [UI/Workflow]: Fixed bug where users could not submit large analyses due to an HTTP 414 "Request URI Too Long" error.
  • [Developer]: Removed old gulp dependencies from the package.json file.
  • [Developer]: Update to stable releases of node and yarn.
  • [Administration]: Disabled automated SISTR results from saving to sample metadata. Also disabled retrospective results from being added during the database update. Installations that have already performed the 0.20.0 update will have their retrospective automated SISTR results automatically added to sample metadata. Installations that jump directly to 0.20.1 and above will not have this data added to sample metadata. (0.20.1)
  • [UI/Workflow]: Preview analysis output files in a tabular or plain-text view in the analysis details page under the Preview tab.

0.19.0 to 0.20.0

  • [Developer]: Fixed exception being thrown related to permission denied for updating samples when a normal user (collaborator on a project) runs the assembly pipeline (0.19.1).
  • [UI]: Allowing admins to manually prioritize high importance analyses.
  • [Developer]: Removed dandelion from project > samples page.
  • [UI]: Fixed issue where Projects table could not be exported (0.19.2).
  • [UI]: Fixed user menu icons misaligning in Firefox (0.19.2).
  • [Developer]: Updated front end templating engine to Thymeleaf v3.
  • [Administration]: Added option to expire passwords after a configured number of days. Set security.password.expiry in /etc/irida/irida.conf to configure.
  • [Administration]: Limiting users from reusing passwords.
  • [Developer]: Updated webpack compile path to be resources/dist.
  • [Developer]: Webpack now extracts css / scss into its own bundles.
  • [UI]: Added minification to production javascript.
  • [UI]: Fixed issue where delete project button was always enabled, and created an error when clicked. (0.19.3)
  • [UI]: Clean up of the main navigation bar code, and removed its dependency on angular-ui.
  • [UI]: Fixed reflow layout of pipeline launch page.
  • [UI]: Changed the wording of 'copying' samples to 'sharing' samples.
  • [UI]: Allow users to share (copy) samples from a remote project. Disabled menu items for move and merge.
  • [Developer]: Ran prettier on all javascript files within resources/js.
  • [Developer]: Ran prettier on all scss files within resources/sass.
  • [Developer]: Add a git pre-commit hook to ensure prettier formatting.
  • [UI]: Fixed issue where all activities page could not be displayed.
  • [UI]: Fixed issue where time stamps where not displayed on activities pages.
  • [UI]: Fixed issue where breadcrumbs were not displaying on the Project > Line List and Project > Analyses pages.
  • [UI]: Cleaned up sub-navigation elements on samples and files.
  • [UI]: Updated Remote API pages (datatables, and removed Noty modals).
  • [UI]: Fixed issue where breadcrumbs not displaying on the Samples > File > QC Analsis pages.
  • [UI]: Removed search box from sequencing run page.
  • [UI/Workflow]: Galaxy job error info retrieved from Galaxy if a workflow submission fails. Job error info is shown in Analyses table and on the Analysis page if it exists.
  • [UI]: Fixed issue with Upload Sequence Files button when SequenceFiles page resized.
  • [UI]: SISTR able to write metadata back to samples.

0.18.0 to 0.19.0

  • [Developer]: Removed the requirement for pipeline developers to add an Analysis subclass and database tables for pipelines. All pipeline results can now be stored in the Analysis class.
  • [Developer]: Fixed issue where bootstrap was being loaded twice onto the page. (0.18.1)
  • [UI]: Fixed URL for concatenation of sample sequence files. (0.18.1)
  • [Developer]: Removed dandelion from: Announcements, Cart, Sequencing Runs, Login, Project Settings - Landing, Events, Create Sample, Line List, Announcements - Create & Read, Livestampjs, Pipelines Launch, lodash, NCBI Export Page, Session Handler, Project Members and Groups Server Side, NCBI export lists, Groups Listing, Group Members.
  • [UI]: Added empty state if no files exist in a sample.
  • [UI]: Added ability to associate assemblies with a sample.
  • [UI]: Fix broken link for concatenating files. (0.18.2)
  • [UI]: Fix broken permissions for downloading reference files not associated with a project. (0.18.2)
  • [UI]: Fixed issued with layout of the events panel on the dashboard page. (0.18.2)
  • [UI]: Fixed issue with local samples causing problems in synchronized projects. (0.18.2)
  • [API]: Fixed permission issue when asking for permission for analysis results using sequencing objects with no associated samples (0.18.3).
  • [UI]: Cleaned up styles on DataTables with fixed columns.
  • [Developer]: Upgraded to v5.3.0 of npm, and changed build process to use yarn.
  • [API]: NCBI uploads automatically retry after failure.
  • [UI]: Added global project and sample search from top toolbar.
  • [UI]: Changed user's modified date to "Last Login" in user list.
  • [Developer]: Created production and development webpack builds.
  • [UI]: Fixed issue with uploading .fastqc files in IE, and allow for uploading for fastqc.gz in all browsers (0.18.4).
  • [UI]: Added ability to update an analysis submission name after it's been submitted.
  • [Developer]: Added run-tests.sh script for running local integration tests.
  • [UI]: Fixed issue with exporting csv and excel from Project > Samples pages (0.18.5).
  • [UI]: Fixed bug with importing large excel file that contained columns with only a header and no other data in column.
  • [UI]: Fixed project sync settings from resetting themselves.

0.17.0 to 0.18.0

  • [Developer]: Removed old javascript build configuration files.
  • [Developer]: Cleaned up javascript imports (removed all require statements).
  • [UI]: Removed phylocanvas context menu from analysis > details page.
  • [Workflow]: Made workflows applying to a single sample to include sample name in all output files. Updated previous output files in database to also include sample name if corresponding workflow used only a single sample.
  • [UI]: Added buttons on the project settings page, and metadata template page to download an excel template.
  • [Developer]: Reorganized permissions classes into subpackages.
  • [UI]: Added maximum coverage quality control option.
  • [UI]: Allowing admins to delete synchronized data so it will be resynchronized if there was a problem. Note any changes made to synchronized samples will be overwritten on the next sync job. (0.17.1)
  • [Developer]: Checking if single end files have been synchronized to stop duplication.
  • [Developer]: Changed relationship of sequence files to a single collection in AnalysisSubmission instead of a collection for each file type.
  • [Documentation]: Rewrote Galaxy installation guide, added sections for linking IRIDA to existing Galaxy or to a pre-build Docker image.
  • [Developer]: Removed Dandelion dependencies from the dashboard, projects listing, & users listing pages.
  • [Developer]: Created new DataTables request handler to enable removing Dandelion DataTables.
  • [API]: Performance improvements when listing analyses of a specific type in the REST API.
  • [Developer]: Changed file processing chain to try to avoid errors in processing.
  • [API]: Added REST API endpoints for accessing all analyses associated with a project and for accessing automated analyses.
  • [UI]: Added ability to concatenate sequence files in a sample.
  • [UI]: New feature to export metadata through the Project line list view.
  • [UI]: Fixed bug allowing empty library name for Galaxy exporting.
  • [UI]: Added ability to download individual analysis output files.

0.16.0 to 0.17.0

  • [Developer]: Updated how project samples ajax controller handles datatables column sort functionality.
  • [UI]: Disallow spaces in Remote API and Client Details creation.
  • [UI]: Added ability for admins and project owners to delete a project.
  • [UI]: Added Technician system role which allows technicians to view results of all sequencing runs in the system.
  • [Developer]: Fixed permissions for NCBI submission uploads failing with Access Denied error. (0.16.1)
  • [Developer]: Removed thymeleaf-extras-conditionalcomments. Not used anymore.
  • [UI]: Fixed bug causing reference file uploads to fail when launching a pipeline. (0.16.2)
  • [UI]: In SISTR report, changed incorrect label Percent shared k-mers to Mash distance and report the mash distance instead of converting to percent.
  • [Developer]: Changed gitlab CI builds to run with Docker. See ci/README.md for more information.
  • [Developer]: Removed deprecated RemoteRelatedProject and *Snapshot classes and all associated services, repositories, and web features. Note this feature will remove some tables from the databse such as remote_related_project and remote_sequence_file. While these were likely unused it is strongly recommended to backup your database before this upgrade.
  • [UI]: Fixed bug with permission not allowing users to view automated SISTR results. (0.16.3)
  • [Developer]: Fixed permissions for NCBI submission uploads failing with Access Denied error. (0.16.1)
  • [UI]: New Line List page for displaying sample metadata for all samples within a project.
  • [UI]: New upload excel spreadsheet of metadata for samples within a project.
  • [UI]: New project sample metadata templates.
  • [UI]: New advanced phylogenetic tree with metadata visualization.
  • [UI]: Fixed bug where a project collaborator could try to change the role of a group.
  • [UI]: Fix bug where notifications were not being displayed when samples where copied between projects.
  • [Workflow]: The SISTR pipeline has been upgraded to use sistr_cmd version 1.0.2.

0.15.0 to 0.16.0

  • [Developer]: Upgraded to AngularJS 1.6.2 https://github.com/angular/angular.js/blob/master/CHANGELOG.md
  • [Developer]: Removed FontAwesome thymeleaf dialect, updated developer documentation https://irida.corefacility.ca/documentation//developer/interface/icons/.
  • [Workflow]: Added version 0.1 of a pipeline for Salmonella typing (SISTR) using the sistr_cmd.
  • [UI]: Removing commas (,) and replacing spaces with underscores (_) in download filenames as they confuse browsers. (0.15.1)
  • [Workflow]: The software SPAdes has been updated in all workflows to version 3.9.0. This requires installing an updated spades tool in Galaxy.
  • [Workflow]: The parameters to Prokka were changed to avoid crashing when a contig (and so sample) name was too long.
  • [UI]: Fixed issue caused when trying to use the command line linker to export a large number of samples from a project.
  • [Developer]: Fixed issue caused when trying to create a new pipeline with no parameters.
  • [UI]: Moved "Members", "Groups", "Associated Projects", "Reference Files" to a new "Settings" tab in projects.
  • [UI]: Fixed bug where collaborators on a project had access to the sample tools. These buttons are now hidden from collaborators.
  • [UI]: Fixed bug with email subscriptions where users were emailed events from all their projects if they were subscribed to one.

0.14.0 to 0.15.0

  • [API]: Added a checksum to files on upload so uploaders can validate upload was successful.
  • [UI]: Project sync jobs ignore bad files and set a sample to error when it can't transfer files, but gracefully continues the rest of the sync. (0.14.1)
  • [Workflow]: Removed @Transactional from the AnalysisExecutionServiceGalaxyAsync.executeAnalysis method as transactions were timing out while waiting for files to upload to galaxy. (0.14.2)
  • [Developer]: Cleaned up old use deprecated method CrudService.update(Long, Map) and removed the method from the project.
  • [API]: Added configurable maximum number of workflows IRIDA will schedule at a time irida.workflow.max-running. Default 4.
  • [UI]: Fixed login error message that requested an email instead of username.
  • [Developer]: Added quick failure on detection of an upload error in Galaxy.
  • [Developer]: Added ability to adjust size of thread pool for polling Galaxy after uploading files with galaxy.library.upload.threads.
  • [Workflow]: Upgraded SNVPhyl from 1.0 to 1.0.1. Details of changes found at http://snvphyl.readthedocs.io/en/latest/install/versions/#version-101.
  • [Workflow]: Removed @Transactional from methods in AnalysisExecutionServiceGalaxy as this was causing occasional conflicts between database entries written under different threads, causing analysis pipelines to get stuck in an invalid state.
  • [Administration]: Recommending enabling prod profile for dandelion for performance improvements.
  • [UI]: Fixed bug for users the could not select all samples on the Project > Samples page.
  • [UI]: Fixed bug where pipeline customization button could not be clicked in browser width > 758px and < 991px.
  • [UI]: Added a QC indicator to the project/samples table to indicate file processing failure or low coverage. Also visible in the sample/files page.

0.13.0 to 0.14.0

  • [UI]: Added ability to select or deselect viewing all associated projects. (0.13.1)
  • [UI]: Fixed issue with missing settings tab when in export view within a Project. (0.13.2)
  • [UI]: Fixed bug preventing sample selection while filtered by file. (0.13.2)
  • [UI]: Fixed bug with selecting samples with associated projects. (0.13.3)
  • [UI]: Fixed bug when displaying samples names from associated projects when filtering by file. (0.13.3)
  • [UI]: Fixed a bug when selecting samples after filter by file with a large number of sample names. (0.13.4)
  • [UI]: Added filtering project samples by organism.
  • [API]: Added ability to upload sequencing runs as regular user as long as you have access to required projects.
  • [UI]: Share analyses with projects so anyone on the project can view analysis results.

0.12.0 to 0.13.0

  • [Developer]: Updated node to v6.4.0.
  • [UI]: Fixed bug where sample edit button wouldn't show up when users had permission (0.12.1)
  • [UI]: Fixed bug where announcements couldn't be marked as read (0.12.1)
  • [UI]: Changed the user icon in recent events to a basic icon instead of a gravatar (0.12.1)
  • [API]: Fixed a bug with the sequencingObject/sequence file REST endpoint that was throwing 404s when it should read a file. (0.12.2)
  • [Developer]: Added ability to build IRIDA package .zip file and tools-list.yml for distribution and easy installation of tools in Galaxy.
  • [UI]: Major update to the Project > Samples page.
  • [Administation]: Added configurable values for the number of threads to use for file processing.
  • [Developer]: Creating the file processors as Spring beans and wrapping their processing methods in transactions.

0.11.0 to 0.12.0

  • [UI]: Removed bootstrap tooltip and extra script from dashboard page.
  • [UI]: Remove bower dependency for angular-notification-icons.
  • [UI]: Remove bower dependency for AngularJS-toaster.
  • [UI]: Removed qTip2 dependency.
  • [UI]: Removed bower dependency for bootstrap-sass-official.
  • [UI]: Remove bower dependency for 'MagnificPopup'.
  • [UI]: Removed client side dependency on angular-gravatar and replace with server gravatar url creation.
  • [UI]: Fix issue with Dandelion filters throwing nullpointerexceptions (0.11.4)
  • [Developer]: Added FetchMode.SELECT to SequenceFilePair.files as Hibernate was including the children multiple times in the result set. (0.11.1)
  • [Developer]: Packer now waits for tomcat to start during the build so that the database is fully deployed before distribution.
  • [Developer]: Packer renames the VM on output.
  • [Developer]: The Virtualbox appliance that's built now uses the virtio network adapter because the Intel one had serious performance issues over NAT.
  • [UI]: FastQC images were not rendering in Firefox because the request behaviour changed. (0.11.2)
  • [UI]: Fixed a permissions issue with reading NCBI submissions. (0.11.3)
  • [Developer]: Paths in the database (for sequence files, output files, references, remote) are stored as relative paths instead of absolute. This will make it easier to migrate filesystems in the future.
  • [UI]: Implemented a project synchronization feature to pull remote samples and data from other IRIDA installations.
  • [Developer]: Added FastQC metrics to the REST API
  • [Workflow]: Upgraded SNVPhyl from 0.3 to 1.0.

1.0.0 to 0.11.0

  • [UI]: Fixed issue were login page was being displayed even though the user was logged in.
  • [UI]: Full analysis name is now displayed in table
  • [UI]: Added the project ID to all project specific pages.
  • [UI]: Added the time to modified dates.
  • [UI]: Fixed issue with IE11 caching ajax calls.
  • [UI]: Samples in the cart are now sorted by created date.
  • [UI]: Fixed a bug where exporting to Galaxy from the cart was not working.
  • [Database] Fixed an issue with migrating single end sequence files to the new SequencingObject model in cases where samples with single files had been merged. IRIDA installs should skip directly to v1.0.2 from 1.0.0alpha-10 to avoid database update problems. (1.0.2)
  • [Developer]: Added a complete docker image for Galaxy, updated the VirtualBox appliance to use the Docker image.
  • [UI]: Fixed a bug when the launch pipeline page was opened on a small display (<1000px) the "Launch Pipeline" button disappeared.
  • [Developer]: Added support for a wider variety of naming patters when pairing uploaded sequence files.
  • [UI]: Fixed a bug where the hashCode method on SequenceFilePair was only using the date the pair was created, causing Sets of pairs to be much smaller than expected. (1.0.3)
  • [UI]: Fixed a UI bug in Internet Explorer 11 where the IRIDA logo and the Projects menu were overlapping.
  • [Developer]: Fixed a couple of broken links in documentation.
  • [Developer]: Re-fixed the hashCode bug so that the files collection is a List instead of a Set. The Set was throwing a NullPointerException from Hibernate. (1.0.4)
  • [UI]: Displaying the modification time of samples in the project/samples table.
  • [UI]: Refactored Sequencing Runs list to use dandelion datatables.
  • [UI]: Fixed a bug where groups on a project with manager role were not allowed to behave like a manager. (1.0.5)
  • [UI]: Added a project event for removing samples from a project.
  • [UI]: Updated NCBI SRA uploader UI to be easier to prepare large numbers of samples.
  • [Developer]: Dropped version down to a slightly lower number.

1.0.0-alpha10 to 1.0.0

  • [UI]: Fixed a bug where project filtering on the projects table excluded projects that did not have an organism
  • [Developer]: Make all of the responses when working with samples have the same set of links.
  • [UI]: Show the version of the pipeline on the pipeline details page.
  • [Developer]: Fixed a bug where updating project modified time on addition of a sample caused the uploader to fail.
  • [UI]: Help links and contact information shown on page are now configurable.
  • [UI]: Show the current version of IRIDA in the UI under the 'Help' menu.
  • [Developer] Change integration tests to use Liquibase instead of Hibernate hbm2ddl, to more closely resemble production environment.
  • [Developer] Change service-layer integration tests to use MySQL database instead of in-memory database
  • [UI] Added description box for describing a new analysis before submission to a pipeline.
  • [UI] Added password restriction list when creating or editing user info, and when resetting a password.
  • [Developer] Changed organization of sequencing data to make it easier to add other types of sequencing objects and automate tasks on data upload.
  • [UI/Workflow] Added per-project option to automatically assemble uploaded sequence data.
  • [UI]: Added active tokens count to OAuth client list page.

1.0.0-alpha9 to 1.0.0-alpha10

  • [Developer]: Upgraded to angularjs 1.5.0.
  • [Developer]: When building the VM, don't install a tool more than once (even if multiple workflows depend on the tool).
  • [UI]: Fixed a bug where the Send to Galaxy button was enabled on the samples table even if you didn't come to IRIDA through a Galaxy.
  • [UI]: Fixed a bug where uploading a reference file with IUPAC ambiguous bases was reporting a very bad error message, and was inconsistently applied in the different places where you can upload reference files.
  • [Developer]: Database initialization for integration tests is now 1) managed by liquibased to match our production environment, and 2) runs much more quickly by loading up a pre-populated database rather than building the database by changesets from the beginning of time.
  • [UI]: Removed the bottom footer and moved links into the Help menu.
  • [UI]: Fixed a bug where sorting users on the users table didn't actually sort the users correctly.
  • [Developer]: Added support to Galaxy integration to allow different sets of states, (hopefully) allowing the use of newer versions of Galaxy that we prescribe.
  • [UI]: New feature: user group management for creating collections of users to apply permissions to projects.

1.0.0-alpha8 to 1.0.0-alpha9

  • [Developer]: Added maven package to install node, npm, and front end assets, then it will build all front end dependencies.
  • [Developer]: Replaced Grunt with Gulp for better front-end compilation of assets.
  • [UI]: Fixed a bug where clicking on FastQC quality charts attempted to download the images instead of viewing them in the browser.
  • [Developer]: Added thread pool for scheduled task submission with new configuration key irida.scheduled.threads.
  • [UI]: Made navigation tabs on the project samples page instead of buttons below breadcrumbs.
  • [Developer]: Chrome is launched only one time for the entire testing suite instead of once per class.
  • [UI]: Polling for updates is removed from the analysis details page so that browser sessions don't stay open forever.
  • [UI]: Session timeouts increased to 5 minutes from 2 minutes.
  • [UI]: Enforce some restrictions on NCBI submissions (at least one set of samples, at least one set of files per sample).
  • [UI]: Allow removal of samples from the NCBI submission page.
  • [UI]: Administrators may now view all NCBI export submissions from the admin panel.
  • [Developer]: Replace grunt with gulp.
  • [UI]: Fixed an issue with filtering by file where the sample name file was generated on a Windows machine.
  • [Developer]: Add a maven plugin for handling downloading node.js and npm.
  • [Developer]: Test suites are executed in parallel instead of in serial, improving test execution times.
  • [UI]: Fixed the admin events monitoring page.
  • [Developer]: Added some docs and features for doing browser sync with gulp on css and javascript changes.
  • [UI]: Reference files may now be uploaded at pipeline submission time in addition to being added to a project.
  • [UI]: Fixed a bug where the password reset page was not styled in the same way as the rest of the application.

1.0.0-alpha7 to 1.0.0-alpha8

  • [Developer]: Fix an issue where having multiple forward slashes in a URI would result in part of the URI being duplicated in links generated as part of the response.
  • [UI]: Fixed a bug where users would have permission to view a project page, but not view a sample page if the sample is attached to multiple projects.
  • [Developer]: Upgraded to Dandelion Core, Thymeleaf, and Datatables 1.1.1
  • [UI]: Ignore the __workflow_invocation_uuid__ parameter from Galaxy when importing execution provenance from Galaxy.
  • [UI]: Password reset e-mails now include your username.
  • [Developer]: Fix up inconsistencies with tables created by Liquibase and tables created by Hibernate.
  • [Developer] Removed several unused properties and classes to simplify data model.
  • [UI]: Analysis list page reworked to use Datatables. Now does server side paging for performance increases.
  • [UI]: Replace large checkboxes on Project Samples page with standard platform dependant checkboxes.
  • [UI]: Allow deleting and cancelling an analysis.
  • [UI]: Updated pipeline selection interface by adding the pipeline colour to the background of the name and making the panels equal in height.
  • [UI]: Fixed issue where samples in the cart could not be sent to galaxy.
  • [UI]: Added ability to upload sequence files to NCBI from the Project/Samples table.
  • [UI]: New feature to download complete list of projects either in excel or csv format.
  • [UI]: Fixed bug on Analysis Details page and updated style of the progress bar.

1.0.0-alpha6 to 1.0.0-alpha7

  • [UI] Feature: When new data is added to a project, both the project and sample modified times are changed so that you can find the most recently uploaded files in a project by sorting on the date modified column of the samples table.
  • [UI] Feature: All metadata fields for sample are shown on the samples details page, even if the field does not have an entered value.
  • [Workflow]: Upgraded SNVPhyl from version 0.2 to 0.3.
  • [Workflow]: Upgraded Prokka in assembly and annotation pipelines from 1.4.0 to 1.11.0 (assembly and annotation to 0.3, assembly and annotation collection to 0.2).
  • [UI]: Fixed issue where the organism would overflow on the project page sidebar.
  • [UI]: Fixed issue with Analyses Filter overlapping the Analyses table on smaller screens.
  • [Developer]: Removed magnific-popups from the project samples page and replace with bootstrap modals through angular-ui.
  • [UI]: Fixed issue with downloading a sample with duplicate filenames. Duplicates are now renamed with Windows style "file (1).fastq" names.
  • [UI]: Fixed error with date a user joined a project on the Project Members Page.

1.0.0-alpha5 to 1.0.0-alpha6

  • [UI] Feature: Added IRIDA logo to the header, and added a footer with some contact information. Also added a favicon.
  • [UI] Feature: Added ability to remove sequencing runs and all uploaded files from the web interface.
  • [UI] Feature: Upgrade to the latest version of Phylocanvas for rendering phylogenetic trees from SNVPhyl runs. We were falling back to PhyloSVG in Firefox on Linux because of a bug in Phylocanvas, but the bug has since been fixed, so now everyone gets Phylocanvas!
  • [UI] Feature/Bugfix: Updated the "Recent Activities" section to use angular directives. Also fixed a bug with how the links in recent activities were rendered.
  • [UI] Feature: Added a feature to filter samples in a project using a file with sample names.
  • [UI] Feature: Paging is now down server side for the projects list, improving performance.
  • [Tools] Bugfix: Updated some of the permissions for listing projects for ROLE_SEQUENCER so that the new GUI uploader tool works.
  • [Developer] Feature: Fixed up a lot of the testing code to evaluate pass or fail based on the content of the page rather than the URL. This fixed timing issues in tests and actually validated some behaviour instead of assuming that stuff worked.
  • [Developer] Feature: Add forward and reverse links on paired-end sequencing files to the REST API.
  • [Developer] Bugfix: Moved the install directories in the VM to reside on /home from /opt because packer makes a giant home partition and we were running out of space when Galaxy was running in /opt.

1.0.0-alpha4 to 1.0.0-alpha5

  • [UI] Feature: Announcements section added to dashboard.
  • [UI] Feature: Updated the logo in the top, right-hand corner to use the real IRIDA logo.
  • [UI] Feature: Project e-mail subscriptions; you may now subscribe to a project to receive daily digest e-mails showing project events.
  • [UI] Papercut: Show better error messages when a problem occurs with sequence file uploads by the web interface. (Issue #318)
  • [Workflow]: SNVPhyl is updated to version 0.2 (in sync with NML Galaxy).
  • [Tools] Bugfix: Resolved issue where multiple OAuth token requests by the same client using the same user credentials was resulting in duplicated OAuth access tokens being issued. (Issue #324)
  • [Tools] Papercut: Remove sequencer ID column from back-end, only use the sample name field from sample sheets to reduce confusion about how data is uploaded to samples.
  • [Developer] Removed all unused code for transferring files to arbitrary instances of Galaxy, feature is supported by IRIDA Import tool in NML Galaxy.
  • [Developer] Add new top-level data model classes to help distinguish mutable from immutable objects.

1.0.0-alpha3 to 1.0.0-alpha4

  • [UI] Bugfix: Fixed adding samples to the cart from associated projects.

  • [UI] Bugfix: File downloads should now start instantly instead of after a long delay; Upgraded Dandelion library to work resolve issues with downloading files.

  • [Workflow] Bugfix: Pipelines are now executed in the background with the user account that submitted them rather than a system user. This change was made to facilitate running pipelines with federated data sources.

  • [UI] Bugfix: Samples from remote associated projects are displayed even if the project has no local associated projects.

  • [UI] Bugfix: Fixed showing a "Page not found" page was shown after editing sample details. (Thanks to Matt Walker for finding this one)

  • [Developer] removed several unused and unnecessary css files.

  • [Developer] conditionally hide certain fields and buttons if an e-mail server is not configured.

  • [Developer] Bugfix: fixed a long-standing bug where expressions for showing Thymeleaf properties would sometimes randomly break page rendering by 1) updating the Thymeleaf library to actually show the errors instead of silently ignoring them, and 2) disabling expression caching in Thymeleaf (due to a bug in Spring, bug reported upstream at: https://jira.spring.io/browse/SPR-13247).

1.0.0-alpha2 to 1.0.0-alpha3

  • [Workflow] Synchronize the assembly and annotation workflow(s) with NML production Galaxy versions.

  • [UI] Updated the projects list UI with an improved table view.

  • [UI] Fixed the feature to delete sequence files and sequence file pairs.

  • [UI] When viewing a sample, immediately navigate to the files page instead of showing the sample metadata first.

  • [UI] Show upload progress when uploading sequence files through a web browser.

  • [UI] Update modified date on projects when sequencing data is uploaded.

  • [UI] Added recent event for top-up data.

  • [UI] Add administrator function to revoke client tokens.

  • [UI/Workflow] Add feature to load data from remote instances of IRIDA for local workflow analysis.

  • [Developer] Added a feature to help maintain common icon and glyph usage throughout the platform web interface.

  • [Developer] Complete sequencing runs can now be deleted from the REST API.

  • [Documentation] Various improvements in the install guides for Galaxy, and improved install documentation including download links.

  • [Developer] Add build scripts for building complete, self-contained instances of IRIDA in a virtual appliance.

  • [Developer] Started migration to using Dandelion for asset management on pages.

  • [Developer] Add REST API for interacting with analyses.