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@JeffreyThiessen JeffreyThiessen released this Nov 25, 2020 · 184 commits to development since this release

  • [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)
Assets 4

@tom114 tom114 released this Oct 8, 2020 · 187 commits to development since this release

  • [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 addded in 20.09. (20.09.2)
Assets 4

@tom114 tom114 released this Oct 5, 2020 · 206 commits to development since this release

[UI]: Fixed bug where sequencing runs could not be deleted on sequencing runs details page. (20.09.1)
[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)

Assets 4

@tom114 tom114 released this Sep 24, 2020 · 222 commits to development since this release

  • [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.
Assets 4

@tom114 tom114 released this Aug 13, 2020 · 869 commits to development since this release

  • [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)
Assets 4

@tom114 tom114 released this Jul 29, 2020 · 872 commits to development since this release

[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)

Assets 4
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@tom114 tom114 released this Jun 25, 2020 · 876 commits to development since this release

  • [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)
Assets 4

@tom114 tom114 released this Jun 17, 2020 · 881 commits to development since this release

  • [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)
Assets 4

@tom114 tom114 released this May 28, 2020 · 885 commits to development since this release

  • [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.
Assets 4

@tom114 tom114 released this Mar 5, 2020 · 2298 commits to development since this release

  • [UI]: Fixed UI bugs preventing users from selecting single-end input files for analysis pipelines. (20.01.2)
Assets 4
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