From ae5ae68cd2ec4b5b66ae26e58de34b660151d1ca Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Tue, 30 Jan 2024 10:32:30 +0100
Subject: [PATCH] feat: adding StrucvarToolsCard (#42)

---
 .../StrucvarToolsCard.spec.ts                 |  37 ++++
 .../StrucvarToolsCard/StrucvarToolsCard.vue   | 178 ++++++++++++++++++
 2 files changed, 215 insertions(+)
 create mode 100644 src/components/StrucvarToolsCard/StrucvarToolsCard.spec.ts
 create mode 100644 src/components/StrucvarToolsCard/StrucvarToolsCard.vue

diff --git a/src/components/StrucvarToolsCard/StrucvarToolsCard.spec.ts b/src/components/StrucvarToolsCard/StrucvarToolsCard.spec.ts
new file mode 100644
index 0000000..a5c0ada
--- /dev/null
+++ b/src/components/StrucvarToolsCard/StrucvarToolsCard.spec.ts
@@ -0,0 +1,37 @@
+import { describe, expect, it } from 'vitest'
+
+import { type Strucvar } from '../../lib/genomicVars'
+import { setupMountedComponents } from '../../lib/testUtils'
+import StrucvarToolsCard from './StrucvarToolsCard.vue'
+
+/** Example Strucvar */
+const strucvarInfo: Strucvar = {
+  genomeBuild: 'grch37',
+  svType: 'DEL',
+  chrom: '17',
+  start: 41176312,
+  stop: 41277500,
+  userRepr: 'DEL-grch37-17-41176312-41277500'
+}
+
+describe.concurrent('StrucvarToolsCard.vue', async () => {
+  it('renders content', async () => {
+    // arrange:
+    const { wrapper } = await setupMountedComponents(
+      { component: StrucvarToolsCard },
+      {
+        props: {
+          strucvar: structuredClone(strucvarInfo),
+          genomeBuild: 'grch37'
+        }
+      }
+    )
+
+    // act: nothing, only test rendering
+
+    // assert:
+    expect(wrapper.text()).toContain('Variant Tools')
+    const vButtons = wrapper.findAllComponents({ name: 'VBtn' })
+    expect(vButtons.length).toBe(7)
+  })
+})
diff --git a/src/components/StrucvarToolsCard/StrucvarToolsCard.vue b/src/components/StrucvarToolsCard/StrucvarToolsCard.vue
new file mode 100644
index 0000000..17f9446
--- /dev/null
+++ b/src/components/StrucvarToolsCard/StrucvarToolsCard.vue
@@ -0,0 +1,178 @@
+<script setup lang="ts">
+import { computed } from 'vue'
+
+import type { GenomeBuild } from '../../lib/genomeBuilds'
+import { type Strucvar } from '../../lib/genomicVars'
+import DocsLink from '../DocsLink/DocsLink.vue'
+
+/** Type for this component's props. */
+export interface Props {
+  genomeBuild?: GenomeBuild
+  // eslint-disable-next-line vue/require-default-prop
+  strucvar?: Strucvar
+}
+
+/** The component's props, fallback for genome build is GRCh37. */
+const props = withDefaults(defineProps<Props>(), {
+  genomeBuild: 'grch37'
+})
+
+const ucscLinkout = computed((): string => {
+  if (!props.strucvar) {
+    return '#'
+  }
+  const db = props.genomeBuild === 'grch37' ? 'hg19' : 'hg38'
+  return (
+    `https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=${db}&position=` +
+    `${props.strucvar.chrom}:${props.strucvar.start}-` +
+    `${props.strucvar.stop}`
+  )
+})
+
+const ensemblLinkout = computed((): string => {
+  if (!props.strucvar) {
+    return '#'
+  }
+  const loc = `${props.strucvar.chrom}:${props.strucvar.start}-${props.strucvar.stop}`
+  if (props.genomeBuild === 'grch37') {
+    return `https://grch37.ensembl.org/Homo_sapiens/Location/View?r=${loc}`
+  } else if (props.genomeBuild === 'grch38') {
+    return `https://ensembl.org/Homo_sapiens/Location/View?r=${loc}`
+  }
+  return '#'
+})
+
+const dgvLinkout = computed((): string => {
+  if (!props.strucvar) {
+    return '#'
+  }
+  const db = props.genomeBuild === 'grch37' ? 'hg19' : 'hg38'
+  return (
+    `http://dgv.tcag.ca/gb2/gbrowse/dgv2_${db}/?name=${props.strucvar.chrom}:` +
+    `${props.strucvar.start}-${props.strucvar.stop};search=Search`
+  )
+})
+
+const gnomadLinkout = computed((): string => {
+  if (!props.strucvar) {
+    return '#'
+  }
+  const dataset = props.genomeBuild === 'grch37' ? 'gnomad_r2_1' : 'gnomad_r3'
+  return (
+    `https://gnomad.broadinstitute.org/region/${props.strucvar.chrom}:` +
+    `${props.strucvar.start}-${props.strucvar.stop}?dataset=${dataset}`
+  )
+})
+
+const varsomeLinkout = computed((): string => {
+  if (!props.strucvar) {
+    return '#'
+  }
+  const urlRelease = props.genomeBuild === 'grch37' ? 'hg19' : 'hg38'
+  const chrom = props.strucvar.chrom.startsWith('chr')
+    ? props.strucvar.chrom
+    : `chr${props.strucvar.chrom}`
+  return `https://varsome.com/cnv/${urlRelease}/${chrom}:${props.strucvar.start}:${props.strucvar.stop}:${props.strucvar.svType}`
+})
+
+const franklinLinkout = computed((): string => {
+  if (!props.strucvar) {
+    return '#'
+  }
+  const { chrom, start, stop, svType } = props.strucvar
+  const urlRelease = props.genomeBuild === 'grch37' ? 'hg19' : 'hg38'
+  return `https://franklin.genoox.com/clinical-db/variant/sv/chr${chrom}-${start}-${stop}-${svType}-${urlRelease}`
+})
+
+const jumpToLocus = async () => {
+  const chrPrefixed = props.strucvar?.chrom.startsWith('chr')
+    ? props.strucvar?.chrom
+    : `chr${props.strucvar?.chrom}`
+  // NB: we allow the call to fetch here as it goes to local IGV.
+  await fetch(
+    `http://127.0.0.1:60151/goto?locus=${chrPrefixed}:${props.strucvar?.start}-${props.strucvar?.stop}`
+  ).catch((e) => {
+    const msg = "Couldn't connect to IGV. Please make sure IGV is running and try again."
+    alert(msg)
+    console.error(msg, e)
+  })
+}
+
+interface Linkout {
+  href: string
+  label: string
+}
+
+const genomeBrowsers = computed<Linkout[]>(() => {
+  return [
+    { label: 'ENSEMBL', href: ensemblLinkout.value },
+    { label: 'UCSC', href: ucscLinkout.value }
+  ]
+})
+
+const resources = computed<Linkout[]>(() => {
+  return [
+    { label: 'DGV', href: dgvLinkout.value },
+    { label: 'gnomAD', href: gnomadLinkout.value },
+    { label: 'varsome', href: varsomeLinkout.value },
+    { label: 'genoox Franklin', href: franklinLinkout.value }
+  ]
+})
+</script>
+
+<template>
+  <v-card class="mt-3">
+    <v-card-title class="pb-0 pr-2">
+      Variant Tools
+      <DocsLink anchor="clinvar-information" />
+    </v-card-title>
+
+    <v-card-subtitle class="text-overline"> Genome Browsers </v-card-subtitle>
+    <v-card-text>
+      <v-btn
+        v-for="linkout in genomeBrowsers"
+        :key="linkout.label"
+        :href="linkout.href"
+        target="_blank"
+        prepend-icon="mdi-launch"
+        variant="tonal"
+        rounded="sm"
+        class="mr-2"
+      >
+        {{ linkout.label }}
+      </v-btn>
+    </v-card-text>
+
+    <v-card-subtitle class="text-overline"> Other Resources </v-card-subtitle>
+    <v-card-text>
+      <v-btn
+        v-for="linkout in resources"
+        :key="linkout.label"
+        :href="linkout.href"
+        target="_blank"
+        prepend-icon="mdi-launch"
+        variant="tonal"
+        rounded="sm"
+        class="mr-2"
+      >
+        {{ linkout.label }}
+      </v-btn>
+    </v-card-text>
+
+    <v-card-actions>
+      <v-btn prepend-icon="mdi-launch" @click.prevent="jumpToLocus()"> Jump in Local IGV </v-btn>
+    </v-card-actions>
+  </v-card>
+</template>
+
+<style scoped>
+.external-resource-item {
+  float: left;
+  margin-right: 10px;
+}
+
+.external-resource-item:last-child {
+  float: none;
+  margin-right: 0;
+}
+</style>