capybara_spec.rb in sequenceserver-2.0.0.beta4

- old
+ new

@@ -12,55 +12,54 @@
   it 'properly controls interaction with database listing' do
     visit '/'
     fill_in('sequence', with: nucleotide_query)
     check(nucleotide_databases.first)
     page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
-      .should eq(true)
+        .should eq(true)
   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.save_screenshot('screenshot.png')
     page.has_css?('button.dropdown-toggle').should eq(true)
   end
 
   it 'can run a simple blastn search' do
     perform_search query: nucleotide_query,
-      databases: nucleotide_databases
+                   databases: nucleotide_databases
     page.should have_content('BLASTN')
   end
 
   it 'can run a simple blastp search' do
     perform_search query: protein_query,
-      databases: protein_databases
+                   databases: protein_databases
     page.should have_content('BLASTP')
   end
 
   it 'can run a simple blastx search' do
     perform_search query: nucleotide_query,
-      databases: protein_databases
+                   databases: protein_databases
     page.should have_content('BLASTX')
   end
 
   it 'can run a simple tblastx search' do
     perform_search query: nucleotide_query,
-      databases: nucleotide_databases,
-      method: 'tblastx'
+                   databases: nucleotide_databases,
+                   method: 'tblastx'
     page.should have_content('TBLASTX')
   end
 
   it 'can run a simple tblastn search' do
     perform_search query: protein_query,
-      databases: nucleotide_databases
+                   databases: nucleotide_databases
     page.should have_content('TBLASTN')
   end
 
   ### Test aspects of the generated report.
 
-  it "can download FASTA of each hit" do
+  it 'can download FASTA of each hit' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
                    databases: protein_databases.values_at(0))
 
@@ -68,17 +67,17 @@
     # download to finish.
     page.execute_script("$('.download-fa:eq(0)').click()")
     wait_for_download
 
     # Test name and content of the downloaded file.
-    expect(File.basename(downloaded_file)).
-      to eq('sequenceserver-SI2.2.0_06267.fa')
-    expect(File.read(downloaded_file)).
-      to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
+    expect(File.basename(downloaded_file))
+      .to eq('sequenceserver-SI2.2.0_06267.fa')
+    expect(File.read(downloaded_file))
+      .to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
   end
 
-  it "can download FASTA of selected hits" do
+  it 'can download FASTA of selected hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
                    databases: protein_databases.values_at(0))
 
@@ -87,28 +86,28 @@
     page.check('Query_2_hit_1_checkbox')
     page.click_link('FASTA of 2 selected hit(s)')
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sequenceserver-2_hits.fa'))
   end
 
-  it "can download FASTA of all hits" do
+  it 'can download FASTA of all hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
                    databases: protein_databases.values_at(0))
 
     # Click 'FASTA of all hits'.
     page.click_link('FASTA of all hits')
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sequenceserver-2_hits.fa'))
   end
 
-  it "can download alignment for each hit" do
+  it 'can download alignment for each hit' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
                    databases: protein_databases.values_at(0))
 
@@ -117,15 +116,15 @@
     page.execute_script("$('.download-aln:eq(0)').click()")
     wait_for_download
 
     # Test name and content of the downloaded file.
     expect(File.basename(downloaded_file)).to eq('Query_1_SI2_2_0_06267.txt')
-    expect(File.read(downloaded_file)).
-      to eq(File.read("#{__dir__}/sequences/Query_1_SI2_2_0_06267.txt"))
+    expect(File.read(downloaded_file))
+      .to eq(File.read("#{__dir__}/sequences/Query_1_SI2_2_0_06267.txt"))
   end
 
-  it "can download Alignment of selected hits" do
+  it 'can download Alignment of selected hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
                    databases: protein_databases.values_at(0))
 
@@ -134,25 +133,25 @@
     page.check('Query_2_hit_1_checkbox')
     page.click_link('Alignment of 2 selected hit(s)')
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-2_hits.txt'))
   end
 
-  it "can download Alignment of all hits" do
+  it 'can download Alignment of all hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
                    databases: protein_databases.values_at(0))
 
     # Click 'Alignment of all hits'.
     page.click_link('Alignment of all hits')
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-2_hits.txt'))
   end
 
   it 'can download BLAST results in XML and tabular formats' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
@@ -230,11 +229,11 @@
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
                    databases: protein_databases.values_at(0))
 
     ## Check that there is a circos vis and unfold it.
-    page.should have_content('Circos')
+    page.should have_content('Chord diagram: queries and their top hits')
     page.execute_script("$('.circos > .grapher-header > h5').click()")
     sleep 1
 
     page.execute_script("$('.export-to-svg:eq(0)').click()")
     wait_for_download
@@ -244,11 +243,10 @@
     page.execute_script("$('.export-to-png:eq(0)').click()")
     wait_for_download
     expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
     clear_downloads
 
-
     ## Check that there is a graphical overview of hits.
     page.should have_content('Graphical overview of hits')
 
     page.execute_script("$('.export-to-svg:eq(1)').click()")
     wait_for_download
@@ -258,11 +256,10 @@
     page.execute_script("$('.export-to-png:eq(1)').click()")
     wait_for_download
     expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.png')
     clear_downloads
 
-
     ## Check that there is a length distribution of hits.
     page.should have_content('Length distribution of hits')
     page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
     sleep 1
 
@@ -290,10 +287,10 @@
     clear_downloads
   end
 
   ## Helpers ##
 
-  def perform_search(query: , databases: , method: nil)
+  def perform_search(query:, databases:, method: nil)
     # Load search form.
     visit '/'
 
     # Fill in query, select databases, submit form.
     fill_in('sequence', with: query)