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
andsequencing_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.