Towards reading XLSX files

Author: lmrodriguezr

app/models/register.rb

@@ -420,6 +420,39 @@ def pending_genomes?
     names.any? { |n| n.type_genome.try(:pending?) }
   end
 
+  # ============ --- FILES --- ============
+  %i[publication supplementary].each do |file|
+    define_method(:"#{file}_file") do
+      send(:"#{file}_pdf")
+    end
+
+    define_method(:"#{file}_file?") do
+      send(:"#{file}_file").attached?
+    end
+  end
+
+  def file?(file)
+    %i[publication supplementary].include?(file.to_sym) &&
+      send(:"#{file}_file?")
+  end
+
+  def file(file)
+    return unless file?(file)
+    send(:"#{file}_pdf")
+  end
+
+  def file_is_pdf?(file)
+    file = file(file) or return false
+    file.filename.extension == 'pdf' || file.content_type == 'application/pdf'
+  end
+
+  def file_is_xlsx?(file)
+    file = file(file) or return false
+    file.filename.extension == 'xlsx' ||
+      file.content_type ==
+        'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
+  end
+
   private
 
   def assign_accession

app/models/register/status.rb

@@ -272,55 +272,68 @@ def automated_validation
   end
 
   ##
-  # Check if the PDF file(s) include accession and all list names, and report
-  # results as register list notes
+  # Check if the PDF and XLSX file(s) include accession and all list names, and
+  # report results as register list notes
   #
   # Returns boolean, with true indicating all checks passed and false otherwise
   #
   # IMPORTANT: Notes are soft-registered, remember to +save+ to make them
-  # persistent
+  # persistent, but the individual +Check+ entries are actually saved
   def check_pdf_files
-    inames = Hash[names.map { |n| [n, false] }]
-    anames = Hash[names.map { |n| [n, false] }]
-    [publication_pdf, supplementary_pdf].each do |as|
-      next unless as.attached?
-      break if anames.values.all? && inames.values.all?
-
-      if as.filename.extension == 'pdf' || as.content_type == 'application/pdf'
-        as.open do |file|
-          render = PDF::Reader.new(file.path)
+    xnames = Hash[names.map { |n| [n, [false, false]] }]
+    %i[publication supplementary].each do |file|
+      next unless file?(file)
+      break if xnames.values.flatten.all?
+
+      file(file).open do |fh|
+        if file_is_pdf?(file)
+          render = PDF::Reader.new(fh.path)
           render.pages.each do |page|
-            txt = page.text.unicode_normalize(:nfkc)
-            anames.each { |n, _| anames[n] = true } if txt.index(accession)
-            names.each do |n|
-              inames[n] ||= n.pdf_variants.find { |i| txt.index(i) }.present?
-              anames[n] ||= txt.index(n.seqcode_url(false)).present?
-            end
-            break if anames.values.all? && inames.values.all?
+            break if _search_names_in_text(
+              xnames, names, accession,
+              page.text.unicode_normalize(:nfkc)
+            )
+          end
+        elsif file_is_xlsx?(file)
+          xlsx = Roo::Spreadsheet.open(fh.path)
+          xlsx.each do |row|
+            break if _search_names_in_text(
+              xnames, names, accession,
+              row.select(&:present?).join(' ')
+            )
           end
         end
-      elsif as.filename.extension == 'xlsx'
-        # TODO
-        # Parse spreadsheets!
       end
     end
 
     names.each do |n|
-      par = { pass: anames[n], user: nil }
+      par = { pass: xnames[n][0], user: nil }
       Check.create_with(par).find_or_create_by(
         name: n, kind: :effective_publication_missing_accession
       ).update(par)
 
-      par = { pass: inames[n], user: nil }
+      par = { pass: xnames[n][1], user: nil }
       Check.create_with(par).find_or_create_by(
         name: n, kind: :name_missing_in_effective_publication
       ).update(par)
     end
 
     add_note('The effective publication files have been parsed')
-    anames.values.all? && inames.values.all?
+    xnames.values.flatten.all?
   rescue => e
     add_note('ERROR: The effective publication files could not be parsed')
     raise e
   end
+
+  private
+
+  def _search_names_in_text(xnames, names, accession, txt)
+    xnames.each { |n, _| xnames[n][0] = true } if txt.index(accession)
+    names.each do |n|
+      xnames[n][0] ||= txt.index(n.seqcode_url(false)).present?
+      xnames[n][1] ||= n.pdf_variants.find { |i| txt.index(i) }.present?
+    end
+    xnames.values.flatten.all?
+  end
 end
+

app/views/registers/_citation.html.erb

@@ -104,15 +104,21 @@
             <%= @register.publication.long_citation_html %>
           </p>
           <% if @register.can_view_publication?(current_user) %>
-            <% %i[publication_pdf supplementary_pdf].each do |attach| %>
-              <% as = @register.send(attach) %>
-              <% if as.attached? %>
+            <% %i[publication supplementary].each do |attach| %>
+              <% if @register.file?(attach) %>
                 <%= link_to(
-                      rails_blob_path(as, disposition: 'attachment'),
-                      class: 'btn btn-secondary btn-sm'
+                      rails_blob_path(
+                        @register.file(attach), disposition: 'attachment'
+                      ), class: 'btn btn-secondary btn-sm'
                     ) do %>
-                  <%= fa_icon('file-pdf') %>
-                  <%= attach.to_s.sub(/_.*/, '') %>
+                  <% if @register.file_is_pdf?(attach) %>
+                    <%= fa_icon('file-pdf') %>
+                  <% elsif @register.file_is_xlsx?(attach) %>
+                    <%= fa_icon('file-excel') %>
+                  <% else %>
+                    <%= fa_icon('file-alt') %>
+                  <% end %>
+                  <%= attach %>
                 <% end %>
               <% end %>
             <% end %>