Support for selecting multiple origins in geneVariant term

[gavrielm]

Description

This PR supports selection of one or more mutation origins for geneVariant term. In the geneVariant search handler,
if a mutation type (e.g. SNV/indel) has multiple origins (e.g. somatic and germline), then checkboxes are rendered to select one or more of these origins. The selected origins are stored on tw.term.origins[].

Since now origin is a dynamic property, dtTerms and predefined groupsets that were defined by origin have been removed. Legacy geneVariant termwrapper structure is still supported.

Labels for selected origins and sample types are stored on term.originLabel and term.sampleTypeLabel, respectively, and then concatenated into term.label. The term.label is displayed along with term.name in the plot title and in the term pill.

Please test using DISCOVER portal.

Checklist

Check each task that has been performed or verified to be not applicable.

• Tests: Added and/or passed unit and integration tests, or N/A
• Todos: Commented or documented, or N/A
• Notable Changes: updated release.txt, prefixed a commit message with "fix:" or "feat:", added to an internal tracking document, or N/A
• Rust: Checked to see whether Rust needs to be re-compiled because of this PR, or N/A

[Copilot]

Copilot review overview

🟡 Changes recommended

Several state-reset, label-generation, compatibility, and legacy-migration defects can produce incorrect filtering or failing tests.

Review effort: Balanced
Findings: 2 · 4

Open (6)

• Clear stale origin state when no origin selector exists · New
• Migrate legacy origins in custom groupsets · New
• Fall back to sample type name when plural name is absent · New
• Put sample type before origin in combined labels · New
• Include selector labels in custom groupset titles · New
• Preserve generic sample labels for legacy matrix requests · New

What changed in this PR

Adds multi-origin selection and labeling for geneVariant terms across client and server processing.

Changes:

• Makes mutation data-type terms origin-agnostic.
• Adds reusable origin/sample-type selectors and labels.
• Filters and aggregates variants across selected origins.

File	Description
shared/​utils/​src/​test/​terms.unit.spec.ts	Tests origin-agnostic data-type terms.
shared/​utils/​src/​common.ts	Simplifies shared data-type terms.
shared/​types/​src/​terms/​geneVariant.ts	Updates current and legacy origin types.
server/​src/​test/​mds3.init.unit.spec.js	Tests server-side origin filtering.
server/​src/​termdb.matrix.ts	Adjusts sample-type labels.
server/​src/​termdb.barchart.js	Attaches origins to chart terms.
server/​src/​routes/​termdb.categories.ts	Supports dynamic origin categories.
server/​src/​mds3.init.js	Filters variants and availability by origins.
client/​tw/​test/​geneVariant.integration.spec.ts	Tests term-wrapper migration.
client/​tw/​geneVariant.ts	Migrates legacy terms and updates groupsets.
client/​termsetting/​handlers/​geneVariant.ts	Displays combined labels.
client/​termdb/​handlers/​test/​rememberedGvQ.unit.spec.ts	Updates remembered-setting expectations.
client/​termdb/​handlers/​test/​geneVariant.integration.spec.ts	Tests origin and label selection.
client/​termdb/​handlers/​test/​geneExpression.unit.spec.ts	Tests sample-type labels.
client/​termdb/​handlers/​rememberedGvQ.ts	Matches settings by data type.
client/​termdb/​handlers/​geneVariant.ts	Implements origin selection and submission.
client/​termdb/​handlers/​geneExpression.ts	Reuses sample-type labeling.
client/​filter/​tvs.dt.js	Merges selected-origin values.
client/​filter/​test/​tvs.dt.unit.spec.ts	Tests origin value merging.
client/​dom/​test/​checkboxSelect.unit.spec.ts	Tests the checkbox selector.
client/​dom/​sampleTypeSelect.ts	Generalizes sample-type selection and labels.
client/​dom/​index.ts	Exports checkbox utilities.
client/​dom/​checkboxSelect.ts	Adds reusable checkbox selection UI.

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[Copilot]

Copilot review overview

🟡 Changes recommended

Legacy saved sessions can be misinterpreted, and current label, matrix, and type-definition issues cause incorrect behavior or test/type-check failures.

Review effort: Balanced
Findings: 3 · 2

Open (5)

• Handle trimmed legacy germline selections during migration · New
• Declare originLabel and label on geneVariant term types · New
• Migrate legacy origins in custom groupsets
• Include selector labels in custom groupset titles
• Fall back to sample type name when plural name is absent

Resolved since last review (3)

• Clear stale origin state when no origin selector exists
• Preserve generic sample labels for legacy matrix requests
• Put sample type before origin in combined labels