From edebc21e57b8faa6a3a8f9c828760bbf2e6c63df Mon Sep 17 00:00:00 2001 From: Felix Hennig Date: Wed, 29 Jul 2026 10:42:26 +0200 Subject: [PATCH] fix(mpox): rename lineage field to outbreakLineage and update values Pathoplexus restructured mpox lineages: the LAPIS field is now `outbreakLineage` (old `lineage` field no longer has a lineage index, causing the lineage definition fetch to fail). Lineage values are now prefixed with the outbreak identifier (e.g. `sh2017/F.1`). - Labels updated to "Outbreak & Lineage" throughout - Predefined variants and compare-side-by-side defaults updated to use `sh2017/F.*` values - E2E test helper updated with new field placeholder and lineage value Co-Authored-By: Claude Sonnet 4.6 --- website/src/views/mpox.ts | 14 +++++++------- website/tests/helpers/organisms.ts | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/website/src/views/mpox.ts b/website/src/views/mpox.ts index 7fb713f4f..5d8d1879b 100644 --- a/website/src/views/mpox.ts +++ b/website/src/views/mpox.ts @@ -37,7 +37,7 @@ import { ALL_TIMES_LABEL, defaultDateRangeOption } from '../util/defaultDateRang const earliestDate = '1960-01-01'; -const LINEAGE_FIELD_NAME = 'lineage'; +const LINEAGE_FIELD_NAME = 'outbreakLineage'; const CLADE_FIELD_NAME = 'clade'; class MpoxConstants implements OrganismConstants { @@ -48,7 +48,7 @@ class MpoxConstants implements OrganismConstants { public readonly lineageFilters: LineageFilterConfig[] = [ { lapisField: LINEAGE_FIELD_NAME, - placeholderText: 'Lineage', + placeholderText: 'Outbreak & Lineage', filterType: 'lineage' as const, }, { @@ -88,10 +88,10 @@ class MpoxConstants implements OrganismConstants { public readonly accessionDownloadFields = PATHOPLEXUS_ACCESSION_DOWNLOAD_FIELDS; public readonly predefinedVariants = [ { - lineages: { [LINEAGE_FIELD_NAME]: 'F.1' }, + lineages: { [LINEAGE_FIELD_NAME]: 'sh2017/F.1' }, }, { - lineages: { [LINEAGE_FIELD_NAME]: 'F.2' }, + lineages: { [LINEAGE_FIELD_NAME]: 'sh2017/F.2' }, }, { lineages: { [CLADE_FIELD_NAME]: 'Ia' }, @@ -102,7 +102,7 @@ class MpoxConstants implements OrganismConstants { public get aggregatedVisualizations() { return getPathoplexusSequencingEffortsAggregatedVisualizations(this, { sublineages: { - label: 'Sub-Lineages', + label: 'Outbreak & Lineage', fields: [LINEAGE_FIELD_NAME, CLADE_FIELD_NAME], }, }); @@ -142,12 +142,12 @@ export class MpoxCompareSideBySideView extends BaseView< const defaultPageState = makeCompareSideBySideData(defaultDatasetFilter, [ { lineages: { - [LINEAGE_FIELD_NAME]: 'F.1', + [LINEAGE_FIELD_NAME]: 'sh2017/F.1', }, }, { lineages: { - [LINEAGE_FIELD_NAME]: 'F.2', + [LINEAGE_FIELD_NAME]: 'sh2017/F.2', }, }, ]); diff --git a/website/tests/helpers/organisms.ts b/website/tests/helpers/organisms.ts index 8f0c16a4b..4900cddbd 100644 --- a/website/tests/helpers/organisms.ts +++ b/website/tests/helpers/organisms.ts @@ -17,7 +17,7 @@ export const organismOptions = { [Organisms.westNile]: { lineage: '1A', lineageFieldPlaceholder: 'Lineage', gene: 'NS1' }, [Organisms.rsvA]: { lineage: 'A.D.5.2', lineageFieldPlaceholder: 'Lineage', gene: 'NS1' }, [Organisms.rsvB]: { lineage: 'B.D.E.1', lineageFieldPlaceholder: 'Lineage', gene: 'NS1' }, - [Organisms.mpox]: { lineage: 'F.1', lineageFieldPlaceholder: 'Lineage', gene: 'OPG001' }, + [Organisms.mpox]: { lineage: 'sh2017/F.1', lineageFieldPlaceholder: 'Outbreak & Lineage', gene: 'OPG001' }, [Organisms.ebolaSudan]: { mutation: 'G5902T', gene: 'NP' }, [Organisms.ebolaZaire]: { mutation: 'T18365C', gene: 'NP' }, [Organisms.cchf]: { mutation: 'M:G3565A', gene: 'RdRp' },