├── .ruby-version ├── test ├── empty_config.yml ├── database │ ├── funky_ids │ │ ├── funky_ids.fa.nsi │ │ ├── funky_ids.fa.nhr │ │ ├── funky_ids.fa.nin │ │ ├── funky_ids.fa.nog │ │ ├── funky_ids.fa.nsq │ │ ├── funky_ids.fa.nsd │ │ └── funky_ids.fa │ ├── without_parse_seqids │ │ ├── without_parse_seqids.fa.phr │ │ ├── without_parse_seqids.fa.pin │ │ ├── without_parse_seqids.fa.psq │ │ └── without_parse_seqids.fa │ └── sample │ │ ├── proteins │ │ └── Solenopsis_invicta │ │ │ ├── Sinvicta2-2-3.prot.subset.fasta.phr │ │ │ ├── Sinvicta2-2-3.prot.subset.fasta.pin │ │ │ ├── Sinvicta2-2-3.prot.subset.fasta.pog │ │ │ └── Sinvicta2-2-3.prot.subset.fasta.psi │ │ └── transcripts │ │ └── Solenopsis_invicta │ │ ├── Sinvicta2-2-3.cdna.subset.fasta.nhr │ │ ├── Sinvicta2-2-3.cdna.subset.fasta.nin │ │ ├── Sinvicta2-2-3.cdna.subset.fasta.nog │ │ ├── Sinvicta2-2-3.cdna.subset.fasta.nsi │ │ ├── Sinvicta2-2-3.cdna.subset.fasta.nsq │ │ └── Sinvicta2-2-3.cdna.subset.fasta.nsd └── test_route_spec.rb ├── public ├── web_files │ ├── json │ │ └── .gitkeep │ ├── img │ │ └── gene.png │ └── fonts │ │ ├── FontAwesome.otf │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.ttf │ │ └── fontawesome-webfont.woff ├── src │ ├── js │ │ ├── jquery.cookie.min.js │ │ ├── bionode-seq.min.js │ │ ├── genevalidator.js │ │ ├── jquery.validate.min.js │ │ ├── bootstrap.min.js │ │ └── jquery.tablesorter.min.js │ └── css │ │ ├── custom.css │ │ └── font-awesome.min.css └── GeneValidator │ └── loading.html ├── config.ru ├── lib ├── genevalidatorapp │ ├── version.rb │ ├── logger.rb │ ├── server.rb │ ├── config.rb │ ├── database.rb │ ├── routes.rb │ ├── exceptions.rb │ └── genevalidator.rb └── genevalidatorapp.rb ├── Gemfile ├── views ├── 500.slim ├── results.slim ├── layout.slim └── index.slim ├── .gitignore ├── .travis.yml ├── README.md ├── genevalidatorapp.gemspec └── Rakefile /.ruby-version: -------------------------------------------------------------------------------- 1 | 2.2 -------------------------------------------------------------------------------- /test/empty_config.yml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /public/web_files/json/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config.ru: -------------------------------------------------------------------------------- 1 | require 'genevalidatorapp' 2 | GeneValidatorApp.init 3 | run GeneValidatorApp 4 | -------------------------------------------------------------------------------- /lib/genevalidatorapp/version.rb: -------------------------------------------------------------------------------- 1 | module GeneValidatorApp 2 | VERSION = '2.1.8'.freeze 3 | end 4 | -------------------------------------------------------------------------------- /test/database/funky_ids/funky_ids.fa.nsi: -------------------------------------------------------------------------------- 1 | m @m4>123#4562 -------------------------------------------------------------------------------- /public/web_files/img/gene.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/public/web_files/img/gene.png -------------------------------------------------------------------------------- /Gemfile: -------------------------------------------------------------------------------- 1 | source 'https://rubygems.org' 2 | 3 | gemspec 4 | 5 | gem 'passenger', '~>5.3.4' 6 | gem 'genevalidator', '2.1.5' 7 | -------------------------------------------------------------------------------- /public/web_files/fonts/FontAwesome.otf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/public/web_files/fonts/FontAwesome.otf -------------------------------------------------------------------------------- /test/database/funky_ids/funky_ids.fa.nhr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/funky_ids/funky_ids.fa.nhr -------------------------------------------------------------------------------- /test/database/funky_ids/funky_ids.fa.nin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/funky_ids/funky_ids.fa.nin -------------------------------------------------------------------------------- /test/database/funky_ids/funky_ids.fa.nog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/funky_ids/funky_ids.fa.nog -------------------------------------------------------------------------------- /test/database/funky_ids/funky_ids.fa.nsq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/funky_ids/funky_ids.fa.nsq -------------------------------------------------------------------------------- /public/web_files/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/public/web_files/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /public/web_files/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/public/web_files/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /public/web_files/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/public/web_files/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /test/database/without_parse_seqids/without_parse_seqids.fa.phr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/without_parse_seqids/without_parse_seqids.fa.phr -------------------------------------------------------------------------------- /test/database/without_parse_seqids/without_parse_seqids.fa.pin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/without_parse_seqids/without_parse_seqids.fa.pin -------------------------------------------------------------------------------- /test/database/funky_ids/funky_ids.fa.nsd: -------------------------------------------------------------------------------- 1 | 123#4562 2 | 123456#3 3 | abc#def1 4 | abcdef#0 5 | lcl|123#4562 6 | lcl|1234564 7 | lcl|123456#3 8 | lcl|abc#def1 9 | lcl|abcdef#0 10 | -------------------------------------------------------------------------------- /test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr -------------------------------------------------------------------------------- /test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin -------------------------------------------------------------------------------- /test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog -------------------------------------------------------------------------------- /test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi -------------------------------------------------------------------------------- /test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr -------------------------------------------------------------------------------- /test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin -------------------------------------------------------------------------------- /test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog -------------------------------------------------------------------------------- /test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi -------------------------------------------------------------------------------- /test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wurmlab/genevalidatorapp/HEAD/test/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq -------------------------------------------------------------------------------- /views/500.slim: -------------------------------------------------------------------------------- 1 | .alert.alert-danger role="alert" 2 | h3.error_header Oops! Something went Wonky! 3 | p Apologies, there was an error with your request. Please try again. 4 | p Error Message: #{request.env['sinatra.error'].message} 5 | p If the error persists, please contact the administrator. -------------------------------------------------------------------------------- /test/database/funky_ids/funky_ids.fa: -------------------------------------------------------------------------------- 1 | >abcdef# 2 | GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAG 3 | >abc#def 4 | GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAG 5 | >123#456 6 | GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAG 7 | >123456# 8 | GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAG 9 | >123456 10 | GATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAG 11 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.gem 2 | *.rbc 3 | .bundle 4 | .config 5 | .yardoc 6 | .DS_Store 7 | Gemfile.lock 8 | InstalledFiles 9 | _yardoc 10 | coverage 11 | doc/ 12 | lib/bundler/man 13 | pkg 14 | rdoc 15 | spec/reports 16 | test/tmp 17 | test/version_tmp 18 | tmp 19 | *.bundle 20 | *.so 21 | *.o 22 | *.a 23 | mkmf.log 24 | .DS_Store 25 | passenger* -------------------------------------------------------------------------------- /test/database/without_parse_seqids/without_parse_seqids.fa.psq: -------------------------------------------------------------------------------- 1 |     2 |    3 |           4 |   5 | 6 |    7 |        8 | 9 |    10 |  11 |          12 |  13 | 14 |  15 |            16 |  17 |  18 | 19 |       20 | 21 |  22 |     23 |               -------------------------------------------------------------------------------- /test/database/without_parse_seqids/without_parse_seqids.fa: -------------------------------------------------------------------------------- 1 | >SI2.2.0_06267 locus=Si_gnF.scaffold02592[1282609..1284114].pep_2 quality=100.00 2 | MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIR 3 | TNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD 4 | ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGE 5 | KENKIKEGMKMMGLNDSVF 6 | >SI2.2.0_13722 locus=Si_gnF.scaffold06207[1925625..1928536].pep_1 quality=100.00 7 | MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIIC 8 | DGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS 9 | EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINEL 10 | TSYCGP 11 | -------------------------------------------------------------------------------- /lib/genevalidatorapp/logger.rb: -------------------------------------------------------------------------------- 1 | require 'logger' 2 | 3 | module GeneValidatorApp 4 | class Logger < Logger 5 | def initialize(dev, verbose = false) 6 | super dev 7 | self.level = verbose ? DEBUG : INFO 8 | self.formatter = Formatter.new 9 | end 10 | 11 | # We change Logging format so that it is consistent with Sinatra's 12 | class Formatter < Formatter 13 | Format = "[%s] %s %s\n".freeze 14 | 15 | def initialize 16 | self.datetime_format = '%Y-%m-%d %H:%M:%S' 17 | end 18 | 19 | def call(severity, time, _progname, msg) 20 | format(Format, format_datetime(time), severity, msg2str(msg)) 21 | end 22 | end 23 | end 24 | end 25 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: ruby 2 | rvm: 3 | - "2.2.10" 4 | - "2.3.7" 5 | - "2.4.4" 6 | - "2.5.1" 7 | before_install: 8 | # Install MAFFT 9 | - mkdir dependencies 10 | - mkdir dependencies/mafft 11 | - curl -L --fail https://mafft.cbrc.jp/alignment/software/mafft-7.397-linux.tgz | tar -xzf - --strip-components=1 -C dependencies/mafft 12 | - MAFFT_DIR="$PWD/dependencies/mafft/mafftdir" 13 | - MAFFT_BINARIES="${MAFFT_DIR}/libexec"; export MAFFT_BINARIES; 14 | # BLAST 15 | - mkdir dependencies/blast 16 | - curl -L --fail https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz | tar -xzf - --strip-components=1 -C dependencies/blast 17 | - BLAST_BIN="$PWD/dependencies/blast/bin" 18 | - export PATH=${MAFFT_DIR}/bin:${BLAST_BIN}:$PATH 19 | script: bundle exec rake test 20 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # GeneValidatorApp 2 | [![Build Status](https://travis-ci.org/wurmlab/genevalidatorapp.svg?branch=master)](https://travis-ci.org/wurmlab/genevalidatorapp) 3 | [![Gem Version](https://badge.fury.io/rb/genevalidatorapp.svg)](http://badge.fury.io/rb/genevalidatorapp) 4 | [![Scrutinizer Code Quality](https://scrutinizer-ci.com/g/wurmlab/genevalidatorapp/badges/quality-score.png?b=master)](https://scrutinizer-ci.com/g/wurmlab/genevalidatorapp/?branch=master) 5 | 6 | 7 | ## Introduction 8 | 9 | This repository is part of the GeneValidator Package and is used internally by GeneValidator - Please see [https://github.com/wurmlab/genevalidator](https://github.com/wurmlab/genevalidator) for more information. 10 | 11 | 12 |
13 | 14 | This program was developed at [Wurm Lab](https://wurmlab.github.io), [QMUL](http://sbcs.qmul.ac.uk) with the support of a BBSRC grant. 15 | -------------------------------------------------------------------------------- /public/src/js/jquery.cookie.min.js: -------------------------------------------------------------------------------- 1 | !function(a){"function"==typeof define&&define.amd?define(["jquery"],a):"object"==typeof exports?a(require("jquery")):a(jQuery)}(function(a){function c(a){return h.raw?a:encodeURIComponent(a)}function d(a){return h.raw?a:decodeURIComponent(a)}function e(a){return c(h.json?JSON.stringify(a):String(a))}function f(a){0===a.indexOf('"')&&(a=a.slice(1,-1).replace(/\\"/g,'"').replace(/\\\\/g,"\\"));try{return a=decodeURIComponent(a.replace(b," ")),h.json?JSON.parse(a):a}catch(c){}}function g(b,c){var d=h.raw?b:f(b);return a.isFunction(c)?c(d):d}var b=/\+/g,h=a.cookie=function(b,f,i){if(void 0!==f&&!a.isFunction(f)){if(i=a.extend({},h.defaults,i),"number"==typeof i.expires){var j=i.expires,k=i.expires=new Date;k.setTime(+k+864e5*j)}return document.cookie=[c(b),"=",e(f),i.expires?"; expires="+i.expires.toUTCString():"",i.path?"; path="+i.path:"",i.domain?"; domain="+i.domain:"",i.secure?"; secure":""].join("")}for(var l=b?void 0:{},m=document.cookie?document.cookie.split("; "):[],n=0,o=m.length;o>n;n++){var p=m[n].split("="),q=d(p.shift()),r=p.join("=");if(b&&b===q){l=g(r,f);break}b||void 0===(r=g(r))||(l[q]=r)}return l};h.defaults={},a.removeCookie=function(b,c){return void 0===a.cookie(b)?!1:(a.cookie(b,"",a.extend({},c,{expires:-1})),!a.cookie(b))}}); -------------------------------------------------------------------------------- /genevalidatorapp.gemspec: -------------------------------------------------------------------------------- 1 | lib = File.expand_path('lib', __dir__) 2 | $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib) 3 | require 'genevalidatorapp/version' 4 | 5 | Gem::Specification.new do |s| 6 | s.name = 'genevalidatorapp' 7 | s.version = GeneValidatorApp::VERSION 8 | s.authors = ['Monica Dragan', 'Ismail Moghul', 'Anurag Priyam', 9 | 'Yannick Wurm'] 10 | s.email = 'y.wurm@qmul.ac.uk' 11 | s.summary = 'A Web App wrapper for GeneValidator.' 12 | s.description = 'A Web App wrapper for GeneValidator, a program for' \ 13 | ' validating gene predictions.' 14 | s.homepage = 'https://wurmlab.github.io/tools/genevalidator/' 15 | s.license = 'AGPL' 16 | 17 | s.files = `git ls-files -z`.split("\x0") 18 | s.test_files = s.files.grep(%r{^(test|spec|features)/}) 19 | s.require_paths = ['lib'] 20 | 21 | s.required_ruby_version = '>= 2.2.0' 22 | 23 | s.add_development_dependency 'capybara', '~> 2.4', '>= 2.4.4' 24 | s.add_development_dependency 'minitest', '~> 5.10' 25 | s.add_development_dependency 'rake', '~> 12.3' 26 | # s.add_development_dependency 'w3c_validators', '~>1.1' 27 | 28 | s.add_dependency 'bio', '~>1.4' 29 | s.add_dependency 'sinatra', '~> 2.0' 30 | s.add_dependency 'sinatra-cross_origin', '~> 0.3' 31 | s.add_dependency 'slim', '~>3.0' 32 | end 33 | -------------------------------------------------------------------------------- /lib/genevalidatorapp/server.rb: -------------------------------------------------------------------------------- 1 | require 'rack/handler/webrick' 2 | 3 | module GeneValidatorApp 4 | # Simple wrapper around WEBrick and Rack::Handler::WEBrick to host 5 | # GeneValidatorApp standalone. 6 | class Server 7 | class << self 8 | def run(*args) 9 | new(*args).start 10 | end 11 | end 12 | 13 | def initialize(app) 14 | @app = app 15 | end 16 | 17 | attr_reader :app 18 | 19 | # Start server. Raises Errno::EADDRINUSE if port is in use by another 20 | # process. Raises Errno::EACCES if binding to the port requires root 21 | # privilege. 22 | def start 23 | setup_signal_handlers 24 | @server = WEBrick::HTTPServer.new(options) 25 | @server.mount '/', Rack::Handler::WEBrick, app 26 | @server.start 27 | end 28 | 29 | # Stop server. 30 | def stop 31 | @server.shutdown 32 | end 33 | 34 | # Options Hash passed to WEBrick::HTTPServer. 35 | # rubocop:disable Metrics/AbcSize 36 | def options 37 | @options ||= { 38 | BindAddress: app.config[:host], 39 | Port: app.config[:port], 40 | StartCallback: proc { app.on_start }, 41 | StopCallback: proc { app.on_stop }, 42 | OutputBufferSize: 5, 43 | AccessLog: [[logdev, WEBrick::AccessLog::COMMON_LOG_FORMAT]], 44 | Logger: WEBrick::Log.new(logdev) 45 | } 46 | end 47 | # rubocop:enable Metrics/AbcSize 48 | 49 | private 50 | 51 | def setup_signal_handlers 52 | %i[INT TERM].each do |sig| 53 | trap sig do 54 | stop 55 | end 56 | end 57 | end 58 | 59 | def logdev 60 | @logdev ||= app.verbose? ? STDERR : '/dev/null' 61 | end 62 | end 63 | end 64 | -------------------------------------------------------------------------------- /Rakefile: -------------------------------------------------------------------------------- 1 | require 'rake/testtask' 2 | GEMSPEC = Gem::Specification.load('genevalidatorapp.gemspec') 3 | 4 | task default: [:build] 5 | 6 | desc 'Builds and installs' 7 | task install: [:build] do 8 | sh "gem install #{Rake.original_dir}/genevalidatorapp-#{GEMSPEC.version}.gem" 9 | end 10 | 11 | desc 'Runs tests and builds gem (default)' 12 | task build: [:test] do 13 | sh "gem build #{Rake.original_dir}/genevalidatorapp.gemspec" 14 | end 15 | 16 | desc 'Runs tests' 17 | task :test do 18 | Rake::TestTask.new do |t| 19 | t.libs.push 'lib' 20 | t.test_files = FileList['test/test_*.rb'] 21 | t.verbose = false 22 | t.warning = false 23 | end 24 | end 25 | 26 | desc 'Build Assets' 27 | task :assets do 28 | # Requires uglifycss and uglifyjs 29 | # npm install uglifycss -g 30 | # npm install uglify-js -g 31 | src_assets_dir = File.expand_path('public/src', __dir__) 32 | assets_dir = File.expand_path('public/web_files', __dir__) 33 | `rm #{assets_dir}/css/gv.compiled.min.css` 34 | `rm #{assets_dir}/js/gv.compiled.min.js` 35 | sh "uglifycss --output '#{assets_dir}/css/gv.compiled.min.css'" \ 36 | " '#{src_assets_dir}/css/bootstrap1.min.css'" \ 37 | " '#{src_assets_dir}/css/font-awesome.min.css'" \ 38 | " '#{src_assets_dir}/css/custom.css'" 39 | 40 | sh "uglifyjs '#{src_assets_dir}/js/jquery.min.js'" \ 41 | " '#{src_assets_dir}/js/bootstrap.min.js'" \ 42 | " '#{src_assets_dir}/js/jquery.tablesorter.min.js'" \ 43 | " '#{src_assets_dir}/js/jquery.validate.min.js'" \ 44 | " '#{src_assets_dir}/js/jquery.cookie.min.js'" \ 45 | " '#{src_assets_dir}/js/d3.v3.min.js'" \ 46 | " '#{src_assets_dir}/js/plots.js'" \ 47 | " '#{src_assets_dir}/js/genevalidator.js'" \ 48 | " -m -c -o '#{assets_dir}/js/gv.compiled.min.js'" 49 | end 50 | -------------------------------------------------------------------------------- /public/GeneValidator/loading.html: -------------------------------------------------------------------------------- 1 | GeneValidator: identify problems with gene predictions 2 | 4 | 5 |
6 |

GeneValidator

7 |

Identify Problems with Protein-Coding Gene Predictions

8 | 9 |

Calculating...

10 |

This may take some time. Please leave this page open.

11 |
12 | 13 | -------------------------------------------------------------------------------- /test/test_route_spec.rb: -------------------------------------------------------------------------------- 1 | require 'minitest/autorun' 2 | require 'capybara/minitest' 3 | 4 | require 'genevalidatorapp' 5 | 6 | # Basic unit tests for HTTP / Rack interface. 7 | module GeneValidatorApp 8 | # include W3CValidators 9 | describe 'Routes' do 10 | ENV['RACK_ENV'] = 'production' 11 | include Rack::Test::Methods 12 | 13 | let 'root' do 14 | GeneValidatorApp.root 15 | end 16 | 17 | let 'empty_config' do 18 | File.join(root, 'test', 'empty_config.yml') 19 | end 20 | 21 | let 'database_dir' do 22 | File.join(root, 'test', 'database') 23 | end 24 | 25 | before :each do 26 | GeneValidatorApp.init(config_file: empty_config, 27 | database_dir: database_dir) 28 | 29 | validations = %w[lenc lenr dup merge align frame orf] 30 | sequence = 'AGCTAGCTAGCT' 31 | database = Database.first.name 32 | 33 | @params = { 34 | 'validations' => validations, 35 | 'seq' => sequence, 36 | 'database' => database 37 | } 38 | end 39 | 40 | let 'app' do 41 | GeneValidatorApp 42 | end 43 | 44 | it 'should start the app' do 45 | get '/' 46 | assert_equal(true, last_response.ok?) 47 | end 48 | 49 | it 'returns Bad Request (400) if no sequence is provided' do 50 | @params.delete('seq') 51 | post '/', @params 52 | assert_equal(400, last_response.status) 53 | end 54 | 55 | it 'returns Bad Request (400) if no validations is provided' do 56 | @params.delete('validations') 57 | post '/', @params 58 | assert_equal(400, last_response.status) 59 | end 60 | 61 | it 'returns Bad Request (400) if no database is provided' do 62 | @params.delete('database') 63 | post '/', @params 64 | assert_equal(400, last_response.status) 65 | end 66 | 67 | # W3C_Validator Gem is broken - https://github.com/alexdunae/w3c_validators/issues/16 68 | # it 'validate the html' do 69 | # get '/' 70 | # html = last_response.body 71 | 72 | # validator = MarkupValidator.new 73 | # results = validator.validate_text(html.to_s) 74 | # results.errors.each { |err| puts err.to_s } if results.errors.length > 0 75 | # puts results.errors 76 | # results.errors.length.should == 0 77 | # end 78 | end 79 | end 80 | -------------------------------------------------------------------------------- /lib/genevalidatorapp/config.rb: -------------------------------------------------------------------------------- 1 | require 'forwardable' 2 | 3 | # Define Config class. 4 | module GeneValidatorApp 5 | # Capture our configuration system. 6 | class Config 7 | extend Forwardable 8 | 9 | def_delegators GeneValidatorApp, :logger 10 | 11 | def initialize(data = {}) 12 | @data = symbolise data 13 | @config_file = @data.delete(:config_file) || default_config_file 14 | @config_file = File.expand_path(@config_file) 15 | @data = parse_config_file.update @data 16 | @data = defaults.update @data 17 | end 18 | 19 | attr_reader :data, :config_file 20 | 21 | # Get. 22 | def [](key) 23 | data[key] 24 | end 25 | 26 | # Set. 27 | def []=(key, value) 28 | data[key] = value 29 | end 30 | 31 | # Exists? 32 | def include?(key) 33 | data.include? key 34 | end 35 | 36 | # Write config data to config file. 37 | def write_config_file 38 | return unless config_file 39 | 40 | File.open(config_file, 'w') do |f| 41 | f.puts(data.delete_if { |_, v| v.nil? }.to_yaml) 42 | end 43 | end 44 | 45 | private 46 | 47 | # Symbolizes keys. Changes `database` key to `database_dir`. 48 | def symbolise(data) 49 | return {} unless data 50 | # Symbolize keys. 51 | Hash[data.map { |k, v| [k.to_sym, v] }] 52 | end 53 | 54 | # Parses and returns data from config_file if it exists. Returns {} 55 | # otherwise. 56 | def parse_config_file 57 | unless file? config_file 58 | logger.debug "Configuration file not found: #{config_file}" 59 | return {} 60 | end 61 | 62 | logger.debug "Reading configuration file: #{config_file}." 63 | symbolise YAML.load_file(config_file) 64 | rescue StandardError => error 65 | raise CONFIG_FILE_ERROR.new(config_file, error) 66 | end 67 | 68 | def file?(file) 69 | file && File.exist?(file) && File.file?(file) 70 | end 71 | 72 | # Default configuration data. 73 | def defaults 74 | { 75 | num_threads: 1, 76 | mafft_threads: 1, 77 | port: 5678, 78 | ssl: false, 79 | host: '0.0.0.0', 80 | serve_public_dir: File.join(Dir.home, '.genevalidatorapp/'), 81 | max_characters: 'undefined' 82 | } 83 | end 84 | 85 | def default_config_file 86 | '~/.genevalidatorapp.conf' 87 | end 88 | end 89 | end 90 | -------------------------------------------------------------------------------- /lib/genevalidatorapp/database.rb: -------------------------------------------------------------------------------- 1 | require 'find' 2 | require 'digest/md5' 3 | require 'forwardable' 4 | 5 | module GeneValidatorApp 6 | # class on the BLAST databases 7 | class Database < Struct.new(:name, :title, :type) 8 | class << self 9 | extend Forwardable 10 | 11 | def_delegators GeneValidatorApp, :config, :logger 12 | 13 | def collection 14 | @collection ||= {} 15 | end 16 | 17 | private :collection 18 | 19 | def <<(database) 20 | collection[database.id] = database 21 | end 22 | 23 | def [](ids) 24 | ids = Array ids 25 | collection.values_at(*ids) 26 | end 27 | 28 | def ids 29 | collection.keys 30 | end 31 | 32 | def all 33 | collection.values 34 | end 35 | 36 | def each(&block) 37 | all.each(&block) 38 | end 39 | 40 | def include?(path) 41 | collection.include? Digest::MD5.hexdigest path 42 | end 43 | 44 | def group_by(&block) 45 | all.group_by(&block) 46 | end 47 | 48 | def first 49 | all.first 50 | end 51 | 52 | def default_db 53 | if config[:default_db] && Database.include?(config[:default_db]) 54 | all.find { |a| a.name == config[:default_db] } 55 | else 56 | all.first 57 | end 58 | end 59 | 60 | def non_default_dbs 61 | all.find_all { |a| a != Database.default_db } 62 | end 63 | 64 | # Returns the original structure that the title is within. 65 | def obtain_original_structure(db_title) 66 | all.find_all { |a| a.title.chomp == db_title } 67 | end 68 | 69 | # Recurisvely scan `database_dir` for blast databases. 70 | def scan_databases_dir 71 | database_dir = config[:database_dir] 72 | cmd = "blastdbcmd -recursive -list #{database_dir} -list_outfmt" \ 73 | ' "%p::%f::%t"' 74 | list = `#{cmd} 2>&1` 75 | list.each_line do |line| 76 | type, name, title = line.split('::', 3) 77 | next if multipart_database_name?(name) 78 | next unless type.casecmp('protein').zero? 79 | self << Database.new(name, title, type) 80 | end 81 | end 82 | 83 | # Returns true if the database name appears to be a multi-part database 84 | # name. 85 | # 86 | # e.g. 87 | # /home/ben/pd.ben/sequenceserver/db/nr.00 => yes 88 | # /home/ben/pd.ben/sequenceserver/db/nr => no 89 | # /home/ben/pd.ben/sequenceserver/db/img3.5.finished.faa.01 => yes 90 | def multipart_database_name?(db_name) 91 | !db_name.match(%r{.+\/\S+\d{2}$}).nil? 92 | end 93 | end 94 | 95 | def initialize(*args) 96 | args.last.downcase! 97 | args.each(&:freeze) 98 | super 99 | 100 | @id = Digest::MD5.hexdigest args.first 101 | end 102 | 103 | attr_reader :id 104 | 105 | def to_s 106 | "#{type}: #{title} #{name}" 107 | end 108 | end 109 | end 110 | -------------------------------------------------------------------------------- /views/results.slim: -------------------------------------------------------------------------------- 1 | h3 Overview 2 | #overview.text-left 3 | span 4 | strong BLAST Database Used: 5 | = @params[:database] 6 | br 7 | strong BLAST E-Value Used: 8 | | 10-5 9 | br 10 | #overview_text 11 | button#overview_btn.btn.btn-primary.btn-sm style="margin-bottom:10px" data-toggle="button" onclick="GV.toggleOverviewBtn();" data-overviewjson="/GeneValidator/#{@gv_results[:unique_id]}/output/html_files/json/overview.json" 12 | br 13 | 14 | - output_dir = "/GeneValidator/#{@gv_results[:unique_id]}/output/" 15 | - csv_file = File.join(output_dir, 'input_file_results.csv') 16 | - json_file = File.join(output_dir, 'input_file_results.json') 17 | - summary_file = File.join(output_dir, 'input_file_summary.csv') 18 | a.btn.btn-primary.btn-sm target="_blank" download="" style="margin-right:10px;" href="#{csv_file}" CSV Output File 19 | a.btn.btn-primary.btn-sm target="_blank" download="" style="margin-right:10px;" href="#{json_file}" JSON Output File 20 | a.btn.btn-primary.btn-sm target="_blank" download="" style="margin-right:10px;" href="#{summary_file}" Summary CSV Output File 21 | 22 | br/ 23 | hr/ 24 | h3#results_header GeneValidator Results Table 25 | table#sortable_table.table.table-striped.table-collapsed.table-bordered.table-condensed.tablesorter 26 | thead 27 | tr#header 28 | th # 29 | th Ranking 30 | th 31 | | Sequence Definition  32 | span data-placement="top" data-toggle="tooltip" title=("Query definition as it apears in the input fasta file.") 33 | i.fa.fa-question-circle 34 | th 35 | | No. Hits  36 | span data-placement="top" data-toggle="tooltip" title=("Number of non-identical hits found by BLAST.") 37 | i.fa.fa-question-circle 38 | - @json_data_section[0][:validations].each do |_short_header, item| 39 | th.sorter-false 40 | strong 41 | = item[:header] 42 | | 43 | - if item[:header] == "Length Cluster" || item[:header] == "Gene Merge" || item[:header] == "Main ORF" || item[:header] == "Missing/Extra Sequences" 44 | span data-placement="top" data-toggle="tooltip" title=("Charts available for this validation") 45 | i.fa.fa-bar-chart-o.chartIcon 46 | | 47 | span data-placement="top" data-toggle="tooltip" title="#{item[:description]}" 48 | i.fa.fa-question-circle 49 | th.sorter-false.chart-column 50 | tbody 51 | - @json_data_section.each do |row| 52 | - json_file = "/GeneValidator/#{@gv_results[:unique_id]}/output/html_files/json/input_file_#{row[:idx]}.json" 53 | tr data-jsonfile="#{json_file}" data-target="toggle#{row[:idx]}" 54 | td title="idx" = row[:idx] 55 | td data-score="#{row[:overall_score]}" 56 | .ratings 57 | .empty-stars 58 | .full-stars style=("width:#{row[:overall_score]}%;") 59 | td title="Definition" = row[:definition] 60 | td title=("No. Hits") = row[:no_hits] 61 | - row[:validations].each do |_short_header, item| 62 | td class="#{item[:status]}" title="#{item[:header]}" 63 | == item[:print].gsub(' ', ' ').gsub('; ', '; ') 64 | - if row[:validations].select { |_short_header, item| item[:graphs] != nil }.map{ |_short_header, item| item[:graphs].length }.inject(0) { |r, e| r + e } != 0 65 | td 66 | button.plot_btn.btn.btn-default title=("Show plots") 67 | i.fa.fa-bar-chart-o 68 | - else 69 | td 70 | -------------------------------------------------------------------------------- /views/layout.slim: -------------------------------------------------------------------------------- 1 | doctype html 2 | html lang="en" 3 | head 4 | meta charset="utf-8" 5 | meta content="IE=edge" http-equiv="X-UA-Compatible" 6 | meta content="width=device-width, initial-scale=1" name="viewport" 7 | meta content="GeneValidator | Identify problems with Gene Predictions" name="description" 8 | meta content="Wurmlab" name="author" 9 | title GeneValidator | Identify problems with Gene Predictions 10 | 11 | link href="/web_files/css/gv.compiled.min.css" rel="stylesheet" type="text/css" 12 | 13 | script type="text/javascript" src="/web_files/js/gv.compiled.min.js" 14 | /! HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries 15 | /![if lt IE 9] 16 | script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js" 17 | script src="https://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js" 18 | 19 | body#mainbody 20 | .navbar.navbar-default.navbar-fixed-top role="navigation" 21 | .nav-container 22 | .navbar-header 23 | button.navbar-toggle data-target=".navbar-responsive-collapse" data-toggle="collapse" type="button" 24 | span.icon-bar 25 | span.icon-bar 26 | span.icon-bar 27 | span.navbar-brand 28 | a href="#" GeneValidator 29 | .navbar-collapse.collapse.navbar-responsive-collapse 30 | ul.nav.navbar-nav 31 | li 32 | a href="https://wurmlab.github.io/tools/genevalidator/" target="_blank" GeneValidator 33 | li 34 | a href="https://wurmlab.github.io/tools/genevalidator/api" target="_blank" API 35 | li 36 | a href="https://wurmlab.github.io" target="_blank" Wurm Lab 37 | li 38 | a href="http://doi.org/10.1093/bioinformatics/btw015" target="_blank" Publication 39 | 40 | ul.nav.navbar-nav.navbar-right 41 | li 42 | a.nav_github_icon href="https://github.com/wurmlab/genevalidatorapp" target="_blank" 43 | span.i.fa.fa-2x.fa-github 44 | ==yield 45 | #spinner.modal aria-hidden="true" aria-labelledby="spinner" role="dialog" tabindex="-1" 46 | .modal-dialog 47 | .modal-content 48 | .modal-body.text-center 49 | h2 Calculating... 50 | p.results_link This may take some time. Please leave this page open. 51 | i.fa.fa-spinner.fa-5x.fa-spin 52 | footer#footer 53 | p.text-muted.text-center 54 | | Please cite: 55 | Dragan M‡, Moghul I‡, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problematic gene predictions. 56 | Bioinformatics, doi: 10.1093/bioinformatics/btw015. 57 | br 58 | | Developed at 59 | a href="https://wurmlab.github.io" target="_blank" Wurm Lab 60 | | , 61 | a href="http://www.sbcs.qmul.ac.uk" target="_blank" QMUL 62 | | with funding by 63 | a href="http://www.bbsrc.ac.uk/home/home.aspx" target="_blank" BBSRC 64 | | and 65 | a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank" Google Summer of Code 2013 66 | br 67 | | This page was created by 68 | a href="https://github.com/wurmlab/genevalidatorapp" target="_blank" GeneValidator Web Application 69 | | v#{GeneValidatorApp::VERSION} (using 70 | a href="https://github.com/wurmlab/genevalidator" target="_blank" GeneValidator 71 | | v#{@current_gv_version}) -------------------------------------------------------------------------------- /views/index.slim: -------------------------------------------------------------------------------- 1 | section#search 2 | h1.page-header 3 | span GeneValidator  4 | span.small Identify problems with gene predictions 5 | form#input action="/" method="POST" 6 | .form-group#input_seq_group 7 | label.control-label.input_seq-label for="seq" Input Sequences: 8 | - if @max_characters != 'undefined' 9 | textarea#seq.form-control autofocus="" name="seq" placeholder="Paste your sequence(s) here..." rows="10" spellcheck="false" data-maxCharacters="#{@max_characters}" 10 | - else 11 | textarea#seq.form-control autofocus="" name="seq" placeholder="Paste your sequence(s) here..." rows="10" spellcheck="false" 12 | .clearfix 13 | .form-group 14 | button#input_btn.btn.btn-lg.btn-primary type="submit" value="input" 15 | i.fa.fa-search 16 | |   Analyse Sequences 17 | button#adv_params_btn.btn.btn-primary type="button" onclick="changeAdvParamsBtnText()" 18 | i.fa.fa-pencil-square-o 19 | |   Show Advanced Parameters 20 | .clearfix 21 | #adv_params.collapse 22 | .form-group.form-inline#validations_group 23 | br/ 24 | label.control-label Advanced Parameters: Validations Types 25 | br/ 26 | label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12 27 | Length Validation (via clusterization) 28 | label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12 29 | Length Validation (via ranking) 30 | label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12 31 | Duplication Check 32 | label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12 33 | Gene Merge Validation 34 | label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12 35 | Multiple Alignment Validation (proteins) 36 | label.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12 37 | Blast Reading Frame Validation (nucleotides) 38 | label#lastValidation.checkbox-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12 39 | Open Reading Frame Validation (nucleotides) 40 | .clearfix 41 | br/ 42 | .form-group.form-inline 43 | label.control-label Advanced Parameters: Database 44 | br/ 45 | label.radio-inline.no_indent.col-xs-12 46 | #{@default_db.title.chomp} 47 | - unless @non_default_dbs.empty? 48 | - @non_default_dbs.each do |db| 49 | label.radio-inline.no_indent.col-xs-12 50 | #{db.title.chomp} 51 | .clearfix 52 | .show_examples_text 53 | span 54 | a#protein_example onclick="examplarSequence('protein')" 55 | | Show a protein example 56 | span 57 | |  |  58 | span 59 | a#dna_example onclick="examplarSequence('dna')" 60 | | Show a DNA example 61 | section#results 62 | #results_box style="display:none;" 63 | h1#output_header.page-header 64 | span Results 65 | #output -------------------------------------------------------------------------------- /lib/genevalidatorapp/routes.rb: -------------------------------------------------------------------------------- 1 | require 'sinatra/base' 2 | require 'sinatra/cross_origin' 3 | require 'genevalidator/version' 4 | require 'genevalidatorapp/version' 5 | require 'slim' 6 | 7 | module GeneValidatorApp 8 | # The Sinatra Routes 9 | class Routes < Sinatra::Base 10 | register Sinatra::CrossOrigin 11 | 12 | configure do 13 | # We don't need Rack::MethodOverride. Let's avoid the overhead. 14 | disable :method_override 15 | 16 | # Ensure exceptions never leak out of the app. Exceptions raised within 17 | # the app must be handled by the app. We do this by attaching error 18 | # blocks to exceptions we know how to handle and attaching to Exception 19 | # as fallback. 20 | disable :show_exceptions, :raise_errors 21 | 22 | # Make it a policy to dump to 'rack.errors' any exception raised by the 23 | # app so that error handlers don't have to do it themselves. But for it 24 | # to always work, Exceptions defined by us should not respond to `code` 25 | # or http_status` methods. Error blocks errors must explicitly set http 26 | # status, if needed, by calling `status` method. 27 | enable :dump_errors 28 | 29 | # We don't want Sinatra do setup any loggers for us. We will use our own. 30 | set :logging, nil 31 | 32 | # This is the app root... 33 | set :root, -> { GeneValidatorApp.root } 34 | 35 | # This is the full path to the public folder... 36 | set :public_folder, -> { GeneValidatorApp.public_dir } 37 | end 38 | 39 | helpers do 40 | # Overide default URI helper method - to hardcode a https:// 41 | # In our setup, we are running passenger on http:// (not secure) and then 42 | # reverse proxying that onto a 443 port (i.e. https://) 43 | # Generates the absolute URI for a given path in the app. 44 | # Takes Rack routers and reverse proxies into account. 45 | def uri(addr = nil, absolute = true, add_script_name = true) 46 | return addr if addr =~ /\A[a-z][a-z0-9\+\.\-]*:/i 47 | uri = [host = ''] 48 | if absolute 49 | host << (GeneValidatorApp.ssl? ? 'https://' : 'http://') 50 | host << if request.forwarded? || request.port != (request.secure? ? 443 : 80) 51 | request.host_with_port 52 | else 53 | request.host 54 | end 55 | end 56 | uri << request.script_name.to_s if add_script_name 57 | uri << (addr || request.path_info).to_s 58 | File.join uri 59 | end 60 | 61 | def host_with_port 62 | forwarded = request.env['HTTP_X_FORWARDED_HOST'] 63 | if forwarded 64 | forwarded.split(/,\s?/).last 65 | else 66 | request.env['HTTP_HOST'] || "#{request.env['SERVER_NAME'] || 67 | request.env['SERVER_ADDR']}:#{request.env['SERVER_PORT']}" 68 | end 69 | end 70 | 71 | # Remove port number. 72 | def host 73 | host_with_port.to_s.sub(/:\d+\z/, '') 74 | end 75 | 76 | def base_url 77 | @base_url ||= "#{GeneValidatorApp.ssl? ? 'https' : 'http'}://#{host}" 78 | end 79 | end 80 | 81 | # Set up global variables for the templates... 82 | before '/' do 83 | @default_db = Database.default_db 84 | @non_default_dbs = Database.non_default_dbs 85 | @max_characters = GeneValidatorApp.config[:max_characters] 86 | @current_gv_version = GeneValidator::VERSION 87 | end 88 | 89 | get '/' do 90 | slim :index 91 | end 92 | 93 | post '/' do 94 | cross_origin # Required for the API to work... 95 | RunGeneValidator.init(request.url, params) 96 | @gv_results = RunGeneValidator.run 97 | @json_data_section = @gv_results[:parsed_json] 98 | if @params[:results_url] 99 | @gv_results[:results_url] 100 | elsif @params[:json_url] 101 | @gv_results[:json_url] 102 | else 103 | slim :results, layout: false 104 | end 105 | end 106 | 107 | # This error block will only ever be hit if the user gives us a funny 108 | # sequence or incorrect advanced parameter. Well, we could hit this block 109 | # if someone is playing around with our HTTP API too. 110 | error RunGeneValidator::ArgumentError do 111 | status 400 112 | slim :"500", layout: false 113 | end 114 | 115 | # This will catch any unhandled error and some very special errors. Ideally 116 | # we will never hit this block. If we do, there's a bug in GeneValidatorApp 117 | # or something really weird going on. 118 | # TODO: If we hit this error block we show the stacktrace to the user 119 | # requesting them to post the same to our Google Group. 120 | error Exception, RunGeneValidator::RuntimeError do 121 | status 500 122 | slim :"500", layout: false 123 | end 124 | 125 | not_found do 126 | status 404 127 | slim :"500" # TODO: Create another Template 128 | end 129 | end 130 | end 131 | -------------------------------------------------------------------------------- /lib/genevalidatorapp/exceptions.rb: -------------------------------------------------------------------------------- 1 | # This file defines all possible exceptions that can be thrown by 2 | # GeneValidatorApp on startup. 3 | # 4 | # Exceptions only ever inform another entity (downstream code or users) of an 5 | # issue. Exceptions may or may not be recoverable. 6 | # 7 | # Error classes should be seen as: the error code (class name), human readable 8 | # message (to_s method), and necessary attributes to act on the error. 9 | # 10 | # We define as many error classes as needed to be precise about the issue, thus 11 | # making it easy for downstream code (bin/genevalidatorapp or config.ru) to act 12 | # on them. 13 | 14 | module GeneValidatorApp 15 | # Error in config file. 16 | class CONFIG_FILE_ERROR < StandardError 17 | def initialize(ent, err) 18 | @ent = ent 19 | @err = err 20 | end 21 | 22 | attr_reader :ent, :err 23 | 24 | def to_s 25 | < at , but 44 | # didn't". 45 | # 46 | # ENOENT is raised if and only if an entity was set, either using CLI or 47 | # config file. For instance, it's compulsory to set database_dir. But ENOENT 48 | # is not raised if database_dir is not set. ENOENT is raised if database_dir 49 | # was set, but does not exist. 50 | class ENOENT < StandardError 51 | def initialize(des, ent) 52 | @des = des 53 | @ent = ent 54 | end 55 | 56 | attr_reader :des, :ent 57 | 58 | def to_s 59 | "Could not find #{des}: #{ent}" 60 | end 61 | end 62 | 63 | # Raised if bin dir set, but does not exist. 64 | class BIN_DIR_NOT_FOUND < ENOENT 65 | def initialize(ent) 66 | super 'bin dir', ent 67 | end 68 | end 69 | 70 | # Raised if extension file set, but does not exist. 71 | class EXTENSION_FILE_NOT_FOUND < ENOENT 72 | def initialize(ent) 73 | super 'extension file', ent 74 | end 75 | end 76 | 77 | # Raised if database dir set, but does not exist. 78 | class DATABASE_DIR_NOT_FOUND < ENOENT 79 | def initialize(ent) 80 | super 'database dir', ent 81 | end 82 | end 83 | 84 | ## MAFFT NOT INSTALLED OR NOT COMPATIBLE ## 85 | 86 | # Raised if GV could not locate MAFFT binaries on 87 | # user's system. 88 | class MAFFT_NOT_INSTALLED < StandardError 89 | def to_s 90 | 'Could not locate MAFFT binaries.' 91 | end 92 | end 93 | 94 | ## BLAST NOT INSTALLED OR NOT COMPATIBLE ## 95 | 96 | # Raised if GV could not locate NCBI BLAST+ installation on 97 | # user's system. 98 | class BLAST_NOT_INSTALLED < StandardError 99 | def to_s 100 | 'Could not locate BLAST+ binaries.' 101 | end 102 | end 103 | 104 | # Raised if GV could not successfully execute 'blastp -version' 105 | # on user's system (see #141). 106 | class BLAST_NOT_EXECUTABLE < StandardError 107 | def to_s 108 | 'Error executing BLAST+ binaries.' 109 | end 110 | end 111 | 112 | # Raised if GV determined NCBI BLAST+ present on the user's 113 | # system but not meeting GV's minimum version requirement. 114 | class BLAST_NOT_COMPATIBLE < StandardError 115 | def initialize(version) 116 | @version = version 117 | end 118 | 119 | attr_reader :version 120 | 121 | def to_s 122 | <Submitted:'\ 140 | "#{Time.now.strftime('%H:%M-%B_%d_%Y')}\n") 141 | end 142 | sequence.gsub!(/^\>(\S+)/) do |s| 143 | if unique_queries.key?(s) 144 | unique_queries[s] += 1 145 | s + '_' + (unique_queries[s] - 1).to_s 146 | else 147 | unique_queries[s] = 1 148 | s 149 | end 150 | end 151 | @params[:seq] = sequence 152 | end 153 | 154 | # Asserts that the input file has been generated and is not empty 155 | def assert_input_file_present 156 | return if File.exist?(@input_file) && !File.zero?(@input_file) 157 | raise 'GeneValidatorApp was unable to create the input file.' 158 | end 159 | 160 | # Runs GeneValidator 161 | def run_genevalidator 162 | create_gv_log_file 163 | run_gv 164 | assert_json_output_file_produced 165 | rescue SystemExit 166 | raise 'GeneValidator failed to run properly' 167 | end 168 | 169 | def run_gv 170 | run_opt = gv_params 171 | GeneValidator.init(run_opt) 172 | GeneValidator.run 173 | end 174 | 175 | def gv_params 176 | { 177 | validations: @params[:validations], 178 | db: @db, 179 | num_threads: config[:num_threads], 180 | mafft_threads: config[:mafft_threads], 181 | min_blast_hits: 5, 182 | input_fasta_file: @input_file, 183 | output_formats: %w[html csv json summary], 184 | output_dir: File.join(@run_dir, 'output') 185 | } 186 | end 187 | 188 | def create_gv_log_file 189 | @gv_log_file = File.join(@run_dir, 'log_file.txt') 190 | logger.debug("Log file: #{@gv_log_file}") 191 | end 192 | 193 | # Assets whether the results file is produced by GeneValidator. 194 | def assert_json_output_file_produced 195 | @json_file = File.join(@run_dir, 'output/input_file_results.json') 196 | return if File.exist?(@json_file) 197 | raise 'GeneValidator did not produce the required output file.' 198 | end 199 | 200 | # Reuturns the URL of the results page. 201 | def produce_result_url_link(url) 202 | url.gsub(/input/, '').gsub(%r{/*$}, '') + 203 | "/GeneValidator/#{@unique_id}/output/results.html" 204 | end 205 | 206 | # Reuturns the URL of the results page. 207 | def produce_json_url_link(url) 208 | url.gsub(/input/, '').gsub(%r{/*$}, '') + 209 | "/GeneValidator/#{@unique_id}/output/input_file_results.json" 210 | end 211 | 212 | def parse_output_json 213 | json_contents = File.read(output_json_file_path) 214 | JSON.parse(json_contents, symbolize_names: true) 215 | end 216 | 217 | def output_json_file_path 218 | File.join(@run_dir, 'output/input_file_results.json') 219 | end 220 | 221 | def individual_json_path 222 | "/GeneValidator/#{@unique_id}/output/html_files/json" 223 | end 224 | end 225 | end 226 | end 227 | -------------------------------------------------------------------------------- /public/src/js/bionode-seq.min.js: -------------------------------------------------------------------------------- 1 | require=function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o=threshold||acgMatch+uMatch>=threshold){if(tMatch>=uMatch){return"dna"}else if(uMatch>=tMatch){return"rna"}else{return"dna"}}else if(proteinMatch>=threshold){return"protein"}};seq.createComplementBase=function(sequenceType){var complementBasesMatrix=sequenceType==="rna"||sequenceType==="ambiguousRna"?_rnaComplementBasesMatrix:_dnaComplementBasesMatrix;var getComplementBase=function(base){var complement=complementBasesMatrix[base];return complement||base};return getComplementBase};seq.reverse=function(sequence){return sequence.split("").reverse().join("")};seq.complement=function(sequence,reverse){var reverse=reverse||false;var sequenceType=seq.checkType(sequence);var getComplementBase=seq.createComplementBase(sequenceType);if(reverse){return sequence.split("").reverse().map(getComplementBase).join("")}else{return sequence.split("").map(getComplementBase).join("")}};seq.reverseComplement=function(sequence){return seq.complement(sequence,true)};seq.getTranscribedBase=function(base){return _transcribeBasesMatrix[base]||base};seq.getTranslatedAA=function(codon){return _translateCodonsMatrix[codon]};seq.removeIntrons=function(sequence,exonsRanges){var sequenceWithoutIntrons="";var exonsRangesSorted=exonsRanges.sort(function(a,b){return a[0]-b[0]});exonsRangesSorted.forEach(function(exonRange){sequenceWithoutIntrons+=sequence.substring(exonRange[0],exonRange[1])});return sequenceWithoutIntrons};seq.transcribe=function(sequence,exonsRanges){if(exonsRanges){var sequenceWithoutIntrons=seq.removeIntrons(sequence,exonsRanges);sequence=sequenceWithoutIntrons}var sequenceType=seq.checkType(sequence);if(sequenceType==="dna"||sequenceType==="ambiguousDna"){return sequence.replace(/t/g,"u").replace(/T/g,"U")}else if(sequenceType==="rna"||sequenceType==="ambiguousRna"){return sequence.replace(/u/g,"t").replace(/U/g,"T")}};seq.translate=function(sequence,exonsRanges){if(exonsRanges){var sequenceWithoutIntrons=seq.removeIntrons(sequence,exonsRanges);sequence=sequenceWithoutIntrons}var sequenceType=seq.checkType(sequence);var rna;if(sequenceType==="protein"){return sequence}else if(sequenceType==="dna"||sequenceType==="ambiguousDna"){if(sequenceType==="ambiguousDna")sequence.replace(/[wsmkrybdhv]/g,"x").replace(/[WSMKRYBDHV]/g,"X");rna=seq.transcribe(sequence,exonsRanges)}else if(sequenceType==="rna"||sequenceType==="ambiguousRna"){if(sequenceType==="ambiguousRna")sequence.replace(/[wsmkrybdhv]/g,"x").replace(/[WSMKRYBDHV]/g,"X");rna=sequence}return rna.match(/.{1,3}/g).map(seq.getTranslatedAA).join("")};seq.reverseExons=function(exonsRanges,referenceLength){var reversedExonsRanges=[];exonsRanges.forEach(function(exonRange){var start=referenceLength-exonRange[1];var stop=referenceLength-exonRange[0];reversedExonsRanges.push([start,stop])});return reversedExonsRanges};seq.findNonCanonicalSplices=function(sequence,exonsRanges){var nonCanonicalSplices=[];var exonsRangesSorted=exonsRanges.sort(function(a,b){return a[0]-b[0]});exonsRangesSorted.forEach(checkNonCanonicalIntron);function checkNonCanonicalIntron(exonRange,i){var donor=exonRange;var acceptor=exonsRangesSorted[i+1];if(!acceptor)return null;var intronRange=[donor[1],acceptor[0]];var intronStartBases=sequence.slice(intronRange[0],intronRange[0]+2).toLowerCase().replace("t","u");var intronStopBases=sequence.slice(intronRange[1]-2,intronRange[1]).toLowerCase();if(intronStartBases!=="gu")nonCanonicalSplices.push(intronRange[0]);if(intronStopBases!=="ag")nonCanonicalSplices.push(intronRange[1])}return nonCanonicalSplices};seq.checkCanonicalTranslationStartSite=function(sequence){return sequence.substring(0,3).toLowerCase().replace("t","u")==="aug"};seq.getReadingFrames=function(sequence){var reverse=seq.reverseComplement(sequence);return[sequence,sequence.substring(1),sequence.substring(2),reverse,reverse.substring(1),reverse.substring(2)]};seq.getOpenReadingFrames=function(sequence){var sequenceType=seq.checkType(sequence);var stopCodons;if(sequenceType==="dna"||sequenceType==="ambiguousDna"){stopCodons=["TAA","TGA","TAG","taa","tga","tag"]}else if(sequenceType==="rna"||sequenceType==="ambiguousRna"){stopCodons=["UAA","UGA","UAG","uaa","uga","uag"]}var openReadingFrames=[];var openReadingFrame="";sequence.match(/.{1,3}/g).forEach(function(codon){openReadingFrame+=codon;if(stopCodons.indexOf(codon)!==-1&&openReadingFrame.length>0){openReadingFrames.push(openReadingFrame);openReadingFrame=""}});openReadingFrames.push(openReadingFrame);return openReadingFrames};seq.getAllOpenReadingFrames=function(sequence){var readingFrames=seq.getReadingFrames(sequence);var allOpenReadingFrames=readingFrames.map(seq.getOpenReadingFrames);return allOpenReadingFrames};seq.findLongestOpenReadingFrame=function(sequence,frameSymbol){var frameSymbols=["+1","+2","+3","-1","-2","-3"];if(frameSymbol){var framePosition=frameSymbols.indexOf(frameSymbol);var readingFrame=seq.getReadingFrames(sequence)[framePosition];var openReadingFrames=seq.getOpenReadingFrames(readingFrame);var longestOpenReadingFrame=getLongestOpenReadingFrame(openReadingFrames);return longestOpenReadingFrame}else{var longestOpenReadingFrames=seq.getAllOpenReadingFrames(sequence).map(getLongestOpenReadingFrame);var longestOpenReadingFrame=getLongestOpenReadingFrame(longestOpenReadingFrames.slice());var framePosition=longestOpenReadingFrames.indexOf(longestOpenReadingFrame);var frameSymbol=frameSymbols[framePosition];return[longestOpenReadingFrame,frameSymbol]}function sortReadingFrames(a,b){var aSort=a.length;var bSort=b.length;if(bSort-aSort===0){var aStartCodon=a.slice(0,3).toUpperCase().replace("T","U");var bStartCodon=b.slice(0,3).toUpperCase().replace("T","U");if(aStartCodon==="AUG"){aSort++}if(bStartCodon==="AUG"){bSort++}}return bSort-aSort}function getLongestOpenReadingFrame(array){return array.sort(sortReadingFrames)[0]}}},{}],"bionode-seq":[function(require,module,exports){module.exports=require("./lib/bionode-seq")},{"./lib/bionode-seq":1}]},{},["bionode-seq"]); -------------------------------------------------------------------------------- /lib/genevalidatorapp.rb: -------------------------------------------------------------------------------- 1 | require 'yaml' 2 | require 'fileutils' 3 | 4 | require 'genevalidatorapp/config' 5 | require 'genevalidatorapp/database' 6 | require 'genevalidatorapp/exceptions' 7 | require 'genevalidatorapp/genevalidator' 8 | require 'genevalidatorapp/logger' 9 | require 'genevalidatorapp/routes' 10 | require 'genevalidatorapp/server' 11 | require 'genevalidatorapp/version' 12 | 13 | module GeneValidatorApp 14 | # Use a fixed minimum version of BLAST+ 15 | MINIMUM_BLAST_VERSION = '2.11.0+'.freeze 16 | 17 | class << self 18 | def environment 19 | ENV['RACK_ENV'] 20 | end 21 | 22 | def verbose? 23 | @verbose ||= (environment == 'development') 24 | end 25 | 26 | def root 27 | File.dirname(File.dirname(__FILE__)) 28 | end 29 | 30 | def ssl? 31 | @config[:ssl] 32 | end 33 | 34 | def logger 35 | @logger ||= Logger.new(STDERR, verbose?) 36 | end 37 | 38 | # Setting up the environment before running the app... 39 | def init(config = {}) 40 | @config = Config.new(config) 41 | 42 | init_binaries 43 | init_database 44 | 45 | init_dirs 46 | 47 | load_extension 48 | check_num_threads 49 | check_max_characters 50 | self 51 | end 52 | 53 | attr_reader :config, :temp_dir, :public_dir 54 | 55 | # Starting the app manually 56 | def run 57 | check_host 58 | Server.run(self) 59 | rescue Errno::EADDRINUSE 60 | puts "** Could not bind to port #{config[:port]}." 61 | puts " Is GeneValidator already accessible at #{server_url}?" 62 | puts ' No? Try running GeneValidator on another port, like so:' 63 | puts 64 | puts ' genevalidator app -p 4570.' 65 | rescue Errno::EACCES 66 | puts "** Need root privilege to bind to port #{config[:port]}." 67 | puts ' It is not advisable to run GeneValidator as root.' 68 | puts ' Please use Apache/Nginx to bind to a privileged port.' 69 | end 70 | 71 | def on_start 72 | puts '** GeneValidator is ready.' 73 | puts " Go to #{server_url} in your browser and start analysing genes!" 74 | puts ' Press CTRL+C to quit.' 75 | open_in_browser(server_url) 76 | end 77 | 78 | def on_stop 79 | puts 80 | puts '** Thank you for using GeneValidator :).' 81 | puts ' Please cite: ' 82 | puts ' Dragan M, Moghul MI, Priyam A, Bustos C, Wurm Y. 2016.' 83 | puts ' GeneValidator: identify problems with protein-coding gene' 84 | puts ' predictions. Bioinformatics, doi: 10.1093/bioinformatics/btw015.' 85 | end 86 | 87 | # Rack-interface. 88 | # 89 | # Inject our logger in the env and dispatch request to our controller. 90 | def call(env) 91 | env['rack.logger'] = logger 92 | Routes.call(env) 93 | end 94 | 95 | private 96 | 97 | def init_dirs 98 | config[:serve_public_dir] = File.expand_path(config[:serve_public_dir]) 99 | unique_start_id = 'GV_' + Time.now.strftime('%Y%m%d-%H-%M-%S').to_s 100 | @public_dir = File.join(config[:serve_public_dir], unique_start_id) 101 | init_public_dir 102 | end 103 | 104 | # Create the Public Dir and copy files from gem root - this public dir 105 | # is served by the app is accessible at URL/... 106 | def init_public_dir 107 | FileUtils.mkdir_p(File.join(@public_dir, 'GeneValidator')) 108 | root_web_files = File.join(GeneValidatorApp.root, 'public/web_files') 109 | root_gv = File.join(GeneValidatorApp.root, 'public/GeneValidator') 110 | FileUtils.cp_r(root_web_files, @public_dir) 111 | FileUtils.cp_r(root_gv, @public_dir) 112 | end 113 | 114 | def init_binaries 115 | config[:bin] = init_bins if config[:bin] 116 | assert_blast_installed_and_compatible 117 | assert_mafft_installed 118 | end 119 | 120 | def init_database 121 | set_database_from_env unless config[:database_dir] 122 | raise DATABASE_DIR_NOT_SET unless config[:database_dir] 123 | 124 | config[:database_dir] = File.expand_path(config[:database_dir]) 125 | unless File.exist?(config[:database_dir]) && 126 | File.directory?(config[:database_dir]) 127 | raise DATABASE_DIR_NOT_FOUND, config[:database_dir] 128 | end 129 | 130 | assert_blast_databases_present_in_database_dir 131 | logger.debug("Will use BLAST+ databases at: #{config[:database_dir]}") 132 | 133 | Database.scan_databases_dir 134 | Database.each do |database| 135 | logger.debug("Found #{database.type.chomp} database" \ 136 | " '#{database.title.chomp}' at '#{database.name.chomp}'") 137 | end 138 | end 139 | 140 | # attempt to set the database dir to GV_BLAST_DB_DIR if it exists 141 | def set_database_from_env 142 | config[:database_dir] = ENV['GV_BLAST_DB_DIR'] 143 | end 144 | 145 | def load_extension 146 | return unless config[:require] 147 | config[:require] = File.expand_path config[:require] 148 | unless File.exist?(config[:require]) && File.file?(config[:require]) 149 | raise EXTENSION_FILE_NOT_FOUND, config[:require] 150 | end 151 | 152 | logger.debug("Loading extension: #{config[:require]}") 153 | require config[:require] 154 | end 155 | 156 | def assert_blast_databases_present_in_database_dir 157 | cmd = "blastdbcmd -recursive -list '#{config[:database_dir]}'" 158 | out = `#{cmd}` 159 | errpat = /BLAST Database error/ 160 | raise NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty? 161 | raise BLAST_DATABASE_ERROR, cmd, out if out.match(errpat) || 162 | !$CHILD_STATUS.success? 163 | type = [] 164 | out.lines.each { |l| type << l.split[1] } 165 | return if type.include? 'Protein' 166 | raise NO_PROTEIN_BLAST_DATABASE_FOUND, config[:database_dir] 167 | end 168 | 169 | def check_num_threads 170 | num_threads = Integer(config[:num_threads]) 171 | raise NUM_THREADS_INCORRECT unless num_threads > 0 172 | 173 | logger.debug "Will use #{num_threads} threads to run BLAST." 174 | if num_threads > 256 175 | logger.warn "Number of threads set at #{num_threads} is unusually high." 176 | end 177 | rescue StandardError 178 | raise NUM_THREADS_INCORRECT 179 | end 180 | 181 | def check_max_characters 182 | if config[:max_characters] != 'undefined' 183 | config[:max_characters] = Integer(config[:max_characters]) 184 | end 185 | rescue StandardError 186 | raise MAX_CHARACTERS_INCORRECT 187 | end 188 | 189 | def init_bins 190 | bins = [] 191 | Array(config[:bin]).each do |bin| 192 | bins << File.expand_path(bin) 193 | unless File.exist?(bin) && File.directory?(bin) 194 | raise BIN_DIR_NOT_FOUND, config[:bin] 195 | end 196 | export_bin_dir(bin) 197 | end 198 | bins 199 | end 200 | 201 | ## Checks if dir is in $PATH and if not, it adds the dir to the $PATH. 202 | def export_bin_dir(bin_dir) 203 | return unless bin_dir 204 | return if ENV['PATH'].split(':').include?(bin_dir) 205 | ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}" 206 | end 207 | 208 | def assert_blast_installed_and_compatible 209 | raise BLAST_NOT_INSTALLED unless command? 'blastdbcmd' 210 | version = `blastdbcmd -version`.split[1] 211 | return if is_compatible(version, MINIMUM_BLAST_VERSION) 212 | raise BLAST_NOT_COMPATIBLE, version 213 | end 214 | 215 | def assert_mafft_installed 216 | raise MAFFT_NOT_INSTALLED unless command? 'mafft' 217 | end 218 | 219 | # Check and warn user if host is 0.0.0.0 (default). 220 | def check_host 221 | return unless config[:host] == '0.0.0.0' 222 | logger.warn 'Will listen on all interfaces (0.0.0.0).' \ 223 | ' Consider using 127.0.0.1 (--host option).' 224 | end 225 | 226 | def server_url 227 | host = config[:host] 228 | host = 'localhost' if host == '127.0.0.1' || host == '0.0.0.0' 229 | "http://#{host}:#{config[:port]}" 230 | end 231 | 232 | def open_in_browser(server_url) 233 | return if using_ssh? || verbose? 234 | if RUBY_PLATFORM =~ /linux/ && xdg? 235 | `xdg-open #{server_url}` 236 | elsif RUBY_PLATFORM =~ /darwin/ 237 | `open #{server_url}` 238 | end 239 | end 240 | 241 | def using_ssh? 242 | true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION'] 243 | end 244 | 245 | def xdg? 246 | true if ENV['DISPLAY'] && command?('xdg-open') 247 | end 248 | 249 | # Return `true` if the given command exists and is executable. 250 | def command?(command) 251 | system("which #{command} > /dev/null 2>&1") 252 | end 253 | 254 | # Returns true if the given version is higher than the minimum expected 255 | # version string. 256 | def is_compatible(given, expected) 257 | # The speceship operator (<=>) below returns -1, 0, 1 depending on 258 | # on whether the left operand is lower, same, or higher than the 259 | # right operand. We want the left operand to be the same or higher. 260 | (parse_version(given) <=> parse_version(expected)) >= 0 261 | end 262 | 263 | # Turn version string into an arrary of its component numbers. 264 | def parse_version(version_string) 265 | version_string.split('.').map(&:to_i) 266 | end 267 | end 268 | end 269 | -------------------------------------------------------------------------------- /public/src/css/custom.css: -------------------------------------------------------------------------------- 1 | html { 2 | /* This is required in order to make the footer stick to the bottom..*/ 3 | /* There is a js function that controls the bottom margin...*/ 4 | position: relative; 5 | min-height: 100%; 6 | } 7 | 8 | body { 9 | margin: 0; 10 | margin-top: 60px; 11 | background-color:#F5F5F5; 12 | } 13 | 14 | section { 15 | width: 100%; 16 | padding: 0 5%; 17 | display: table; 18 | margin: 0; 19 | max-width: none; 20 | padding-bottom: 35px; 21 | } 22 | 23 | .nav-container { 24 | width:100%; 25 | padding: 0 5%; 26 | margin: 0; 27 | } 28 | 29 | .navbar-brand { 30 | padding-left: 0; 31 | } 32 | 33 | footer { 34 | bottom: 0; 35 | width: 100%; 36 | margin: 0 auto; 37 | position: absolute; 38 | border-top: 2px solid #DBDBDB; 39 | padding-top:10px; 40 | } 41 | 42 | .alert-danger{ 43 | background-color: #f2dede; 44 | } 45 | 46 | .alert-danger p { 47 | font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; 48 | font-size: 14px; 49 | line-height: 20px; 50 | text-align: left; 51 | font-weight: 400; 52 | color: #ff1c21; 53 | } 54 | 55 | .alert-danger h3 { 56 | color: #ff1c21; 57 | } 58 | 59 | 60 | /* Navbar 61 | -------------------------------------------------- */ 62 | .navbar-nav>li>a, .navbar-brand { 63 | line-height: 27px; 64 | } 65 | 66 | .navbar-brand a { 67 | color:#fff; 68 | } 69 | 70 | .navbar-brand a:hover { 71 | text-decoration: none; 72 | } 73 | 74 | .navbar-nav > li > a.nav_github_icon { 75 | padding-top: 0; 76 | padding-bottom: 0; 77 | } 78 | 79 | .fa-github { 80 | color: #fff; 81 | padding-top: 18px; 82 | padding-bottom: 18px; 83 | } 84 | 85 | h1 .small { 86 | color: #2C3E50; 87 | } 88 | 89 | .input_seq-label { 90 | font-size: 26px; 91 | } 92 | 93 | #protein_example, #dna_example { 94 | cursor: pointer; 95 | } 96 | 97 | #adv_params_btn { 98 | display: block; 99 | margin-left: auto; 100 | margin-right: auto; 101 | margin-top: 20px; 102 | } 103 | 104 | #input_btn { 105 | display: block; 106 | margin-left: auto; 107 | margin-right: auto; 108 | } 109 | 110 | .show_examples_text { 111 | font-size: 17px; 112 | text-align: center; 113 | margin-top: 10px; 114 | } 115 | 116 | .control-label{ 117 | font-size: 1.25em; 118 | font-weight: normal; 119 | } 120 | 121 | label, .radio label, .checkbox label, .help-block { 122 | font-size: 0.9em; 123 | font-weight: inherit; 124 | } 125 | 126 | .checkbox.inline.no_indent+.checkbox.inline.no_indent { 127 | margin-left: 0; 128 | margin-right: 10px; 129 | 130 | } 131 | .checkbox.inline.no_indent:last-child { 132 | margin-right: 0px; 133 | } 134 | 135 | label.checkbox-inline.no_indent { 136 | margin-left: 0; 137 | margin-right: 10px; 138 | } 139 | 140 | label.radio-inline.no_indent { 141 | margin-left: 0; 142 | margin-right: 10px; 143 | } 144 | 145 | #results_header { 146 | margin-top: 0; 147 | margin-bottom: 30px; 148 | } 149 | 150 | #results_link_btn { 151 | margin-top: 0; 152 | margin-right: -15px; 153 | } 154 | 155 | /* Table 156 | -------------------------------------------------- */ 157 | .table { 158 | color: #333; 159 | } 160 | 161 | .table thead tr { 162 | border-bottom: 3px solid #DDD; 163 | } 164 | 165 | .table td { 166 | font-size: 13px !important; 167 | border-color: rgb(221, 221, 221) !important; 168 | } 169 | 170 | table .success, 171 | .table .success, 172 | table .warning, 173 | .table .warning, 174 | table .danger, 175 | .table .danger, 176 | table .info, 177 | .table .info { 178 | color: #333; 179 | } 180 | 181 | .table-bordered { 182 | border: none; 183 | } 184 | 185 | .danger { 186 | background-color: rgb(242, 222, 222) !important; 187 | } 188 | 189 | .danger:hover { 190 | background-color: rgb(242, 203, 203) !important; 191 | } 192 | 193 | .success { 194 | background-color: rgb(223, 240, 216) !important; 195 | } 196 | 197 | .success:hover{ 198 | background-color: rgb(204, 228, 200) !important; 199 | } 200 | 201 | .warning { 202 | background-color: rgb(252, 248, 227) !important; 203 | } 204 | 205 | .alert-info { 206 | background-color: rgb(217, 237, 247); 207 | border-color: rgb(188, 232, 241); 208 | border-style: solid; 209 | border-width: 1px; 210 | border-collapse: collapse; 211 | box-sizing: border-box; 212 | color: rgb(49, 112, 143); 213 | display: block; 214 | margin-bottom: 0px; 215 | padding-bottom: 15px; 216 | padding-left: 15px; 217 | padding-right: 15px; 218 | padding-top: 15px; 219 | } 220 | 221 | .explanation_alert p { 222 | font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; 223 | font-size: 14px; 224 | line-height: 20px; 225 | text-align: left; 226 | font-weight: 400; 227 | } 228 | 229 | .plot_btn { 230 | color: #333; 231 | background-color: #fff; 232 | border-color: #ccc; 233 | } 234 | 235 | .plot_btn:hover { 236 | color: #333; 237 | background-color: #ebebeb; 238 | border-color: #adadad 239 | } 240 | 241 | .table-bordered>thead>tr>th, 242 | .table-bordered>tbody>tr>th, 243 | .table-bordered>tfoot>tr>th, 244 | .table-bordered>thead>tr>td, 245 | .table-bordered>tbody>tr>td, 246 | .table-bordered>tfoot>tr>td { 247 | border:none; 248 | } 249 | 250 | .table-bordered>tbody>tr { 251 | border-bottom: 2px solid #DDD; 252 | } 253 | 254 | .error_header { 255 | margin-top: 10px; 256 | } 257 | 258 | 259 | /* GeneValidator Results... 260 | -------------------------------------------------- */ 261 | .explanation_alert{ 262 | margin-bottom: 0; 263 | } 264 | 265 | /* TABLE 266 | ___________________________*/ 267 | 268 | .table-responsive { 269 | overflow-x: auto; 270 | } 271 | 272 | .table td { 273 | vertical-align: middle !important; 274 | border-collapse: collapse; 275 | background-clip: padding-box; 276 | text-align: left; 277 | } 278 | 279 | .table th, 280 | .table thead td { 281 | background-color: #E8E8E8; 282 | white-space: nowrap; 283 | } 284 | 285 | tr { 286 | height: 39px; 287 | } 288 | 289 | .expanded-child{ 290 | display: block; 291 | text-align: center; 292 | } 293 | 294 | /* table sorter ___________*/ 295 | 296 | 297 | .tablesorter-default .header, 298 | .tablesorter-default .tablesorter-header { 299 | background-image: url(data:image/gif;base64,R0lGODlhFQAJAIAAACMtMP///yH5BAEAAAEALAAAAAAVAAkAAAIXjI+AywnaYnhUMoqt3gZXPmVg94yJVQAAOw==); 300 | background-position: center right; 301 | background-repeat: no-repeat; 302 | cursor: pointer; 303 | padding: 4px 20px 4px 4px; 304 | } 305 | .tablesorter-default thead .headerSortUp, 306 | .tablesorter-default thead .tablesorter-headerSortUp, 307 | .tablesorter-default thead .tablesorter-headerAsc { 308 | background-image: url(data:image/gif;base64,R0lGODlhFQAEAIAAACMtMP///yH5BAEAAAEALAAAAAAVAAQAAAINjI8Bya2wnINUMopZAQA7); 309 | border-bottom: #000 3px solid !important; 310 | } 311 | .tablesorter-default thead .headerSortDown, 312 | .tablesorter-default thead .tablesorter-headerSortDown, 313 | .tablesorter-default thead .tablesorter-headerDesc { 314 | background-image: url(data:image/gif;base64,R0lGODlhFQAEAIAAACMtMP///yH5BAEAAAEALAAAAAAVAAQAAAINjB+gC+jP2ptn0WskLQA7); 315 | border-bottom: #000 3px solid !important; 316 | } 317 | .tablesorter-default thead .sorter-false { 318 | background-image: none; 319 | cursor: default; 320 | padding: 4px; 321 | } 322 | 323 | /* table processing indicator */ 324 | .tablesorter-default .tablesorter-processing { 325 | background-position: center center !important; 326 | background-repeat: no-repeat !important; 327 | background-image: url('data:image/gif;base64,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') !important; 328 | } 329 | 330 | /* table icons ___________*/ 331 | 332 | .table tbody td.success, 333 | .table tbody td.danger, 334 | .table tbody td.warning { 335 | padding-left:30px !important; 336 | position:relative; 337 | } 338 | 339 | .table tbody td.success:before, 340 | .table tbody td.danger:before, 341 | .table tbody td.warning:before { 342 | font-family: FontAwesome; 343 | position: absolute; 344 | margin-left:-25px; 345 | font-size: 1.5em; 346 | margin-top: -0.75em; 347 | top:50%; 348 | } 349 | 350 | .table tbody td.success:before { 351 | content: "\f058"; 352 | color:#1AA882; 353 | } 354 | 355 | .table tbody td.danger:before { 356 | content: "\f057"; 357 | color:#FC585A; 358 | } 359 | 360 | .table tbody td.warning:before{ 361 | content: "\f06a"; 362 | color:#FCB83F; 363 | } 364 | 365 | .table tbody td.success, 366 | .table tbody td.danger { 367 | cursor: pointer !important; 368 | } 369 | 370 | /* Tooltips 371 | ___________________________*/ 372 | 373 | .tooltip > .tooltip-inner { 374 | background-color: #fff; 375 | color: #000; 376 | border: 1px solid #CCCCCC; 377 | max-width:275px; 378 | } 379 | 380 | .tooltip.top > .tooltip-arrow { 381 | bottom:0; 382 | left:50%; 383 | margin-left:-5px; 384 | border-left:5px solid transparent; 385 | border-right:5px solid transparent; 386 | border-top:5px solid #CCC 387 | } 388 | 389 | /* D3Js & Axis 390 | ___________________________*/ 391 | .axis path, 392 | .axis line { 393 | fill: none; 394 | stroke: #000; 395 | shape-rendering: crispEdges; 396 | } 397 | 398 | .dot { 399 | stroke: #000; 400 | opacity:0.7; 401 | } 402 | 403 | .line1 { 404 | fill: green; 405 | stroke: black; 406 | stroke-width: 1.5px; 407 | opacity:0.5; 408 | } 409 | 410 | svg:not(:root) { 411 | overflow: visible; 412 | } 413 | 414 | svg { 415 | margin:15px; 416 | } 417 | 418 | /* Ratings... 419 | ___________________________*/ 420 | 421 | .ratings { 422 | position: relative; 423 | vertical-align: middle; 424 | display: inline-block; 425 | color: #b1b1b1; 426 | overflow: hidden; 427 | } 428 | 429 | .full-stars{ 430 | position: absolute; 431 | left: 0; 432 | top: 0; 433 | white-space: nowrap; 434 | overflow: hidden; 435 | color: #fde16d; 436 | } 437 | 438 | .empty-stars:before, 439 | .full-stars:before { 440 | font-family: FontAwesome; 441 | content: "\f005\f005\f005\f005\f005"; 442 | font-size: 14pt; 443 | } 444 | 445 | .empty-stars:before { 446 | -webkit-text-stroke: 1px #848484; 447 | } 448 | 449 | .full-stars:before { 450 | -webkit-text-stroke: 1px orange; 451 | } 452 | 453 | /* Other 454 | ___________________________*/ 455 | 456 | .menu_icon { 457 | padding-left: 10px; 458 | font-weight: bold; 459 | } 460 | 461 | #toggle { 462 | text-align:center; 463 | } 464 | 465 | .tooltip-inner { 466 | white-space: pre-wrap; 467 | min-width: 100px; 468 | } 469 | 470 | #report { 471 | text-align: left; 472 | } 473 | 474 | 475 | /* Responsive CSS 476 | ___________________________*/ 477 | 478 | @media (min-width: 768px) { 479 | #adv_params_btn { 480 | float:left !important; 481 | margin-top:0; 482 | } 483 | 484 | #input_btn { 485 | float:right !important; 486 | } 487 | 488 | .show_examples_text { 489 | text-align: left; 490 | } 491 | 492 | .container{ 493 | width:90%; 494 | } 495 | } 496 | 497 | 498 | /* Browser Specific 499 | ___________________________*/ 500 | 501 | /* Border on Stars ________*/ 502 | /* Webkit-text-stroke not support on firefox or IE */ 503 | /* Firefox */ 504 | @-moz-document url-prefix() { 505 | .full-stars{ 506 | color: #ECBE24; 507 | } 508 | } 509 | /* IE */ 510 | 516 | -------------------------------------------------------------------------------- /public/src/js/genevalidator.js: -------------------------------------------------------------------------------- 1 | $(document).ready(function() { 2 | 'use strict'; 3 | checkCollapseState(); 4 | keepFooterFixedToBottom(); 5 | addSeqValidation(); 6 | inputValidation(); 7 | bindTdClicks(); 8 | 9 | $(document).bind('keydown', function (e) { 10 | if (e.ctrlKey && e.keyCode === 13 ) { 11 | $('#input').trigger('submit'); 12 | } 13 | }); 14 | }); 15 | 16 | // Looks for a cookie (called 'GeneValidator_adv_params_status') to check the state of the adv_params box when it was last closed. 17 | // This function is called upon as soon as the website is loaded; 18 | var checkCollapseState = function () { 19 | 'use strict'; 20 | if ($.cookie('GeneValidator_adv_params_status')){ 21 | var adv_params_status = $.cookie('GeneValidator_adv_params_status'); 22 | if (adv_params_status === 'open') { 23 | var btn = document.getElementById('adv_params_btn'); 24 | btn.innerHTML = '  Hide Advanced Parameters'; 25 | $('#adv_params').addClass('in'); 26 | } 27 | } 28 | }; 29 | 30 | // This function simply ensures that the footer stays to fixed to the bottom of the window 31 | var keepFooterFixedToBottom = function () { 32 | 'use strict'; 33 | $('#mainbody').css({'margin-bottom': (($('#footer').height()) + 15)+'px'}); 34 | $(window).resize(function(){ 35 | $('#mainbody').css({'margin-bottom': (($('#footer').height()) + 15)+'px'}); 36 | }); 37 | }; 38 | 39 | // Creates a custom Validation for Jquery Validation plugin... 40 | // It ensures that sequences are either protein or DNA data... 41 | // If there are multiple sequences, ensures that they are of the same type 42 | // It utilises the checkType function (further below)... 43 | var addSeqValidation = function () { 44 | 'use strict'; 45 | jQuery.validator.addMethod('checkInputType', function(value, element) { 46 | var types = [], 47 | type = ''; 48 | if (value.charAt(0) === '>') { 49 | var seqs_array = value.split('>'); 50 | for (var i = 1; i < seqs_array.length; i++) { 51 | var lines = seqs_array[i].split('\n'); 52 | if (lines.length !== 0) { 53 | var clean_lines = jQuery.grep(lines,function(n){ return(n); }); 54 | if (clean_lines.length !== 0){ 55 | clean_lines.shift(); 56 | var seq = clean_lines.join(''); 57 | type = checkType(seq, 0.9); 58 | types.push(type); 59 | if ((type !== 'protein') && (type !== 'dna') && (type !== 'rna')) { 60 | return false; 61 | } 62 | } 63 | } 64 | } 65 | var firstType = types[0]; 66 | for (var j = 0; j < types.length; j++) { 67 | if (types[j] !== firstType){ 68 | return false; 69 | } 70 | } 71 | return true; 72 | } else { 73 | type = checkType(value, 0.9); 74 | if ((type !== 'protein') && (type !== 'dna') && (type !== 'rna')) { 75 | return false; 76 | } else { 77 | return true; 78 | } 79 | } 80 | }, '* The Input must be either DNA or protein sequence(s). Please ensure that your sequences do not contains any non-letter character(s). If there are multiple sequences, ensure that they are all of one type. '); 81 | }; 82 | 83 | 84 | // A function that validates the input - Utilises Jquery.Validator.js 85 | var inputValidation = function () { 86 | 'use strict'; 87 | var maxCharacters = $('#seq').attr('data-maxCharacters'); // returns a number or undefined 88 | $('#input').validate({ 89 | rules: { 90 | seq: { 91 | minlength: 5, 92 | required: true, 93 | checkInputType: true, 94 | maxlength: maxCharacters // when undefined, maxlength is unlimited 95 | }, 96 | 'validations[]': { 97 | required: true, 98 | }, 99 | }, 100 | highlight: function(element) { 101 | $(element).closest('.form-group').addClass('has-error'); 102 | }, 103 | unhighlight: function(element) { 104 | $(element).closest('.form-group').removeClass('has-error'); 105 | }, 106 | errorElement: 'span', 107 | errorClass: 'help-block', 108 | errorPlacement: function(error, element) { 109 | if (element.parent().parent().attr('id') === 'validations_group') { 110 | var helpText = document.getElementById('lastValidation'); 111 | error.insertAfter(helpText); 112 | } else { 113 | if (element.parent('.input-group').length) { 114 | error.insertAfter(element.parent()); 115 | } else { 116 | error.insertAfter(element); 117 | } 118 | } 119 | }, 120 | submitHandler: function(form) { 121 | $('#spinner').modal({ 122 | backdrop: 'static', 123 | keyboard: 'false' 124 | }); 125 | ajaxFunction(); 126 | } 127 | }); 128 | }; 129 | 130 | var bindTdClicks = function () { 131 | $( document ).on( "click", "td, .plot_btn", function( event ) { 132 | if ($(this).hasClass('success') || $(this).hasClass('danger')){ 133 | var title = $(this).attr('title'); 134 | var val = title.replace(/[ \/]/g, ''); 135 | GV.addData(this, val); 136 | } else if ($(this).hasClass('plot_btn')){ 137 | GV.addData(this, 'all'); 138 | } 139 | }); 140 | }; 141 | 142 | // Sends the data within the form to the Server 143 | var ajaxFunction = function () { 144 | 'use strict'; 145 | $.ajax({ 146 | type: 'POST', 147 | url: $('#input').attr('action'), 148 | data: $('#input').serialize(), 149 | success: function(response){ 150 | $('#results_box').show(); 151 | $('#output').html(response); 152 | GV.toggleOverviewBtn(); // add overview info from JSON 153 | initTableSorter(); // initiate the table sorter 154 | $("[data-toggle='tooltip']").tooltip(); // Initiate the tooltips 155 | 156 | $('#mainbody').css({'background-color': '#fff'}); 157 | $('#search').css({'background-color': '#F5F5F5'}); 158 | $('#results').css({'border-top': '3px solid #DBDBDB'}); 159 | $('#search').css({'margin-bottom': '0'}); 160 | 161 | $('#spinner').modal('hide'); // remove progress notification 162 | }, 163 | error: function (e, status) { 164 | var errorMessage; 165 | if (e.status == 500 || e.status == 400) { 166 | errorMessage = e.responseText; 167 | $('#results_box').show(); 168 | $('#output').html(errorMessage); 169 | $('#spinner').modal('hide'); // remove progress notification 170 | } else { 171 | errorMessage = e.responseText; 172 | $('#results_box').show(); 173 | $('#output').html('There seems to be an unidentified Error.'); 174 | $('#spinner').modal('hide'); // remove progress notification 175 | } 176 | } 177 | }); 178 | }; 179 | 180 | // Table sortert Initialiser 181 | // Contains a custom parser that allows the Stars to be sorted. 182 | var initTableSorter = function () { 183 | 'use strict'; 184 | $.tablesorter.addParser({ 185 | id: 'star_scores', 186 | is: function(s) {return false;}, 187 | format: function(s, table, cell, cellIndex) { 188 | var $cell = $(cell); 189 | if (cellIndex === 1) { 190 | return $cell.attr('data-score') || s; 191 | } 192 | return s; 193 | }, 194 | parsed: false, 195 | type: 'numeric' 196 | }); 197 | 198 | $('table').tablesorter({ 199 | headers: { 200 | 1 : { sorter: 'star_scores' } 201 | }, 202 | sortList: [[0,0]], 203 | }); 204 | }; 205 | 206 | // Function is called each time the Adv. Params button is pressed... 207 | var changeAdvParamsBtnText = function () { 208 | 'use strict'; 209 | var btn = document.getElementById('adv_params_btn'); 210 | if (btn.innerHTML === '  Show Advanced Parameters') { 211 | btn.innerHTML = '  Hide Advanced Parameters'; 212 | $('#adv_params').collapse('show'); 213 | $.cookie('GeneValidator_adv_params_status', 'open'); 214 | } 215 | else { 216 | btn.innerHTML = '  Show Advanced Parameters'; 217 | $('#adv_params').collapse('hide'); 218 | $.cookie('GeneValidator_adv_params_status', 'closed'); 219 | } 220 | }; 221 | 222 | // Changes the input to an examplar dna or protein sequence... 223 | var examplarSequence = function (type){ 224 | 'use strict'; 225 | var dna = '>Insulin\n' + 226 | 'ATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG\n' + 227 | '>Insulin (with a duplication)\n' + 228 | 'ATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGACAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG'; 229 | var protein = '>Methylmalonyl-CoA carboxyltransferase 12S \n' + 230 | 'MAENNNLKLASTMEGRVEQLAEQRQVIEAGGGERRVEKQHSQGKQTARERLNNLLDPHSFDEVGAFRKHRTTLFGMDKAVVPADGVVTGRGTILGRPVHAASQDFTVMGGSAGETQSTKVVETMEQALLTGTPFLFFYDSGGARIQEGIDSLSGYGKMFFANVKLSGVVPQIAIIAGPCAGGASYSPALTDFIIMTKKAHMFITGPQVIKSVTGEDVTADELGGAEAHMAISGNIHFVAEDDDAAELIAKKLLSFLPQNNTEEASFVNPNNDVSPNTELRDIVPIDGKKGYDVRDVIAKIVDWGDYLEVKAGYATNLVTAFARVNGRSVGIVANQPSVMSGCLDINASDKAAEFVNFCDSFNIPLVQLVDVPGFLPGVQQEYGGIIRHGAKMLYAYSEATVPKITVVLRKAYGGSYLAMCNRDLGADAVYAWPSAEIAVMGAEGAANVIFRKEIKAADDPDAMRAEKIEEYQNAFNTPYVAAARGQVDDVIDPADTRRKIASALEMYATKRQTRPAKKPWKLPLLSEEEIMADEEEKDLMIATLNKRVASLESELGSLQSDTQGVTEDVLTAISAVAAYLGNDGSAEVVHFAPSPNWVREGRRALQNHSIR\n' + 231 | '>locus=Si_gnF\n' + 232 | 'MWFPVVLLLLVGVAVAMPDHEHAWEPQNEYQYSVFVRTLTGVDTLKQQYTGIQLKGVLVIQVKSEELLQAKYINPRYAHIHQELSNGPYSKIPEENLEYRDIPMSGKPFEIKLKHGVIRDLLFDRNVPTWEVNMLKGIVGQLQIDTQGENAIDSQSTQIPSNSEPSSATFKAMEDSVGGKCEVLYEITPLPQHVAQTRPDRVPMSSVPSKGHHYEVKKLKNYEKCQERQLYHYGMDVKMTKENMMKRNKVVSELSTTHIVITGTLKSFTIQSTEMKNEITVQPESSDSPIGTVYSITKLTLAKINKISNSWFGPLELSNVESTGNLVYIFNNPFSDSEQRRVGQPSISRNSEQENSLETKKRSFHSHSSSSSSSSSSSSEEENESVMQSKASLRNIFMAPNVPLLPYFIGFKGKTIMKSNEHNVMQLAKDLLLQIAKEIQNPSEGYENTLEKYVNLKNLIRTMDRKQYTELEQYVSQFNKATVEGENAWYTLRDAVVHAGTGPAFVTIENWLKSGQVKGEEAAELLSKIPKSVHQPTPDYIKEFFKLIKSSVVTQQEYVNVSAPLAFAELLRNNYVVPSYYPVHSFGRMTLKGNEEIDNYISYLANQLQQGYLENNTQKIQTFIFALGVTAHPKIISVFEPYLEGKLPTTKYQRMLMVAALYDLSRDIPKLVGPIFYKLYMNENEAHEVRCMAVQQFILTDPPMITLQRVAKYTNYDQSDQVNSAVKSTLNSIINTKRPEWRNLANKARSVRYLVNPKNYDTWYSKGYYIDFENWVFKGLNVKMVASNDAVLPRYVYVGLDSIFNFLRKPTFEVGYAVSSYRQVYDLINELWNSYQFEEMREKSQGSRVEKLAQELKIKSGQKNNLEGHVLFNSVYGSMVYPYDKHRIREAVAALKKLLTSDSKLKTTAFNNFEKIVSFPMEMGVPFVYSFELPVFVKSEINFKKGEPITSRSGVYETLFCNRVQKRFGFIAPFEYQNYIAGIDKNGIMRVPLKYETNIDIKQKNFALKIHPNIPQSGTSTGLTHYSVVPFTTRQNIFNLQPVSNEGNTRPVITSEIHKMTKEKGPFSIKIESDTTKKESVLEDIVTGISKSSNSNNERYMKIDTTFESKQVAKCEIQIDMTFDAVTIHGKNQQPSHKEMQHHSKLDWKPNSKERREEIVNVLSAGLKSGTVFVADVSFSLPRLQDNTYVFTVGSVRSNIDQKLRHYFYVNTNAAQEVKYELCYSQEVQYAYPTPLNFEYAINNEPKDKLKGVLRYGRTCNTGNEIVITGSSSQSPQLRDMIENSSITKQCMEEIQKGKKSVRTCNKATDVAQVRDQLNFHIDASQLSEIRQKYDQVIGLLNYTNLSQYNVQQNSETNTIVVQNPWVMVPTVQEPWYRWAIKPSESQRQSEIDVLLDEVSQPSCTLDNDKILTFDNQLYNVQLGKCKHVLLTTYPQDSHNRRNYIPESSKVAVLAKDTDNDSRNVYVWLGNLEIELKKVGNDLKVAINGQNVEIPEKGHQESNGNEIIFEIVQLPDGSLSVISEKYGITVIFDGKHVRLYANGATYRNAIRGLCGNYDSRRDNDFLTPKNCLLTKPEEFAATYAMTNENCQGPAPENKRKAEGAMCIEVPEQQQMNVISDREAGRMMTEGGNWGYHQSNRKKEHGQDSKRGHGHKKYNQKDSQEGGSNESQYRKKHNIVYRTRVVEMDDKICFTTTPVPGCLQDTRPVERVPKKYDLYCLSKNNESMDLKRRVEEGAKPDFTQKPVNKIQNFQIPVSCSAA'; 233 | 234 | if (type === 'dna'){ 235 | document.getElementById('seq').value = dna; 236 | } else if (type === 'protein') { 237 | document.getElementById('seq').value = protein; 238 | } 239 | }; 240 | 241 | // FROM BIONODE-Seq - See https://github.com/bionode/bionode-seq 242 | // Checks whether a sequence is a protein or dna sequence... 243 | var checkType = function (sequence, threshold, length, index) { 244 | 'use strict'; 245 | if (threshold === undefined) { 246 | threshold = 0.9; 247 | } 248 | if (length === undefined) { 249 | length = 10000; 250 | } 251 | if (index === undefined) { 252 | index = 1; 253 | } 254 | var seq = sequence.slice(index - 1, length); 255 | 256 | var dnaSeq = seq.replace(/N/gi,''); 257 | var dnaTotal = dnaSeq.length; 258 | var acgMatch = ((dnaSeq.match(/[ACG]/gi) || []).length) / dnaTotal; 259 | var tMatch = ((dnaSeq.match(/[T]/gi) || []).length) / dnaTotal; 260 | var uMatch = ((dnaSeq.match(/[U]/gi) || []).length) / dnaTotal; 261 | 262 | var proteinSeq = seq.replace(/X/gi,''); 263 | var proteinTotal = proteinSeq.length; 264 | var proteinMatch = ((seq.match(/[ARNDCQEGHILKMFPSTWYV\*]/gi) || []).length) / proteinTotal; 265 | 266 | if (((acgMatch + tMatch) >= threshold) || ((acgMatch + uMatch) >= threshold)) { 267 | if (tMatch >= uMatch) { 268 | return 'dna'; 269 | } else if (uMatch >= tMatch) { 270 | return 'rna'; 271 | } else { 272 | return 'dna'; 273 | } 274 | } else if (proteinMatch >= threshold) { 275 | return 'protein'; 276 | } 277 | }; 278 | -------------------------------------------------------------------------------- /public/src/css/font-awesome.min.css: -------------------------------------------------------------------------------- 1 | /*! 2 | * Font Awesome 4.1.0 by @davegandy - http://fontawesome.io - @fontawesome 3 | * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License) 4 | 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c,d=a(b),e=b.type;return"radio"===e||"checkbox"===e?a("input[name='"+b.name+"']:checked").val():"number"===e&&"undefined"!=typeof b.validity?b.validity.badInput?!1:d.val():(c=d.val(),"string"==typeof c?c.replace(/\r/g,""):c)},check:function(b){b=this.validationTargetFor(this.clean(b));var c,d,e,f=a(b).rules(),g=a.map(f,function(a,b){return b}).length,h=!1,i=this.elementValue(b);for(d in f){e={method:d,parameters:f[d]};try{if(c=a.validator.methods[d].call(this,i,b,e.parameters),"dependency-mismatch"===c&&1===g){h=!0;continue}if(h=!1,"pending"===c)return void(this.toHide=this.toHide.not(this.errorsFor(b)));if(!c)return this.formatAndAdd(b,e),!1}catch(j){throw this.settings.debug&&window.console&&console.log("Exception occurred when checking element "+b.id+", check the '"+e.method+"' method.",j),j}}if(!h)return this.objectLength(f)&&this.successList.push(b),!0},customDataMessage:function(b,c){return a(b).data("msg"+c.charAt(0).toUpperCase()+c.substring(1).toLowerCase())||a(b).data("msg")},customMessage:function(a,b){var c=this.settings.messages[a];return c&&(c.constructor===String?c:c[b])},findDefined:function(){for(var a=0;aWarning: No message defined for "+b.name+"")},formatAndAdd:function(b,c){var d=this.defaultMessage(b,c.method),e=/\$?\{(\d+)\}/g;"function"==typeof d?d=d.call(this,c.parameters,b):e.test(d)&&(d=a.validator.format(d.replace(e,"{$1}"),c.parameters)),this.errorList.push({message:d,element:b,method:c.method}),this.errorMap[b.name]=d,this.submitted[b.name]=d},addWrapper:function(a){return this.settings.wrapper&&(a=a.add(a.parent(this.settings.wrapper))),a},defaultShowErrors:function(){var a,b,c;for(a=0;this.errorList[a];a++)c=this.errorList[a],this.settings.highlight&&this.settings.highlight.call(this,c.element,this.settings.errorClass,this.settings.validClass),this.showLabel(c.element,c.message);if(this.errorList.length&&(this.toShow=this.toShow.add(this.containers)),this.settings.success)for(a=0;this.successList[a];a++)this.showLabel(this.successList[a]);if(this.settings.unhighlight)for(a=0,b=this.validElements();b[a];a++)this.settings.unhighlight.call(this,b[a],this.settings.errorClass,this.settings.validClass);this.toHide=this.toHide.not(this.toShow),this.hideErrors(),this.addWrapper(this.toShow).show()},validElements:function(){return this.currentElements.not(this.invalidElements())},invalidElements:function(){return a(this.errorList).map(function(){return this.element})},showLabel:function(b,c){var d,e,f,g=this.errorsFor(b),h=this.idOrName(b),i=a(b).attr("aria-describedby");g.length?(g.removeClass(this.settings.validClass).addClass(this.settings.errorClass),g.html(c)):(g=a("<"+this.settings.errorElement+">").attr("id",h+"-error").addClass(this.settings.errorClass).html(c||""),d=g,this.settings.wrapper&&(d=g.hide().show().wrap("<"+this.settings.wrapper+"/>").parent()),this.labelContainer.length?this.labelContainer.append(d):this.settings.errorPlacement?this.settings.errorPlacement(d,a(b)):d.insertAfter(b),g.is("label")?g.attr("for",h):0===g.parents("label[for='"+h+"']").length&&(f=g.attr("id"),i?i.match(new RegExp("\b"+f+"\b"))||(i+=" "+f):i=f,a(b).attr("aria-describedby",i),e=this.groups[b.name],e&&a.each(this.groups,function(b,c){c===e&&a("[name='"+b+"']",this.currentForm).attr("aria-describedby",g.attr("id"))}))),!c&&this.settings.success&&(g.text(""),"string"==typeof this.settings.success?g.addClass(this.settings.success):this.settings.success(g,b)),this.toShow=this.toShow.add(g)},errorsFor:function(b){var c=this.idOrName(b),d=a(b).attr("aria-describedby"),e="label[for='"+c+"'], label[for='"+c+"'] *";return d&&(e=e+", #"+d.replace(/\s+/g,", #")),this.errors().filter(e)},idOrName:function(a){return this.groups[a.name]||(this.checkable(a)?a.name:a.id||a.name)},validationTargetFor:function(a){return this.checkable(a)&&(a=this.findByName(a.name).not(this.settings.ignore)[0]),a},checkable:function(a){return/radio|checkbox/i.test(a.type)},findByName:function(b){return a(this.currentForm).find("[name='"+b+"']")},getLength:function(b,c){switch(c.nodeName.toLowerCase()){case"select":return a("option:selected",c).length;case"input":if(this.checkable(c))return this.findByName(c.name).filter(":checked").length}return b.length},depend:function(a,b){return this.dependTypes[typeof a]?this.dependTypes[typeof a](a,b):!0},dependTypes:{"boolean":function(a){return a},string:function(b,c){return!!a(b,c.form).length},"function":function(a,b){return a(b)}},optional:function(b){var c=this.elementValue(b);return!a.validator.methods.required.call(this,c,b)&&"dependency-mismatch"},startRequest:function(a){this.pending[a.name]||(this.pendingRequest++,this.pending[a.name]=!0)},stopRequest:function(b,c){this.pendingRequest--,this.pendingRequest<0&&(this.pendingRequest=0),delete this.pending[b.name],c&&0===this.pendingRequest&&this.formSubmitted&&this.form()?(a(this.currentForm).submit(),this.formSubmitted=!1):!c&&0===this.pendingRequest&&this.formSubmitted&&(a(this.currentForm).triggerHandler("invalid-form",[this]),this.formSubmitted=!1)},previousValue:function(b){return a.data(b,"previousValue")||a.data(b,"previousValue",{old:null,valid:!0,message:this.defaultMessage(b,"remote")})}},classRuleSettings:{required:{required:!0},email:{email:!0},url:{url:!0},date:{date:!0},dateISO:{dateISO:!0},number:{number:!0},digits:{digits:!0},creditcard:{creditcard:!0}},addClassRules:function(b,c){b.constructor===String?this.classRuleSettings[b]=c:a.extend(this.classRuleSettings,b)},classRules:function(b){var c={},d=a(b).attr("class");return d&&a.each(d.split(" "),function(){this in a.validator.classRuleSettings&&a.extend(c,a.validator.classRuleSettings[this])}),c},attributeRules:function(b){var c,d,e={},f=a(b),g=b.getAttribute("type");for(c in a.validator.methods)"required"===c?(d=b.getAttribute(c),""===d&&(d=!0),d=!!d):d=f.attr(c),/min|max/.test(c)&&(null===g||/number|range|text/.test(g))&&(d=Number(d)),d||0===d?e[c]=d:g===c&&"range"!==g&&(e[c]=!0);return e.maxlength&&/-1|2147483647|524288/.test(e.maxlength)&&delete e.maxlength,e},dataRules:function(b){var c,d,e={},f=a(b);for(c in a.validator.methods)d=f.data("rule"+c.charAt(0).toUpperCase()+c.substring(1).toLowerCase()),void 0!==d&&(e[c]=d);return e},staticRules:function(b){var c={},d=a.data(b.form,"validator");return d.settings.rules&&(c=a.validator.normalizeRule(d.settings.rules[b.name])||{}),c},normalizeRules:function(b,c){return a.each(b,function(d,e){if(e===!1)return void delete b[d];if(e.param||e.depends){var f=!0;switch(typeof e.depends){case"string":f=!!a(e.depends,c.form).length;break;case"function":f=e.depends.call(c,c)}f?b[d]=void 0!==e.param?e.param:!0:delete b[d]}}),a.each(b,function(d,e){b[d]=a.isFunction(e)?e(c):e}),a.each(["minlength","maxlength"],function(){b[this]&&(b[this]=Number(b[this]))}),a.each(["rangelength","range"],function(){var c;b[this]&&(a.isArray(b[this])?b[this]=[Number(b[this][0]),Number(b[this][1])]:"string"==typeof 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this.optional(b)||/^[a-zA-Z0-9.!#$%&'*+\/=?^_`{|}~-]+@[a-zA-Z0-9](?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?(?:\.[a-zA-Z0-9](?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?)*$/.test(a)},url:function(a,b){return this.optional(b)||/^(https?|s?ftp):\/\/(((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:)*@)?(((\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5]))|((([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.)+(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.?)(:\d*)?)(\/((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)+(\/(([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)*)*)?)?(\?((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)|[\uE000-\uF8FF]|\/|\?)*)?(#((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)|\/|\?)*)?$/i.test(a)},date:function(a,b){return 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