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@northwestwitch northwestwitch released this 12 Jun 11:23
v1.0.0
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Learn about vigilant mode.

[1.0.0]

Added

  • Instructions on how to install and run the app on a Conda environment
  • Test for heartbeat endpoint
  • Automated tests GitHub workflow
  • Instructions on how to run a demo connected to a database in README
  • Add Codecov steps to Tests GitHub action
  • Vulture GitHub action to remove unused code
  • Colored logs for development and debugging
  • Common test fixtures
  • Some badges on README page
  • Tests for cases and samples endpoints
  • Save samples with coverage files stored on a remote HTTP(s) server
  • Demo data (D4 file containing coverage data for a panel of 4 genes)
  • Endpoint for coverage queries over a single interval of a provided D4 file
  • Demo case and demo sample loaded with demo instance startup
  • Endpoint for coverage queries over the intervals of a BED file
  • Include a default .env file loaded on app startup
  • Filter genes, transcripts and exons by Ensemble id, HGNC id, HGNC symbol
  • Demo genes, transcripts and exons loaded on demo instance startup
  • Return coverage over a list of genes for a sample in the database
  • Remove a sample from the database by providing its name
  • Return coverage and coverage completeness (custom thresholds) over a list of genes for a case or a list of samples
  • Return transcripts coverage and coverage completeness (custom thresholds) over a list of genes for a case or a list of
    samples
  • Return exons coverage and coverage completeness (custom thresholds) over a list of genes for a case or a list of
    samples
  • Remove a sample and all associated samples from the database by providing its name
  • Created the basic structure of the howto using mkdocs
  • Created a GitHub action for publishing the documentation on the GitHub pages
  • Documentation on how to load cases and samples into the database
  • Documentation on how to query the server for coverage stats
  • Documentation on how to load genes, transcripts and exons into the database
  • Improve documentation on how to customise the .env file to use a production database

Fixed

  • Bugs preventing the gunicorn app to launch
  • Code to compose DB url to work when app is invoked from docker-compose
  • Dockerfile building error due to missing d4tools lib
  • Add VARCHAR length to sample.coverage_file_path SQL field
  • Format of Build field in genes, transcripts and exons tables
  • Increased size of allowed HGNC symbols in the MySQL gene model
  • Remove old exons and transcripts data when updating genes
  • Test warnings regarding Case-Sample database relationship
  • Error when removing a case that is not found in the database
  • Updated and faster GitHub actions
  • Format of mean coverage and coverage completeness returned in responses

Changed

  • Renamed root endpoint to heartbeat
  • Use a multi-stage build in Dockerfile to reduce its size
  • SQLite database launched instead of MySQL as the default demo database
  • Simpler docker-compose file and additional docker-compose file to show MySQL connection howto
  • Removed broken BumpVersion GitHub action
  • Use a temporary file when running the demo app
  • Modified the command to run a demo instance in README file
  • Renamed table Individuals table to the more general Samples
  • Renamed table Regions table to Intervals
  • Use uvicorn logging and avoid printing logs twice
  • Modified samples and cases endpoints to interact with database via CRUD utils
  • Use SQLAlchemy 1.4 Declarative which is now integrated into the ORM to avoid deprecation warning
  • Start SQL engine and sessions using the future tag to prepare migration to SQLAlchemy 2.0
  • Updated a few python dependencies
  • Moved validation of sample's coverage file path to sample's pydantic model
  • Installing the pyd4 module as a requirement of this repository
  • Moved the endpoints constants to a class in test fixtures
  • More explicit names for two endpoints
  • Load genes, transcripts and exons in batches of 10K records
  • Simpler code to load genes and transcripts into the database
  • Updated version of several GitHub actions
  • Validate sample coverage queries so that only one gene list format can be provided
  • Speed up queries by optimizing Genes, Transcripts and Exons tables and indexes
  • Custom algorithm to speed up coverage completeness thresholds calculation
  • Replaced deprecated pkg_resources lib with importlib_resources lib
  • Modified Python version in Dockerfile from 3.8 to 3.11
  • Introduced a "track_name" key in sample database objects to be used in multitrack D4 files analysis
  • One sample can belong to more than one case
  • Practical howto in README file and moved deployment instructions to the docs
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