Merge pull request #661 from tadast/tt/fix-tests

Fix flaky capybara tests

.gitignore

@@ -15,7 +15,7 @@ doc
 # jeweler generated
 pkg
 
-# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore:
 #
 # * Create a file at ~/.gitignore
 # * Include files you want ignored
@@ -54,3 +54,6 @@ pkg
 .gems/*
 Gemfile.lock
 node_modules
+
+spec/dotdir/*
+spec/downloads/*

.rubocop.yml

@@ -8,6 +8,7 @@ Metrics/AbcSize:
   Exclude:
     # TODO
     - 'lib/sequenceserver.rb'
+    - 'spec/**'
 Metrics/MethodLength:
   # Because 15 lines in a method is just about as good as 10 (default). And we
   # have a couple that can't be helped.
@@ -30,6 +31,7 @@ Metrics/BlockLength:
   Exclude:
     - 'bin/sequenceserver'
     - 'sequenceserver.gemspec'
+    - 'spec/**'
 
 Style/UnlessElse:
   # TODO:

Gemfile.lock

@@ -14,7 +14,7 @@ GEM
     addressable (2.8.4)
       public_suffix (>= 2.0.2, < 6.0)
     ast (2.4.2)
-    capybara (3.39.0)
+    capybara (3.39.2)
       addressable
       matrix
       mini_mime (>= 0.1.3)
@@ -23,7 +23,7 @@ GEM
       rack-test (>= 0.6.3)
       regexp_parser (>= 1.5, < 3.0)
       xpath (~> 3.2)
-    capybara-screenshot (1.0.24)
+    capybara-screenshot (1.0.26)
       capybara (>= 1.0, < 4)
       launchy
     childprocess (3.0.0)
@@ -32,16 +32,16 @@ GEM
     docile (1.3.2)
     json (2.3.0)
     json_pure (2.6.3)
-    launchy (2.4.3)
-      addressable (~> 2.3)
+    launchy (2.5.2)
+      addressable (~> 2.8)
     matrix (0.4.2)
     method_source (1.0.0)
     mini_mime (1.1.2)
-    mini_portile2 (2.8.1)
+    mini_portile2 (2.8.2)
     mustermann (2.0.2)
       ruby2_keywords (~> 0.0.1)
-    nokogiri (1.14.3)
-      mini_portile2 (~> 2.8.0)
+    nokogiri (1.15.3)
+      mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     ox (2.14.16)
     parallel (1.23.0)
@@ -51,8 +51,8 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.1)
-    racc (1.6.2)
-    rack (2.2.6.4)
+    racc (1.7.1)
+    rack (2.2.7)
     rack-protection (2.2.4)
       rack
     rack-test (1.1.0)
@@ -64,15 +64,15 @@ GEM
       rspec-core (~> 3.9.0)
       rspec-expectations (~> 3.9.0)
       rspec-mocks (~> 3.9.0)
-    rspec-core (3.9.1)
-      rspec-support (~> 3.9.1)
+    rspec-core (3.9.3)
+      rspec-support (~> 3.9.3)
     rspec-expectations (3.9.0)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.9.0)
     rspec-mocks (3.9.1)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.9.0)
-    rspec-support (3.9.2)
+    rspec-support (3.9.4)
     rubocop (1.50.2)
       json (~> 2.3)
       parallel (~> 1.10)

public/js/report.js

@@ -487,7 +487,7 @@ class Report extends Component {
             // remove attributes from link if sequence_ids array is empty
             $('.download-alignment-of-selected').attr('href', '#').removeAttr('download');
             return;
-                
+
         }
         if(this.state.alignment_blob_url){
             // always revoke existing url if any because this method will always create a new url
@@ -503,7 +503,7 @@ class Report extends Component {
                 }
             });
         }, this));
-        const filename = 'alignment-' + sequence_ids.length + '_hits';
+        const filename = 'alignment-' + sequence_ids.length + '_hits.txt';
         const blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, filename);
         // set required download attributes for link
         $('.download-alignment-of-selected').attr('href', blob_url).attr('download', filename);
@@ -528,7 +528,7 @@ class Report extends Component {
         );
 
         var aln_exporter = new AlignmentExporter();
-        var file_name = `alignment-${num_hits}_hits`;
+        var file_name = `alignment-${num_hits}_hits.txt`;
         const blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, file_name);
         $('.download-alignment-of-all')
             .attr('href', blob_url)

spec/capybara_spec.rb

@@ -7,67 +7,70 @@
     visit '/'
     fill_in('sequence', with: nucleotide_query)
 
-    prot = page.evaluate_script("$('.protein .database').text().trim()")
-    prot.should eq("2020-11 Swiss-Prot insecta 2020-11-Swiss-Prot insecta (subset taxid 102803) Sinvicta 2-2-3 prot subset without_parse_seqids.fa")
-
-    nucl = page.evaluate_script("$('.nucleotide .database').text().trim()")
-    nucl.should eq("Sinvicta 2-2-3 cdna subset Solenopsis invicta gnG subset funky ids (v5)")
+    expect(page).to have_selector('.protein .database', text: /\A2020-11 Swiss-Prot insecta\z/)
+    expect(page).to have_selector('.protein .database', text: '2020-11-Swiss-Prot insecta (subset taxid 102803)')
+    expect(page).to have_selector('.protein .database', text: 'Sinvicta 2-2-3 prot subset')
+    expect(page).to have_selector('.protein .database', text: 'without_parse_seqids.fa')
+
+    expect(page).to have_selector('.nucleotide .database', text: 'Sinvicta 2-2-3 cdna subset')
+    expect(page).to have_selector('.nucleotide .database', text: 'Solenopsis invicta gnG subset')
+    expect(page).to have_selector('.nucleotide .database', text: 'funky ids (v5)')
   end
 
-  it 'properly controls blast button' do
+  it 'keeps the CTA disabled until a sequence is provided and database selected' do
     visit '/'
 
     fill_in('sequence', with: nucleotide_query)
-    page.evaluate_script("$('#method').is(':disabled')").should eq(true)
+    expect(page).to have_selector('#method:disabled')
 
     check(nucleotide_databases.first)
-    page.evaluate_script("$('#method').is(':disabled')").should eq(false)
+    expect(page).to have_selector('#method:enabled')
   end
 
-  it 'properly controls interaction with database listing' do
+  it 'disables protein DB selection if a nucleotide DB is already selected' do
     visit '/'
     fill_in('sequence', with: nucleotide_query)
     check(nucleotide_databases.first)
-    page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
-        .should eq(true)
+
+    expect(page).to have_no_selector('.protein .database:enabled')
   end
 
   it 'shows a dropdown menu when other blast methods are available' do
     visit '/'
     fill_in('sequence', with: nucleotide_query)
     check(nucleotide_databases.first)
-    page.has_css?('#methods button.dropdown-toggle').should eq(true)
+    expect(page).to have_selector('#methods button.dropdown-toggle')
   end
 
   it 'can run a simple blastn search' do
     perform_search query: nucleotide_query,
                    databases: nucleotide_databases
-    page.should have_content('BLASTN')
+    expect(page).to have_content('BLASTN')
   end
 
   it 'can run a simple blastp search' do
     perform_search query: protein_query,
                    databases: protein_databases
-    page.should have_content('BLASTP')
+    expect(page).to have_content('BLASTP')
   end
 
   it 'can run a simple blastx search' do
     perform_search query: nucleotide_query,
                    databases: protein_databases
-    page.should have_content('BLASTX')
+    expect(page).to have_content('BLASTX')
   end
 
   it 'can run a simple tblastx search' do
     perform_search query: nucleotide_query,
                    databases: nucleotide_databases,
                    method: 'tblastx'
-    page.should have_content('TBLASTX')
+    expect(page).to have_content('TBLASTX')
   end
 
   it 'can run a simple tblastn search' do
     perform_search query: protein_query,
                    databases: nucleotide_databases
-    page.should have_content('TBLASTN')
+    expect(page).to have_content('TBLASTN')
   end
 
   ### Test aspects of the generated report.
@@ -80,7 +83,7 @@
 
     # Click on the first FASTA download button on the page and wait for the
     # download to finish.
-    page.execute_script("$('.download-fa:eq(0)').click()")
+    page.first('.download-fa').click
     wait_for_download
 
     # Test name and content of the downloaded file.
@@ -141,7 +144,7 @@
 
     # Click on the first Alignment download button on the page and wait for the
     # download to finish.
-    page.execute_script("$('.download-aln:eq(0)').click()")
+    page.first('.download-aln').click
     wait_for_download
 
     # Test name and content of the downloaded file.
@@ -222,7 +225,7 @@
     href = page.find('#sendEmail')['href']
     expect(href).to include('mailto:?subject=SequenceServer%20BLASTP%20analysis')
     expect(href).to include(page.current_url)
-    expect(href).to include(protein_databases.values_at(0).join() && '%20')
+    expect(href).to include(protein_databases.values_at(0).join && '%20')
   end
 
   it 'can show hit sequences in a modal' do
@@ -232,7 +235,7 @@
                    databases: protein_databases.values_at(0))
 
     # Click on the first sequence viewer link in the report.
-    page.execute_script("$('.view-sequence:eq(0)').click()")
+    page.first('.view-sequence').click
 
     within('.sequence-viewer') do
       page.should have_content('SI2.2.0_06267')
@@ -245,11 +248,12 @@
       SEQ
     end
 
-    # Dismiss the first modal.
-    page.execute_script("$('.sequence-viewer').modal('hide')")
+    # Dismiss the modal.
+    page.find('.sequence-viewer').send_keys(:escape)
+    expect(page).to have_no_css('.sequence-viewer')
 
     # Click on the second sequence viewer link in the report.
-    page.execute_script("$('.view-sequence:eq(1)').click()")
+    page.find_all('.view-sequence')[1].click
 
     within('.sequence-viewer') do
       page.should have_content('SI2.2.0_13722')
@@ -272,7 +276,7 @@
                    databases: nucleotide_databases.values_at(0))
 
     # Check that the sequence viewer links are disabled.
-    page.evaluate_script("$('.view-sequence').is(':disabled')").should eq(true)
+    expect(page).to have_selector('.view-sequence:disabled')
   end
 
   it 'can download visualisations in svg and png format' do
@@ -282,60 +286,66 @@
                    databases: protein_databases.values_at(0))
 
     ## Check that there is a circos vis and unfold it.
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > h4').click()")
-    sleep 1
+    page.find('.circos > .grapher-header > h4', text: 'Queries and their top hits: chord diagram').click
 
-    page.execute_script("$('.export-to-svg:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
-    clear_downloads
+    within('.circos.grapher') do
+      page.click_on('SVG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+      clear_downloads
 
-    page.execute_script("$('.export-to-png:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+      page.click_on('PNG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+    end
     clear_downloads
 
     ## Check that there is a graphical overview of hits.
-    page.should have_content('Graphical overview of hits')
-
-    page.execute_script("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.svg')
-    clear_downloads
-
-    page.execute_script("$('.export-to-png:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.png')
-    clear_downloads
+    expect(page).to have_content('Graphical overview of hits')
+
+    within('#Query_1 .alignment-overview.grapher') do
+      page.click_on('SVG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.svg')
+      clear_downloads
+
+      page.click_on('PNG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.png')
+      clear_downloads
+    end
 
     ## Check that there is a length distribution of matching sequences.
-    page.should have_content('Length distribution of matching sequences')
-    page.execute_script("$('.length-distribution > .grapher-header > h4').click()")
-    sleep 1
-
-    page.execute_script("$('.export-to-svg:eq(2)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.svg')
-    clear_downloads
-
-    page.execute_script("$('.export-to-png:eq(2)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.png')
-    clear_downloads
+    expect(page).to have_content('Length distribution of matching sequences')
+    page.find('#Query_1 .length-distribution > .grapher-header > h4',
+              text: 'Length distribution of matching sequences').click
+
+    within('#Query_1 .length-distribution.grapher') do
+      page.click_on('SVG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.svg')
+      clear_downloads
+
+      page.click_on('PNG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.png')
+      clear_downloads
+    end
 
     ## Check that there is a kablammo vis of query vs hit.
-    page.should have_content('Graphical overview of aligning region(s)')
-
-    page.execute_script("$('.export-to-svg:eq(3)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.svg')
-    clear_downloads
-
-    page.execute_script("$('.export-to-png:eq(3)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.png')
-    clear_downloads
+    expect(page).to have_content('Graphical overview of aligning region(s)')
+
+    within('#Query_1_hit_1 .kablammo.grapher') do
+      page.click_on('SVG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.svg')
+      clear_downloads
+
+      page.click_on('PNG')
+      wait_for_download
+      expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.png')
+      clear_downloads
+    end
   end
 
   ## Helpers ##