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fix: bump rfl to support new annonars ClinVar XML format (#719) (#720)
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holtgrewe authored Jun 4, 2024
1 parent 929f45b commit a521bc1
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Showing 4 changed files with 6 additions and 3 deletions.
2 changes: 1 addition & 1 deletion frontend/package.json
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Expand Up @@ -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"
},
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2 changes: 1 addition & 1 deletion frontend/src/ext/reev-frontend-lib
Submodule reev-frontend-lib updated 79 files
+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
3 changes: 3 additions & 0 deletions frontend/src/plugins/vuetify.ts
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Expand Up @@ -42,6 +42,9 @@ export default createVuetify({
},
VSheet: {
rounded: 'lg'
},
VChip: {
rounded: 'xl'
}
},
theme: {
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2 changes: 1 addition & 1 deletion frontend/src/views/SeqvarDetailsView/SeqvarDetailsView.vue
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Expand Up @@ -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" />
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