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fix: ugprade rfl to adjust to latest annonars and ClinVar XML changes (
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holtgrewe authored Jun 4, 2024
1 parent f98c060 commit e209961
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Showing 5 changed files with 9 additions and 2 deletions.
3 changes: 3 additions & 0 deletions cases/vueapp/src/plugins/vuetify.ts
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Expand Up @@ -51,6 +51,9 @@ export const vuetify = createVuetify({
VSheet: {
rounded: 'lg',
},
VChip: {
rounded: 'xl',
},
},
theme: {
defaultTheme: 'customLightTheme',
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1 change: 1 addition & 0 deletions varfish/vueapp/.eslintignore
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@@ -0,0 +1 @@
ext/reev-frontend-lib/src/pbs/google/protobuf/*
3 changes: 3 additions & 0 deletions varfish/vueapp/.storybook/plugins/vuetify.ts
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Expand Up @@ -42,6 +42,9 @@ export const vuetify = createVuetify({
},
VSheet: {
rounded: 'lg'
},
VChip: {
rounded: 'xl'
}
},
theme: {
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2 changes: 1 addition & 1 deletion varfish/vueapp/ext/reev-frontend-lib
Submodule reev-frontend-lib updated 76 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
+78 −0 src/components/SeqvarClinvarCard/GermlineClassification.vue
+186 −0 src/components/SeqvarClinvarCard/RcvRow.vue
+6 −6 src/components/SeqvarClinvarCard/SeqvarClinvarCard.spec.ts
+7 −5 src/components/SeqvarClinvarCard/SeqvarClinvarCard.stories.ts
+101 −98 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
+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
+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
2 changes: 1 addition & 1 deletion variants/vueapp/src/views/SeqvarDetails/SeqvarDetails.vue
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Expand Up @@ -279,7 +279,7 @@ onMounted(async () => {
</div>
<div id="seqvar-clinvar" class="mt-3">
<SeqvarClinvarCard
:clinvar-record="seqvarInfoStore.varAnnos?.clinvar"
:clinvar-records="seqvarInfoStore.varAnnos?.clinvar"
/>
</div>
<div id="seqvar-scores" class="mt-3">
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