Changelog

Starting with version 2.0 will the project use semantic versioning.

[Unreleased]

Added

Changed

Fixed

  • Fixed bug in generating mongodb URI

  • Fixed crash if vcf type was not recognized

[v0.5.0]

Added

  • Show the same metadata in grapetree as in the sample table from the groups and group view.

  • Added optional LDAP based authentication system

Changed

  • Show disabled IGV button for samples without BAM or reference genome.

  • Updated LIMS export format

Fixed

[v0.4.1]

Added

  • Display LIMS id in samples view

Changed

  • Sample name is being displayed instead of sample id on the samples view

  • Dockerfile chown step for api and frontend

Fixed

  • Fix minhash sample id lookup by storing sample_id as signautre name when signature is written to disk.

  • Links to a sample from the samples tables now works when Bonsai is hosted under a sub-path

  • Fixed so the samples could be added to the minhash index

  • Fixed nameing of signature sketches and updating filename

  • Fixed broken URL that prevented finding similar samples

  • Fixed storing of selected samples in browser session that prevented samples to be added to the basket from the groups view.

  • Fixed broken URLs in dendrogram in samples view

  • Fixed crash when reading empty sourmash index

  • Fixed crash in resistance/variants view when a samples did not have SNVs or SV variants

[v0.4.0]

Added

  • Added Sample name, LIMS ID, and Sequencing run as selectable columns

  • Sample name in sample view table links to sample

  • New upload script (upload_sample.py) that takes a upload config in YAML format as input

Fixed

Changed

  • Sample id is assigend by concating lims_id and sequencing_run

  • Sample id is not displayed by default

  • API route POST /samples/ returns sample_id

  • Removed upload_sample.sh

[v0.3.0]

Added

  • Add button to remove samples from the group- and groups view.

  • Added view for analyszing variants with filtering

  • Added IGV genome browser integration to variant analysis view.

  • Bonsai support display of SV and SNV variants.

  • A user can classify variant as accepted or as rejected based and annotate why it was dissmissed.

  • A user can annotate that a variant yeilds resistance to additional anitbiotics

  • Placeholder Export to LIMBS button to the sidebar in the variants view

  • Added CLI command for exporting AMR prediction to a LIMS tsv file

Fixed

  • 500 error when trying to get a sample removed from the database

  • Frontend properly handles non-existing samples and group

  • Fixed typo in similar samples card that caused invalid URLs

  • Fixed default fontend config to work with default docker-compose file

Changed

  • Removed “passed qc” column from tbprofiler result

  • Changed default app port to 8000 and api port to 8001

[v0.2.1]

Added

  • Bulk QC status dropdown in group view

Fixed

  • Fixed crash when clustering on samples without a MLST profile

  • Fixed bug that prevented adding samples to the basket in groups without “analysis profile” column

  • Fixed issue that prevented finding similar samples in group view

Changed

  • Display the sum of kraken assigned reads and added reads in spp card by default.

  • Froze uvicorn to version 0.25.0

  • Updated fastapi to version 0.108.0

[v0.2.0]

Added

  • Improved output of create_user API CLI command

  • bonsai_api create-user command have options for mail, first name and last name.

  • Open samples by clicking on labels in the similar samples card in the samples view.

  • Optional “extended” HTTP argument to sample view to view extended prediction info

Fixed

  • Fixed crash in create_user API CLI command

  • Resistance_report now render work in progress page

  • Removed old project name from GrapeTree header

  • Fixed issue that prevented node labels in GrapeTree from being displayed.

Changed

  • The role “user” have permission to comment and classify QC

  • Updated PRP to version 0.3.0

[v0.1.0]

Added

  • Find similar samples by calculating MinHash distance

  • Added async similarity searches and clustering

  • User can choose clustering method from the sample basket

  • Added spp prediction result to sample view

  • Find similar samples default to 50

  • Added STX typing for Escherichia coli samples

  • CLI command for updating tags for all samples

Fixed

  • Fixed calculation of missing and novel cgmlst alleles

  • Fixed so sample metadata is displayed in GrapeTree

Changed

  • Renamed client to frontent and server to api

  • Renamed cgvis to Bonsai

  • Complete rewrite of the project

  • Removed N novel cgmlst alleles from cgmlst qc card

  • Use data models from JASEN Pipleine Result Processing application

  • Use pre-defined table columns in edit groups view

Previous release

Starting with version 2.0, the project was renamed from cgvis to Bonsai.