Merge branch 'seek-1.14' into fairdomhub

Gemfile

@@ -15,7 +15,7 @@ gem 'hpricot', '~>0.8.2'
 gem 'libxml-ruby', '~>2.9.0', require: 'libxml'
 gem 'uuid', '~>2.3'
 gem 'RedCloth', '>=4.3.0'
-gem 'simple-spreadsheet-extractor', '~> 0.18.0'
+gem 'simple-spreadsheet-extractor', '0.18.1'
 gem 'open4'
 gem 'sample-template-generator', '~>0.7'
 gem 'rmagick', '4.2.5'

Gemfile.lock

@@ -186,7 +186,7 @@ GEM
     citeproc-ruby (2.0.0)
       citeproc (~> 1.0, >= 1.0.9)
       csl (~> 2.0)
-    climate_control (0.2.0)
+    climate_control (1.2.0)
     code_analyzer (0.5.5)
       sexp_processor
     coderay (1.1.3)
@@ -774,9 +774,9 @@ GEM
     rubyntlm (0.6.3)
     rubyzip (2.0.0)
     rugged (1.1.0)
-    sample-template-generator (0.7.0)
+    sample-template-generator (0.7.1)
       rdoc (~> 6.0)
-      terrapin (~> 0.6)
+      terrapin (~> 1.0)
     sass-rails (6.0.0)
       sassc-rails (~> 2.1, >= 2.1.1)
     sassc (2.4.0)
@@ -821,9 +821,9 @@ GEM
       rdf-xsd (~> 3.2)
       sparql (~> 3.2)
       sxp (~> 1.2)
-    simple-spreadsheet-extractor (0.18.0)
+    simple-spreadsheet-extractor (0.18.1)
       libxml-ruby (~> 2.9)
-      terrapin (~> 0.6)
+      terrapin (~> 1.0)
     simplecov (0.21.2)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
@@ -875,8 +875,8 @@ GEM
     teaspoon-mocha (2.3.3)
       teaspoon (>= 1.0.0)
     temple (0.8.2)
-    terrapin (0.6.0)
-      climate_control (>= 0.0.3, < 1.0)
+    terrapin (1.0.1)
+      climate_control
     terser (1.1.8)
       execjs (>= 0.3.0, < 3)
     test-prof (1.0.7)
@@ -1073,7 +1073,7 @@ DEPENDENCIES
   sass-rails (>= 6)
   savon (= 1.1.0)
   seedbank
-  simple-spreadsheet-extractor (~> 0.18.0)
+  simple-spreadsheet-extractor (= 0.18.1)
   simplecov
   sprockets-rails
   sqlite3 (~> 1.4)

app/views/search/partials/_biomodels_resource_list_item.html.erb

@@ -25,7 +25,7 @@
           </div>
         <% end %>
       </div>
-      <% unless resource.unreleased %>
+      <% unless resource.unreleased || resource.main_filename.blank? %>
         <div class="col-sm-2 text-right list_item_actions">
           <%
              biomodel_download_link = resource.download_link

lib/seek/biomodels_search/search_biomodels_adaptor.rb

@@ -12,7 +12,12 @@ def perform_search(query)
 
         json = JSON.parse(json)
         json['models'].collect do |result|
-          BiomodelsSearchResult.new result['id']
+          begin
+            BiomodelsSearchResult.new result['id']
+          rescue NoMethodError=>exception
+            Seek::Errors::ExceptionForwarder.send_notification(exception, data: { error: 'error reading response from BioModels', item_id: result['id'], query: query })
+            nil
+          end
         end.compact.reject do |biomodels_result|
           biomodels_result.title.blank?
         end
@@ -62,14 +67,15 @@ def populate
           self.publication_title = json.dig('publication', 'title')
           self.authors = (json.dig('publication', 'authors') || []).collect { |author| author['name'] }
           self.published_date = Time.at(json['firstPublished'] / 1000)
-          latest_version = json['history']['revisions'].sort { |rev| rev['version'] }.first
-          self.last_modification_date = Time.at(latest_version['submitted'] / 1000)
-          self.main_filename = json['files']['main'].first['name']
+          latest_version = (json.dig('history','revisions') || []).sort { |rev| rev['version'] }&.first
+          if latest_version&.fetch('submitted')
+            self.last_modification_date = Time.at(latest_version['submitted'] / 1000)
+          end
+          self.main_filename = (json.dig('files','main') || []).first&.fetch('name')
           self.unreleased = false
         else
           self.unreleased = true
         end
-
       end
     end
   end

test/factories/content_blobs.rb

@@ -313,6 +313,12 @@
     content_type { 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' }
     data { File.new("#{Rails.root}/test/fixtures/files/blank-master-template.xlsx", 'rb').read }
   end
+
+  factory(:spreadsheet_with_error_logs_content_blob, parent: :content_blob) do
+    original_filename { 'spreadsheet-with-poi-error-logs.xlsx' }
+    content_type { 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' }
+    data { File.new("#{Rails.root}/test/fixtures/files/spreadsheet-with-poi-error-logs.xlsx", 'rb').read }
+  end
 
   factory(:blank_content_blob, class: ContentBlob) do
     url { nil }

test/factories/data_files.rb

@@ -121,6 +121,10 @@
   factory(:small_test_spreadsheet_datafile, parent: :data_file) do
     association :content_blob, factory: :small_test_spreadsheet_content_blob
   end
+
+  factory(:spreadsheet_with_error_logs_datafile, parent: :data_file) do
+    association :content_blob, factory: :spreadsheet_with_error_logs_content_blob
+  end
 
   factory(:strain_sample_data_file, parent: :data_file) do
     association :content_blob, factory: :strain_sample_data_content_blob

test/functional/data_files_controller_test.rb

@@ -1255,6 +1255,13 @@ def test_show_item_attributed_to_jerm_file
     assert_response :success
   end
 
+  test 'explore spreadsheet with error logs' do
+    data = FactoryBot.create :spreadsheet_with_error_logs_datafile, policy: FactoryBot.create(:public_policy)
+    get :explore, params: { id: data }
+    assert_response :success
+    assert_select 'div#spreadsheet_1 table.sheet td#cell_B4',text:'ProjectDescription'
+  end
+
   test 'explore earlier version' do
 
     df = FactoryBot.create(:small_test_spreadsheet_datafile)

test/unit/search_biomodels_adaptor_test.rb

@@ -52,6 +52,7 @@ class SearchBiomodelsAdaptorTest < ActiveSupport::TestCase
       assert_equal DateTime.parse('2012-12-14 14:24:40 +0000'), result.last_modification_date
       assert_equal 'search/partials/test_partial', result.partial_path
       assert_equal 'EBI Biomodels', result.tab
+      assert_equal 'BIOMD0000000429_url.xml', result.main_filename
     end
 
   end
@@ -64,5 +65,13 @@ class SearchBiomodelsAdaptorTest < ActiveSupport::TestCase
     end
   end
 
+  test 'search does not files' do
+    VCR.use_cassette('biomodels/search-2024') do
+      adaptor = Seek::BiomodelsSearch::SearchBiomodelsAdaptor.new('partial_path' => 'search/partials/test_partial')
+      results = adaptor.search('2024')
+      assert_equal 25, results.count
+    end
+  end
+
 
 end