Feature/unified variants#7

Merged

JamesKane merged 28 commits intomainfrom

feature/unified-variants

Dec 14, 2025

Commits on Dec 13, 2025

**chore(variants): Remove unused legacy variant group and alias code**
JamesKane
committed
Template for maintenance page
JamesKane
committed
DU Naming Authority API
JamesKane
committed
**refactor(variants): Update forms and backend for simplified reference genome and variant metadata handling**
JamesKane
committed
**chore(curator): Remove legacy Cytoband and STR Marker templates and models**
JamesKane
committed
**chore(curator): Remove legacy Cytoband and STR Marker templates and models**
JamesKane
committed
**refactor(views/utils): Centralize badge and variant rendering utilities**
JamesKane
committed
**refactor(views): Extract and reuse breadcrumb, flash message, and search input components**
JamesKane
committed
**refactor(views): Extract and reuse breadcrumb, flash message, and search input components**
JamesKane
committed

Commits on Dec 14, 2025

feat(tree): add user opt-in preference for block layout
JamesKane
committed
**refactor(sql): Optimize variant migration script for performance and clarity**
JamesKane
committed
**refactor(views/controllers): Simplify variant and haplogroup pagination with dynamic fragment loading**
JamesKane
committed
**chore(models): Remove deprecated STR Marker model and table**
JamesKane
committed
**feat(variants): Add smart ingestion and deduplication for YBrowse variants**
JamesKane
committed
**refactor(sql): Optimize and consolidate variant migration script for better performance and maintainability**
JamesKane
committed
Fixing some SQL issues
JamesKane
committed
Enhance the block tree layout to use SVG and similar design language to the original.
JamesKane
committed
Search the tree by SNP name as well as subclade name
JamesKane
committed
Using the more correct terminology for cladograms
JamesKane
committed
Fixing the download location. Was still trying to refer to the VCF.
JamesKane
committed
Reducing the number of connections from the pool we allow the variant ingestion to use. Prioritizing the user experience.
JamesKane
committed
Fixing some UI odditities
JamesKane
committed
Remove dead code
JamesKane
committed
Split the DB side OR to live in the application code. It was causing problems with PostgreSQL's planner and inducing full table scans.
JamesKane
committed
Try optimizing the queries.
JamesKane
committed
Comment out the logging to reduce noise. Need to rethink it so we still see progress, but not tons of 0 new variants. This is the DEFAULT case.
JamesKane
committed
Back to logging total records examined, since the Perf issues seems resolved.
JamesKane
committed
Split the universal variant details into smaller chunks retaining the original as a link source to the final status.
JamesKane
committed

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Feature/unified variants#7

Feature/unified variants#7
JamesKane merged 28 commits intomainfrom
feature/unified-variants

Commits on Dec 13, 2025

chore(variants): Remove unused legacy variant group and alias code

Template for maintenance page

DU Naming Authority API

refactor(variants): Update forms and backend for simplified reference genome and variant metadata handling

chore(curator): Remove legacy Cytoband and STR Marker templates and models

chore(curator): Remove legacy Cytoband and STR Marker templates and models

refactor(views/utils): Centralize badge and variant rendering utilities

refactor(views): Extract and reuse breadcrumb, flash message, and search input components

refactor(views): Extract and reuse breadcrumb, flash message, and search input components

Commits on Dec 14, 2025

feat(tree): add user opt-in preference for block layout

refactor(sql): Optimize variant migration script for performance and clarity

refactor(views/controllers): Simplify variant and haplogroup pagination with dynamic fragment loading

chore(models): Remove deprecated STR Marker model and table

feat(variants): Add smart ingestion and deduplication for YBrowse variants

refactor(sql): Optimize and consolidate variant migration script for better performance and maintainability

Fixing some SQL issues

Enhance the block tree layout to use SVG and similar design language to the original.

Search the tree by SNP name as well as subclade name

Using the more correct terminology for cladograms

Fixing the download location. Was still trying to refer to the VCF.

Reducing the number of connections from the pool we allow the variant ingestion to use. Prioritizing the user experience.

Fixing some UI odditities

Remove dead code

Split the DB side OR to live in the application code. It was causing problems with PostgreSQL's planner and inducing full table scans.

Try optimizing the queries.

Comment out the logging to reduce noise. Need to rethink it so we still see progress, but not tons of 0 new variants. This is the DEFAULT case.

Back to logging total records examined, since the Perf issues seems resolved.

Split the universal variant details into smaller chunks retaining the original as a link source to the final status.

Feature/unified variants#7JamesKane merged 28 commits intomainJamesKane/decodingus:mainfrom feature/unified-variantsJamesKane/decodingus:feature/unified-variantsCopy head branch name to clipboard

Commits

Commits on Dec 13, 2025

Commits on Dec 14, 2025

Feature/unified variants#7
JamesKane merged 28 commits intomainfrom
feature/unified-variants