sequenceserver 2.0.0.beta1 → 2.0.0.beta3

data/spec/sequences/alignment-2_hits.txt

@@ -0,0 +1,12 @@
+>Query_1:1-199
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+>Query_1:1-199_alignment_SI2.2.0_06267:1-199
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+>SI2.2.0_06267:1-199
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+>SI2.2.0_13722:1-186
+MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP
+>SI2.2.0_13722:1-186_alignment_SI2.2.0_13722:1-186
+MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP
+>SI2.2.0_13722:1-186
+MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP

data/spec/sequences/sequenceserver-2_hits.fa

@@ -0,0 +1,10 @@
+>SI2.2.0_06267 locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
+TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
+KENKIKEGMKMMGLNDSVF
+>SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00
+MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC
+DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL
+TSYCGP

data/spec/spec_helper.rb

@@ -45,7 +45,7 @@ RSpec.configure do |config|
 
       # Suppress "open with / save" dialog for FASTA, XML, and TSV file types.
       options.profile['browser.helperApps.neverAsk.saveToDisk'] =
-        'text/fasta,text/xml,text/tsv'
+        'text/fasta,text/xml,text/tsv,image/png'
 
       Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
     end

data/views/layout.erb

@@ -94,8 +94,8 @@
         </a>
         <br>
         Please cite relevant data sources and:
-        <a href="http://www.biorxiv.org/content/early/2015/11/27/033142">
-          Priyam et al. (2015) Sequenceserver: a modern graphical user interface for custom BLAST databases</a>.
+        <a href="https://doi.org/10.1093/molbev/msz185">
+          Priyam et al. (2019) Sequenceserver: a modern graphical user interface for custom BLAST databases</a>.
       </p>
     </div> <!-- /container -->
   </div>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 2.0.0.beta1
+  version: 2.0.0.beta3
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-24 00:00:00.000000000 Z
+date: 2019-08-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -57,62 +57,62 @@ dependencies:
   name: sinatra
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.0'
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '2.0'
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: slop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.6'
     - - ">="
       - !ruby/object:Gem::Version
         version: 3.6.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.6'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.6'
     - - ">="
       - !ruby/object:Gem::Version
         version: 3.6.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.6'
 - !ruby/object:Gem::Dependency
   name: capybara
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: '3.15'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.12.0
+        version: 3.15.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: '3.15'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.12.0
+        version: 3.15.1
 - !ruby/object:Gem::Dependency
   name: capybara-screenshot
   requirement: !ruby/object:Gem::Requirement
@@ -134,45 +134,25 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 1.0.23
 - !ruby/object:Gem::Dependency
-  name: codeclimate-test-reporter
+  name: rack-test
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.8
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.8
-- !ruby/object:Gem::Dependency
-  name: rack-test
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -197,22 +177,22 @@ dependencies:
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.7'
     - - ">="
       - !ruby/object:Gem::Version
         version: 3.7.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.7'
     - - ">="
       - !ruby/object:Gem::Version
         version: 3.7.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.7'
 - !ruby/object:Gem::Dependency
   name: sauce_whisk
   requirement: !ruby/object:Gem::Requirement
@@ -239,20 +219,40 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.141'
+        version: '3.142'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.141.0
+        version: 3.142.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.141'
+        version: '3.142'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.142.3
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.141.0
+        version: 0.17.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.17.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.17.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.17.0
 description: |
   SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
   user interface for use locally or over the web.
@@ -3714,7 +3714,6 @@ files:
 - spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb
 - spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb
 - spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb
-- spec/capybara_spec.local.rb
 - spec/capybara_spec.rb
 - spec/config_spec.rb
 - spec/database/funky_ids/funky_ids.fa
@@ -3964,10 +3963,12 @@ files:
 - spec/sequences/Nucleotide_TP53_COX41.fasta
 - spec/sequences/Protein_TP53_COX41.fasta
 - spec/sequences/Query_1_SI2_2_0_06267.txt
+- spec/sequences/alignment-2_hits.txt
 - spec/sequences/nucleotide_query.fa
 - spec/sequences/problematic_query.fa
 - spec/sequences/protein_query.fa
 - spec/sequences/sample_query_fire_ant_obps.fa
+- spec/sequences/sequenceserver-2_hits.fa
 - spec/sequences/sequenceserver-SI2.2.0_06267.fa
 - spec/sequenceserver_spec.rb
 - spec/spec_helper.rb
@@ -4006,8 +4007,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.2.3
+rubygems_version: 3.0.1
 signing_key: 
 specification_version: 4
 summary: BLAST search made easy!

data/spec/capybara_spec.local.rb

@@ -1,190 +0,0 @@
-describe 'a browser', type: :feature, js: true do
-  it 'properly controls blast button' do
-    visit '/'
-
-    fill_in('sequence', with: nucleotide_query)
-    page.evaluate_script("$('#method').is(':disabled')").should eq(true)
-
-    check(nucleotide_databases.first)
-    page.evaluate_script("$('#method').is(':disabled')").should eq(false)
-  end
-
-  it 'properly controls interaction with database listing' do
-    visit '/'
-    fill_in('sequence', with: nucleotide_query)
-    check(nucleotide_databases.first)
-    page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
-      .should eq(true)
-  end
-
-  it 'shows a dropdown menu when other blast methods are available' do
-    visit '/'
-    fill_in('sequence', with: nucleotide_query)
-    check(nucleotide_databases.first)
-    page.save_screenshot('screenshot.png')
-    page.has_css?('button.dropdown-toggle').should eq(true)
-  end
-
-  it 'can run a simple blastn search' do
-    perform_search query: nucleotide_query,
-      databases: nucleotide_databases
-    page.should have_content('BLASTN')
-  end
-
-  it 'can run a simple blastp search' do
-    perform_search query: protein_query,
-      databases: protein_databases
-    page.should have_content('BLASTP')
-  end
-
-  it 'can run a simple blastx search' do
-    perform_search query: nucleotide_query,
-      databases: protein_databases
-    page.should have_content('BLASTX')
-  end
-
-  it 'can run a simple tblastx search' do
-    perform_search query: nucleotide_query,
-      databases: nucleotide_databases,
-      method: 'tblastx'
-    page.should have_content('TBLASTX')
-  end
-
-  it 'can run a simple tblastn search' do
-    perform_search query: protein_query,
-      databases: nucleotide_databases
-    page.should have_content('TBLASTN')
-  end
-
-  ### Test aspects of the generated report.
-
-  it 'can show hit sequences in a modal' do
-    # Do a BLASTP search. protein_query refers to the first two sequence in
-    # protein_databases[0], so the top hits are the query sequences themselves.
-    perform_search(query: protein_query,
-                   databases: protein_databases.values_at(0))
-
-    # Click on the first sequence viewer link in the report.
-    page.execute_script("$('.view-sequence:eq(0)').click()")
-
-    within('.sequence-viewer') do
-      page.should have_content('SI2.2.0_06267')
-      page.should have_content(<<~SEQ.chomp)
-        MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIP
-        LAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPIS
-        CRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
-        ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPL
-        YMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
-      SEQ
-    end
-
-    # Dismiss the first modal.
-    page.execute_script("$('.sequence-viewer').modal('hide')")
-
-    # Click on the second sequence viewer link in the report.
-    page.execute_script("$('.view-sequence:eq(1)').click()")
-
-    within('.sequence-viewer') do
-      page.should have_content('SI2.2.0_13722')
-      page.should have_content(<<~SEQ.chomp)
-        MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSA
-        VSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNK
-        RHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
-        EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYR
-        RESRGIHEECCINGCTINELTSYCGP
-      SEQ
-    end
-  end
-
-  it "can download hit sequences" 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 on the first FASTA download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.download-fa:eq(0)').click()")
-    wait_for_download
-
-    # Test name and content of the downloaded file.
-    expect(File.basename(downloaded_file)).
-      to eq('sequenceserver-SI2.2.0_06267.fa')
-    expect(File.read(downloaded_file)).
-      to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
-  end
-
-  it "can download alignment for each hit" do
-    # Do a BLASTP search. protein_query refers to the first two sequence in
-    # protein_databases[0], so the top hits are the query sequences themselves.
-    perform_search(query: protein_query,
-                   databases: protein_databases.values_at(0))
-
-    # Click on the first Alignment download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.download-aln:eq(0)').click()")
-    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"))
-  end
-
-  it 'disables sequence viewer links if hits are longer than 10kb' do
-    # BLASTN transcripts against genome. nucleotide_query refers to two fire
-    # ant transcripts and nucleotide_databases[0] is subset of the fire ant
-    # genome (few longest scaffolds). We expect sequence viewer links to be
-    # disabled for all hits of this search.
-    perform_search(query: nucleotide_query,
-                   databases: nucleotide_databases.values_at(0))
-
-    # Check that the sequence viewer links are disabled.
-    page.evaluate_script("$('.view-sequence').is(':disabled')").should eq(true)
-  end
-
-  ## Helpers ##
-
-  def perform_search(query: , databases: , method: nil)
-    # Load search form.
-    visit '/'
-
-    # Fill in query, select databases, submit form.
-    fill_in('sequence', with: query)
-    databases.each { |db| check db }
-    if method == 'tblastx'
-      find('.dropdown-toggle').click
-      find('.dropdown-menu li').click
-    end
-    click_button('method')
-
-    # Switch to new window because link opens in new window
-    page.driver.browser.switch_to.window(page.driver.browser.window_handles.last)
-
-    # It is important to have this line or the examples end prematurely with a
-    # failure.
-    page.should have_content('Query')
-  end
-
-  def nucleotide_query
-    File.read File.join(__dir__, 'sequences', 'nucleotide_query.fa')
-  end
-
-  def protein_query
-    File.read File.join(__dir__, 'sequences', 'protein_query.fa')
-  end
-
-  def nucleotide_databases
-    [
-      'Solenopsis invicta gnG subset',
-      'Sinvicta 2-2-3 cdna subset'
-    ]
-  end
-
-  def protein_databases
-    [
-      'Sinvicta 2-2-3 prot subset',
-      '2018-04 Swiss-Prot insecta'
-    ]
-  end
-end