sequenceserver 2.0.0.beta3 → 2.0.0.beta4

data/spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt

@@ -0,0 +1,6 @@
+>sp|P04637|P53_HUMAN:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>sp|P04637|P53_HUMAN:1-393_alignment_gi|1099170394|ref|XP_018868681.1|:16-408
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSP LNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>gi|1099170394|ref|XP_018868681.1|:16-408
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPTLNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

data/spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt

@@ -0,0 +1,6 @@
+>sp|P04637|P53_HUMAN:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>sp|P04637|P53_HUMAN:1-393_alignment_gi|120407068|ref|NP_000537.3|:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>gi|120407068|ref|NP_000537.3|:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

data/spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt

@@ -0,0 +1,6 @@
+>sp|P04637|P53_HUMAN:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEXXXXXXXXXXXXXXXXXXXXXXXXXXXSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>sp|P04637|P53_HUMAN:1-393_alignment_gi|1484127324|gb|MG595988.1|:1-1179
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>gi|1484127324|gb|MG595988.1|:1-1179
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

data/spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt

@@ -0,0 +1,6 @@
+>sp|P04637|P53_HUMAN:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEXXXXXXXXXXXXXXXXXXXXXXXXXXXSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>sp|P04637|P53_HUMAN:1-393_alignment_gi|395440626|gb|JQ694049.1|:24-1202
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>gi|395440626|gb|JQ694049.1|:24-1202
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

data/spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt

@@ -0,0 +1,6 @@
+>sp|P04637|P53_HUMAN:1-394
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPXXXXXXXXXXXXXXXXXXXXXXXXSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>sp|P04637|P53_HUMAN:1-394_alignment_sp|P04637|P53_HUMAN:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPXXXXXXXXXXXXXXXXXXXXXXXXSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
+>sp|P04637|P53_HUMAN:1-393
+MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPXXXXXXXXXXXXXXXXXXXXXXXXSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

data/spec/spec_helper.rb

@@ -1,5 +1,6 @@
 require 'simplecov'
 require 'capybara/rspec'
+require 'capybara-screenshot/rspec'
 require 'selenium-webdriver'
 
 require_relative 'download_helper'
@@ -30,7 +31,7 @@ RSpec.configure do |config|
   config.before :context, type: :feature do
     Capybara.app = SequenceServer.init
     Capybara.server = :webrick
-    Capybara.default_max_wait_time = 10
+    Capybara.default_max_wait_time = 30
 
     Capybara.register_driver :selenium do |app|
       options = Selenium::WebDriver::Firefox::Options.new
@@ -43,10 +44,9 @@ RSpec.configure do |config|
       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.
+      # Suppress "open with / save" dialog for FASTA, XML, TSV and PNG file types.
       options.profile['browser.helperApps.neverAsk.saveToDisk'] =
         'text/fasta,text/xml,text/tsv,image/png'
-
       Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
     end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 2.0.0.beta3
+  version: 2.0.0.beta4
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-21 00:00:00.000000000 Z
+date: 2019-12-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -57,42 +57,42 @@ dependencies:
   name: sinatra
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.0.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.0.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.0.0
 - !ruby/object:Gem::Dependency
   name: slop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 3.6.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.6.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 3.6.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.6'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.6.0
 - !ruby/object:Gem::Dependency
   name: capybara
   requirement: !ruby/object:Gem::Requirement
@@ -137,82 +137,62 @@ dependencies:
   name: rack-test
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '10.3'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 10.3.2
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.3'
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 10.3.2
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 3.7.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.7.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 3.7.0
     - - "~>"
       - !ruby/object:Gem::Version
         version: '3.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.7.0
 - !ruby/object:Gem::Dependency
-  name: sauce_whisk
+  name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
+        version: '0.75'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.19
+        version: 0.75.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
+        version: '0.75'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.19
+        version: 0.75.1
 - !ruby/object:Gem::Dependency
   name: selenium-webdriver
   requirement: !ruby/object:Gem::Requirement
@@ -237,20 +217,20 @@ dependencies:
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
         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: |
@@ -268,19 +248,22 @@ files:
 - ".codeclimate.yml"
 - ".csslintrc"
 - ".eslintignore"
-- ".eslintrc"
+- ".eslintrc.json"
 - ".gitignore"
 - ".mailmap"
 - ".rspec"
 - ".rubocop.yml"
 - ".travis.yml"
+- AppImage/recipe.yml
+- AppImage/sequenceserver.desktop
+- AppImage/sequenceserver.png
+- AppImage/sequenceserver.sh
 - COPYRIGHT.txt
 - Dockerfile
 - LICENSE.txt
 - LICENSE/Apache.txt
 - LICENSE/d3.txt
 - README.md
-- Rakefile
 - bin/sequenceserver
 - config.ru
 - lib/sequenceserver.rb
@@ -3871,7 +3854,6 @@ files:
 - 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
@@ -3883,7 +3865,6 @@ files:
 - 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
@@ -3956,20 +3937,48 @@ files:
 - spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml
 - spec/download_helper.rb
 - spec/empty_config.yml
-- spec/import_spec_capybara_local.rb
 - spec/routes_spec.rb
 - spec/sample.conf
 - spec/sequence_spec.rb
+- spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt
+- spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt
+- spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt
+- spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt
 - 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/alignment-35_hits_diamond_blastp.txt
+- spec/sequences/alignment-35_hits_diamond_blastx.txt
+- spec/sequences/alignment-3_hits.txt
+- spec/sequences/alignment-40_hits_blastn.txt
+- spec/sequences/alignment-40_hits_blastp.txt
+- spec/sequences/alignment-40_hits_blastp_2.2.30.txt
+- spec/sequences/alignment-40_hits_blastx.txt
+- spec/sequences/alignment-40_hits_tblastn.txt
+- spec/sequences/alignment-40_hits_tblastn_2.2.30.txt
+- spec/sequences/alignment-40_hits_tblastx.txt
+- spec/sequences/alignment-4_hits.txt
+- spec/sequences/alignment-4_hits_blastn.txt
+- spec/sequences/alignment-4_hits_blastp.txt
+- spec/sequences/alignment-4_hits_blastp_2.2.30.txt
+- spec/sequences/alignment-4_hits_blastx.txt
+- spec/sequences/alignment-4_hits_diamond_blastp.txt
+- spec/sequences/alignment-4_hits_diamond_blastx.txt
+- spec/sequences/alignment-4_hits_tblastn.txt
+- spec/sequences/alignment-4_hits_tblastn_2.2.30.txt
+- spec/sequences/alignment-4_hits_tblastx.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/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt
+- spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt
+- spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt
+- spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt
+- spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt
 - spec/sequenceserver_spec.rb
 - spec/spec_helper.rb
 - views/_options.erb
@@ -4007,7 +4016,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubygems_version: 3.0.1
+rubyforge_project: 
+rubygems_version: 2.5.2.3
 signing_key: 
 specification_version: 4
 summary: BLAST search made easy!

data/.eslintrc

@@ -1,213 +0,0 @@
-ecmaFeatures:
-  modules: true
-  jsx: true
-
-env:
-  amd: true
-  browser: true
-  es6: true
-  jquery: true
-  node: true
-
-# http://eslint.org/docs/rules/
-rules:
-  # Possible Errors
-  comma-dangle: [2, never]
-  no-cond-assign: 2
-  no-console: 0
-  no-constant-condition: 2
-  no-control-regex: 2
-  no-debugger: 2
-  no-dupe-args: 2
-  no-dupe-keys: 2
-  no-duplicate-case: 2
-  no-empty: 2
-  no-empty-character-class: 2
-  no-ex-assign: 2
-  no-extra-boolean-cast: 2
-  no-extra-parens: 0
-  no-extra-semi: 2
-  no-func-assign: 2
-  no-inner-declarations: [2, functions]
-  no-invalid-regexp: 2
-  no-irregular-whitespace: 2
-  no-negated-in-lhs: 2
-  no-obj-calls: 2
-  no-regex-spaces: 2
-  no-sparse-arrays: 2
-  no-unexpected-multiline: 2
-  no-unreachable: 2
-  use-isnan: 2
-  valid-jsdoc: 0
-  valid-typeof: 2
-
-  # Best Practices
-  accessor-pairs: 2
-  block-scoped-var: 0
-  complexity: [2, 6]
-  consistent-return: 0
-  curly: 0
-  default-case: 0
-  dot-location: 0
-  dot-notation: 0
-  eqeqeq: 2
-  guard-for-in: 2
-  no-alert: 2
-  no-caller: 2
-  no-case-declarations: 2
-  no-div-regex: 2
-  no-else-return: 0
-  no-empty-label: 2
-  no-empty-pattern: 2
-  no-eq-null: 2
-  no-eval: 2
-  no-extend-native: 2
-  no-extra-bind: 2
-  no-fallthrough: 2
-  no-floating-decimal: 0
-  no-implicit-coercion: 0
-  no-implied-eval: 2
-  no-invalid-this: 0
-  no-iterator: 2
-  no-labels: 0
-  no-lone-blocks: 2
-  no-loop-func: 2
-  no-magic-number: 0
-  no-multi-spaces: 0
-  no-multi-str: 0
-  no-native-reassign: 2
-  no-new-func: 2
-  no-new-wrappers: 2
-  no-new: 2
-  no-octal-escape: 2
-  no-octal: 2
-  no-proto: 2
-  no-redeclare: 2
-  no-return-assign: 2
-  no-script-url: 2
-  no-self-compare: 2
-  no-sequences: 0
-  no-throw-literal: 0
-  no-unused-expressions: 2
-  no-useless-call: 2
-  no-useless-concat: 2
-  no-void: 2
-  no-warning-comments: 0
-  no-with: 2
-  radix: 2
-  vars-on-top: 0
-  wrap-iife: 2
-  yoda: 0
-
-  # Strict
-  strict: 0
-
-  # Variables
-  init-declarations: 0
-  no-catch-shadow: 2
-  no-delete-var: 2
-  no-label-var: 2
-  no-shadow-restricted-names: 2
-  no-shadow: 0
-  no-undef-init: 2
-  no-undef: 0
-  no-undefined: 0
-  no-unused-vars: 0
-  no-use-before-define: 0
-
-  # Node.js and CommonJS
-  callback-return: 2
-  global-require: 2
-  handle-callback-err: 2
-  no-mixed-requires: 0
-  no-new-require: 0
-  no-path-concat: 2
-  no-process-exit: 2
-  no-restricted-modules: 0
-  no-sync: 0
-
-  # Stylistic Issues
-  array-bracket-spacing: 0
-  block-spacing: 0
-  brace-style: 0
-  camelcase: 0
-  comma-spacing: 0
-  comma-style: 0
-  computed-property-spacing: 0
-  consistent-this: 0
-  eol-last: 0
-  func-names: 0
-  func-style: 0
-  id-length: 0
-  id-match: 0
-  indent: 0
-  jsx-quotes: 0
-  key-spacing: 0
-  linebreak-style: 0
-  lines-around-comment: 0
-  max-depth: 0
-  max-len: 0
-  max-nested-callbacks: 0
-  max-params: 0
-  max-statements: [2, 30]
-  new-cap: 0
-  new-parens: 0
-  newline-after-var: 0
-  no-array-constructor: 0
-  no-bitwise: 0
-  no-continue: 0
-  no-inline-comments: 0
-  no-lonely-if: 0
-  no-mixed-spaces-and-tabs: 0
-  no-multiple-empty-lines: 0
-  no-negated-condition: 0
-  no-nested-ternary: 0
-  no-new-object: 0
-  no-plusplus: 0
-  no-restricted-syntax: 0
-  no-spaced-func: 0
-  no-ternary: 0
-  no-trailing-spaces: 0
-  no-underscore-dangle: 0
-  no-unneeded-ternary: 0
-  object-curly-spacing: 0
-  one-var: 0
-  operator-assignment: 0
-  operator-linebreak: 0
-  padded-blocks: 0
-  quote-props: 0
-  quotes: 0
-  require-jsdoc: 0
-  semi-spacing: 0
-  semi: 0
-  sort-vars: 0
-  space-after-keywords: 0
-  space-before-blocks: 0
-  space-before-function-paren: 0
-  space-before-keywords: 0
-  space-in-parens: 0
-  space-infix-ops: 0
-  space-return-throw-case: 0
-  space-unary-ops: 0
-  spaced-comment: 0
-  wrap-regex: 0
-
-  # ECMAScript 6
-  arrow-body-style: 0
-  arrow-parens: 0
-  arrow-spacing: 0
-  constructor-super: 0
-  generator-star-spacing: 0
-  no-arrow-condition: 0
-  no-class-assign: 0
-  no-const-assign: 0
-  no-dupe-class-members: 0
-  no-this-before-super: 0
-  no-var: 0
-  object-shorthand: 0
-  prefer-arrow-callback: 0
-  prefer-const: 0
-  prefer-reflect: 0
-  prefer-spread: 0
-  prefer-template: 0
-  require-yield: 0