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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning

About changelog here

[Unreleased]

Added

  • --force flag to gens loads sample for overwriting any existing sample in case of key conflict.
  • --force flag prints a warning to stderr when overwriting an existing sample.
  • gens delete sample command
  • Height ordering for variants track.

Fixed

  • Pan able to exit chrosome when using genome build 17
  • --force flag update_one call not being called properly
  • Incorrect total sample count on home page.
  • Some typos and documentation.
  • Labels often not being visible on larger variants.

Merged for Solna from Lund 2.1.2

Changed

  • Changed cached method from simple to file system as it would be thread safe

Fixed

  • Fixed cache issue that could result in chromosome information not being updated
  • Fixed max arg error when searching for some genes
  • Fixed bug that prevented updating annotation tracks

[2.3]

Added

  • Link out to Scout: introduce config variable for base URL
  • Link out to Scout: case links on home sample list
  • Link out to Scout: click variant to open Scout page

Changed

  • Archive prod docker image with release tag name. Update action versions.

Fixed

  • Error image background static path
  • GitHub action DockerHub push on release

[2.2]

Added

  • Document track processing and loading
  • OAuth authentication

Changed

  • Use sample id instead of display name for variant retrieval
  • Hide balanced variants
  • Keyboard pan speed increased
  • Don't shrink pan window when attemting to pan over start

[2.1.1b]

Added

Changed

  • Changes the main view's page title to be sample_name and adds sample_name and case_id to the header title
  • Updated external images used in GitHub actions, including tj-actions/branch-names to v7 (fixes a security issue)
  • Updated Python and MongoDB version used in tests workflow to 3.8 and 7 respectively

[2.1.2 Lund only - Solna version in Unreleased/2.4]

Added

Changed

  • Changed cached method from simple to file system as it would be thread safe

Fixed

  • Fixed cache issue that could result in chromosome information not being updated
  • Fixed max arg error when searching for some genes
  • Fixed bug that prevented updating annotation tracks

[2.1.1]

Added

Changed

  • Updated flask and pinned connexion to v2
  • Updated node version of github action to 17.x

Fixed

  • Fixed annotation tracks being hidden behind other elements
  • Use sample id as individual id to link out from Gens home sample list
  • Some fixes from MHKC CG-Lund, e.g. status codes and a JSON error
  • Removes some leading / that were breaking links
  • Increased contrast of region selector
  • Chromosome bands are displayed properly

[2.1.0]

Added

  • Added seperate error page for when accessing a sample not in the database
  • load chromosome-info stores centromere position and cyto band info
  • Display viewed chromosome region in cytogenetic ideogram figure

Changed

Fixed

  • Can now display samples that doesnt have data on all chromosomes

[2.0.1]

Added

Changed

  • Do not warn when using default configuration
  • Renamed cli gens load chrom-sizes to gens load chromosome-info
  • Removed gens load chromosome-info dependancy on additional files

Fixed

  • Missing tbi files now returns 404 status code
  • Fixed sort order of samples table
  • Prevent "internal error" when trying to access sample not in database

[2.0.0]

Added

  • Command line interface for manageing Gens
  • Commands for loading transcripts, annotations and chromosome size into database
  • Include api spec, html and static files in distribution
  • Display when databases last updated in /about.html
  • Display current configuration /about.html
  • Added landing page that show uploaded samples
  • Added load sample command for loading samples into gens database
  • Added index command for creating new indexes
  • Added view sample command for displaying sample information
  • Added pagination samples table

Changed

  • Changed development status from Alpha to Stable
  • Samples are loaded based on the paths given when uploading the sample
  • Gens no longer uses HG38_PATH and HG37_PATH variables
  • Use genome build instead of hg_type throughout the codebase and in API calls

Fixed

  • Fixed typo in variable name

[1.2.1]

Added

  • Reinstated tooltips to display additional information on genetic elements

Changed

  • Use popper for positioning tooltips
  • Prettier for code formatting

Fixed

[1.2.0]

Added

  • Added github workflow for running pytest on PRs
  • Added unit tests
  • Added labels to the annotation tracks
  • Added js unit tests with jest and linting with eslint

Changed

  • Changed positive strand color of transcripts to a more constrasting color
  • Temporarily disabled on hover popups in annotation tracks
  • Transcripts are represented as arrows in lower resolutions
  • Highlight MANE transcript in name and with a brighter color
  • Annotaion tracks are disabled if api returns an error at some point
  • Annotation track DOMs are constructed with template macros
  • Don't show "Loading..." when panning the interactive view with the mouse
  • Changed default chromosome region to display to entire chromosome 1
  • Restored ability to view entire chromosome when zoomed in by clicking on it in the chromosome overview.
  • Build js package with webpack instead of gulp
  • Remove dependency on three.js

Fixed

  • Gene names are now centered below transcript
  • Fixed assignement of height order when updating transcript data
  • get-variant-data returns 404 if case cant be found
  • Hide trancscript tracks when requesting new data from api
  • Fixed alignment of annotation tracks near chromosome end

[1.1.2]

Added

  • Added error pages for 404, 416, 500 and missing samples
  • Added watch cmd to npm run to launch a gulp server watches and updates js/css assets
  • Shift - Click now Zoom in

Changed

  • Refactored page definitions into blueprint module
  • Removed entrypoint script

Fixed

  • Navigation shortcuts does not trigger in text fields
  • Fixed crash when searching for only chromosome
  • Restored ability to search for transcripts by gene name
  • Fixed crash when Shift - Click in interactive canvas
  • Fixed checking of api return status in drawInteractiveContent
  • Aligned highlight in interactive canvas
  • Bumped Three to version 0.125.0

[1.1.1]

Fixed

  • Reincluded gunicorn in docker image

[1.1.0]

Added

  • Runnable Gens development environment in docker
  • Added Change log document
  • Added development environment
  • Set default annotation file with annotation="name" url argument
  • Added tack with variants from the Scout database where the selected variant is highlighted
  • Github action to enforce the use of a changelog
  • Described Gens APIs in openAPI specification file
  • Add possibility to load overview data from a JSON, which substantially improves initial load times.
  • Ctrl + Mouse click in interacive canvas zooms out
  • Shift + Mouse to select a region in the interactive canvas to zoom in on
  • Annotation tracks pan with the coverage track
  • Annotation tracks are rendered by blitting sections from an offscreen canvas
  • Added logo to README and Gens webpage

Changed

  • Added description on how to use the containerized version of Gens
  • Replaced print statements with logging to stderr
  • Refactored Gens as a python package
  • Updated start.sh to work with packaged Gens
  • Improved loading of genome overview track
  • Made Gens (and db update scripts) read db configuration from env variables
  • Increased the expanded annoation track width to 300px
  • All annotations are allways being displayed
  • Eliminate use of offScreenCanvas in order to support Firefox/Gecko
  • Removed select region to zoom functionality from overview canvas
  • Dropped jquery as a dependency
  • General GUI updates

Fixed

  • Replaced depricated update() with update_one() in update_transcripts.py.
  • Adjust the "Loading..." div to avoid drawing it above UI elements
  • Made SASS more readable

[1.0.0]

Added

  • Initial release of Gens