Fix search by accession and lineage functionality #489

dbmanager_test.js

@@ -3,7 +3,7 @@ const { readTree } = require('./server/phylo')
 const fs = require('fs');
 
 const { $DATA_FOLDER } = require('./config/config');
-
+const dbstats = require(`./${$DATA_FOLDER}/dbstats.json`)
 require("./globalVariables")
 
 class TestDBManager {
@@ -64,6 +64,18 @@ class TestDBManager {
         })
     }
 
+    get_display(cindex) {
+        return new Promise((resolve,reject)=>{
+            var rawLineage = dbstats["lineages"][global.clusters[cindex].lineage]["raw_lineage"];
+            if (rawLineage.startsWith("XBB"))
+                resolve(["XBB Lineages"]);
+            else if (rawLineage.startsWith("X"))
+                resolve(["Recombinants"]);
+            else
+                resolve(["Non-Recombinants"]);
+        });
+    }
+
     get_accession(accession) {
         return new Promise((resolve,reject)=>{
             resolve(global.accn_to_cid[accession]);

js/covizu.js

@@ -303,7 +303,7 @@ req.done(async function() {
 
   // Maps id to a cidx
   const reverse_recombinant_tips = [...recombinant_tips].reverse()
-  var all_tips = [...tips, ...reverse_recombinant_tips]
+  var all_tips = [...tips, ...reverse_recombinant_tips, ...df_xbb]
   console.log("tips = ",tips)
   console.log("recombinant_tips = ",recombinant_tips)
   console.log("all_tips = ",all_tips)
@@ -417,7 +417,6 @@ req.done(async function() {
     $('#error_message').text(``);
     $('#search-button').removeAttr("disabled");
     $('#clear_button').removeAttr("disabled");
-    reset_tree();
     wrap_search();
     enable_buttons();
 
@@ -471,7 +470,6 @@ req.done(async function() {
       $('#error_message').text(``);
       $("#loading").show();
       $("#loading_text").text(i18n_text.loading);
-      await reset_tree(partial_redraw=true);
       await wrap_search();
       enable_buttons();
 
@@ -548,7 +546,6 @@ req.done(async function() {
     $('#error_message').text(``);
     $("#loading").show();
     $("#loading_text").text(i18n_text.loading);
-    await reset_tree(partial_redraw=true);
     await wrap_search();
     enable_buttons();
     $("#loading").hide();

js/drawtree.js

@@ -549,10 +549,10 @@ $("#select-tree-colours").change(function() {
 });
 
 
-$("#display-tree").change(async function() {
+async function changeDisplay() {
   var curr_date = new Date();
   curr_date.setFullYear(curr_date.getFullYear() - 1);
-  const tree_multiplier = 100000000; 
+  const tree_multiplier = 100000000;
 
   var handle = $( "#tree-slider-handle" );
   var cutoff_date = $( "#cutoff-date" );
@@ -580,14 +580,13 @@ $("#display-tree").change(async function() {
   $("#tree-slider").slider("option", "min", min);
   $("#tree-slider").slider("option", "max", max);
   $("#tree-slider").slider("option", "value",  (start_value > min && start_value < max) ? start_value : min);
-  
+
   $("#cutoff-date").text(xaxis_to_date($("#tree-slider").slider("option", "value")/tree_multiplier, tips_obj[0], d3.min(tips_obj, function(d) {return d.first_date}), d3.max(tips_obj, function(d) {return d.last_date})));
   $("#tree-cutoff").css('left',  $("#tree-slider-handle").position().left);
 
-  $("#tree-slider").slider("option", "slide", async function( event, ui ) {        
+  $("#tree-slider").slider("option", "slide", async function( event, ui ) {
     cutoff_date.text(xaxis_to_date(ui.value/tree_multiplier, tips_obj[0], d3.min(tips_obj, function(d) {return d.first_date}), d3.max(tips_obj, function(d) {return d.last_date})));
     await handle.change()
-
     cutoff_line.css('visibility', 'visible');
     var cutoff_pos = handle.position().left;
     cutoff_line.css('left', cutoff_pos + 29);
@@ -602,12 +601,16 @@ $("#display-tree").change(async function() {
   cindex = node.__data__.cluster_idx;
   d3.select('#cidx-' + cindex).attr("class", "clicked");
   draw_cluster_box(d3.select(node));
-  
+
   await beadplot(cindex);
   gentable(node.__data__);
   draw_region_distribution(node.__data__.allregions);
   gen_details_table(points);  // update details table with all samples
   gen_mut_table(mutations[cindex]);
+}
+
+$("#display-tree").change(async function() {
+  await changeDisplay();
 });
 
 

js/search.js

@@ -236,6 +236,16 @@ async function lineage_search(text_query) {
     return;
   }
 
+  // Get the lineage to determine if the tree needs to be redrawn
+  var display = await getdata(`/api/display/${cidx}`);
+
+  if (!($("#display-tree").val() === display[0])) {
+    await $("#display-tree").val(display[0])
+    await changeDisplay();
+  }
+
+  await reset_tree(partial_redraw=true);
+
   var cluster = select_cluster("cidx-"+cidx);
 
   // Reduces the opacity of all clusters
@@ -268,6 +278,16 @@ async function accession_search(text_query) {
     return;
   }
 
+  // Get the lineage to determine if the tree needs to be redrawn
+  var display = await getdata(`/api/display/${cidx}`);
+
+  if (!($("#display-tree").val() === display[0])) {
+    await $("#display-tree").val(display[0])
+    await changeDisplay();
+  }
+
+  await reset_tree(partial_redraw=true);
+
   var cluster = select_cluster("cidx-"+cidx);
 
   d3.select("#svg-timetree")

server.js

@@ -68,6 +68,12 @@ app.get('/api/xbbtips', (req, res) => {
   })
 });
 
+app.get('/api/display/:cindex', (req, res) => {
+  dbManager.get_display(req.params.cindex).then(result=>{
+    res.send(result);
+  })
+});
+
 app.get('/api/df', (req, res) => {
   dbManager.get_df().then(result=>{
     res.send(result)