V2.4.1 (#454)

* Add grouping columns (and indices) to sequence-mtuation tables

* bump version

* Add omicron

* Fix capitalization in group label

* Add group aggregate download (#437)

package.json

@@ -1,6 +1,6 @@
 {
   "name": "covidcg",
-  "version": "2.4.0",
+  "version": "2.4.1",
   "description": "",
   "engines": {
     "node": ">=8",
@@ -174,4 +174,4 @@
     },
     "globals": {}
   }
-}
+}

src/components/Sidebar/StatusBox.js

@@ -33,6 +33,7 @@ const serializeCoordinates = (coordinateRanges) => {
 
 const DOWNLOAD_OPTIONS = {
   AGGREGATE_DATA: 'Aggregate Data',
+  GROUP_COUNTS: 'Group Counts',
   CONSENSUS_MUTATIONS: 'Consensus Mutations',
   SELECTED_SEQUENCE_METADATA: 'Sequence Metadata',
   SELECTED_GENOMES: 'Selected Genomes',
@@ -64,6 +65,8 @@ const StatusBox = observer(() => {
   const handleDownloadSelect = (option) => {
     if (option === DOWNLOAD_OPTIONS.AGGREGATE_DATA) {
       dataStore.downloadAggSequences();
+    } else if (option === DOWNLOAD_OPTIONS.GROUP_COUNTS) {
+      dataStore.downloadAggGroup();
     } else if (option === DOWNLOAD_OPTIONS.CONSENSUS_MUTATIONS) {
       showModal('downloadConsensusMutations');
     } else if (option === DOWNLOAD_OPTIONS.SELECTED_SEQUENCE_METADATA) {
@@ -154,6 +157,7 @@ const StatusBox = observer(() => {
 
   const downloadOptions = [
     DOWNLOAD_OPTIONS.AGGREGATE_DATA,
+    DOWNLOAD_OPTIONS.GROUP_COUNTS,
     DOWNLOAD_OPTIONS.CONSENSUS_MUTATIONS,
   ];
   if (config.allow_metadata_download) {

src/stores/configStore.js

@@ -420,9 +420,9 @@ export class ConfigStore {
       return config.group_cols[groupKey].title;
     } else if (groupKey === GROUP_MUTATION) {
       if (dnaOrAa === DNA_OR_AA.DNA) {
-        return 'NT mutation';
+        return 'NT Mutation';
       } else {
-        return 'AA mutation';
+        return 'AA Mutation';
       }
     }
   }

src/stores/dataStore.js

@@ -355,6 +355,30 @@ export class DataStore {
     downloadBlobURL(url, 'aggregate_sequences.csv');
   }
 
+  downloadAggGroup() {
+    let csvString = `${rootStoreInstance.configStore.getGroupLabel()},count,percent\n`;
+    let intToMutationMap = rootStoreInstance.configStore.getIntToMutationMap();
+
+    this.groupCounts.forEach((row) => {
+      // Group
+      if (rootStoreInstance.configStore.groupKey === GROUP_MUTATION) {
+        csvString += `"${intToMutationMap[row.group_id].mutation_str}",`;
+      } else {
+        csvString += `"${row.group_id}",`;
+      }
+
+      // Counts
+      csvString += `${row.counts},`;
+      // Percent
+      csvString += `${row.counts / this.numSequencesAfterAllFiltering}\n`;
+    });
+
+    const blob = new Blob([csvString]);
+    const url = URL.createObjectURL(blob);
+
+    downloadBlobURL(url, `group_counts.csv`);
+  }
+
   downloadAggGroupDate() {
     // Write to a CSV string
     let csvString = `collection_date,"${rootStoreInstance.configStore.getGroupLabel()}",count\n`;

src/stores/groupDataStore.js

@@ -13,7 +13,7 @@ import { mutationHeatmapToPymolScript } from '../utils/pymol';
 
 export const initialValues = {
   activeGroupType: Object.keys(config['group_cols'])[0],
-  selectedGroups: ['AY.4', 'B.1.617.2', 'B.1.1.7', 'B.1.351', 'P.2'],
+  selectedGroups: ['B.1.1.529', 'AY.4', 'B.1.617.2', 'B.1.1.7', 'B.1.351', 'P.2'],
   groupMutationType: 'protein_aa',
 };
 

src/utils/version.js

@@ -1 +1 @@
-export const version = '2.4.0';
+export const version = '2.4.1';