Feature/ybrowse integration #5
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…n service - Added `VariantController` with a search endpoint for variants by rsId or common name. - Implemented `YBrowseVariantIngestionService` for batch processing YBrowse VCF files with liftover support. - Expanded `VariantRepository` to support variant search and batch operations. - Updated `GenbankContigRepository` to allow fetching contigs by common names. - Included `htsjdk` library for VCF parsing and liftover functionality.
…on and integrate with ingestion service - Introduced `GenomicsConfig` for managing genomics-related settings, including reference genome aliases, supported references, FASTA paths, and liftover chains. - Extended `YBrowseVariantIngestionService` to utilize `GenomicsConfig` for canonical genome name resolution, reference FASTA loading, and liftover chain management. - Added normalization logic for variants, including left-alignment and allele trimming using reference sequences.
…scheduled ingestion - Introduced `GenomicsAdminController` for triggering on-demand YBrowse variant updates via an admin-only API. - Added `YBrowseVariantUpdateActor` for downloading and ingesting Y-DNA SNP data from YBrowse. - Scheduled periodic ingestion of YBrowse VCF files using Quartz. - Updated `GenomicsConfig` with YBrowse configuration parameters (VCF URL, storage path).
… curator-centric workflows - Introduced `TreeCurator` role with specific permissions for haplogroup and variant curation. - Added comprehensive curator audit logging, including schemas, tables, and services for create/update/delete actions. - Implemented `AuditLogEntry` model and `AuditLogTable` for audit trail tracking. - Developed `CuratorController` with forms and workflows for creating haplogroups and variants. - Enhanced UI with haplogroup and variant creation views.
…ta into variant workflows - Introduced `VariantWithContig` to combine variant and GenbankContig data for improved context. - Extended `VariantRepository` with `findByIdWithContig` and `searchWithContig` methods. - Updated curator interface to display contig and reference genome details. - Refactored variant detail and list views to use `VariantWithContig`.
… and audit logging - Introduced UI panels for managing haplogroup-variant associations: `variantHistoryPanel`, `variantSearchResults`, and `variantsPanel`. - Enabled variant addition/removal workflows with search and modal interfaces. - Added audit logging for haplogroup-variant actions, including revision history. - Updated routes, controllers, and services for new association management features.
…SNP grouping across application - Added `VariantGroup` to represent logical SNPs across reference builds. - Updated `VariantRepository` with grouping methods: `fromVariants`, `searchGrouped`, and `groupVariants`. - Refactored curator UIs (`variantsPanel`, `variantSearchResults`) to display grouped SNPs. - Updated controllers and routes to support grouped variant management, with addition/removal workflows. - Enhanced audit logging for haplogroup-variant group actions.
…d split operations - Added `TreeRestructuringService` for handling `merge` and `split` operations on haplogroups. - Updated UI to include forms for merge and split workflows (`mergeConfirmForm`, `splitBranchForm`). - Enhanced `CuratorController` with routes and actions for tree restructuring. - Integrated new actions into curator interface (`detailPanel` buttons for merge/split). - Added audit logging for merge and split operations in `CuratorAuditService`.
…options and validations - Added radio buttons for tree placement (root, above existing root, leaf). - Included dynamic parent selection with live search results. - Updated backend validations for parent and tree placement conflicts. - Introduced new `searchHaplogroupsJson` endpoint for haplogroup search. - Refactored form handling in `CuratorController` to support advanced tree placement workflows. - Updated repository with methods for fetching root haplogroups (`findRoots`).
…ant liftover - Introduced methods in `GenbankContigRepository` to retrieve all contigs and filter Y-DNA/mtDNA contigs. - Enhanced variant creation form to include a dropdown for selecting reference genome/contig. - Implemented liftover workflow in `YBrowseVariantIngestionService` to support cross-reference genome lifting. - Updated `CuratorController` logic to handle Y-DNA/mtDNA contig selection and variant liftover during creation. - Added audit logging and user feedback for successful variant creation and liftover results.
…operties - Introduced `editVariantGroupForm` and `updateVariantGroup` actions in `CuratorController`. - Created `editGroupForm.scala.html` for managing grouped variant properties. - Enhanced `VariantGroup` workflows with UI updates for list, detail, and edit views. - Integrated routing for group editing and updates. - Improved list and detail panels to display Variant Group builds and variants.
… 0.5 progress - Marked regression tests as completed in planning documentation. - Added detailed scope, deliverables, and outcomes of Phase 0.5 (Base Curator Functionality). - Updated Phase 3 and Phase 4 sections to reflect Phase 0.5 dependencies and completed functionality.
…tive SNP names - Added `variant_alias` table to store alternative names for variants with support for multiple sources (e.g., YBrowse, ISOGG, publications). - Migrated existing `common_name` and `rs_id` data into alias records. - Created `VariantAlias` model, table mappings, and repository (`VariantAliasRepository`) with CRUD operations. - Enhanced `VariantRepository` to handle alias recording during batch operations. - Updated curator detail views to display all aliases, grouped by type, with primary designation support. - Refactored variant search logic to include alias-based matches. - Updated controllers, modules, and UI workflows to integrate alias functionality.
…c and UI - Integrated `VariantAliasRepository` to fetch aliases in batch for variants. - Extended `VariantDTO` to include alias mappings grouped by type. - Updated `HaplogroupTreeService` to map aliases and combine them across grouped variants. - Enhanced SNP detail sidebar UI to display aliases with improved styling and layout. - Added utility methods for formatting reference genome keys and alias types.
- Added SQL migrations to introduce branch age columns (`formed_ybp`, `tmrca_ybp`, and confidence intervals) in `haplogroup` table. - Updated models (`Haplogroup`, `TreeNodeDTO`, and `TreeViewModel`) to support branch age data. - Enhanced curator forms and views to allow editing and displaying branch age estimates, with input fields for CI ranges and source attribution. - Integrated feature flag (`showBranchAgeEstimates`) to control visibility in the tree UI. - Adjusted tree layout to account for larger node dimensions with age data shown.
… variants panel - Introduced a dynamic input field for filtering variants in the panel. - Added badge to display the total variant count. - Updated UI with live filter functionality and status indicator for visible variants. - Adjusted layout for improved alignment and responsiveness.
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