sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/dotdir/diamond_0.9.24/blastx/job.yaml

@@ -0,0 +1,8 @@
+--- !ruby/object:SequenceServer::BLAST::Job
+id: 'diamond_0.9.24/blastx'
+submitted_at: 2019-06-18 15:49:12.135304300 +01:00
+imported_xml_file: DIAMOND_BLASTX_0.9.24.xml
+advanced_params: {}
+databases: []
+completed_at: 2019-06-18 15:49:12.144588000 +01:00
+exitstatus: 0

data/spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml

@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastx</BlastOutput_program>
+  <BlastOutput_version>diamond 0.9.24</BlastOutput_version>
+  <BlastOutput_reference>Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), &quot;Fast and sensitive protein alignment using DIAMOND&quot;, Nature Methods 12:59-60.</BlastOutput_reference>
+  <BlastOutput_db>nr.dmnd</BlastOutput_db>
+  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
+  <BlastOutput_query-def>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1</BlastOutput_query-def>
+  <BlastOutput_query-len>704</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>blosum62</Parameters_matrix>
+      <Parameters_expect>0.001</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>F</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+<BlastOutput_iterations>
+<Iteration>
+  <Iteration_iter-num>1</Iteration_iter-num>
+  <Iteration_query-ID>Query_1</Iteration_query-ID>
+  <Iteration_query-def>SI2.2.0_13722 Si_gnF.scaffold06207[1925625..1928536].pep_1</Iteration_query-def>
+  <Iteration_query-len>704</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>459708</Statistics_db-num>
+      <Statistics_db-len>170771147</Statistics_db-len>
+      <Statistics_hsp-len>0</Statistics_hsp-len>
+      <Statistics_eff-space>0</Statistics_eff-space>
+      <Statistics_kappa>0.041000</Statistics_kappa>
+      <Statistics_lambda>0.267000</Statistics_lambda>
+      <Statistics_entropy>0</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+</BlastOutput_iterations>
+</BlastOutput>

data/spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml

@@ -0,0 +1,8 @@
+--- !ruby/object:SequenceServer::BLAST::Job
+id: 'diamond_0.9.24/blastx_nohits'
+submitted_at: 2019-07-01 14:20:40.624064600 +01:00
+imported_xml_file: DIAMOND_BLASTX_NOHITS_0.9.24.xml
+advanced_params: {}
+databases: []
+completed_at: 2019-07-01 14:20:40.627058200 +01:00
+exitstatus: 0

data/spec/download_helper.rb

@@ -0,0 +1,32 @@
+# Based on https://stackoverflow.com/a/29544674
+module DownloadHelpers
+  def downloads_dir
+    File.join(__dir__, 'downloads')
+  end
+
+  def wait_for_download
+    Timeout.timeout(Capybara.default_max_wait_time) do
+      sleep 1 until downloaded?
+    end
+  end
+
+  def downloaded_file
+    downloads.first
+  end
+
+  def clear_downloads
+    FileUtils.rm_f(downloads)
+  end
+
+  def downloaded?
+    !downloading? && downloads.any?
+  end
+
+  def downloading?
+    downloads.grep(/\.part$/).any?
+  end
+
+  def downloads
+    Dir[File.join(downloads_dir, "*")]
+  end
+end

data/spec/import_spec_capybara_local.rb

@@ -0,0 +1,61 @@
+require 'spec_helper'
+require 'sauce_whisk'
+require 'capybara/rspec'
+require 'selenium-webdriver'
+
+RSpec.configure do |config|
+  config.include Capybara::DSL
+end
+
+SequenceServer::DOTDIR = File.join(__dir__, 'imported_xml_reports')
+
+describe 'report generated from imported XML', :js => true do
+  before do |scenario|
+    Capybara.app = SequenceServer.init
+    Capybara.server = :webrick
+    Capybara.javascript_driver = :selenium
+    Capybara.default_max_wait_time = 10
+
+    options = ::Selenium::WebDriver::Firefox::Options.new
+    options.args << '--headless'
+    Capybara.register_driver :selenium do |app|
+      Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
+    end
+  end
+
+  # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
+  it 'loads BLASTP xml output' do
+    access_by_uuid('ea347d79-6397-44e5-9048-c90e58c56200')
+  end
+
+  it 'loads BLASTX xml output' do
+    access_by_uuid('e39d30a2-304f-4b85-ad1c-a114cc0b383f')
+  end
+
+  it 'loads BLASTN xml output' do
+    access_by_uuid('85ca3be1-b495-43d3-b267-2e50aced9cc7')
+  end
+
+  it 'loads TBLASTN xml output' do
+    access_by_uuid('148e0664-4ab8-41af-86cb-127ff19f2d33')
+  end
+
+  it 'loads TBLASTX xml output' do
+    access_by_uuid('752b6b87-2670-47a0-aa57-d0dc8cdd7667')
+  end
+
+  it 'loads diamond_BLASTP xml output' do
+    access_by_uuid('043110ae-faf9-4258-8098-3384fb16fbb1')
+  end
+
+  it 'loads diamond_BLASTX xml output' do
+    access_by_uuid('8e400eed-4ef2-48e6-aee8-a55a45606e77')
+  end
+
+  ## Helpers ##
+
+  def access_by_uuid(id)
+    visit "/#{id}"
+    page.should have_content('Query')
+  end
+end

data/spec/sequence_spec.rb

@@ -41,8 +41,7 @@ module SequenceServer
   end
 
   describe 'Sequence retrieval' do
-    root = SequenceServer.root
-    database_dir = File.join(root, 'spec', 'database')
+    database_dir = File.join(__dir__, 'database')
 
     let 'a_normal_database_id' do
       Digest::MD5.hexdigest File.join(database_dir, 'sample', 'proteins',

data/spec/sequences/Nucleotide_TP53_COX41.fasta

@@ -0,0 +1,15 @@
+>MH011443.1 Homo sapiens TP53 (TP53) gene, exon 5 and partial cds
+TGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCGTGGCCATCTACAAGCAGTCACAGCACA
+TGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGAT
+>NM_001861.5 Homo sapiens cytochrome c oxidase subunit 4I1 (COX4I1), transcript variant 1, mRNA
+CTCTTCCGGTCGCGGGACACCGGGTGTAGAGGGCGGTCGCGGCGGGCAGTGGCGGCAGAATGTTGGCTAC
+CAGGGTATTTAGCCTAGTTGGCAAGCGAGCAATTTCCACCTCTGTGTGTGTACGAGCTCATGAAAGTGTT
+GTGAAGAGCGAAGACTTTTCGCTCCCAGCTTATATGGATCGGCGTGACCACCCCTTGCCGGAGGTGGCCC
+ATGTCAAGCACCTGTCTGCCAGCCAGAAGGCATTGAAGGAGAAGGAGAAGGCCTCCTGGAGCAGCCTCTC
+CATGGATGAGAAAGTCGAGTTGTATCGCATTAAGTTCAAGGAGAGCTTTGCTGAGATGAACAGGGGCTCG
+AACGAGTGGAAGACGGTTGTGGGCGGTGCCATGTTCTTCATCGGTTTCACCGCGCTCGTTATCATGTGGC
+AGAAGCACTATGTGTACGGCCCCCTCCCGCAAAGCTTTGACAAAGAGTGGGTGGCCAAGCAGACCAAGAG
+GATGCTGGACATGAAGGTGAACCCCATCCAGGGCTTAGCCTCCAAGTGGGACTACGAAAAGAACGAGTGG
+AAGAAGTGAGAGATGCTGGCCTGCGCCTGCACCTGCGCCTGGCTCTGTCACCGCCATGCAACTCCATGCC
+TATTTACTGGAAACCTGTTATGCCAAACAGTTGTACCACTGCTAATAAATGACCAGTTTACCTGAAACCC
+TTTGTGATCAGTTCTTTAATGATACCTAAATGAAAGCTAATTAAAACAA

data/spec/sequences/Protein_TP53_COX41.fasta

@@ -0,0 +1,12 @@
+>sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens OX=9606 GN=TP53 PE=1 SV=4
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
+DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
+SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
+RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
+SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
+PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
+GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>sp|P13073|COX41_HUMAN Cytochrome c oxidase subunit 4 isoform 1, mitochondrial OS=Homo sapiens OX=9606 GN=COX4I1 PE=1 SV=1
+MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQK
+ALKEKEKASWSSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMW
+QKHYVYGPLPQSFDKEWVAKQTKRMLDMKVNPIQGLASKWDYEKNEWKK

data/spec/sequences/Query_1_SI2_2_0_06267.txt

@@ -0,0 +1,6 @@
+>Query_1:1-199
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+>Query_1:1-199_alignment_SI2.2.0_06267:1-199
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+>SI2.2.0_06267:1-199
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF

data/spec/sequences/problematic_query.fa

@@ -0,0 +1,5 @@
+>PB10005-PA maker-pbar_scf7180000346129-snap-gene-0.2-mRNA-1 protein AED:0.0281413612565444 QI:53|1|0.5|1|1|1|4|-1|223
+MKQLACILIALAIVGVYGEDPEKLVNGYPVNIEDNPQCVSIQVRGSHFCGGSIISDRYIL
+TAGHCVDGLNPYRLPSAVVVTGTSRLSSGGQSFKIKRMVLHENYNARTMDGYDIGLIELA
+TPIQFNARQRPVCLTTRRAAQNDPVKITAWGSTGYRQNVHDDLRQLTAVVMPPNVCRPYH
+QRIMSINEKEFCTLIRSGTGACNGDSGSGVVRTTDGCIIGLVS

data/spec/sequences/protein_query.fa

@@ -0,0 +1,9 @@
+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/sequences/sample_query_fire_ant_obps.fa

@@ -0,0 +1,44 @@
+>SiOBP1-mRNA [organism=Solenopsis invicta]
+ATGCACGTGTCGGTGATTCTCGGCGTAGTGTTGCTACAGGCGATTTACGTGTCCGCCGCGCCACCCGACTGGATACCCCCGGAAATGTTGGAGATGGTTCAAGGTGACAAGGAGCGATGCATGGCCGAACACGGAACGAGTCAAGCGCTTATTGACGAAGTTAACGATGGGAAACTCTCGAATGACCGGTCTATCACGTGCTACATGAACTGCCTTCTCGACGCCTTCAGTTTGGTCGATGAAGACGGTAATTTGGAAGCTGAGATGCTGATAAGTGTTATCCCGGAAGAATTTCAAGAGATAGGTAACAAGATTTTGAACAAATGCGCCGTACAAGACGGCGCGGATAAATGCGAAAAGATCTACAATGTGGCGAAATGCGTCCAAGGAACAGTACCAGAGCTGTGGTTTATGGTTTAA
+>SiOBP2-mRNA [organism=Solenopsis invicta]
+ATGGAGAAGGTCGCGTTTTTCGTTTTAGCACTCATTGCTGTCGTAGTTGCAAATGAGATTGTAGAAGAGATGGCAAAGAAATTCGAGACCGATTCAGCAACAGTACAGAAATGTCTGGATGACACTGGAATTACGATGGAGGAATTAGGTACTTCATTGAAAGAGTGGGCCGAATTAAAGGACGAAGATATCAATGAAATGACTAAACAATCTCTTATGAAATACGTTAATTTCCTGGCTTGTATGATGGAGAAGAATGAAATGATGATCGATTCGAAATTGGTTGTTGACAAAATCGTTGAAAGTGCTCAAAATGACAAGGATCTCTTACCACCTGTACCAAAGGAAGTTCTAACGGAATGCCTGACTGCATTGAACGAAAATAGCGAAATATCTCGAGAAGACAGAGTCTTTGGTTTAATGTTTTGCATGATGGATGGTCAAACGGACAAAAAATAA
+>SiOBP3-mRNA [organism=Solenopsis invicta]
+ATGAAGACGTTCGTATTGCATATTTTTATTTTTGCTCTCGTGGCTTTCGCTTCTGCATCTCGTGATAGCGCGAGGAAGATAGGATCCCAATATGACAATTACGCGACTTGCTTAGCCGAACATAGTCTAACAGAGGATGACATCTTCTCGATTGGTGAAGTATCAAGTGGCCAGCACAAAACCAATCATGAAGATACCGAACTACACAAAAATGGTTGCGTCATGCAATGTTTGTTAGAAAAAGATGGACTGATGTCTGGAGCTGATTATGATGAAGAGAAAATGCGTGAGGACTATATCAAGGAAACAGGTGCTCAACCAGGAGATCAAAGGATAGAAGCTCTGAATGCCTGCATGCAAGAAACAAAAGaCATGGAGGATAAATGTGACAAAAGCTTGCTCCTTGTAGCATGTGTCTTAGCAGCTGAAGCTGTGCTCGCCGATTCTAACGAAGGAGCATAA
+>SiOBP4-mRNA [organism=Solenopsis invicta]
+ATGAAAACGCTCGTATTTCATATTTTCATTTTTGCTCTCATAGCTTTTGCCTCTGCATCTTGTAATAGCGCAAAGAAGATAGGATCCCACTATGACCATTACCAAACTTGCTTAACCGAACTTGGTGTAACAGAGGATGAGCTCTTCTCGGTTGGTGAAGTAACAAATGGCCAGCACAAAACCAAGCATGAAGATACCAAACAACACAAGAATGGTTGCATCATGCAATGTGTGTTTGAAAAATTGGGACTAATGATTGGAGCGGATTTTGATGAAGAGAAAATGCGTGAGTATTATATTAAGGAAAAAGGTCTTCAACCAGGAGATCAAAGAATAGATTTTCTGAGTAGCTGCATGGAACAAACAAAAAACATGGAAGATAAATGTGACAAAAGCTTGGGCTTTATAGGATGTGTCTTAATGAACGAAGTTAGTCTCCCCGCTTCTAACGAAGAAGCATGA
+>SiOBP5-mRNA [organism=Solenopsis invicta]
+ATGTGCGCGCGTTTACTAATCTGCATGATTACAATTGCGCTATTCGCAGTACATCAAACAAATGCTGCAATGACAATGGAACAAATTGAAAAAACCGCGCTAAACGTGCGAAATACGTGTACGTCGAAATCTCATGCAGACCCTGGAGCTGTCGCAGGAATACAAAATGGCGTATTTCCAGATGACAATAAACCTTTGAAATGCTATACACTATGTGTAATGAAGACAATGCGAACTTTCAAAAATGGACGCATAGATGACGGTATGATGATTAAaCAAGTGGATCTAATGTTGCCAGCTGAAATGGCGGGTCCTTTGAAAGCAGTTGCGACTAAATGCGCAGCAGAACCACCTACTGGCGATGATTGCTCAACCACTTATCAGTTTGTGAAATGTAGTTATTCCACGGATCCAGATCACTTCTTCTTTCCTTAA
+>SiOBP6-mRNA [organism=Solenopsis invicta]
+ATGAAAGAAACTGGTACAATCTTCTTCATTTCGCTTGTGTTTATGGCAAATCTTCAAAATATCGAGAGTAAAAGATATACCTTCGAAGATATAAAGGTGGCTCTGGAACCATTGAAGAAACATTGCATTGATAGAGTGGGCAAGGATCAAAAGGTGATCGATGATGCAAACAATTTTAAAATAGTACCGGACTGGAAAACGCAATGTTACTATAAGTGTATAATGCTGAATACAAAAATGATGAAAAATGATAAGATAGTCGAAAAAGCTTTAATAAATATAGCGGAACACATGTTACTGGAGGAATATTTGCCAGTTGTCGTAAAAACGATAGAACAATGTCATTCAACTGCAACTAAATCGATGGAAGGATGTGCGTTAGCATACGAATATTACAAATGCCTCTATGATGTTAATCCAACGATTGCCATGTATGCATGA
+>SiOBP7-mRNA [organism=Solenopsis invicta]
+ATGAAAGCAATCATTATCGTGCTTGCCATTTCTTTTGTTGCTGTTTTGGGTCAACTCACAGATGAACAAAAAGCAAAATTGAGAACGTACAAGGAATCCTGTATCAATGAATCTGGTGTCGATACTACCATACTTGAAAATGCAAAAAAAGGAGAGGTAGCTGAAAGTGACGAAAAGCTTGCTTGTTTCAGTACCTGTTTGTTAAAGAAAATCGGAATTATGAATGCGGATGAAGACATTAACTGGGAAGTAGCTCGTGCTAAATTGCCACCAGGCGTACCGCAAGAACAGGCCGATCAAATATATAATGCCTGCAAAGACATTACTGGAACAGGTTGTGAAAAAGGAGGCAAAGTGTTCAAATGCTTCTTGGACAACAAACATTTTCATCTTTTATCATAA
+>SiOBP8-mRNA [organism=Solenopsis invicta]
+ATGCATCATAGTGCAAGTACTCATGCTATTGCTATCTTTATGTCGGTAATATATATCCTCTTTGTGGTTgTTATTATTACTCGTTTCAAAGAGaCATACTTGTCTGAAAATAGTCCATTCACAGAGAAGGAAACAGAAAAATTAAGAGGCTACAGAACATTATGTATGAACAAATATGATGTTGATACGACAATAATTaAAAAAGCAAAGGAAATGGAAAACATAATTGATTATATTGACGAAAGACTTGTTTCCTATGTTATTTGTTTATATaAAAACTGGGGAATTATAAATGCAGATGGACACATTGACTGGAAGGTAACTCTTTCTATGTTGCCAGGTGTACCACAAAAAGTATTCAATGAAATATACAGTGCATGCAATCGTACCACTGGTACGGATTATGAAAGAGGATACGAGTTATTTAAGTGCTTCTTACAAAACGAAGTAGATCTTCTATAA
+>SiOBP9-mRNA [organism=Solenopsis invicta]
+ATGAAAATTATAAATATATTACTTGTTATTTTATTCCTTCTGTTAGTTGGAGCACGAGCGGACATTAAACGAGAATGTCGCCAACAAACAAATGTGTCTTGGGCATCTTTAAAGCAATTAAAGGCTGGAAACATTGAACAAAATGATATGAAATTAAAATGCTATTTGAAATGCTTTATGGTGAAAATTGGTATTCTTAATGAAGACAGCAATGTAGATGTTGAAAAAGCTCTGCGTCATTTGCCGCGCAGTATGCAAGAATCATCAAAAAGAATTCTTAATCAATGTAAATTGATCCAAGCGGAGAATGCATGCGATAGAGCATTTCAAATAGCTATATGTTACGTTAAAGCGCAACCTGAAATCTTAAAAAACGTATCGTTTATTTAA
+>SiOBP10-mRNA [organism=Solenopsis invicta]
+ATGAGGCTCCTCACGGTCGCCTTGGGTTTCCTCCTTCAGGCGTGGATCGTGTACTGCGGGACGAAGAGACCCAGCTTCGTTTCCGAGCAGATGATCGCGACCGCAGCGAGTGTCGTAAACGCCTGCCAAACGCAAACGGGAGTCGCCACAGCTGACATAGAAGCAGTAAGAAACGGACAGTGGCCGGAAACACGTCAATTGAAGTGCTATATGTATTGCCTCTGGGAGCAATTTGGTCTGGTCGACGACAAGAGAGAGCTAAGTCTGAACGGGATGCTGACGTTCTTCCAGAGAATACCCGCTTACAGAGCCGAGGTTGAGAAAGCAATCGGCGAGTGCAAGGGGCTCGCAAAGGGTGATAACTGCGAGTACGCGTACGCGTTTAACAAGTGTTACGCGCAGCTATCTCCGAGGACTTACTATCTATTCTAA
+>SiOBP11-mRNA [organism=Solenopsis invicta]
+ATGGCAAGAAAAAGCCTAATTCTCGTCTGTGTCTCTGTGGTTCTCACGCAGCTCGTCGTTGTGAGTTTTAGTGCCAAAACAGATGAAATAGATTGGACTACTGTTCATGATGATCTAAGAAAACTGGGTGCTACTTTTCGAAAAAAATGTTTAGCAGAGACTGGCGTGACGATTGATAAGTTAGAAGGAGCAGAAATGGGTCAATTTCCGGATGACAGAAAATTGGCATGTTATTTCAAATGCGTGATGGAAAAAGGCGGAGTGATGAAAAAGGATGGCACTATAAACTACAAAGTATTGGCCAAATtGCTTCCGCAAGCATATAAACAAATTGGAATAGACATGATGGATGAGTGTCGCGATATAGAGGGTAGCGACAGTTGTGAGAAAGGCATGAAATTTCATCAATGCATGTACAACGCAAATCCTGTGGCGTTCTTCGTTATCTAG
+>SiOBP12-mRNA [organism=Solenopsis invicta]
+ATGAAACATCTAGTGCTGTGCGCATGTGTTTTGTTATTCACTTTTTAGTTGTCTAACTCATCAGAACTAAAACAAAAGATTCAAGAAGAAGTAAAGATCAAGCAACGGATTGATTTTGAAGCTTGCTTGAGTGAAAATGGTATAAATGAAAGTGACTTGTACGGTCCGACAGAAATAGTGTCTAATGTACATACCGAAACAGCAAATGAAGAAAAAACGAGAAAGAATGGCTGCTTTATGGCGTGTTTTTTAAAAAAACAAAATTTAATGGAAGGAACCAACATTAAAGAAGATGAAGTTATTGCACGATTAAATGAAGTAGTAGTTACTGATGATGTTGaAAAAAAATTGCGCACAATTGTGCGTAAATGCATaAAAGAAAAGAAGGACATTACGCAAGAATGTGATAAATGTTTCTCTATATACGTATGTATTATAAAAGCTGTAAGTGAAGAAAGAAAATGTATGCAGGAAGAAAACGTAAGAACTGAAGAAGAAGAAACAGGAGAACCAAATAAAAAGAAGTAG
+>SiOBP13-mRNA [organism=Solenopsis invicta]
+ATGAAACATCTAGTGCTGTGCGCATGTGTTTTGATATTTGCTTTGTCTAACGCAACAGAAATACAACAAGAGATCCAAAATGAGATCAAACTACGGCTTGATTTAGAAGCTTGCTTGATTGAAAATGGTTTAAATAACAGTGGCTTGTACAGTATGAACGAAGTATCCATTAACGTACATACCAAACCAGGAAATGAAGAAAGAACGAGAAAGAATGGCTGCTTTATGGCGTGTGTTTTGAAAAAACAAAATTTAATGGAAGGAACAAACATTAAAGAAGACGAAGTTATTGCACGATTATATGAATTAACTAGGCAAGATTTAAAAGTGATATTGGGCAAAATTGTGCGAAAATGCCTAGAAGAAAAGAGGGATATTACGCAAGAATGTGCTAAATGTTTCTCTATATTCGAATGCATAATACAAACTATGGATAAATTCCCAAGAGAACATGAACATGAAGAAATCGTAACAACTGAATGA
+>SiOBP14-mRNA [organism=Solenopsis invicta]
+atgaaaggtttcatactctgggTCTGTGtttttAtttttgctTCGTCTAGTTCGTCAAAACTAAAAGAAGAGAAACACATAAATACAAATGTAAGAGCTATTCAAGATGAAATTAAACCTTGTTTAAGTGAAATTGGTATAGCTTATGAGGCTTTATACCCACCAGCCGAAATAATAGCTAACGTACATACTCAACCAGCAAATAAAGAAAGAACGAAAAATCATGGCTGTTTCATGGCGTGTGTTTTGAAAAAACAGAATTTAATAGAAGGAACAAACATTAAAGAAGCACAAGTTTATTCAAGGTTACATGAAATACTTGACGAAGAACTTGATGGACCAGGACACCAAATTATACGTAAATGCATGGAAGAAGTGAGGAATATGACACAAGAATGTGAGAAAGGTTTTTCTCTGTACGTATGTATCGTAAAAGAAGCGGCTGCGCATGAAGAAGAAGCAAAACGTCAGAAAAATaAAAAAAATTGA
+>SiOBP15-mRNA [organism=Solenopsis invicta]
+ATGAAAACTTTCGTACTTTGTGCTTGCGTCTTCGTTCTTGCTGTATACTTTCAGTCGTCTAGTTCATCAGAACTAAATGAACAAGAACTCAGAAAGATAGGAATATCTATTCGGAATGATTTTAACACTTGCCTCAGTGAAATTGGTATAACTCCTGCTGACTTTGTCAAACCGATGGAAATAGTTACTAACGTACATCTGCAACCTGCAAATGAAGAAAGAACAAACAAACATGGCTGCTTTATAGCGTGTGTTTTAAAGAAACAGAATTTGATTGAAGGAACAAAGATTAAAGAAGAGCAAGTTTATGAAAGATTACAATTAATATTTGACGAAAATCCTGGCGGACCAATGCACCAAATTGTACAAAAATGCATGGAAAAAGTGAGGAATGACGCACAAGAATGTGAGAAATGCTTCTCTGTCTATGTTTGTACCATCAAAGATATGTATGAAGAAGAACAACGCAGAAAAAATGAAAGAAACTAA
+>SiOBP16-mRNA [organism=Solenopsis invicta]
+ATGAAAAGTCTCGTGCTTTGCGCCTGTGTTTTATTACTTGCTTTTCAGCTGTCTAGCTCAACAGAACTTAAAGAAAAGCTAAAGAATGAAGAAAAAAATATTGAGAATATTCTTGAAACTTGTCTAAATGAACAGGGTTTATCTCGGAATGACATGTACAAGGAGGAGGAACTAATGACTAAAGTACATACTGAATCTGTGAATGCAGAAAGAACAAGAAAAGTTGGTTGCTTTGTTGCATGTGCCATGGAAAAGCTGAATTTAATGGATGAAGCAACCATTAAGGAAACACAAATTCATGaAAAAATAAATGAACTATTTGAAGGTCGTGACCAAGGTATAGCACACAAAATTGCGCGTAAATGTTTaAAAAAAGCGAGAAGTATTACGCAAAAATGTGAGAAATGTTTTTCTCTATACGTATGCATCGCAGAAAGTGTGCATAAATTACAAGGACACGAAGAACATGTAAGAGAAGAAACAGAAGAGATAGAAGAAACAGAAGAACAGATCTAA
+>SiOBPZ1-mRNA [organism=Solenopsis invicta]
+ATGACCAGACTGCTCCTCGTTGTCCTGTTCAGCCTTTGCTTGTTGCTGATAGAATCAGTAAATTCATTAAAATGCAGAACAGGTATTCAGCAGACGGACGATCAATACCGCAAGATTATGCAAACTTGCAAGAAACGATTTACGACCGATGATGATGACGACGACGATTATAGCAATGATTCATCATCAAATGAAAATGACGATAATGATTCTTCAAGCGTAGATTTATTTGGTACAAGGTTCTTCGTGAGTGGCGGTAGCAAGTTTTCCAATATGCGCTCTTGGAAAGATCCTAATGAAAATCGGAATCGAGGAAATGATCAGAGAAATGGTAACGACCGACGCTATTCCGTCAGTTATACAAATGGGAATTGGAAAAATGCTCAATATCCTTTTCAAGGCAGCAATAATCGCGATTATAGTTATTCTGAGGGAGCTGGCAGACCAAGCTATGACCAAATGTATAATGGCAACTCTGAGAATTATGATAAGCAACAAAAACAAACCTGCATCAATCAGTGTTTCTTCAACGAATTAAATATGGTAGATCAAAGGGGTTTCCCAGAGCAAGTTTCGGTCATCCAATTTTTGACACGTAATATACACAACCCAGAATTACAGGACTTTATAGAGGAAGCTGTCATAGAATGTTTTCATTATTTGAATTCAGATATAAGGCAAAACAAATGTTATTTCTCAGAAAATCTCGTGACTTGTTTGATTGATAAAGGAAAGGAAAGATGCGAAGATTGGGATAATTAA
+>SiOBPZ2-mRNA [organism=Solenopsis invicta]
+ATGAAAGCAATCATTATCGTGCTCACCATTTCTTTCATCGCCGTTTTGGGAGATCAACTCAGAGATGAACAAAAaGTAAAATTGAGAGGGTACAAAGAATCCTGTATTAACGAATCTGGTGTCGATATTACCGTAATTGAAAATGCAAAGAAaGGAAAAATAGCTGAAAATGACAAAAAGTTTGCTTGTTTTGCTACCTGTTTGCTAAATAAAGCCAGAATTATGAATGCAGATGGAGACGTTGACTGGGACCGAGCTCGTTTTATATTTTCAAGTATACCACAAGAACGACTTGATGAAATTTATGATGCATGCAAACACATTACTGGAACAGGTTGTGAAAAGGGAGGCAAACTGTTTAAATGTTTCATCGACAACAACATTAATATTTTATAA
+>SiOBPZ3-mRNA [organism=Solenopsis invicta]
+ATGAAAAGTCTCGTGCTTTGTGCCTGTGTTTTAGTACTTGCTTTTCAGCCGTCTAGCTCAACAAAACTAAAACAAAAGCTAAAGAATGAAATAGACAATCTTCGCGATAATATTGAAATTTGCGTATTTGAACAGGGTTTATCTCCGAGTGATATATACAGAGAGGAAGAAATAATGACTAACGTACATACTGAATCTGTGAATGCAGAAAAATCGAGAAAATTTGGTTGCTTTGTTGCGTGTGTCTTGAAAAAATTGAATTTAATGGATGGAGCAACCATTAAAGAAATACAAATTCATGCAAAAATAAATAAAACAGTTGATCATAATATGCAAGATGTAGCACACAAAATTGCGCGTAAATGCTTGAAAAAAGCGAGAAGTATTACGCAAGAATGTGAGAAATGTTTTTCTCTATACGTATGCATCATAGAAAATATGCATAAATTGGAAGGACACGAAGAACATGTATAA
+>SiOBPZ4-mRNA [organism=Solenopsis invicta]
+ATGAAAACAATCGTTATCGTGCTCACCATTTCTTTCATCGCCGTTTTGGGTCAACTCACAGATGAACAAAAAGCAAATTTGAGAGAGTACAAAGAATCCTGTATAAACGAAACTGGTGTTGACACTGTTTTAATTGAAAATGCAAAGAAAGGACAAATAGCTGAAAATGACGAAAAGCTTGCTTGTTTCGCTACCTGTTTGTTAAAGAAAGCCGAAATTATAAATGCAGATGGACACATTGACTGGAAAGTAGCTCGTTCTAAATTTCCAGTACCACGAGAAAGACTCGATCAAATTTATAATGCATGCAAGCACATTACTGAAACAGGCTGTGAAAAAGGAGGCAAACTGTTTAAATGTTTCATGGACAACAACATTTATCTTTTACAATAG
+>SiOBPZ5-mRNA [organism=Solenopsis invicta]
+atgaaacatctagtgctgtgcgcatgtgttttgttattcacttttcagttgtctaattcatcagaactaaaacaaaagtttcaagaagaagtaaagattcagcaacggattgattttgaagcttgcttgagtgaaaatggtataaatgaaagtgaattatacggttggacagaaatattgtctaatgtacataccgaaacagcaaatgaagaaagaacgagaaagaatggctgctttatggcgtgttttttaaaaaaacaaaatttaatggaaggaaccagcattaaagaagatgaagttattgcacgattagatgaagtagttattaatgagactggagtaaaattgcccacaattgtgcataaatgcataaaagaaaagaaggatattacgcaagaatgtgataaatgtttctctatatacgtatgtattataaaagctgcaagtgaagaaaaaaaacgtatgcaggaagaaaacgtaagaactgaagaagaagaaacaggagaaccaaataaaaagaagtag
+>SiOBPZ6-mRNA [organism=Solenopsis invicta]
+ATGCATCGTAGTGCAAGTACTCATGCTATTACTAGCTTTACGTTGGTAATATGTATCCTCTTTGTGATTGTTATTATTACTCGTTTCAAAGAGACATACTTGTCTGAAAATAGTCCATTCACAGAGAAGGAAACAGAAAAATTAAGAGGCTACAGAACATTATGTATGAACAAATATGATGTTGATACGACAATAATTGAAAAAGCAAAGGAAATGGAAAACGTAATTGATTATATTGACGAAAGACTTGTTTCCTATGTTATTTGTTTATATAAAAACTGGGGAATTATAAATGCAGATGGACACATTGACTGGAAGGTAACTCTTTCTATGTTGCGAGGTGTACCACAAAAAGTATTCAATGAAATATACAGTGCATGCAATCGTACCACTGGTACAGATTATGAAAGAGGATACGAGTTATTTAAGTGCTTCTTACGAAACAAAGTAGATCTTCTATAA

data/spec/sequences/sequenceserver-SI2.2.0_06267.fa

@@ -0,0 +1,5 @@
+>SI2.2.0_06267 locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00
+MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR
+TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE
+KENKIKEGMKMMGLNDSVF

data/spec/sequenceserver_spec.rb

@@ -81,10 +81,10 @@ module SequenceServer
     end
 
     it 'has a list of databases after startup' do
-      SequenceServer.init()
-      # assuming database_dir is set to spec/database/sample
-      Database.all.length.should == 4
+      SequenceServer.init(database_dir:
+                          File.join(__dir__, 'database', 'sample'))
       Database.all.should_not be_empty
+      Database.all.length.should == 4
     end
   end
 end

data/spec/spec_helper.rb

@@ -1,4 +1,63 @@
 require 'simplecov'
+require 'capybara/rspec'
+require 'selenium-webdriver'
+
+require_relative 'download_helper'
+
+# Start SimpleCov.
 SimpleCov.start
 
+# Load SequenceServer in testing mode.
+ENV['RACK_ENV'] = 'test'
 require 'sequenceserver'
+
+# For the purpose of testing, set DOTDIR to spec/dotdir.
+SequenceServer::DOTDIR = File.join(__dir__, 'dotdir')
+
+RSpec.configure do |config|
+  # Explicitly enable should syntax of rspec.
+  config.expect_with :rspec do |expectations|
+    expectations.syntax = [:should, :expect]
+  end
+
+  # To use url_encode function in import_spec.
+  config.include ERB::Util, type: :feature
+
+  # For file downloading.
+  config.include DownloadHelpers, type: :feature
+
+  # Setup capybara tests.
+  config.before :context, type: :feature do
+    Capybara.app = SequenceServer.init
+    Capybara.server = :webrick
+    Capybara.default_max_wait_time = 10
+
+    Capybara.register_driver :selenium do |app|
+      options = Selenium::WebDriver::Firefox::Options.new
+
+      # Run the browser in headless mode.
+      options.args << '--headless'
+
+      # Tell the browser where to save downloaded files.
+      options.profile = Selenium::WebDriver::Firefox::Profile.new
+      options.profile['browser.download.dir'] = downloads_dir
+      options.profile['browser.download.folderList'] = 2
+
+      # Suppress "open with / save" dialog for FASTA, XML, and TSV file types.
+      options.profile['browser.helperApps.neverAsk.saveToDisk'] =
+        'text/fasta,text/xml,text/tsv'
+
+      Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
+    end
+
+    FileUtils.mkdir_p downloads_dir
+  end
+
+  config.after :example, type: :feature do
+    clear_downloads
+  end
+
+  config.after :context, type: :feature do
+    FileUtils.rm_rf Dir[SequenceServer::DOTDIR + '/*-*-*-*-*']
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.1.0.beta12
+  version: 2.0.0.beta1
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-09-10 00:00:00.000000000 Z
+date: 2019-07-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -99,20 +99,40 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.18'
+        version: '3.12'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.18.0
+        version: 3.12.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.18'
+        version: '3.12'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.18.0
+        version: 3.12.0
+- !ruby/object:Gem::Dependency
+  name: capybara-screenshot
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.23
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.23
 - !ruby/object:Gem::Dependency
   name: codeclimate-test-reporter
   requirement: !ruby/object:Gem::Requirement
@@ -219,20 +239,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.11'
+        version: '3.141'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.11.0
+        version: 3.141.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.11'
+        version: '3.141'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.11.0
+        version: 3.141.0
 description: |
   SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
   user interface for use locally or over the web.
@@ -286,6 +306,7 @@ files:
 - lib/sequenceserver/routes.rb
 - lib/sequenceserver/sequence.rb
 - lib/sequenceserver/server.rb
+- lib/sequenceserver/sys.rb
 - lib/sequenceserver/version.rb
 - package.json
 - public/config.js
@@ -3673,10 +3694,32 @@ files:
 - public/vendor/system.js.map
 - public/vendor/system.src.js
 - sequenceserver.gemspec
-- spec/blast_spec.rb
+- spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb
+- spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb
+- spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb
+- spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb
+- spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb
+- spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb
+- spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb
+- spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb
+- spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb
+- spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb
+- spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb
+- spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb
+- spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb
+- spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb
+- spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb
+- spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb
+- spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb
+- 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
+- spec/database/funky_ids/funky_ids.fa.nhd
+- spec/database/funky_ids/funky_ids.fa.nhi
 - spec/database/funky_ids/funky_ids.fa.nhr
 - spec/database/funky_ids/funky_ids.fa.nin
 - spec/database/funky_ids/funky_ids.fa.nog
@@ -3792,26 +3835,140 @@ files:
 - spec/database/without_parse_seqids/without_parse_seqids.fa.psq
 - spec/database_spec.rb
 - spec/doctor_spec.disabled.rb
+- spec/dotdir/blast_2.2.30/blastn/BLASTN_XML_2.2.30.xml
+- spec/dotdir/blast_2.2.30/blastn/job.yaml
+- spec/dotdir/blast_2.2.30/blastn_nohits/BLASTN_NO_HITS_XML_2.2.30.xml
+- spec/dotdir/blast_2.2.30/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.2.30/blastp/BLASTP_XML_2.2.30.xml
+- spec/dotdir/blast_2.2.30/blastp/job.yaml
+- spec/dotdir/blast_2.2.30/blastx/BLASTX_XML_2.2.30.xml
+- spec/dotdir/blast_2.2.30/blastx/job.yaml
+- spec/dotdir/blast_2.2.30/tblastn/TBLASTN_XML_2.2.30.xml
+- spec/dotdir/blast_2.2.30/tblastn/job.yaml
+- spec/dotdir/blast_2.2.30/tblastx/TBLASTX_XML_2.2.30.xml
+- spec/dotdir/blast_2.2.30/tblastx/job.yaml
+- spec/dotdir/blast_2.2.31/blastn/BLASTN_XML_2.2.31.xml
+- spec/dotdir/blast_2.2.31/blastn/job.yaml
+- spec/dotdir/blast_2.2.31/blastn_nohits/BLASTN_NO_HITS_XML_2.2.31.xml
+- spec/dotdir/blast_2.2.31/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.2.31/blastp/BLASTP_XML_2.2.31.xml
+- spec/dotdir/blast_2.2.31/blastp/job.yaml
+- spec/dotdir/blast_2.2.31/blastx/BLASTX_XML_2.2.31.xml
+- spec/dotdir/blast_2.2.31/blastx/job.yaml
+- spec/dotdir/blast_2.2.31/tblastn/TBLASTN_XML_2.2.31.xml
+- spec/dotdir/blast_2.2.31/tblastn/job.yaml
+- spec/dotdir/blast_2.2.31/tblastx/TBLASTX_XML_2.2.31.xml
+- spec/dotdir/blast_2.2.31/tblastx/job.yaml
+- spec/dotdir/blast_2.3.0/blastn/BLASTN_XML_2.3.0.xml
+- spec/dotdir/blast_2.3.0/blastn/job.yaml
+- spec/dotdir/blast_2.3.0/blastn_nohits/BLASTN_NO_HITS_XML_2.3.0.xml
+- spec/dotdir/blast_2.3.0/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.3.0/blastp/BLASTP_XML_2.3.0.xml
+- spec/dotdir/blast_2.3.0/blastp/job.yaml
+- spec/dotdir/blast_2.3.0/blastx/BLASTX_XML_2.3.0.xml
+- spec/dotdir/blast_2.3.0/blastx/job.yaml
+- spec/dotdir/blast_2.3.0/tblastn/TBLASTN_XML_2.3.0.xml
+- spec/dotdir/blast_2.3.0/tblastn/job.yaml
+- spec/dotdir/blast_2.3.0/tblastx/TBLASTX_XML_2.3.0.xml
+- spec/dotdir/blast_2.3.0/tblastx/job.yaml
+- spec/dotdir/blast_2.4.0/blastn/BLASTN_XML_2.4.0.xml
+- spec/dotdir/blast_2.4.0/blastn/TBLASTN_XML_2.4.0.xml
+- spec/dotdir/blast_2.4.0/blastn/job.yaml
+- spec/dotdir/blast_2.4.0/blastn_nohits/BLASTN_NO_HITS_XML_2.4.0.xml
+- spec/dotdir/blast_2.4.0/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.4.0/blastp/BLASTP_XML_2.4.0.xml
+- spec/dotdir/blast_2.4.0/blastp/job.yaml
+- spec/dotdir/blast_2.4.0/blastx/BLASTX_XML_2.4.0.xml
+- spec/dotdir/blast_2.4.0/blastx/job.yaml
+- spec/dotdir/blast_2.4.0/tblastn/TBLASTN_XML_2.4.0.xml
+- spec/dotdir/blast_2.4.0/tblastn/job.yaml
+- spec/dotdir/blast_2.4.0/tblastx/TBLASTX_XML_2.4.0.xml
+- spec/dotdir/blast_2.4.0/tblastx/job.yaml
+- spec/dotdir/blast_2.5.0/blastn/BLASTN_LONG_XML_2.5.0.xml
+- spec/dotdir/blast_2.5.0/blastn/BLASTN_XML_2.5.0.xml
+- spec/dotdir/blast_2.5.0/blastn/job.yaml
+- spec/dotdir/blast_2.5.0/blastn_nohits/BLASTN_NO_HITS_XML_2.5.0.xml
+- spec/dotdir/blast_2.5.0/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.5.0/blastp/BLASTP
+- spec/dotdir/blast_2.5.0/blastp/BLASTP_XML_2.5.0.xml
+- spec/dotdir/blast_2.5.0/blastp/job.yaml
+- spec/dotdir/blast_2.5.0/blastx/BLASTX
+- spec/dotdir/blast_2.5.0/blastx/BLASTX_XML_2.5.0.xml
+- spec/dotdir/blast_2.5.0/blastx/job.yaml
+- spec/dotdir/blast_2.5.0/tblastn/TBLASTN
+- spec/dotdir/blast_2.5.0/tblastn/TBLASTN_XML_2.5.0.xml
+- spec/dotdir/blast_2.5.0/tblastn/job.yaml
+- spec/dotdir/blast_2.5.0/tblastx/TBLASTX
+- spec/dotdir/blast_2.5.0/tblastx/TBLASTX_XML_2.5.0.xml
+- spec/dotdir/blast_2.5.0/tblastx/job.yaml
+- spec/dotdir/blast_2.6.0/blastn/BLASTN_XML_2.6.0.xml
+- spec/dotdir/blast_2.6.0/blastn/job.yaml
+- spec/dotdir/blast_2.6.0/blastn_nohits/BLASTN_NO_HITS_XML_2.6.0.xml
+- spec/dotdir/blast_2.6.0/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.6.0/blastp/BLASTP_XML_2.6.0.xml
+- spec/dotdir/blast_2.6.0/blastp/job.yaml
+- spec/dotdir/blast_2.6.0/blastx/BLASTX_XML_2.6.0.xml
+- spec/dotdir/blast_2.6.0/blastx/job.yaml
+- spec/dotdir/blast_2.6.0/tblastn/TBLASTN_XML_2.6.0.xml
+- spec/dotdir/blast_2.6.0/tblastn/job.yaml
+- spec/dotdir/blast_2.6.0/tblastx/TBLASTX_XML_2.6.0.xml
+- spec/dotdir/blast_2.6.0/tblastx/job.yaml
+- spec/dotdir/blast_2.7.1/blastn/BLASTN_XML_2.7.1.xml
+- spec/dotdir/blast_2.7.1/blastn/job.yaml
+- spec/dotdir/blast_2.7.1/blastn_nohits/BLASTN_NO_HITS_XML_2.7.1.xml
+- spec/dotdir/blast_2.7.1/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.7.1/blastp/BLASTP_XML_2.7.1.xml
+- spec/dotdir/blast_2.7.1/blastp/job.yaml
+- spec/dotdir/blast_2.7.1/blastx/BLASTX_XML_2.7.1.xml
+- spec/dotdir/blast_2.7.1/blastx/job.yaml
+- spec/dotdir/blast_2.7.1/tblastn/TBLASTN_XML_2.7.1.xml
+- spec/dotdir/blast_2.7.1/tblastn/job.yaml
+- spec/dotdir/blast_2.7.1/tblastx/TBLASTX_XML_2.7.1.xml
+- spec/dotdir/blast_2.7.1/tblastx/job.yaml
+- spec/dotdir/blast_2.8.1/blastn/BLASTN_XML_2.8.1.xml
+- spec/dotdir/blast_2.8.1/blastn/job.yaml
+- spec/dotdir/blast_2.8.1/blastn_nohits/BLASTN_NO_HITS_XML_2.8.1.xml
+- spec/dotdir/blast_2.8.1/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.8.1/blastp/BLASTP_XML_2.8.1.xml
+- spec/dotdir/blast_2.8.1/blastp/job.yaml
+- spec/dotdir/blast_2.8.1/blastx/BLASTX_XML_2.8.1.xml
+- spec/dotdir/blast_2.8.1/blastx/job.yaml
+- spec/dotdir/blast_2.8.1/tblastn/TBLASTN_XML_2.8.1.xml
+- spec/dotdir/blast_2.8.1/tblastn/job.yaml
+- spec/dotdir/blast_2.8.1/tblastx/TBLASTX_XML_2.8.1.xml
+- spec/dotdir/blast_2.8.1/tblastx/job.yaml
+- spec/dotdir/blast_2.9.0/blastn/BLASTN_XML_2.9.0.xml
+- spec/dotdir/blast_2.9.0/blastn/job.yaml
+- spec/dotdir/blast_2.9.0/blastn_nohits/BLASTN_NO_HITS_XML_2.9.0.xml
+- spec/dotdir/blast_2.9.0/blastn_nohits/job.yaml
+- spec/dotdir/blast_2.9.0/blastp/BLASTP_XML_2.9.0.xml
+- spec/dotdir/blast_2.9.0/blastp/job.yaml
+- spec/dotdir/blast_2.9.0/blastx/BLASTX_XML_2.9.0.xml
+- spec/dotdir/blast_2.9.0/blastx/job.yaml
+- spec/dotdir/blast_2.9.0/tblastn/TBLASTN_XML_2.9.0.xml
+- spec/dotdir/blast_2.9.0/tblastn/job.yaml
+- spec/dotdir/blast_2.9.0/tblastx/TBLASTX_XML_2.9.0.xml
+- spec/dotdir/blast_2.9.0/tblastx/job.yaml
+- spec/dotdir/diamond_0.9.24/blastp/DIAMOND_BLASTP_0.9.24.xml
+- spec/dotdir/diamond_0.9.24/blastp/job.yaml
+- spec/dotdir/diamond_0.9.24/blastx/DIAMOND_BLASTX_0.9.24.xml
+- spec/dotdir/diamond_0.9.24/blastx/job.yaml
+- spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml
+- spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml
+- spec/download_helper.rb
 - spec/empty_config.yml
-- spec/nucleotide_query.fa
-- spec/protein_query.fa
+- spec/import_spec_capybara_local.rb
 - spec/routes_spec.rb
 - spec/sample.conf
-- spec/sample_reports/blastn_sample/job.yaml
-- spec/sample_reports/blastn_sample/stdout
-- spec/sample_reports/blastp_sample/job.yaml
-- spec/sample_reports/blastp_sample/stdout
-- spec/sample_reports/blastx_sample/job.yaml
-- spec/sample_reports/blastx_sample/stdout
-- spec/sample_reports/no_hits_sample/job.yaml
-- spec/sample_reports/no_hits_sample/stdout
-- spec/sample_reports/tblastn_sample/job.yaml
-- spec/sample_reports/tblastn_sample/stdout
-- spec/sample_reports/tblastx_sample/job.yaml
-- spec/sample_reports/tblastx_sample/stdout
-- spec/sample_reports/with_hits_sample/job.yaml
-- spec/sample_reports/with_hits_sample/stdout
 - spec/sequence_spec.rb
+- spec/sequences/Nucleotide_TP53_COX41.fasta
+- spec/sequences/Protein_TP53_COX41.fasta
+- spec/sequences/Query_1_SI2_2_0_06267.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-SI2.2.0_06267.fa
 - spec/sequenceserver_spec.rb
 - spec/spec_helper.rb
 - views/_options.erb
@@ -3850,7 +4007,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.2
+rubygems_version: 2.5.2.3
 signing_key: 
 specification_version: 4
 summary: BLAST search made easy!