Genes coverage report and overview

[1.2]

Added

• Load genes, transcripts and exons from pre-downloaded files
• Demo coverage report endpoint in new report module
• Coverage completeness lines in HTML coverage report
• Default threshold level coverage lines in HTML coverage report
• Hidden table cell showing incompletely covered genes in coverage report
• Display optional case name on gene coverage report
• Display error in coverage report when query genes are not found in the database
• Export coverage report to PDF
• Metrics explanation section on coverage report
• Non-demo coverage report endpoint
• Fixed coverage report filters to update report using other settings
• Demo and non-demo genes coverage overview endpoint
• Incomplete intervals at different coverage thresholds on genes overview page
• Gene coverage overview endpoint
• Documentation to create custom genes coverage and coverage overview reports

Changed

• Moved helper function from endpoints coverage to crud samples
• Deleted unused src/chanjo2/meta/handle_query_intervals.py file
• Non-root user and password for database connections
• Refactor and simplify code in meta.handle_d4 module
• Fixed documentation according to changed coverage API
• Removed unused sqlmodel and updated some other dependencies
• Show only RefSeq transcripts in coverage report and overview
• Refactored HTML templates to reduce repetitions by inheriting code from base template
• Coverage report form to accept genes as Ensembl IDS, HGNC IDs and HGNC symbols
• Moved coverage report "show genes" outside form and just above custom coverage stats table
• Updated several Python libraries including schug

Fixed

• Bump certifi from 2022.12.7 to 2023.7.22
• Database connection parameters in documentation files
• Avoid duplications when retrieving transcripts and exons in gene
• Add upgrade-insecure-requests meta to HTML page to be able to use javascript fetch in requests
• Renamed imported function from schug 1.3