Minor bug fixes for local version displaying snps, disable server db …

install/rivet_env.yml

@@ -4,10 +4,8 @@ channels:
 dependencies:
   - pip
   - seaborn = 0.12.1
-  - google-cloud-storage = 2.7.0
-  - google-cloud-sdk = 412.0.0
-  - flask = 2.2.2
-  - flask-caching = 2.0.1
+  - flask
+  - flask-caching
   - biopython
   - pip:
           - pyyaml

rivet-frontend.py

@@ -623,13 +623,13 @@ def table():
   app.config['recomb_desc'] = recomb_desc_dict
   app.config['desc_data'] = desc_position_table
   app.config['desc_file'] = desc_file
- 
+
   # Parameters for full tree descendants information
   app.config['full_tree_recomb_desc'] = full_tree_desc_position_table
   app.config['full_tree_sample_counts'] = full_tree_sample_counts
   app.config['full_tree_desc_data'] = full_tree_desc_position_table
   app.config['full_tree_desc_file'] = full_tree_desc_file
-  
+
   # App tree and config parameters
   app.config['environment'] = config["environment"]
   app.config['date'] = str(config["date"])
@@ -648,13 +648,15 @@ def table():
   app.config['genome_size'] = genome_size
   app.config['genomic_range'] = genomic_range
   app.config['gene_region_data'] = gene_region_data
-  # Name of persistent database file
-  app.config['db_file'] = config['db_file']
-  app.config['aa_tables'] = (config['aa_public'], config['aa_full'])
-  app.config['sample_table'] = config['sample_table']
-  app.config['desc_col'] = config['desc_col']
-  app.config['aa_col'] = config['aa_col']
-  app.config['node_col'] = config['node_col']
+
+  if config["environment"].lower() != "local":
+      # Server config for persistent database file
+      app.config['db_file'] = config['db_file']
+      app.config['aa_tables'] = (config['aa_public'], config['aa_full'])
+      app.config['sample_table'] = config['sample_table']
+      app.config['desc_col'] = config['desc_col']
+      app.config['aa_col'] = config['aa_col']
+      app.config['node_col'] = config['node_col']
 
   tock = time.perf_counter()
   print(f"Time elapsed: {tock-tick:.2f} seconds")

static/app.js

@@ -26,8 +26,17 @@ function main() {
             init_coordinate_track(svg.append('svg'), init_track_width, data);
           })});
 
-  // On load, show the full tree title by default
-  document.querySelector('#full_title').removeAttribute('hidden');
+  const public_table = document.querySelector('#public_tree');
+  const full_table = document.querySelector('#full_tree');
+  const public_title = document.querySelector('#public_title');
+  const full_title = document.querySelector('#full_title');
+  const search_by_sample = document.querySelector('#search');
+  const search_by_aa = document.querySelector('#search_by_aa');
+
+  if (full_title) {
+    // On load, show the full tree title by default
+    document.querySelector('#full_title').removeAttribute('hidden');
+  }
 
   // SNV plot svg download and copy buttons setup
   /*
@@ -115,30 +124,28 @@ reate_button('copy_svg', 'Copy SNV Plot', 1200, 280);
       download_taxonium();
     }, false);
   }
-  const public_table = document.querySelector('#public_tree');
-  const full_table = document.querySelector('#full_tree');
-  const public_title = document.querySelector('#public_title');
-  const full_title = document.querySelector('#full_title');
-  const search_by_sample = document.querySelector('#search');
-  const search_by_aa = document.querySelector('#search_by_aa');
 
-  // Listen if public tree selected, update title to public tree title
-  // and remove search by EPI identifier and amino acid mutation
-  public_table.addEventListener('click', () => {
-    full_title.setAttribute('hidden', true);
-    search_by_sample.setAttribute('hidden', true);
-    search_by_aa.setAttribute('hidden', true);
-    desc_button.removeAttribute('hidden');
-    full_tree_desc_button.setAttribute('hidden', true);
-    public_title.removeAttribute('hidden');
-  });
-
-  full_table.addEventListener('click', () => {
-    public_title.setAttribute('hidden', true);
-    full_title.removeAttribute('hidden');
-    search_by_sample.removeAttribute('hidden');
-    search_by_aa.removeAttribute('hidden');
-    desc_button.setAttribute('hidden', true);
-    full_tree_desc_button.removeAttribute('hidden');
-  });
+  if (public_table) {
+    // Listen if public tree selected, update title to public tree title
+    // and remove search by EPI identifier and amino acid mutation
+    public_table.addEventListener('click', () => {
+      full_title.setAttribute('hidden', true);
+      search_by_sample.setAttribute('hidden', true);
+      search_by_aa.setAttribute('hidden', true);
+      desc_button.removeAttribute('hidden');
+      full_tree_desc_button.setAttribute('hidden', true);
+      public_title.removeAttribute('hidden');
+    });
+  }
+
+  if (full_table) {
+    full_table.addEventListener('click', () => {
+      public_title.setAttribute('hidden', true);
+      full_title.removeAttribute('hidden');
+      search_by_sample.removeAttribute('hidden');
+      search_by_aa.removeAttribute('hidden');
+      desc_button.setAttribute('hidden', true);
+      full_tree_desc_button.removeAttribute('hidden');
+    });
+  }
 }

templates/local.html

@@ -191,7 +191,7 @@ <h3 class="offcanvas-title" id="offcanvasScrollingLabel">Selected Node Descendan
          processData: false,
          success: function(response){
              $('#main').text(response)
-                 console.log("RESPONSE: ", response);
+                 //console.log("RESPONSE: ", response);
                              track(response);
              }
          })