update simple-spreadsheet-extractor gem to fix #1728

includes updated javacode, and error handling in the gem, to ensure any errors are logged to stderr rather than stdout, and therefore prevent uncritical errors appearing the successful output

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)

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)