Feature/unified variants #7
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- Deleted templates, models, repositories, and controllers related to old variant group and alias handling. - Refactored dependent views and logic to remove references to deprecated components. - Cleaned up accompanying documentation and comments.
…ce genome and variant metadata handling** - Replaced `genbankContigId` with `refGenome` and `contig` in forms and backend logic. - Enhanced `editForm` and `createForm` to support clearer metadata fields and additional variant types. - Made genomic coordinates immutable, restricting edits to metadata fields only. - Added improved validation and context for editable and optional fields. - Streamlined templates and controller logic to align with `VariantV2` schema.
… models** - Deleted unused templates (`createForm`, `editForm`, `detailPanel`) for Cytobands and STR Markers. - Removed associated Scala models (`Cytoband`, `StrMarker`), streamlining codebase maintenance. - Cleaned up controllers and routes referencing deprecated Cytoband and STR Marker logic.
… models** - Deleted unused templates (`createForm`, `editForm`, `detailPanel`) for Cytobands and STR Markers. - Removed associated Scala models (`Cytoband`, `StrMarker`), streamlining codebase maintenance. - Cleaned up controllers and routes referencing deprecated Cytoband and STR Marker logic.
…ties** - Extracted reusable badge class and variant formatting logic into `CuratorViewUtils` and `VariantViewUtils`. - Updated multiple views to utilize the new utilities, reducing redundancy and improving maintainability. - Replaced inline helper methods with calls to centralized utility functions across various curator and variant templates.
…earch input components** - Added reusable templates for breadcrumbs, flash messages, and search inputs in `fragments`. - Updated variant browser and curator views to utilize the new components, reducing redundancy. - Simplified and centralized layout structures for improved maintainability.
…earch input components** - Added reusable templates for breadcrumbs, flash messages, and search inputs in `fragments`. - Updated variant browser and curator views to utilize the new components, reducing redundancy. - Simplified and centralized layout structures for improved maintainability.
This feature allows users to toggle between the standard tree layout and the block layout on the main tree pages. The preference is saved in a cookie and respected across sessions.
…d clarity** - Added a temporary index to speed up grouping and joining during variant migration. - Combined variant name and coordinates insertion into a single pass. - Simplified alias aggregation using filtered JSONB operations. - Improved maintainability by removing redundant steps and optimizing query structure. - Dropped temporary index after migration steps to clean up.
…tion with dynamic fragment loading** - Replaced server-side pagination logic for variants and haplogroups with HTMX-driven fragment updates for improved responsiveness. - Simplified controller actions and templates, removing unused parameters and reducing complexity. - Added loading spinner and placeholder text for better user experience during content updates.
- Deleted `StrMarker` model and its corresponding table definition. - Cleaned up related dependencies and imports, reflecting the shift away from legacy STR marker handling.
…ariants** - Introduced `findMatches` method in `VariantV2Repository` for matching variants by coordinates or aliases. - Enhanced `YBrowseVariantIngestionService` to support GFF3 ingestion with coordinate normalization, alias grouping, and liftover handling. - Added `smartUpsertVariant` logic to merge or create variants based on matching results. - Improved metadata merging for aliases, coordinates, evidence, and primers during upsert process. - Included support for parsing and processing Y-DNA variants from both VCF and GFF files, with batch processing for efficiency.
…r better performance and maintainability** - Enhanced migration with GIN index management for faster inserts. - Redesigned aggregation queries using Common Table Expressions (CTEs) for aliases and coordinates. - Simplified deduplication steps for `haplogroup_variant` FK updates. - Added verification and manual cleanup steps for improved integrity and safety.
… ingestion to use. Prioritizing the user experience.
…problems with PostgreSQL's planner and inducing full table scans.
…ll see progress, but not tons of 0 new variants. This is the DEFAULT case.
… original as a link source to the final status.
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