Merge pull request #536 from PoonLab/dev

Minor: Bug fixes
PoonLab · Sep 20, 2024 · 9daab54 · 9daab54
2 parents b9aada0 + be186af
commit 9daab54
Showing 7 changed files with 36 additions and 14 deletions.
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,23 @@
+#### Front-end checks to do prior to merging pull request:
+- [ ] Search
+    - [ ] Search by accession number
+    - [ ] Search by lineage
+    - [ ] Search by country
+    - [ ] Search by country (with date filter)
+- [ ] Tree filtering
+- [ ] Download Time-scaled tree (nwk)
+- [ ] Download Time-scaled tree (csv)
+- [ ] Download Beadplot (svg)
+- [ ] Download Beadplot (nwk)
+- [ ] Download mutation list (csv)
+- [ ] Beadplot cutoff slider
+- [ ] Expanding Beadplot
+- [ ] Translated pages
+- [ ] Changing the colour of the tree based on divergence, collection date, etc.
+- [ ] View different displays (Non-Recombinants, Recombinants, etc.) 
+- [ ] Left/Right arrow key to move between beads
+- [ ] Ensure Tooltips get rendered
+- [ ] Hover over accession number in the "Samples" tab to ensure that the acknowledgement tooltips get generated
+- [ ] Countries/Samples/Mutations tabs are populating the correct information
+- [ ] Build front-end database without issues
+- [ ] Port front-end change to `epicov` branch
diff --git a/dbmanager.js b/dbmanager.js
@@ -89,19 +89,19 @@ class DBManager {
     }
 
     get_tips() {
-        return this.db_.collection($COLLECTION__TIPS).find().toArray()
+        return this.db_.collection($COLLECTION__TIPS).find({}, { projection: { _id: 0 } }).toArray()
     }
 
     get_df() {
-        return this.db_.collection($COLLECTION__DF_TREE).find().toArray();
+        return this.db_.collection($COLLECTION__DF_TREE).find({}, { projection: { _id: 0 } }).toArray();
     }
 
     get_xbb_df() {
-        return this.db_.collection($COLLECTION__XBB_TREE).find().toArray();
+        return this.db_.collection($COLLECTION__XBB_TREE).find({}, { projection: { _id: 0 } }).toArray();
     }
 
     get_regionMap() {
-        return this.db_.collection($COLLECTION__REGION_MAP).find().toArray().then((docs,err)=>{
+        return this.db_.collection($COLLECTION__REGION_MAP).find({}, { projection: { _id: 0 } }).toArray().then((docs,err)=>{
             if(err){
                 console.log(`dbmanager::get_regionMap error`,err);
                 return ;
@@ -214,7 +214,7 @@ class DBManager {
     }
 
     get_recombinantTips() {
-        return this.db_.collection($COLLECTION__RECOMBINANT_TIPS).find().toArray().then((docs,err)=>{
+        return this.db_.collection($COLLECTION__RECOMBINANT_TIPS).find({}, { projection: { _id: 0 } }).toArray().then((docs,err)=>{
             if(err){
                 console.log(`dbmanager::get_recombinantTips error`,err)
                 return;

diff --git a/index-es.html b/index-es.html
@@ -145,8 +145,8 @@ <h2 class="modal-title">Search Error</h2>
             <option value="Region">Región</option>
             <option value="No. samples">No. muestras</option>
             <option value="Collection date">Fecha de colección</option>
-            <option value="Divergence" selected>Divergencia</option>
-            <option value="Infections">Infecciones</option>
+            <option value="Divergence">Divergencia</option>
+            <option value="Infections" selected>Infecciones</option>
           </select>
           <div class="legend" id="div-region-legend"></div>
           <div class="legend" id="svg-sample-legend"></div>

diff --git a/index-fr.html b/index-fr.html
@@ -145,8 +145,8 @@ <h2 class="modal-title">Search Error</h2>
             <option value="Region">R&eacute;gion</option>
             <option value="No. samples">T. de l'&eacute;chantillon</option>
             <option value="Collection date">Date de collecte</option>
-            <option value="Divergence" selected>Divergence</option>
-            <option value="Infections">Infections</option>
+            <option value="Divergence">Divergence</option>
+            <option value="Infections" selected>Infections</option>
           </select>
           <div class="legend" id="div-region-legend"></div>
           <div class="legend" id="svg-sample-legend"></div>

diff --git a/index-zh.html b/index-zh.html
@@ -146,8 +146,8 @@ <h2 class="modal-title">Search Error</h2>
             <option value="Region">区域</option>
             <option value="No. samples">样本编号</option>
             <option value="Collection date">收集日期</option>
-            <option value="Divergence" selected>趋异</option>
-            <option value="Infections">感染</option>
+            <option value="Divergence">趋异</option>
+            <option value="Infections" selected>感染</option>
           </select>
           <div class="legend" id="div-region-legend"></div>
           <div class="legend" id="svg-sample-legend"></div>

diff --git a/index.html b/index.html
@@ -146,8 +146,8 @@ <h2 class="modal-title">Search Error</h2>
             <option value="Region">Region</option>
             <option value="No. samples">No. samples</option>
             <option value="Collection date">Collection date</option>
-            <option value="Divergence" selected>Divergence</option>
-            <option value="Infections">Infections</option>
+            <option value="Divergence">Divergence</option>
+            <option value="Infections" selected>Infections</option>
           </select>
           <div class="legend" id="div-region-legend"></div>
           <div class="legend" id="svg-sample-legend"></div>

diff --git a/js/beadplot.js b/js/beadplot.js
@@ -1381,7 +1381,6 @@ function serialize_branch(parent, edgelist) {
     // terminal node, emit string
     // TODO: add count information (number of samples per variant)
     coldate = branch[0].x1.toISOString().split('T')[0];
-    console.log("coldate=",coldate);
     return branch[0].child+'|'+coldate+':'+branch[0].dist;  // node name : branch length
   }
   else {