fix: bump rfl to support new annonars ClinVar XML format (#719) (#720)

bihealth · Jun 4, 2024 · a521bc1 · a521bc1
1 parent 929f45b
commit a521bc1
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Showing 4 changed files with 6 additions and 3 deletions.
diff --git a/frontend/package.json b/frontend/package.json
@@ -11,7 +11,7 @@
     "test:unit:nocov": "vitest",
     "build-only": "vite build",
     "type-check": "vue-tsc --noEmit --composite false",
-    "lint": "eslint . --ext .vue,.js,.jsx,.cjs,.mjs,.ts,.tsx,.cts,.mts --fix --ignore-path .gitignore",
+    "lint": "eslint . --ext .vue,.js,.jsx,.cjs,.mjs,.ts,.tsx,.cts,.mts --fix --ignore-path .gitignore --ignore-pattern 'src/ext/reev-frontend-lib/src/pbs/google/protobuf/*'",
     "format": "prettier --write src/ *.ts *.mts *.json",
     "format:check": "prettier --list-different src/ *.ts *.mts *.json"
   },

diff --git a/frontend/src/ext/reev-frontend-lib b/frontend/src/ext/reev-frontend-lib
diff --git a/frontend/src/plugins/vuetify.ts b/frontend/src/plugins/vuetify.ts
@@ -42,6 +42,9 @@ export default createVuetify({
     },
     VSheet: {
       rounded: 'lg'
+    },
+    VChip: {
+      rounded: 'xl'
     }
   },
   theme: {

diff --git a/frontend/src/views/SeqvarDetailsView/SeqvarDetailsView.vue b/frontend/src/views/SeqvarDetailsView/SeqvarDetailsView.vue
@@ -434,7 +434,7 @@ const SECTIONS: { [key: string]: Section[] } = {
                 <SeqvarConsequencesCard :consequences="seqvarInfoStore.txCsq" />
               </div>
               <div id="seqvar-clinvar" class="mt-3">
-                <SeqvarClinvarCard :clinvar-record="seqvarInfoStore.varAnnos?.clinvar" />
+                <SeqvarClinvarCard :clinvar-records="seqvarInfoStore.varAnnos?.clinvar" />
               </div>
               <div id="seqvar-scores" class="mt-3">
                 <SeqvarScoresCard :var-annos="seqvarInfoStore.varAnnos" />
+3 −0		.storybook/plugins/vuetify.ts
+10 −3		Makefile
+1 −1		package.json
+5 −87		protos/annonars/clinvar/minimal.proto
+13 −77		protos/annonars/clinvar/per_gene.proto
+2 −36		protos/annonars/clinvar/sv.proto
+29 −0		protos/annonars/clinvar_data/class_by_freq.proto
+2,708 −0		protos/annonars/clinvar_data/clinvar_public.proto
+75 −0		protos/annonars/clinvar_data/extracted_vars.proto
+89 −0		protos/annonars/clinvar_data/gene_impact.proto
+28 −0		protos/annonars/clinvar_data/phenotype_link.proto
+0 −0		protos/annonars/functional/base.proto
+12 −0		src/api/annonars/__snapshots__/client.spec.ts.snap
+7 −7		src/api/annonars/client.spec.ts
+3,527 −197		src/api/annonars/fixture.geneClinvar.BRCA1.json
+9,556 −3,334		src/api/annonars/fixture.strucvarClinvarResponse.BRCA1.json
+640 −1,711		src/api/annonars/fixture.variantInfo.BRCA1.json
+89 −32		src/api/annonars/fixture.variantInfo.chrMT.json
+3 −3		src/api/annonars/types.ts
+40 −29		src/components/GeneClinvarCard/ClinvarFreqPlot.vue
+37 −29		src/components/GeneClinvarCard/ClinvarImpact.vue
+1 −0		src/components/GeneClinvarCard/GeneClinvarCard.stories.ts
+25 −33		src/components/GeneClinvarCard/VariationLandscape.vue
+23 −31		src/components/GeneClinvarCard/VariationLandscapePlotly.vue
+3,531 −20,021		src/components/GeneClinvarCard/fixture.clinvarPerGene.BRCA1.json
+9,769 −2,377		src/components/GeneClinvarCard/fixture.clinvarPerGene.TGDS.json
+43 −0		src/components/GeneClinvarCard/lib.ts
+0 −2		src/components/GeneLiteratureCard/GeneLiteratureCard.vue
+0 −2		src/components/GenePathogenicityCard/GenePathogenicityCard.vue
+20 −11		src/components/GenomeBrowserCard/GenomeBrowserCard.vue
+78 −0		src/components/SeqvarClinvarCard/GermlineClassification.vue
+186 −0		src/components/SeqvarClinvarCard/RcvRow.vue
+5 −5		src/components/SeqvarClinvarCard/SeqvarClinvarCard.spec.ts
+7 −5		src/components/SeqvarClinvarCard/SeqvarClinvarCard.stories.ts
+124 −118		src/components/SeqvarClinvarCard/SeqvarClinvarCard.vue
+78 −0		src/components/SeqvarClinvarCard/SomaticClinicalImpact.vue
+78 −0		src/components/SeqvarClinvarCard/SomaticOncogenicity.vue
+112 −40		src/components/SeqvarClinvarCard/constants.ts
+18 −0		src/components/SeqvarClinvarCard/helpers.spec.ts
+21 −0		src/components/SeqvarClinvarCard/helpers.ts
+2 −4		src/components/SeqvarConsequencesCard/SeqvarConsequencesCard.vue
+2 −4		src/components/SeqvarToolsCard/SeqvarToolsCard.vue
+4 −0		src/components/SeqvarVariantValidatorCard/SeqvarVariantValidatorCard.stories.ts
+2 −2		src/components/StrucvarClinvarCard/StrucvarClinvarCard.stories.ts
+366 −46		src/components/StrucvarClinvarCard/StrucvarClinvarCard.vue
+9,552 −3,334		src/components/StrucvarClinvarCard/fixture.clinvarSvRecords.BRCA1.json
+3 −5		src/components/StrucvarGeneListCard/GeneDosage.vue
+2 −2		src/components/StrucvarGeneListCard/ScoreChip.vue
+2 −6		src/components/StrucvarToolsCard/StrucvarToolsCard.vue
+30 −405		src/pbs/annonars/clinvar/minimal.ts
+77 −425		src/pbs/annonars/clinvar/per_gene.ts
+9 −256		src/pbs/annonars/clinvar/sv.ts
+205 −0		src/pbs/annonars/clinvar_data/class_by_freq.ts
+17,815 −0		src/pbs/annonars/clinvar_data/clinvar_public.ts
+521 −0		src/pbs/annonars/clinvar_data/extracted_vars.ts
+431 −0		src/pbs/annonars/clinvar_data/gene_impact.ts
+232 −0		src/pbs/annonars/clinvar_data/phenotype_link.ts
+1 −1		src/pbs/annonars/cons/base.ts
+1 −1		src/pbs/annonars/dbsnp/base.ts
+1 −1		src/pbs/annonars/functional/refseq.ts
+1 −1		src/pbs/annonars/genes/base.ts
+1 −1		src/pbs/annonars/gnomad/exac_cnv.ts
+1 −1		src/pbs/annonars/gnomad/gnomad2.ts
+1 −1		src/pbs/annonars/gnomad/gnomad3.ts
+1 −1		src/pbs/annonars/gnomad/gnomad4.ts
+1 −1		src/pbs/annonars/gnomad/gnomad_cnv4.ts
+1 −1		src/pbs/annonars/gnomad/gnomad_sv2.ts
+1 −1		src/pbs/annonars/gnomad/gnomad_sv4.ts
+1 −1		src/pbs/annonars/gnomad/mtdna.ts
+1 −1		src/pbs/annonars/gnomad/vep_common.ts
+1 −1		src/pbs/annonars/gnomad/vep_gnomad2.ts
+1 −1		src/pbs/annonars/gnomad/vep_gnomad3.ts
+1 −1		src/pbs/annonars/gnomad/vep_gnomad4.ts
+1 −1		src/pbs/annonars/helixmtdb/base.ts
+1 −1		src/pbs/annonars/regions/clingen.ts
+317 −0		src/pbs/google/protobuf/timestamp.ts
+1 −1		src/pbs/mehari/server.ts
+1 −1		src/pbs/mehari/txs.ts
+8,720 −634		src/stores/geneInfo/__snapshots__/store.spec.ts.snap