New features and maintenance

[northwestwitch]

[4.58]

Added

• Documentation on how to create/update PanelApp panels
• Add filter by local observations (archive) to structural variants filters
• Add more splicing consequences to SO term definitions
• Search for a specific gene in all gene panels
• Institute settings option to force show all variants on VariantS page for all cases of an institute
• Filter cases by validation pending status
• Link to The Clinical Knowledgebase (CKB) (https://ckb.jax.org/) in cancer variant's page

Fixed

• Added a not-authorized auto-login fixture according to changes in Flask-Login 0.6.2
• Renamed cache_timeout param name of flask.send_file function to max_age (Flask 2.2 compliant)
• Replaced deprecated app.config["JSON_SORT_KEYS"] with app.json.sort_keys in app settings
• Bug in gene variants page (All SNVs and INDELs) when variant gene doesn't have a hgnc id that is found in the database
• Broken export of causatives table
• Query for genes in build 38 on Search SNVs and INDELs page
• Prevent typing special characters ^<>?!=\/ in case search form
• Search matching causatives also among research variants in other cases
• Links to variants in Verified variants page
• Broken filter institute cases by pinned gene
• Better visualization of long lists of genes in large SVs on Causative and Verified Variants page
• Reintroduced missing button to export Causative variants
• Better linking and display of matching causatives and managed variants

Changed

• State that loqusdb observation is in current case if observations count is one and no cases are shown
• Better pagination and number of variants returned by queries in Search SNVs and INDELs page
• Refactored and simplified code used for collecting gene variants for Search SNVs and INDELs page
• Fix sidebar panel icons in Case view
• Fix panel spacing in Case view
• Removed unused database sanger_ordered and case_id,category,rank_score indexes (variant collection)
• Verified variants displayed in a dedicated page reachable from institute sidebar
• Unified stats in dashboard page
• Improved gene info for large SVs and cancer SVs
• Remove the unused variant.str_variant endpoint from variant views
• Easier editing of HPO gene panel on case page
• Assign phenotype panel less cramped on Case page
• Causatives and Verified variants pages to use the same template macro
• Allow hyphens in panel names

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This discussion was created from the release New features and maintenance.