From 838332d1e09a0d588cb9dd44591bbd06262b692c Mon Sep 17 00:00:00 2001 From: Riley Grant Date: Thu, 18 Apr 2024 11:06:25 -0500 Subject: [PATCH 1/2] feat(graphql-api): modify es indices to allow v4.1 deployment Here we temporarily add more aliases to allow for a simultaneous deployment of v4.0 and v4.1, since they will refer to different indices --- graphql-api/src/queries/copy-number-variant-queries.ts | 2 +- graphql-api/src/queries/gene-queries.ts | 2 +- graphql-api/src/queries/structural-variant-queries.spec.ts | 4 +++- graphql-api/src/queries/structural-variant-queries.ts | 2 +- .../src/queries/variant-datasets/gnomad-v4-variant-queries.ts | 2 +- 5 files changed, 7 insertions(+), 5 deletions(-) diff --git a/graphql-api/src/queries/copy-number-variant-queries.ts b/graphql-api/src/queries/copy-number-variant-queries.ts index 8dc57a492..61ad626e8 100644 --- a/graphql-api/src/queries/copy-number-variant-queries.ts +++ b/graphql-api/src/queries/copy-number-variant-queries.ts @@ -1,6 +1,6 @@ import { fetchAllSearchResults } from './helpers/elasticsearch-helpers' -const GNOMAD_COPY_NUMBER_VARIANTS_V4_INDEX = 'gnomad_v4_cnvs' +const GNOMAD_COPY_NUMBER_VARIANTS_V4_INDEX = 'v4p1_gnomad_v4_cnvs' type CnvDatasetId = 'gnomad_cnv_r4' type DatasetDependentQueryParams = { diff --git a/graphql-api/src/queries/gene-queries.ts b/graphql-api/src/queries/gene-queries.ts index ac7858c21..827762fda 100644 --- a/graphql-api/src/queries/gene-queries.ts +++ b/graphql-api/src/queries/gene-queries.ts @@ -4,7 +4,7 @@ import { fetchAllSearchResults } from './helpers/elasticsearch-helpers' const GENE_INDICES = { GRCh37: 'genes_grch37', - GRCh38: 'genes_grch38', + GRCh38: 'v4p1_genes_grch38', } const _fetchGeneById = async (esClient: any, geneId: any, referenceGenome: any) => { diff --git a/graphql-api/src/queries/structural-variant-queries.spec.ts b/graphql-api/src/queries/structural-variant-queries.spec.ts index 86a0fa2b1..3ca19d56f 100644 --- a/graphql-api/src/queries/structural-variant-queries.spec.ts +++ b/graphql-api/src/queries/structural-variant-queries.spec.ts @@ -54,7 +54,9 @@ const makeMockClient = (response: any) => { } const expectedIndex = (datasetId: SvDatasetId) => - datasetId === 'gnomad_sv_r4' ? 'gnomad_structural_variants_v3' : 'gnomad_structural_variants_v2' + datasetId === 'gnomad_sv_r4' + ? 'v4p1_gnomad_structural_variants_v3' + : 'gnomad_structural_variants_v2' describe('fetchStructuralVariantById', () => { const variantId = 'dummy-variant' diff --git a/graphql-api/src/queries/structural-variant-queries.ts b/graphql-api/src/queries/structural-variant-queries.ts index 05e956e09..e21ec191b 100644 --- a/graphql-api/src/queries/structural-variant-queries.ts +++ b/graphql-api/src/queries/structural-variant-queries.ts @@ -3,7 +3,7 @@ import { isEmpty } from 'lodash' import { fetchAllSearchResults } from './helpers/elasticsearch-helpers' const GNOMAD_STRUCTURAL_VARIANTS_V2_INDEX = 'gnomad_structural_variants_v2' -const GNOMAD_STRUCTURAL_VARIANTS_V3_INDEX = 'gnomad_structural_variants_v3' +const GNOMAD_STRUCTURAL_VARIANTS_V3_INDEX = 'v4p1_gnomad_structural_variants_v3' type SvDatasetId = | 'gnomad_sv_r2_1' diff --git a/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts b/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts index 8f16a560d..2c079a54b 100644 --- a/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts +++ b/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts @@ -12,7 +12,7 @@ import { getFlagsForContext } from './shared/flags' import { getConsequenceForContext } from './shared/transcriptConsequence' import largeGenes from '../helpers/large-genes' -const GNOMAD_V4_VARIANT_INDEX = 'gnomad_v4_variants' +const GNOMAD_V4_VARIANT_INDEX = 'v4p1_gnomad_v4_variants' type Subset = 'all' | 'non_ukb' From bf250e0a8daa9b2e8cef5874990b19377ebbd52d Mon Sep 17 00:00:00 2001 From: Riley Grant Date: Thu, 18 Apr 2024 11:14:06 -0500 Subject: [PATCH 2/2] fix(graphql-api): fix joint response if no subset --- .../src/queries/variant-datasets/gnomad-v4-variant-queries.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts b/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts index 2c079a54b..19ea68a6f 100644 --- a/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts +++ b/graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts @@ -259,9 +259,9 @@ const shapeVariantSummary = (subset: Subset, context: any) => { const genomeFilters = variant.genome.filters || [] const jointFilters = variant.joint.filter || [] - const subsetJointFreq = variant.joint.freq[subset].ac_raw - const subsetGenomeFreq = variant.genome.freq[subset] || {} + const subsetJointFreq = variant.joint.freq[subset] || {} + const hasExomeVariant = variant.exome.freq[subset].ac_raw const hasGenomeVariant = subsetGenomeFreq.ac_raw const hasJointVariant = subsetJointFreq.ac_raw