Merge pull request #241 from VariantEffect/release-2024.2.2

Release 2024.2.2

package.json

@@ -1,6 +1,6 @@
 {
   "name": "mavedb-ui",
-  "version": "2024.2.0",
+  "version": "2024.2.2",
   "private": true,
   "scripts": {
     "build": "vite build --mode=${MODE=live}",

src/components/ScoreSetHeatmap.vue

@@ -169,13 +169,18 @@ export default {
       // Count of variants that do not appear to be complex but are don't have a valid substitution
       let numIgnoredVariantInstances = 0
 
+      const distinctAccessions = new Set()
+
       const simpleVariantInstances = _.filter(
         scores.map((score) => {
           const variant = parseSimpleProVariant(score.hgvs_pro)
           if (!variant) {
             numComplexVariantInstances++
             return null
           }
+          if (variant.target) {
+            distinctAccessions.add(variant.target)
+          }
           const row = heatmapRowForVariant(variant.substitution)
           if (row == null) {
             numIgnoredVariantInstances++
@@ -187,6 +192,11 @@ export default {
         }),
         (x) => x != null
       )
+      // TODO(#237) See https://github.com/VariantEffect/mavedb-ui/issues/237.
+      if (distinctAccessions.size > 1) {
+        numComplexVariantInstances += simpleVariantInstances.length
+        simpleVariantInstances = []
+      }
       return {simpleVariantInstances, numComplexVariantInstances, numIgnoredVariantInstances}
     },
 

src/components/common/HighlightsView.vue

@@ -11,8 +11,20 @@
               <ProgressSpinner class="highlights-progress" />
             </div>
             <div v-else>
-              <DataTable :value="leaderboardData" sortField="count" :sortOrder="-1" paginator :rows="5"
-                :rowsPerPageOptions="[5, 10, 20]" size="small">
+              <DataTable
+                :ref="`targetDataTable${tab}`"
+                :exportFilename="`mavedb-${pluralize(tab)}`"
+                paginator
+                :rows="5"
+                :rowsPerPageOptions="[5, 10, 20]"
+                size="small"
+                sortField="count"
+                :sortOrder="-1"
+                :value="leaderboardData"
+              >
+                <template #paginatorstart>
+                  <Button type="button" icon="pi pi-download" text @click="exportCsv('target', tab)" />
+                </template>
                 <Column v-for="col of targetLeaderboardColumns[this.field]" :field="col.field" :header="col.header"
                   :sortable="col.field == 'count'" :key="col.field" :style="`width: ${col.width || auto}`">
                   <!-- Link any identifier columns or `column` (in this compoenent representative of some db key) to a MaveDB search page -->
@@ -84,8 +96,20 @@
               <ProgressSpinner class="highlights-progress" />
             </div>
             <div v-else>
-              <DataTable :value="leaderboardData" sortField="count" :sortOrder="-1" paginator :rows="5"
-                :rowsPerPageOptions="[5, 10, 20]" size="small">
+              <DataTable
+                :ref="`scoreSetDataTable${tab}`"
+                :exportFilename="`mavedb-${pluralize(tab)}`"
+                :value="leaderboardData"
+                sortField="count"
+                :sortOrder="-1"
+                paginator
+                :rows="5"
+                :rowsPerPageOptions="[5, 10, 20]"
+                size="small"
+              >
+                <template #paginatorstart>
+                  <Button type="button" icon="pi pi-download" text @click="exportCsv('scoreSet', tab)" />
+                </template>
                 <Column v-for="col of scoreSetLeaderboardColumns[this.field]" :field="col.field" :header="col.header"
                   :sortable="col.field == 'count'" :key="col.field" :style="`width: ${col.width || auto}`">
                   <!-- Link publication identifiers to their MaveDB page -->
@@ -160,20 +184,23 @@
 
 <script>
 import axios from 'axios'
-import config from '@/config'
-import { defineComponent, ref } from 'vue';
-import useItem from '@/composition/item'
-import DataTable from 'primevue/datatable';
-import Column from 'primevue/column';
+import pluralize from 'pluralize'
+import Button from 'primevue/button'
+import Column from 'primevue/column'
 import Card from 'primevue/card'
+import DataTable from 'primevue/datatable'
 import TabView from 'primevue/tabview'
 import TabPanel from 'primevue/tabpanel'
-import ProgressSpinner from 'primevue/progressspinner';
+import ProgressSpinner from 'primevue/progressspinner'
 import Chart from 'primevue/chart'
+import {defineComponent, ref} from 'vue'
+
+import config from '@/config'
+import useItem from '@/composition/item'
 
 export default defineComponent({
   name: 'HighlightsView',
-  components: { Card, Chart, Column, DataTable, TabView, TabPanel, ProgressSpinner },
+  components: {Button, Card, Chart, Column, DataTable, TabView, TabPanel, ProgressSpinner},
 
   setup: (props) => {
     const targetAccessionAssemblyStatistic = useItem({ itemTypeName: 'target-accession-statistics' })
@@ -343,6 +370,14 @@ export default defineComponent({
   },
 
   methods: {
+    pluralize: function(...args) {
+      return pluralize(...args)
+    },
+
+    exportCsv: function(model, tab) {
+      this.$refs[`${model}DataTable${tab}`][0].exportCSV()
+    },
+
     chartDataForTarget: function (targetData) {
       if (!targetData) {
         return {}

src/components/screens/ScoreSetCreator.vue

@@ -1192,7 +1192,7 @@ export default {
           return i;
         }
       }
-      return numSteps - 1 
+      return numSteps - 1
     },
 
     wizardStepHasError: function(step) {
@@ -1631,16 +1631,33 @@ export default {
     },
 
     addTarget: function () {
-      if (this.taxonomy) {
+      if (this.targetGene.name && this.taxonomy) {
+        if ( !this.targetGene.category ) {
+          this.$toast.add({ severity: 'error', summary: 'Please choose protein coding, regulatory or other noncoding for the target gene type.' })
+          return null
+        }
+        if ( !this.targetGene.targetSequence.sequence ) {
+          this.$toast.add({ severity: 'error', summary: 'Please upload reference sequence FAST file.' })
+          return null
+        }
+        if ( !this.targetGene.targetSequence.sequenceType ) {
+          this.$toast.add({ severity: 'error', summary: 'Please choose DNA or protein for the sequence type.' })
+          return null
+        }
         this.targetGene.targetSequence.taxonomy = this.taxonomy
         delete this.targetGene.targetAccession;
       }
-      else if (this.assembly || this.geneName) {
+      else if (this.geneName && this.assembly) {
+        if ( !this.targetGene.category ) {
+          this.$toast.add({ severity: 'error', summary: 'Please choose protein coding, regulatory or other noncoding for the target gene type.' })
+          return null
+        }
         this.targetGene.targetAccession.assembly = this.assemblyDropdownValue
         this.targetGene.targetAccession.gene = this.geneNameDropdownValue // Name property on string object array
         delete this.targetGene.targetSequence;
       }
       else {
+        this.$toast.add({ severity: 'error', summary: 'Target must include taxonomy or assembly and gene name.' })
         return null // target must include one of the above objects
       }
       this.targetGene.externalIdentifiers = _.keys(
@@ -1704,6 +1721,9 @@ export default {
       if (!this.item) {
         editedFields.supersededScoreSetUrn = this.supersededScoreSet ? this.supersededScoreSet.urn : null
         editedFields.metaAnalyzesScoreSetUrns = this.metaAnalyzesScoreSets.map((s) => s.urn)
+        if ( editedFields.metaAnalyzesScoreSetUrns.length===0 && editedFields.supersededScoreSetUrn ) {
+          editedFields.experimentUrn = this.supersededScoreSet.experiment.urn
+        }
       }
       else {
         // empty item arrays so that deleted items aren't merged back into editedItem object
@@ -1969,8 +1989,10 @@ export default {
   display: table;
 }
 
+/* Ensure the step controls are never off-screen. */
 .mavedb-wizard-step-controls {
   padding-left: 10px;
+  max-width: 100vw;
 }
 
 /* Switches */

src/components/screens/ScoreSetEditor.vue

@@ -1335,6 +1335,7 @@
           delete this.targetGene.targetSequence;
         }
         else {
+          this.$toast.add({ severity: 'error', summary: 'Target must include taxonomy or assembly and gene name.' })
           return null // target must include one of the above objects
         }
         this.targetGene.externalIdentifiers = _.keys(

src/lib/mave-hgvs.ts

@@ -13,6 +13,8 @@ interface SimpleProteinVariation {
    * change of another sort.
    */
   substitution: string
+  /** The genomic target (accession) from a fully qualified MaveHGVS-pro string. */
+  target: null | string
 }
 
 /**
@@ -30,15 +32,19 @@ const proVariantRegex = /^p\.([A-Za-z]{3})([0-9]+)([A-Za-z]{3}|=|\*|-)$/
  * @returns An object with properties indicating
  */
 export function parseSimpleProVariant(variant: string): SimpleProteinVariation | null {
-  const match = variant.match(proVariantRegex)
+  const parts = variant.split(":")
+  const variation = parts.length == 1 ? parts[0] : parts[1]
+  const target = parts.length == 1 ? null : parts[0]
+  const match = variation.match(proVariantRegex)
   if (!match) {
     // console.log(`WARNING: Unrecognized pro variant: ${variant}`)
     return null
   }
   return {
     position: parseInt(match[2]),
     original: match[1],
-    substitution: match[3]
+    substitution: match[3],
+    target: target
   }
 }