19.01.1

• [UI/Developer]: Updated to lodash v4.17.11 to fix security issue. (19.01.1)

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.

0.22.5

• Fixed an issue where metadata entries derived from pipelines were not updating the associated analysis submission and ignoring blank entries (#213)

0.22.4

• [Workflow]: Fixed issue where duplicate filenames were found after running Galaxy workflow in newer Galaxy versions. (0.22.4)

0.22.3

• [UI]: Fixed bug where project samples page would freeze if there where numerous QC Issues.
• [UI]: Fixed error where synchronizing sequence files could lead to truncated files without generating an error.

0.22.2

• [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)

0.22.1

• [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)

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).

0.21.4

• [Workflow]: Fixed bug where auto updating metadata from analysis submission failed for non-admin user. (0.21.4)

0.21.3

• [UI]: Fixed bug where edit groups page would throw a server exception. (0.21.3)