show_tax_string support MiGA

Author: lmrodriguezr

app/helpers/application_helper.rb

@@ -1,17 +1,22 @@
+require 'miga/taxonomy'
+
 module ApplicationHelper
-  def show_tax_string(string, opts = {})
+  def show_tax_string(tax, opts = {})
     opts[:class] ||= 'tax-string'
+    tax ||= []
+    tax = tax.ranks.to_a if tax.is_a?(MiGA::Taxonomy)
+    tax = tax.split(/ (>|»|\/) /) unless tax.is_a?(Array)
+
     content_tag(:span, opts) do
-      string = string.split(/ (>|»|\/) /) unless string.is_a?(Array)
-      string.each_with_index.map do |i, k|
-        r, n  = i.split(':', 2)
+      tax.each_with_index.map do |i, k|
+        r, n  = i.is_a?(String) ? i.split(':', 2) : i
         r_key = r.to_s[0].to_sym
 
         content_tag(:span, k == 0 ? '' : ' » '.html_safe) +
-        content_tag(
-          :span, n, title: Name.rank_keys[r_key],
-          data: { kind: :taxonomy, rank: r_key, value: n }
-        )
+          content_tag(
+            :span, n, title: Name.rank_keys[r_key],
+            data: { kind: :taxonomy, rank: r_key, value: n }
+          )
       end.inject(:+)
     end
   end

app/views/registers/curation_genomics/_ambiguous_type_genome.html.erb

@@ -56,13 +56,9 @@
             <% show_aai(cr) %>
           </td>
           <td rowspan=2>
-            <b>
-              <%= show_tax_string(
-                    (miga_obj&.metadata || {})[:tax]
-                      &.ranks&.map { |k, v| "#{k}:#{v}" } || [],
-                    id: "tax-#{name.id}-miga"
-                  ) %>
-            </b><br/>
+            <% miga_classif = miga_obj&.metadata&.[](:tax) %>
+            <%= show_tax_string(miga_classif, id: "tax-#{name.id}-miga") %>
+            <br/>
             <% cr = miga_obj&.closest_relatives(3, true, :aai) || [] %>
             <% show_aai(cr) %>
           </td>

app/views/registers/curation_genomics/_inconsistent_16s_assignment.html.erb

@@ -50,18 +50,15 @@
         </td>
         <td rowspan=2>
           <% miga_classif = genome&.miga_object&.metadata&.[](:tax) %>
-          <%= show_tax_string(
-                miga_classif.ranks.map { |i| "#{i[0]}:#{i[1]}" }.join(' > '),
-                id: "tax-#{name.id}-miga"
-              ) %>
+          <%= show_tax_string(miga_classif, id: "tax-#{name.id}-miga") %>
         </td>
       </tr>
       <tr>
         <td colspan=2>
           <b>Reported Classification</b><br/>
-          <% show_tax_string(
-                name.lineage.map { |i| "#{i.inferred_rank}:#{i.name}" }
-                    .join(' > ')
+          <%= show_tax_string(
+                name.lineage.map { |i| "#{i.inferred_rank}:#{i.name}" },
+                id: "tax-#{name.id}-reported"
               ) %>
         </td>
       </tr>