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Wire the UI up to the new GET /score-sets/{urn}/variants endpoint that
serves one pre-chewed record per variant (selection key, score,
consequence, annotation bridge ids, and parsed DNA/protein HGVS blocks).
- add LeanVariant/HgvsField types mirrored from the OpenAPI schema
- add getLeanScoreSetVariants and leanScoreSetVariantsUrl to the API
client
- fetch the lean view alongside the legacy CSV scoresData channel in
ScoreSetView, exposing a typed leanVariantRecords handle so consumers
can migrate off the CSV channel slice by slice
- regenerate openapi.d.ts for the new path and schemas
Migrate the heatmap, histogram, score-set view, visualizer, and variant lookup off the legacy CSV-parsed `Variant` model onto the lean `DisplayVariant`/`LeanVariant` API record. The score-set view now fetches a single lean whole-set channel instead of the dual histogram-CSV + lean channels, and variant identity keys move from `accession` to `variantUrn` throughout. - Rework use-variant-coordinates around `coordinateFor(variant, level, frame)` as the single source of truth for the (level × frame) coordinate grid; add `resolveLevel` and `isUnmapped`, and make the (mapped, dna) cell null for protein assays (mavedb-api#784) - Handle unmapped variants: labels fall back to submitted HGVS rather than the URN, mapped/clinical mode is disabled and annotated when a set has no mapped data, and the search matches both frames - Extract VEP consequence bucketing into lib/consequences.ts, replacing the parsed-HGVS effect classifiers (`variantIsMissense`, etc.) in lib/variants.ts; `isStartOrStopLoss` stays as the block-aware heatmap filter - Extract shared d3 chart tooltip builders into lib/tooltips.ts and rebuild the heatmap/histogram tooltips on top of them - Add `isNucleotideHgvs` to lib/mave-hgvs.ts and `inferReferenceSequenceFromBlocks` to lib/variants.ts - Heatmap UX: deferred redraw with a loading indicator, a not-shown breakdown (no-coordinate vs complex), a note when the selection is off the chart, and viewport-aware hover-tooltip positioning - Add tests for consequences, mave-hgvs, and use-variant-coordinates
Consume the reworked GET /variants/{urn} envelope: a self-contained
VariantDetailPanel (assay-level facts, primary classification, gnomAD/ClinVar,
supersession badge, link to the variant page) wired into ScoreSetView on the
?variant= selection, plus use-variant-lookup / VariantScreen / the legacy
measurement-URN redirect repointed off the deleted VariantEffectMeasurementWithScoreSet
onto the flat envelope fields (clingenAlleleId bridge, separately fetched score set).
Clinical controls: drop the hard-coded DEFAULT_CLINICAL_CONTROL_VERSION, accept a
nullable version end to end, and render human-readable ClinVar versions
(formatClinvarVersion) in the heatmap/histogram clinical mode. openapi.d.ts
regenerated for the new API shapes.
Match the API field rename: the detail panel reads the superseding *score set*'s URN (supersession is score-set-versioned), not a variant URN, and the tooltip now reads "Superseded by score set X". Update the generated VariantDetail type to match. The /alleles/* schema regen in openapi.d.ts is deliberately left for the alleles-slice work.
…ram url helper - Support an optional `limit` on getScoreSetScoresPreview and getScoreSetCountsPreview so the preview table fetches only the rows it renders instead of the full dataset; document that `drop_na_columns` is evaluated over the sampled rows - Remove the now-unused histogramScoreSetVariantDataUrl helper and its scoreSetVariantDataParams/namespace constant
Pass the variant's URN as a query param on the ClinGen variant-details link so the destination page can disambiguate which variant to show when a single ClinGen allele maps to multiple variants.
- Show the score set URN under its title when showUrn is set, so correlated score sets with identical facts can be told apart - Add an "Assay level" detail row driven by a new assayLevel prop, surfacing the score-set-wide protein/cdna/genomic measurement level - Scope the 2-col top-border reset to the new assay-facts-grid--2col class so the 1-col layout keeps a divider between every stacked row
- Pass MAX_ROWS as a limit to the scores/counts preview requests instead of fetching the full dataset and slicing client-side - Derive the "Showing X of Y" total from the score set's numVariants rather than the now-truncated fetched rows, since the fetch no longer returns the true total
proteinConsequenceBlock referenced variant.proteinLevelHgvs, a field that no longer exists on DisplayVariant; fall back through variant.mapped.protein (the mapped protein representation) before the submitted protein HGVS, matching the documented fallback order.
- Replace MeasurementType (nucleotide/protein/associatedNucleotide) with a two-way LevelBucket (nucleotide/protein) derived from the mapping record's AssayLevel, since cdna and genomic share one visual bucket - Add assayLevelBucket() to bucket a raw assay level, and dominantAssayLevel() to pick the most common non-null level across a score set's variants - Add ASSAY_LEVEL_LABELS for the three per-level labels and RELATIONSHIP_LABELS for the RT direct/protein_consequence/ nucleotide_encoding relationship display strings - Add unit tests covering bucketing and dominant-level selection, including ties and all-null/undefined inputs
Add memoizeRead, a p-memoize/expiry-map wrapper that dedupes concurrent calls to the same idempotent GET and caches the result for a short TTL. Read data can be rewritten underneath us at any time by the mapping/annotation worker, so the cache is tuned to collapse page-load request bursts rather than to reuse results long-term; a 30s default TTL bounds staleness while composables still handle same-page reuse via their own reactive caches.
- Replace lookupVariantsByClingenId (POST clingen-allele-id-lookups)
with getAlleleMeasurements (GET clingen-alleles/{id}/measurements),
the new entrypoint for the ClinGen-allele-centric variant page;
supports includeSuperseded, includeNucleotideSiblings, and asOf
- Wrap getAlleleByCaId, getScoreSet, getLeanScoreSetVariants, and
getVariantDetail in memoizeRead so repeated reads for the same key
dedupe and share a short-TTL cache instead of refetching
- Consolidate the duplicated getScoreSet into score-sets.ts and drop
the copy from calibrations.ts
- Drop getHistogramVariantData now that its only caller is gone
Add groupAlleles, which collapses a variant detail's allele sidecar into rendered groups: each c<->g projection pair (linked by projectionOf) folds into one entry with deduplicated annotations, while the protein apex and projection-failed candidates stay as one-member groups. Groups carry a measured/pageRoot/derivation summary and sort measured-and-page-root entries first, then bottom-up by level (genomic -> cdna -> protein), so the UI can render one block per real allele instead of one per c/g/p record. Add unit tests covering the nucleotide-assay and protein-assay pairing shapes, divergent-annotation flagging, dangling projectionOf, the measured-vs-null-relation distinction, and page-anchor CAID exclusion from surfaced links.
Drop a leftover console.log(endpoint) call in useEntityCache's fetch path.
- Replace the retired lookupVariantsByClingenId flow with getAlleleMeasurements, consuming the API's own direct-first order instead of re-deriving nucleotide/protein/associatedNucleotide buckets from a nested exactMatch/equivalentAa/equivalentNt shape - Extract per-URN detail/score-set/scores caching into useMeasurementCache, and selection + its derived state (score, calibration resolution, clingen id) into useMeasurementSelection, so useVariantLookup becomes an orchestrating facade over both plus useClingenAllele - Add includeSuperseded and asOf query axes; any change to anchor, superseded scope, or as_of bumps a query epoch, clears the caches, and refetches, so a slower stale response can't clobber a newer one - Add a one-shot citation fallback: an initial `?variant=` deep link to a superseded measurement enables includeSuperseded once so it resolves, without fighting a later manual toggle-off - Cap background prefetch of non-selected measurement details at 4 concurrent requests via p-limit, so a large equivalence class doesn't fire a request storm on load
- Widen SequenceLevel from 'dna'|'protein' to 'cdna'|'genomic'|
'protein', mirroring the backend's AnnotationLayer enum, and route
the mapped frame through the new mapped.{cdna,genomic,protein}
triple instead of the removed assayLevelHgvs/proteinLevelHgvs
fields
- In the raw frame, cdna and genomic both alias hgvsNt since the
submitted string is target-relative and the level split only
exists post-mapping; sequenceTypeOptions collapses them into one
"Nucleotide" option keyed by the variant's assayLevel
- Make getHgvsNt in the mapped frame prefer the coding (cdna)
coordinate over genomic, falling back to genomic only when there
is no coding projection, so it pairs naturally with the protein
change in labels and tooltips
- Update tests for the three-level split, the raw-frame NT aliasing,
the coding-preferred mapped fallback, and the existing protein-only
no-fabricated-coding guarantee (#784)
Reverse translation expands a change into many redundant equivalence- class representations (a protein consequence plus its sibling nucleotide encodings). Add aggregateByStudy to collapse those back into one entry per study — measurement count, assay level(s) (protein/nucleotide/mixed), distinct functional classifications, and functional score range — so search can surface per-study evidence instead of a row per representation. Studies with more corroborating measurements sort first, ties broken by title. Add unit tests covering single- and multi-study collapsing, the mixed-level flag with internal disagreement, and a null score range when no measurement carries a score.
…ship - Rename AlleleResult.variants from nucleotide/protein/ associatedNucleotide to direct/proteinConsequence/nucleotideEncoding, mirroring the API's AlleleMeasurement.relationship, and switch its entries from VariantEffectMeasurementWithShortScoreSet to AlleleMeasurement - Add mergeAlleleSpellings to fold one allele's transcript/genomic/MANE coordinates into another, deduplicating shared MANE entries, so a protein change's several registered transcript alleles collapse into one search result instead of several - Drop the unused `m` regex flag from clinGenAlleleIdRegex/ clinVarVariationIdRegex/rsIdRegex, switch `||` defaults to `??`, and replace a for-in loop with Object.entries in the MANE coordinate walk Add unit tests for mergeAlleleSpellings covering coordinate folding, MANE coordinate dedup, and fill-without-overwrite of genome-build HGVS.
Regenerate src/schema/openapi.d.ts against the API's new GET
/clingen-alleles/{id}/measurements endpoint and its supporting
AlleleIdentity/AlleleMeasurement/SequenceLevel/MeasurementRelationship
schemas, and drop the retired clingen-allele-id-lookups endpoint and
its ClingenAlleleIdVariantLookup*/ClingenAlleleVariants types.
- Read `?variant=` off the variant route and pass it through as highlightVariantUrn, so VariantScreen can highlight one specific measurement without changing the CAID/PAID anchor - Preserve it through the legacy variant-URN redirect: the resolved allele page now carries `?variant=<urn>` so the redirect still points at the cited measurement instead of just its allele
- rename getScoreSetByUrn to getScoreSet at its call site - import getScoreSet from @/api/mavedb/score-sets instead of the variants module - rename getScoreSetClinicalControlOptions to getScoreSetClinvarControlOptions to match the ClinVar naming
- add a --nav-height token and have MvNavBar reference it instead of a hard-coded 58px, giving full-height panels a single source of truth - drop the mave-gradient-bar accent from the external identifiers, targets, score-set metadata, and experiment keyword/metadata cards - move the gradient-bar accent from the abstract to the citation card on the publication identifier view
Writing `{...cache.value, [urn]: await fetch()}` snapshots the spread
baseline before the await resolves, so two concurrent loaders (the
selected measurement plus a prefetch) both capture the same pre-write
map and the later write clobbers the earlier key. Await into a local
first, then spread, in both loadScoreSet and loadScores.
- note in use-variant-lookup that the citation-honoring path triggers a
redundant second fetch cycle, to be deduped by a future query cache
Rename the two coordinate frames throughout the resolver and heatmap: raw -> submitted (target numbering), mapped -> reference. The names now say what the frames mean rather than how they were produced. - alias SequenceLevel to the backend enum so genomic is a first-class level distinct from cdna, not folded into a single "dna" case - rework the heatmap tooltip to pair by level: protein <-> coding share a transcript, genomic stands alone with no coding pair - pass the variant URN to the tooltip details link - drop the now-dead codon-translation helpers and genetic-codes import - relabel the "Mapped HGVS" download option to "Reference-frame HGVS"
…re set - reuse SequenceLevel in measurement-types instead of a parallel AssayLevel alias; drop the "level" suffix from bucket labels and reword relationship labels to read relative to the user's variant - rename the aggregation's "study" concept to "score set" (aggregateByStudy -> aggregateByScoreSet, StudyEvidence -> ScoreSetEvidence) and read preferredClassification - coalesce grouped-allele annotations field-by-field (present-wins) so a missing field on one level is carried through rather than read as divergence; only a real present-vs-present conflict splits the block
Rename clinical-controls to clinvar-controls and build out the ClinVar control data layer the variant page and histogram consume. - add reduceControlPlacement (the D78 divergence fold) producing a representative call plus winning-set classifications and directional flags, exposed as ClinvarControlPlacement - add notables helpers: per-class clinical extremes, consequence exemplars, score extremes, and median/MAD deviation - add the useClinvarControls store composable - alias control types to the generated schema instead of hand-mirroring them, and add isClassifiedSignificance to reject ClinVar's "-" placeholder significances - move formatClinvarVersion in from lib/formats and point ClinvarControlVariant at ClinvarControlPlacement - add tooltipFootnote and tooltipEmptyLine helpers
Build the disclosure-ladder infrastructure: a single Key drawer that any badge can deep-link into, so jargon is explained in one shared place rather than scattered tooltips. - add useKeyDrawer, a module-level singleton store driving one drawer mounted at the variant-page root, opened via open(term) from any subtree - add the v-key-term directive that turns a badge into a keyboard- and screen-reader-accessible deep link into the drawer, centralizing the handlers, ARIA, and hover affordance - add MvKeyDrawer and the variant key-section content definitions - register the directive and brand the PrimeVue tooltip (sage background, body font) as the ladder's first rung
New user-docs section covering variant mapping, reverse translation & projection, and annotation, plus an "Interpreting Annotated Variants" page. Wire the pages into the nav and add "annotated variant(s)" glossary abbreviations.
…s variants Replace the four-dash facts grid shown for a selected variant with no resolvable annotations, which added clutter without information. - Render the facts grid only when a consequence, classification, gnomAD, or ClinVar cell resolves; otherwise show a quiet empty-state message - Keep the identity line in the empty state only when a distinct underlying nucleotide coordinate disambiguates the selection - Move the superseded badge and full-details link into a shared row so both survive the empty state without duplicating markup
The VRS digest lookup returns an empty array rather than a 404 when no MaveDB variants match, so the "not found" warning never fired and the error was rethrown. Trigger the warning on an empty result and let the catch handle only genuine request failures.
The related-allele context on a variant's ClinVar and gnomAD cells could leak the subject's own record back into its "related" list, and ClinVar precedence would silently borrow a projection sibling's call even when the measured allele sat at nucleotide level, where its own absent record is real information rather than a fan-out gap. - add annotation-subject.ts: a shared SubjectDigest type/helper for a measurement's own digest(s), including its c<->g projection twin, so gnomAD and ClinVar resolve "is this my own record" the same way - resolveClinvarRecords/collectGnomadFrequencies now key off the full subject digest set instead of a single assayLevelDigest, and drop cross-frame duplicates of the subject's own record from the related-record enumeration - reduceControlPlacement only falls through to projection siblings at protein assay level; at cdna/genomic level a missing direct record returns null (a new 'absent' ClinvarHeadline kind) instead of borrowing a sibling's call - wire assayLevel/assayLevelDigest through VariantDetailPanel and VariantScreen to the gnomAD/ClinVar stat components
…ion columns
Replace the retired /mapped-variants JSON download with the
substrate-faithful streaming NDJSON /variant-details export, and
extend the custom CSV download with the new annotation namespaces
(gnomAD, VEP, ClinGen, ClinVar).
- remove downloadMappedVariants; the Variant Details button now
streams GET /score-sets/{urn}/variant-details via streamNdjson,
driving a progress bar off the server's X-Total-Count
- fix progress overshooting 100%: count '\n' characters per chunk
instead of split() segments, which overcounted by one per chunk
and double-counted lines split across fetch chunk boundaries;
also clamp the computed percentage to 100
- fix the progress bar rendering under both the Variant Details and
Annotated Variants buttons at once; track which button's stream
is active (streamTarget) and gate each bar on its own target
instead of the shared in-progress flag
- add gnomAD/VEP/ClinGen/ClinVar options to the custom CSV dialog,
wiring ScoreSetView's resolved clinvarVersion through so the
versioned ClinVar column can be offered
- update the downloading and API quickstart docs to describe the
Variant Details export in place of the old mapped-variants JSON
…ence-badge palette "Your variant" read oddly once the same badge could appear on other pages/contexts, so the direct-relationship label and its Key-drawer entry are now phrased as "This variant" instead, with its own dedicated subject color rather than reusing brand sage. MvMeasurementCard's relationship badge now derives its color from the shared RELATIONSHIPS dict instead of a hardcoded class, which is what let the two drift out of sync in the first place. On the confidence axis (measured/resolved/convergent/candidate), "Resolved" gets its own dedicated slate rather than reusing the assay-level "Nucleotide" color — the two answer different questions (was this coordinate measured or derived? vs. what level was it assayed at?) and coloring them identically read as redundant on the same card. "Convergent" and "Candidate" are unified onto one shared color: both represent genuine variant-identity ambiguity, as opposed to "Resolved"'s certain, deterministic re-expression of the same variant.
Replaces the old VariantScreen with the functional-first redesign: functional evidence leads, re-anchoring is per-section and always labeled, and clinical/ population reference is shown per allele rather than pooled across a group. - MvAlleleLedger combines the old separate "related alleles" panel and per-allele clinical/population cells into one card per allele group (this-variant/ this-measurement/collapsed others), each with a role badge and a facts grid. - VariantConsequenceStat factors the molecular-consequence cell out of VariantDetailPanel so the ledger and the score-set panel render it identically. - VariantClinvarStat/VariantGnomadStat fold their "pooled from N related variants" provenance into the stat trigger itself instead of a separate caption. - use-clingen-allele now surfaces every mapped reference-genome build (allGenomicLocationsText) instead of silently keeping only the first, closing a gap versus the old VariantInfoSection card. - clingen.ts extracts the ClinGen registry URL helpers shared by the page and search results. - VariantInfoSection and MvRelatedAlleles are deleted; the ledger fully supersedes both.
The `isOpen` watcher only re-fires on open/close transitions, so clicking a badge while the drawer stays open updated `activeTerm` without scrolling to it. Watch `activeTerm` directly and scroll whenever the drawer is open.
…ecision Cuts redundant restatement (e.g. Convergent said the same thing twice in different words) and fixes a couple of dangling clauses. Also corrects the evidence-strength ladder, which only listed 4 of the 5 schema tiers (MODERATE_PLUS was missing despite being a live badge value).
…rawer The allele ledger's page-role badge and a measurement's direct- relationship badge were two names for the same fact (both use the subject color) — collapse them onto one shared definition instead of each carrying their own. Moves "This variant" to lead the drawer so "Relationship to this variant" reads naturally right after it, and routes MvMeasurementCard's direct-relationship badge to the "this-variant" deep link (matching MvAlleleLedger's existing pattern) instead of a "relationship" section that no longer defines it.
Replaces the standalone tooltip (with its own duplicated wording) on the Superseded badge with a deep link into the shared Key drawer, and moves the supersession banner after the functional-evidence section with copy refocused on the score set rather than the individual measurement. Adds --color-superseded/-light tokens to app.css so the badge, banner, and glossary chip share one source instead of three copies of bg-amber-100/text-amber-800.
"Sibling allele" was scattered across the glossary, the histogram
caption/tooltip, and VariantClinvarStat under three different words
("sibling", "related", "pooled") for the same concept. Renames the
glossary section to "Inferred controls" and threads "inferred"
through the histogram tooltip and popover note so the same word
means the same thing everywhere it shows up.
Also fixes the histogram: the projected-control caption was a global
note that couldn't say which series it applied to; replaces it with a
per-series legend flag computed from that series' own classifier, and
teaches the legend to wrap a title across lines (HistogramSerieOptions
now accepts string | string[]) so the added text doesn't widen the
legend enough to cover plotted data. Drops the asterisk convention,
which collided with an unrelated footnote using the same glyph for a
different caveat.
MvAlleleLedger never declared an "identify" prop, so ScoreSetView's :identify="false" was dead markup. Also reworks the ledger's subtitle for clarity.
Introduce formatScore() + SCORE_DISPLAY_PRECISION in lib/scores.ts as the single source of truth for rendering a variant's functional score (4 significant figures; null for NA/absent, so callers own the empty case). Route the histogram tooltip, variant-page score, and both measurement components through it, replacing scattered toPrecision(4) literals.
Search indexed only scored variants, so a coordinate query for an in-set variant with an NA score returned "No matching variants" — a false negative on the page's only directory surface. Index the whole set instead; unscored matches select normally. Since the histogram can't jump to a scoreless variant, the detail panel now carries a Score headline (4 sig figs, or "Not scored") so a selection always reports its measurement. Also unify the search dropdown's leading dot to one meaning everywhere — a ClinVar control colored by classification — instead of overloading it with consequence-palette and score colors in the empty state.
The API now reaches a CA's protein consequence and sibling nt encodings unconditionally (one behavior on every surface), so the client flag no longer gates anything. Remove includeNucleotideSiblings from the getAlleleMeasurements wrapper (and its memo key) and from the variant search's only call site, which now requests the full equivalence class like the variant page.
MvAlleleLedger never passed assay-gnomad to VariantGnomadStat, so an allele's own direct frequency was neither promoted to the headline nor included in the pooled/related list (its digests are in the subject exclusion set). Only pooled protein-change frequencies from other alleles survived, leaving the actual allele's cell blank. Pass the group's coalesced gnomAD annotation, mirroring the existing vep wiring on the sibling consequence stat, so the allele's own frequency renders as the direct headline.
…enum values Renames "twin"/"sibling" to "projection"/"encodings" in the ClinVar/gnomAD library comments, updates the Cat-VRS `relation` test fixtures from `is_genomic_of` to `coordinate_representation_of`, and adds the confidence- badge color tokens (measured/resolved/convergent/candidate) to app.css.
Trims redundant and overly verbose comments across the variant-detail stack (search screen, variant screen, allele ledger, ClinVar/gnomAD stat cells, the clinvar-controls libs), fixes a couple of typos, and adds section dividers to clinvar-control-placement.ts and allele-grouping.ts so each file's distinct concerns are easier to skim. Also carries pre-existing, unrelated changes in VariantScreen.vue, MvAlleleLedger.vue, and allele-grouping.ts (page-group rename and simplification, "Unclassified" badge label, hasPinnedEntry guard) that landed on the same lines as the comment edits and couldn't be cleanly separated from them.
…allele-data-model
…nnotation state The compact variant picker showed "No reference annotations were found for this variant" whenever the protein allele had no direct consequence and no pooled gnomAD/ClinVar. For a reverse-translated protein change that assertion is false: the change fans out to candidate nucleotide alleles that carry their own VEP consequence. Split the empty state — when candidate-derivation alleles are present, name the fan-out and scope the absence to population/clinical evidence; keep the original message only when there is genuinely nothing. The candidate count reuses groupAlleles so a candidate's c↔g spellings count once.
|
coverage: 20.469% (+10.0%) from 10.496% — feature/bencap/api-redesign-for-allele-data-model into release-2026.3.0 |
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Sep 19, 2026
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Ports the UI onto the redesigned variant/allele API (the allele-centric data model workstream): a rebuilt variant detail page, cross-level allele grouping, a reworked ClinVar clinical-controls pipeline, a new inline glossary system, and gnomAD population-frequency integration. Protein-viewer download options rode along on this branch as well.
See VariantEffect/mavedb-api#791,
Variant detail page
95af0090d)f32ef0270,fc493bd89)16c1d92c0,66355474d)b1e5c3037)00f222840,490d9a174)Allele grouping
969dacab7,a66e07ed1)5ec170c6f,b6a1c4f09)ClinVar clinical controls & calibration
resolveControlSeries(c3c4b0c0c,1c38f90f9,1b5676e32)1bc6f8741,314809a39,95dc00da6)8bfdb2125)Glossary / Key drawer
v-key-termdirective for inline term definitions, wired across surfaces and co-located with the modules that own each term (1931d70b1,3852556ae,42d7a4f18)7f9d7dc7a,f69be88d9,2c2c8b52f)gnomAD
c131d2299)Score-set data & downloads
measurementsendpoint; lean whole-set variant view channel added (94ea6b0f8,13d82a88f)7a8b4be3d,1a2c7095a)8906f9aca,64b4c81fc)Protein structure viewer
de4a30b75,d7f56f6d9,b849101c9,cd8d8cf12,49a42cd64)Search & API surface
include_nucleotide_siblingsflag; retired the ClinGen lookup endpoint in favor of a TTL-cached read wrapper; empty VRS-digest lookups warn instead of 404ing (f3fa94f9e,6baf82935,c92eeec11)