download tree info and studies

app/assets/stylesheets/trees.scss

@@ -109,3 +109,8 @@
   display: inline-block;
   float: left;
 }
+
+#download-tree-info-link {
+  margin-top: 20px !important;
+  margin-bottom: 10px !important;
+}

app/controllers/trees_controller.rb

@@ -2,7 +2,7 @@ class TreesController < ApplicationController
   include TreesHelper
   include ListsHelper
 
-  before_action :find_tree, only: [:destroy, :edit, :update, :show, :download, :metadata]
+  before_action :find_tree, only: [:destroy, :edit, :update, :show, :download, :metadata, :download_tree_info]
 
   def show
     @x = params[:x]
@@ -237,7 +237,10 @@ def download_studies
     respond_to do |format|
       format.js
     end
-
+  end
+
+  def download_tree_info
+    send_data @tree.info.to_json, :filename => @tree.name + "_info.json"
   end
 
   private 

app/models/tree.rb

@@ -125,7 +125,25 @@ def ot_scaled
     end
   end
 
-  def metadata
+  def info
+    begin
+      n = JSON.parse(self.tree)["tree_metadata"]
+      return n.nil? ? "" : n
+    rescue
+      ""
+    end
+  end
+
+  def data
+    begin
+      n = JSON.parse(self.tree)["meta_data"]
+      return n.nil? ? "" : n
+    rescue
+      ""
+    end
+  end
+
+  def supporting_studies
     begin
       n = JSON.parse(self.studies)
       return n.nil? ? "" : n

app/views/trees/_metadata.html.erb

@@ -1,27 +1,87 @@
-<% tree_metadata = tree.metadata %>
-
 <div class="container">
   <div class="row min-page-height">
     <div class="col-md-4">
-      <h3>Tree info</h3>
-
-      <div id="info-wrapper">
-        <% if tree_metadata.empty? %>
-          <div class='center loading w-100'><i class="fa fa-spin fa-4x fa-spinner" aria-hidden="true"></i></div>
-        <% else %>
-          <%= render partial: "info", locals: { tree_metadata: tree_metadata } %>
-        <% end %>
+      <div class="row">
+        <div class="col-md-8">
+          <h3>Tree info</h3>
+        </div>
+        <div class="col-md-4">
+          <div id="download-tree-info-link">
+            <%= link_to "Save", download_tree_info_tree_path(tree, format: :txt), class: "btn btn-primary" %> 
+          </div>
+        </div>
       </div>
+
+      <% tree_info = tree.info %>
+      <% tree_data = tree.data %>
+
+      <table class="table table-hover">
+        <tbody>
+          <tr>
+            <th>Topology ID</th>
+            <td><%= tree_info["topology_id"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Gene or species</th>
+            <td><%= tree_info["gene_or_species"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Rooted</th>
+            <td><%= tree_info["rooted"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Anastomosing</th>
+            <td><%= tree_info["anastomosing"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Consensus type</th>
+            <td><%= tree_info["consensus_type"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Branch length type</th>
+            <td><%= tree_info["branch_length_type"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Branch support type</th>
+            <td><%= tree_info["branch_support_type"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Character matrix</th>
+            <td><%= tree_info["character_matrix"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Alignment method</th>
+            <td><%= tree_info["alignment_method"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Inference method</th>
+            <td><%= tree_info["inference_method"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Number of tips</th>
+            <td><%= tree_info["num_tips"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Creation time</th>
+            <td><%= tree_data["creation_time"] rescue "NA" %></td>
+          </tr>
+          <tr>
+            <th>Execution time (second)</th>
+            <td><%= tree_data["execution_time"] rescue "NA" %></td>
+          </tr>
+        </tbody>
+      </table>
     </div>
 
     <div class="col-md-8">
       <h3>Supporting studies  <a href="#" data-toggle="tooltip" title="Published studies with trees relevant to deriving your Phylotastic tree (trees from OpenTree may lack supporting studies if they are based solely on taxonomy)."><i class="fa fa-question-circle" aria-hidden="true"></i></a></h3>
 
       <div id="studies-wrapper">
-        <% if tree_metadata.empty? %>
+        <% tree_studies = tree.supporting_studies %>
+        <% if tree_studies.empty? %>
           <div class='center loading w-100'><i class="fa fa-spin fa-4x fa-spinner" aria-hidden="true"></i></div>
         <% else %>
-          <%= render partial: "support_studies", locals: { tree_metadata: tree_metadata } %>
+          <%= render partial: "support_studies", locals: { tree_studies: tree_studies } %>
         <% end %>
       </div>
     </div>

app/views/trees/_support_studies.html.erb

@@ -1,4 +1,4 @@
-<% if tree_metadata.empty? || tree_metadata["studies"].empty? %>
+<% if tree_studies.empty? || tree_studies["studies"].empty? %>
   <p>No supporting studies were found. This typically happens when a tree is derived from the OpenTree taxonomy without phylogenetic refinement.</p>
 <% else %>
 
@@ -9,11 +9,15 @@
   <hr>
 
   <%= form_tag trees_download_studies_path, method: :post, remote: true do %>
-    <% tree_metadata["studies"].each_with_index do |s, i| %>
+    <% tree_studies["studies"].each_with_index do |s, i| %>
       <div class="study">
         <div class="study-title">
-          <div class="checkbox-wrapper">  
-            <%= check_box_tag("p[#{s["PublicationDOI"]}]", 1, checked = false, class: "select_pub") %>
+          <div class="checkbox-wrapper">
+            <% if s["PublicationDOI"].include? "dx.doi.org" %>
+              <%= check_box_tag("p[#{s["PublicationDOI"]}]", 1, checked = false, class: "select_pub") %>
+            <% else %>
+              <i class='fa fa-exclamation-triangle ' data-toggle='tooltip' title='Bibtex entry not found'></i>
+            <% end %>
           </div>
           <%= s["Publication"] %>
         </div>
@@ -51,7 +55,7 @@
       </div>
       <div class="modal-footer">
         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
-        <a type="button" class="btn btn-primary" download="citation.txt" id="citation-download">Save</a>
+        <a type="button" class="btn btn-primary" download="citation.bib" id="citation-download">Save</a>
       </div>
     </div>
   </div>
@@ -72,7 +76,10 @@
   });
 
   $("#citation-download").click(function() {
-    console.log("aaa");
     this.href = "data:text/plain;charset=UTF-8," + $('#citation-modal-content').text();
   });
+
+  $(function () {
+    $('[data-toggle="tooltip"]').tooltip()
+  })
 </script>

app/views/trees/metadata.js.erb

@@ -1,2 +1,2 @@
-$("#info-wrapper").html("<%=j render partial: 'info', locals: { tree_metadata: @tree_metadata } %>");
-$("#studies-wrapper").html("<%=j render partial: 'support_studies', locals: { tree_metadata: @tree_metadata } %>");
+<% tree_studies = @tree.supporting_studies %>
+$("#studies-wrapper").html("<%=j render partial: 'support_studies', locals: { tree_studies: tree_studies } %>");

config/routes.rb

@@ -9,6 +9,7 @@
       get 'wf'
       post "wf_update"
       get 'metadata'
+      get 'download_tree_info'
     end
   end