See report history in genomes

Author: lmrodriguezr

app/helpers/application_helper.rb

@@ -3,6 +3,20 @@ def cannonical_url
     url_for(only_path: false, protocol: 'https', host: 'registry.seqco.de')
   end
 
+  def report_history(obj, text: 'Report history')
+    id = modal('Report history') do
+      obj.reports.map do |report|
+        content_tag(:div, class: 'border') do
+          time_ago_with_date(report.created_at, true) +
+            report.html.html_safe
+        end
+      end.inject(:+)
+    end
+    modal_button(id, class: 'btn btn-primary btn-sm') do
+      fa_icon('archive') + ' ' + text
+    end
+  end
+
   def list_preference
     cookies[:list] || 'cards'
   end

app/models/genome/external_resources.rb

@@ -50,7 +50,9 @@ def reload_source_json!
   # Find BioSample accession linked to the SRA entry +acc+ and return as
   # String (or +nil+)
   def external_sra_to_biosample(acc)
-    SequencingExperiment.by_sra(acc).try(:biosample_accession)
+    sr = SequencingExperiment.by_sra(acc)
+    ephemeral_report << sr.try(:ephemeral_report)
+    sr.try(:biosample_accession)
   end
 
   ##
@@ -64,7 +66,8 @@ def external_biosample_to_sra(acc)
     ng = Nokogiri::XML(body)
     ng.xpath('//result/entries/entry').map do |exp|
       sra_acc = exp['acc'] || exp['id'] or next
-      SequencingExperiment.find_or_create_by(sra_accession: sra_acc)
+      sr = SequencingExperiment.find_or_create_by(sra_accession: sra_acc)
+      ephemeral_report << sr.try(:ephemeral_report)
     end
   end
 

app/views/genomes/_curator.html.erb

@@ -2,6 +2,9 @@
   <dl name="curator" class="main-section name-details actions-section">
     <h2>Curator Actions</h2>
     <dd class="pt-2">
+      <%= report_history(@genome) %>
+      &raquo; See the logs from automated tasks
+      <hr/>
       <%= link_to(
             update_external_genome_url(@genome),
             method: :post, class: 'btn btn-primary btn-sm'

lib/ephemeral_report.rb

@@ -17,12 +17,24 @@ def <<(message)
     end
   end
 
-  def to_s
-    @messages.map(&:to_s).join("\n")
+  def title_message
+    EphemeralMessage.new(obj.qualified_id, type: :section)
   end
 
-  def to_html
-    @messages.map(&:to_html).join("\n")
+  def end_messsage
+    EphemeralMessage.new('Report end for %s' % obj.qualified_id)
+  end
+
+  def to_s(section: false)
+    y = @messages.map(&:to_s).join("\n")
+    y = title_message.to_s + "\n" + y if section
+    y + "\n" + end_message.to_s
+  end
+
+  def to_html(section: false)
+    y = @messages.map(&:to_html).join("\n")
+    y = title_message.to_html + "\n" + y if section
+    y.html_safe + "\n" + end_message.to_html
   end
 
   def save
@@ -47,15 +59,15 @@ def initialize(message, type: :info)
 
   def to_s
     @message.is_a?(EphemeralReport) ?
-      @message.to_s :
+      @message.to_s(section: true) :
       '%s: [%s] %s' % [@type.to_s.upcase, @timestamp.to_s, @message.to_s]
   end
 
   def to_html
     @message.is_a?(EphemeralReport) ?
-      @message.to_html :
-      '<div class="%s"><span class="text-muted">[%s]</span> %s</div>' % [
-        html_class, @timestamp.to_s, @message.to_s
+      @message.to_html(section: true) :
+      '<div class="%s %s"><span class="text-muted">[%s]</span> %s</div>' % [
+        'report-message', html_class, @timestamp.to_s, @message.to_s
       ]
   end