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CHANGELOG.md

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[Unreleased]

Added

  • Added SNV clustering using SKA indexes.
  • Added card for displaying EMM typing result from emmtyper.
  • Added mlst scheme to mlst card.

Changed

  • Added dummy SKA indexes for test samples.
  • Updated PRP to version 0.11.3
  • Added underscores to AMRs in LIMS export.

Fixed

  • Fixed padding of sample table in group and groups view.

[v0.8.0]

Added

  • Added select all variants button to tbprofiler and SV cards in Variant report view.
  • Added button to the groups view for adding selected samples to group.
  • Added button to the group view for removing selected samples from group.
  • Added column with comments indicator to group and groups view.
  • Added foundation for testing API routes.
  • Added test for Allele cluster service.

Changed

  • Genome coverage plot to interactive and have an y-range of 0 to 100.
  • Use data-tables instead of w2ui for samples tables.
  • Improved error handling of allele cluster service.
  • Removed swedish characters from LIMS export output.

Fixed

  • Fixed highlight of displayed sample in the dendrogram on the sample view page.
  • Fixed formatting of grapetree metadata that could crash the frontend.
  • Fixed crash in Allele cluster service when clustering samples with the same profile using MsTree or MsTreeV2.

[v0.7.0]

Added

  • Can configure SSL verification and usage of SSL certs for API requests from frontend.
  • Added cards ShigaPass result and function to tag Ecoli and Shigella spp with ShigaPass result.
  • Added option to filter variants on WHO class and variant type in the variants view.
  • Added button to reset variants filter on the variants view.
  • Added support for more IGV annoation file formats.

Changed

  • Bonsai now uses sample ids created by Jasen to identify unique samples.
  • Updated PRP to version 0.10.1
  • Improved installation instructions.
  • Updated requests to version 2.32.0
  • Added startup commands to minhash and allele clustering services Dockerfiles.
  • Use pydantic-settings for config management in frontend.
  • Updated the samples tables to make sample name, sample id, and major spp searchable.
  • Truncate long tbprofiler variant names and show full name on hover.
  • Fixed issue that could prevent IGV from loading.
  • Updated IGVjs to version 3.0.2
  • Updaed how AMR variants are displayed on the sample view page. All varians are displayed if no variant have been processed, otherwise only show passed resistance yielding variants.

Fixed

  • Fixed misalignment of the checkbox in the samples table in the group and groups view.
  • Fixed bug in the TB lineage card that could crash the frontend.
  • Fixed an issue where samples without MLST profiles could crash GrapeTree.
  • Fixed removal of new ChewBBACA alleles call info codes.

[v0.6.0]

Added

  • Added source of tbprofier db entry as badge to result card.
  • Added species and phylogroup prediction from Mykrobe.

Changed

  • Updated IGVjs to version 2.15.11
  • Updated PRP to version 0.8.3
  • Updated the formatting of the results table in the tbprofiler card.

Fixed

  • Fixed bug in generating mongodb URI
  • Fixed crash if vcf type was not recognized
  • Fixed bug that prevented samples to be reomved from the basket.
  • Improved error handling if a sample could not be removed from the basket.

[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