From 1d447608db48f1c44a52e739c2439f9a39cf810d Mon Sep 17 00:00:00 2001
From: Jeremy Stone <74574922+jstone-uw@users.noreply.github.com>
Date: Mon, 17 Jun 2024 12:43:55 -0700
Subject: [PATCH 1/9] Add CSV download buttons to tables on the homepage,
 including the list of genes. (#209)

---
 src/components/common/HighlightsView.vue | 57 +++++++++++++++++++-----
 1 file changed, 46 insertions(+), 11 deletions(-)

diff --git a/src/components/common/HighlightsView.vue b/src/components/common/HighlightsView.vue
index 19beaf87..d8011109 100644
--- a/src/components/common/HighlightsView.vue
+++ b/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 {}

From c2b673463dc47f3d1804252d295f0e1ebc62f2ae Mon Sep 17 00:00:00 2001
From: EstelleDa <baishenlonger@live.com.sg>
Date: Tue, 25 Jun 2024 16:38:07 +1000
Subject: [PATCH 2/9] Debug #211 problem

---
 src/components/screens/ScoreSetCreator.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/screens/ScoreSetCreator.vue b/src/components/screens/ScoreSetCreator.vue
index e54ef84f..905af50f 100644
--- a/src/components/screens/ScoreSetCreator.vue
+++ b/src/components/screens/ScoreSetCreator.vue
@@ -1641,6 +1641,7 @@ export default {
         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(

From 0ee5d43263d49d20ee03918a0840e8f4fab52c6f Mon Sep 17 00:00:00 2001
From: EstelleDa <baishenlonger@live.com.sg>
Date: Tue, 25 Jun 2024 17:06:38 +1000
Subject: [PATCH 3/9] Add message in editing score set page if missing
 taxonomy, target sequence or assembly

---
 src/components/screens/ScoreSetEditor.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/screens/ScoreSetEditor.vue b/src/components/screens/ScoreSetEditor.vue
index c03d7e2a..f8ebd0e6 100644
--- a/src/components/screens/ScoreSetEditor.vue
+++ b/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(

From 75e3be737c4dd36c0cbd7303376c6fe4ba079def Mon Sep 17 00:00:00 2001
From: EstelleDa <baishenlonger@live.com.sg>
Date: Tue, 9 Jul 2024 16:56:30 +1000
Subject: [PATCH 4/9] Modified addTarget condition and added error reminders.
 Not finish assembly part yet. Waiting for actual requirements of this part.

---
 src/components/screens/ScoreSetCreator.vue | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/src/components/screens/ScoreSetCreator.vue b/src/components/screens/ScoreSetCreator.vue
index 905af50f..7cc3e51d 100644
--- a/src/components/screens/ScoreSetCreator.vue
+++ b/src/components/screens/ScoreSetCreator.vue
@@ -1631,11 +1631,27 @@ 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;

From 3510e657e50e79e300c14b2a8b396dced1bc4e58 Mon Sep 17 00:00:00 2001
From: Ben Capodanno <capodb@uw.edu>
Date: Tue, 23 Jul 2024 13:29:31 -0700
Subject: [PATCH 5/9] Fixed: Wizard control flow controls appeared off-screen
 on thin windows

---
 src/components/screens/ScoreSetCreator.vue | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/components/screens/ScoreSetCreator.vue b/src/components/screens/ScoreSetCreator.vue
index e54ef84f..2a966456 100644
--- a/src/components/screens/ScoreSetCreator.vue
+++ b/src/components/screens/ScoreSetCreator.vue
@@ -1192,7 +1192,7 @@ export default {
           return i;
         }
       }
-      return numSteps - 1 
+      return numSteps - 1
     },
 
     wizardStepHasError: function(step) {
@@ -1969,8 +1969,10 @@ export default {
   display: table;
 }
 
+/* Ensure the step controls are never off-screen. */
 .mavedb-wizard-step-controls {
   padding-left: 10px;
+  max-width: 100vw;
 }
 
 /* Switches */

From cc67267056fc9cc46a5aeebb67e6b1541de50959 Mon Sep 17 00:00:00 2001
From: Ben Capodanno <capodb@uw.edu>
Date: Tue, 23 Jul 2024 15:00:20 -0700
Subject: [PATCH 6/9] Fixed: Allow Heatmap to Display Variants Reported w/
 Respect to a Protein Accession

---
 src/lib/mave-hgvs.ts | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/lib/mave-hgvs.ts b/src/lib/mave-hgvs.ts
index a36cb52d..daf5d235 100644
--- a/src/lib/mave-hgvs.ts
+++ b/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
 }
 
 /**
@@ -30,7 +32,10 @@ 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
@@ -38,7 +43,8 @@ export function parseSimpleProVariant(variant: string): SimpleProteinVariation |
   return {
     position: parseInt(match[2]),
     original: match[1],
-    substitution: match[3]
+    substitution: match[3],
+    target: target
   }
 }
 

From 25cf973d098353bcc351ce6b48bbd086080e989d Mon Sep 17 00:00:00 2001
From: Ben Capodanno <capodb@uw.edu>
Date: Wed, 24 Jul 2024 13:02:26 -0700
Subject: [PATCH 7/9] Don't Display Heatmap Variants when Multiple Accessions
 are Defined

---
 src/components/ScoreSetHeatmap.vue | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/src/components/ScoreSetHeatmap.vue b/src/components/ScoreSetHeatmap.vue
index 2e25e57c..74b7ffcc 100644
--- a/src/components/ScoreSetHeatmap.vue
+++ b/src/components/ScoreSetHeatmap.vue
@@ -169,6 +169,8 @@ 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)
@@ -176,6 +178,9 @@ export default {
             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}
     },
 

From ccaa58f271260188968c95b1e08121add855a4f5 Mon Sep 17 00:00:00 2001
From: EstelleDa <baishenlonger@live.com.sg>
Date: Mon, 29 Jul 2024 17:47:30 +1000
Subject: [PATCH 8/9] Debug supersede score set misses experiment urn. Solve
 #239.

---
 src/components/screens/ScoreSetCreator.vue | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/components/screens/ScoreSetCreator.vue b/src/components/screens/ScoreSetCreator.vue
index 7cc3e51d..9c8ea844 100644
--- a/src/components/screens/ScoreSetCreator.vue
+++ b/src/components/screens/ScoreSetCreator.vue
@@ -1721,6 +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

From ad70dbcba21d26091b8def40d1894d1aefb769aa Mon Sep 17 00:00:00 2001
From: Ben Capodanno <capodb@uw.edu>
Date: Tue, 30 Jul 2024 16:28:48 -0700
Subject: [PATCH 9/9] Bump Version Number

---
 package-lock.json | 4 ++--
 package.json      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 4952fc3c..ab00bca7 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "mavedb-ui",
-  "version": "2024.2.0",
+  "version": "2024.2.2",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "mavedb-ui",
-      "version": "2024.2.0",
+      "version": "2024.2.2",
       "dependencies": {
         "@fontsource/raleway": "^5.0.16",
         "axios": "^1.6.2",
diff --git a/package.json b/package.json
index 8c5f7902..e79c53ce 100644
--- a/package.json
+++ b/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}",