sequenceserver 2.0.0.rc3 → 2.0.0.rc8

data/public/vendor/npm/through@2.3.8/.travis.yml

@@ -1,5 +0,0 @@
-language: node_js
-node_js:
-  - 0.6
-  - 0.8
-  - "0.10"

data/public/vendor/npm/underscore@1.8.3/.jspm-hash

@@ -1 +0,0 @@
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data/public/vendor/npm/underscore@1.8.3/.jspm.json

@@ -1,74 +0,0 @@
-{
-  "name": "underscore",
-  "description": "JavaScript's functional programming helper library.",
-  "homepage": "http://underscorejs.org",
-  "keywords": [
-    "util",
-    "functional",
-    "server",
-    "client",
-    "browser"
-  ],
-  "author": {
-    "name": "Jeremy Ashkenas",
-    "email": "jeremy@documentcloud.org"
-  },
-  "repository": {
-    "type": "git",
-    "url": "git://github.com/jashkenas/underscore.git"
-  },
-  "main": "underscore.js",
-  "version": "1.8.3",
-  "devDependencies": {
-    "docco": "*",
-    "eslint": "0.6.x",
-    "karma": "~0.12.31",
-    "karma-qunit": "~0.1.4",
-    "qunit-cli": "~0.2.0",
-    "uglify-js": "2.4.x"
-  },
-  "scripts": {
-    "test": "npm run test-node && npm run lint",
-    "lint": "eslint underscore.js test/*.js",
-    "test-node": "qunit-cli test/*.js",
-    "test-browser": "npm i karma-phantomjs-launcher && ./node_modules/karma/bin/karma start",
-    "build": "uglifyjs underscore.js -c \"evaluate=false\" --comments \"/    .*/\" -m --source-map underscore-min.map -o underscore-min.js",
-    "doc": "docco underscore.js"
-  },
-  "license": "MIT",
-  "files": [
-    "underscore.js",
-    "underscore-min.js",
-    "underscore-min.map",
-    "LICENSE",
-    "package.json"
-  ],
-  "gitHead": "e4743ab712b8ab42ad4ccb48b155034d02394e4d",
-  "bugs": {
-    "url": "https://github.com/jashkenas/underscore/issues"
-  },
-  "_id": "underscore@1.8.3",
-  "_shasum": "4f3fb53b106e6097fcf9cb4109f2a5e9bdfa5022",
-  "_from": ".",
-  "_npmVersion": "1.4.28",
-  "_npmUser": {
-    "name": "jashkenas",
-    "email": "jashkenas@gmail.com"
-  },
-  "maintainers": [
-    {
-      "name": "jashkenas",
-      "email": "jashkenas@gmail.com"
-    }
-  ],
-  "dist": {
-    "shasum": "4f3fb53b106e6097fcf9cb4109f2a5e9bdfa5022",
-    "tarball": "http://registry.npmjs.org/underscore/-/underscore-1.8.3.tgz"
-  },
-  "format": "cjs",
-  "ignore": [
-    "node_modules"
-  ],
-  "registry": "npm",
-  "dependencies": {}
-}

data/public/vendor/npm/util@0.10.3/.jspm-hash

@@ -1 +0,0 @@
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data/public/vendor/npm/util@0.10.3/.jspm.json

@@ -1,58 +0,0 @@
-{
-  "author": {
-    "name": "Joyent",
-    "url": "http://www.joyent.com"
-  },
-  "name": "util",
-  "description": "Node.JS util module",
-  "keywords": [
-    "util"
-  ],
-  "version": "0.10.3",
-  "homepage": "https://github.com/defunctzombie/node-util",
-  "repository": {
-    "type": "git",
-    "url": "git://github.com/defunctzombie/node-util"
-  },
-  "main": "./util.js",
-  "scripts": {
-    "test": "node test/node/*.js && zuul test/browser/*.js"
-  },
-  "license": "MIT",
-  "devDependencies": {
-    "zuul": "~1.0.9"
-  },
-  "browser": {
-    "./support/isBuffer.js": "./support/isBufferBrowser.js"
-  },
-  "bugs": {
-    "url": "https://github.com/defunctzombie/node-util/issues"
-  },
-  "_id": "util@0.10.3",
-  "dist": {
-    "shasum": "7afb1afe50805246489e3db7fe0ed379336ac0f9",
-    "tarball": "http://registry.npmjs.org/util/-/util-0.10.3.tgz"
-  },
-  "_from": ".",
-  "_npmVersion": "1.3.24",
-  "_npmUser": {
-    "name": "shtylman",
-    "email": "shtylman@gmail.com"
-  },
-  "maintainers": [
-    {
-      "name": "shtylman",
-      "email": "shtylman@gmail.com"
-    }
-  ],
-  "format": "cjs",
-  "ignore": [
-    "node_modules"
-  ],
-  "map": {},
-  "registry": "npm",
-  "dependencies": {
-    "inherits": "inherits@2.0.1",
-    "process": "github:jspm/nodelibs-process@^0.1.0"
-  }
-}

data/public/vendor/npm/util@0.10.3/.npmignore

@@ -1 +0,0 @@
-node_modules

data/public/vendor/npm/util@0.10.3/.travis.yml

@@ -1,8 +0,0 @@
-language: node_js
-node_js:
-- '0.8'
-- '0.10'
-env:
-  global:
-  - secure: AdUubswCR68/eGD+WWjwTHgFbelwQGnNo81j1IOaUxKw+zgFPzSnFEEtDw7z98pWgg7p9DpCnyzzSnSllP40wq6AG19OwyUJjSLoZK57fp+r8zwTQwWiSqUgMu2YSMmKJPIO/aoSGpRQXT+L1nRrHoUJXgFodyIZgz40qzJeZjc=
-  - secure: heQuxPVsQ7jBbssoVKimXDpqGjQFiucm6W5spoujmspjDG7oEcHD9ANo9++LoRPrsAmNx56SpMK5fNfVmYediw6SvhXm4Mxt56/fYCrLDBtgGG+1neCeffAi8z1rO8x48m77hcQ6YhbUL5R9uBimUjMX92fZcygAt8Rg804zjFo=

data/public/vendor/npm/util@0.10.3/.zuul.yml

@@ -1,10 +0,0 @@
-ui: mocha-qunit
-browsers:
-  - name: chrome
-    version: 27..latest
-  - name: firefox
-    version: latest
-  - name: safari
-    version: latest
-  - name: ie
-    version: 9..latest

data/public/vendor/npm/webshim@1.15.8/.gitattributes

@@ -1,12 +0,0 @@
-build/ export-ignore
-grunt-tasks/ export-ignore
-src/ export-ignore
-swfs/ export-ignore
-js-webshim/minified/extras/ export-ignore
-js-webshim/dev/extras/ export-ignore
-tests/ export-ignore
-Gruntfile.js export-ignore
-bower.json export-ignore
-package.json export-ignore
-webshims.jquery.json export-ignore
-.* export-ignore

data/public/vendor/npm/webshim@1.15.8/.jspm-hash

@@ -1 +0,0 @@
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data/public/vendor/npm/webshim@1.15.8/.jspm.json

@@ -1,92 +0,0 @@
-{
-  "name": "webshim",
-  "version": "1.15.8",
-  "title": "Webshims - polyfills jQuery with many HTML5 features",
-  "licenses": [
-    {
-      "type": "MIT",
-      "url": "https://raw.github.com/aFarkas/webshim/master/MIT-LICENSE.txt"
-    }
-  ],
-  "author": {
-    "name": "Alexander Farkas",
-    "url": "https://github.com/aFarkas/"
-  },
-  "keywords": [
-    "webshims",
-    "webshim",
-    "polyfill",
-    "HTML5",
-    "forms",
-    "audio",
-    "video",
-    "validation",
-    "canvas",
-    "localstorage",
-    "geolocation",
-    "ui",
-    "widgets",
-    "getUserMedia"
-  ],
-  "homepage": "http://afarkas.github.com/webshim/demos/index.html",
-  "description": "modular capability-based polyfill loading libary, which extends jQuery with HTML5 features in legacy browsers",
-  "docs": "http://afarkas.github.com/webshim/demos/index.html",
-  "demo": "http://afarkas.github.com/webshim/demos/index.html",
-  "bugs": {
-    "url": "https://github.com/aFarkas/webshim/issues"
-  },
-  "repository": {
-    "type": "git",
-    "url": "git+https://github.com/aFarkas/webshim.git"
-  },
-  "main": "js-webshim/minified/polyfiller",
-  "devDependencies": {
-    "phantomjs": ">=1.8.2",
-    "grunt-css": ">=0.5.4",
-    "grunt-contrib-concat": ">=0.1.3",
-    "grunt-contrib-watch": ">=0.3.0",
-    "grunt-contrib-copy": ">=0.4.0",
-    "grunt-contrib-uglify": ">=0.2.7",
-    "grunt": ">=0.4.1",
-    "grunt-contrib-sass": "~0.8.1",
-    "grunt-contrib-compress": "~0.7.0",
-    "grunt-contrib-clean": "~0.5.0",
-    "grunt-bytesize": "~0.1.1",
-    "grunt-contrib-csslint": "~0.2.0",
-    "grunt-contrib-jshint": "~0.10.0"
-  },
-  "gitHead": "82229e75e4482d496e8935b644c08c00019ae402",
-  "_id": "webshim@1.15.8",
-  "scripts": {},
-  "_shasum": "1664e4bbe8f2d8b1b14be63674cf4190ea260544",
-  "_from": ".",
-  "_npmVersion": "2.10.1",
-  "_nodeVersion": "0.12.4",
-  "_npmUser": {
-    "name": "afarkas",
-    "email": "info@corrupt-system.de"
-  },
-  "dist": {
-    "shasum": "1664e4bbe8f2d8b1b14be63674cf4190ea260544",
-    "tarball": "http://registry.npmjs.org/webshim/-/webshim-1.15.8.tgz"
-  },
-  "maintainers": [
-    {
-      "name": "afarkas",
-      "email": "info@corrupt-system.de"
-    }
-  ],
-  "jspm": {
-    "main": "js-webshim/minified/polyfiller"
-  },
-  "format": "cjs",
-  "ignore": [
-    "node_modules"
-  ],
-  "registry": "npm",
-  "dependencies": {
-    "fs": "github:jspm/nodelibs-fs@^0.1.0",
-    "path": "github:jspm/nodelibs-path@^0.1.0",
-    "process": "github:jspm/nodelibs-process@^0.1.0"
-  }
-}

data/public/vendor/npm/webshim@1.15.8/.npmignore

@@ -1,16 +0,0 @@
-*.swp
-*.un~
-*.tmp_*~
-todo.txt
-_extends.css
-tests/performance.html
-dev-playground/*
-node_modules/*
-demos/demo-js/node_modules/*
-
-/tests/form-implementation.html
-/build/yuicompressor.jar
-/tests/tmp_tests.html
-.DS_Store
-.sass-cache
-.idea

data/public/vendor/npm/webshim@1.15.8/.project

@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>webshim</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-	</buildSpec>
-	<natures>
-		<nature>com.aptana.projects.webnature</nature>
-	</natures>
-</projectDescription>

data/sequenceserver.gemspec

@@ -1,55 +0,0 @@
-require File.expand_path('lib/sequenceserver/version.rb',
-                         File.dirname(__FILE__))
-Gem::Specification.new do |s|
-  # meta
-  s.name        = 'sequenceserver'
-  s.version     = SequenceServer::VERSION
-  s.authors     = ['Anurag Priyam', 'Ben J Woodcroft',
-                   'Vivek Rai', 'Yannick Wurm']
-  s.email       = ['anurag08priyam@gmail.com', 'b.woodcroft@uq.edu.au']
-  s.homepage    = 'http://sequenceserver.com'
-  s.license     = 'AGPL-3.0'
-
-  s.summary     = 'BLAST search made easy!'
-  s.description = <<~DESC
-    SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
-    user interface for use locally or over the web.
-  DESC
-
-  # dependencies
-  s.required_ruby_version = '>= 2.3.0'
-
-  s.add_dependency('json_pure', '~> 1.8',  '>= 1.8.2')
-  s.add_dependency('ox',        '~> 2.1',  '>= 2.1.1')
-  s.add_dependency('sinatra',   '~> 2.0',  '>= 2.0.0')
-  s.add_dependency('slop',      '~> 3.6',  '>= 3.6.0')
-
-  s.add_development_dependency('capybara', '~> 3.15', '>= 3.15.1')
-  s.add_development_dependency('capybara-screenshot', '~> 1.0', '>= 1.0.23')
-  s.add_development_dependency('rack-test', '~> 1.0', '>= 1.0.0')
-  s.add_development_dependency('rspec', '~> 3.7', '>= 3.7.0')
-  s.add_development_dependency('rubocop', '~> 0.75', '>= 0.75.1')
-  s.add_development_dependency('selenium-webdriver', '~> 3.142', '>= 3.142.3')
-  s.add_development_dependency('simplecov', '~> 0.17.0', '>= 0.17.0')
-
-  # gem
-  s.files         = `git ls-files`.split("\n") - ['Gemfile', 'Gemfile.lock']
-  s.executables   = ['sequenceserver']
-  s.require_paths = ['lib']
-
-  # post install information
-  s.post_install_message = <<~INFO
-
-    ------------------------------------------------------------------------
-      Thank you for installing SequenceServer :)
-
-      To launch SequenceServer execute 'sequenceserver' from command line.
-
-        $ sequenceserver
-
-
-      Visit http://sequenceserver.com for more.
-    ------------------------------------------------------------------------
-
-  INFO
-end

data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb

@@ -1,228 +0,0 @@
-require 'spec_helper'
-
-# Test BLAST module.
-module SequenceServer
- with_hits = Job.fetch('blast_2.2.30/blastn')
-  no_hits = Job.fetch('blast_2.2.30/blastn_nohits')
-
-  init
-
-  describe 'Report' do
-    hits_report = BLAST::Report.new(with_hits)
-    no_hits_report = BLAST::Report.new(no_hits)
-
-    it 'will return an Array of queries' do
-      hits_report.queries.should be_a Array
-      no_hits_report.queries.should be_a Array
-    end
-
-    it 'will return a Hash of stats' do
-      hits_report.stats.should be_a Hash
-      no_hits_report.stats.should be_a Hash
-    end
-
-    it 'contains all the necessary stats' do
-      hits_report.stats.length.should eql(7)
-      no_hits_report.stats.length.should eql(7)
-    end
-  end
-
-  describe 'Query' do
-    hits_report = BLAST::Report.new(with_hits)
-    no_hits_report = BLAST::Report.new(no_hits)
-
-    it 'will return queries with valid length' do
-      hits_report.queries.first.length.should be_a Integer
-      hits_report.queries.first.length.should satisfy { |n| n > 0 }
-      no_hits_report.queries.first.length.should be_a Integer
-      no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
-    end
-
-    it 'will return an Array of hits' do
-      hits_report.queries.first.hits.should be_a Array
-      no_hits_report.queries.first.hits.should be_a Array
-    end
-  end
-
-  describe 'Hits' do
-    hits_report = BLAST::Report.new(with_hits)
-    no_hits_report = BLAST::Report.new(no_hits)
-
-    it 'will have non zero length' do
-      hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
-    end
-
-    it 'will return an Array of HSPs' do
-      hits_report.queries.first.hits.first.hsps.should be_a Array
-    end
-
-    it 'will return an Array with atleast one HSP' do
-      hits_report.queries.first.hits.first.hsps.length.should be >= 1
-    end
-
-    it 'will contain no element if no hits were obtained' do
-      no_hits_report.queries.first.hits.length.should eql(0)
-    end
-  end
-
-  # Test general features of HSPs. Algorithm specific customizations are
-  # tested separetly.
-  describe 'HSPs' do
-    hits_report = BLAST::Report.new(with_hits)
-
-    # Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
-    # hit object it belongs to.
-    it 'have all the necessary values' do
-      hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
-    end
-
-    # Test Random HSPs to ensure that all the values from HSP struct are valid.
-    it 'have correct alignment values' do
-      hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
-      hits_report.queries.last.hits.first.hsps.last.score.should be_a Integer
-
-      hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
-      hits_report.queries.first.hits.first.hsps.first.evalue
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Integer
-      hits_report.queries.first.hits.last.hsps.first.qstart
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.first.hits.last.hsps.first.qend.should be_a Integer
-      hits_report.queries.first.hits.last.hsps.first.qend
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Integer
-      hits_report.queries.last.hits.last.hsps.last.sstart
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.first.hits.first.hsps.last.send.should be_a Integer
-      hits_report.queries.first.hits.first.hsps.last.send
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Integer
-      hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Integer
-
-      hits_report.queries.first.hits.first.hsps.last.identity.should be_a Integer
-      hits_report.queries.first.hits.first.hsps.last.identity
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Integer
-      hits_report.queries.first.hits.first.hsps.last.gaps
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.first.hits.first.hsps.last.positives
-        .should be_a Integer
-      hits_report.queries.first.hits.first.hsps.last.positives
-        .should_not satisfy { |n| n < 0 }
-
-      hits_report.queries.first.hits.first.hsps.last.length.should be_a Integer
-      hits_report.queries.first.hits.first.hsps.last.length
-        .should satisfy { |n| n > 0 }
-
-      hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
-      hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
-      hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
-    end
-
-    it 'have correctly matched query, hit and midline alignments' do
-      hsp = hits_report.queries.last.hits.last.hsps.first
-      hsp.qseq.length.should eql(hsp.sseq.length)
-      hsp.sseq.length.should eql(hsp.midline.length)
-      hsp.midline.length.should eql(hsp.qseq.length)
-    end
-  end
-
-  # Individually test different BLAST+ algorithms
-  #
-  describe 'BLASTN' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.2.30/blastn'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      [1, -1].should include(hsp.qframe)
-      [1, -1].should include(hsp.sframe)
-    end
-
-    it 'have correct qstart, qend, sstart, send' do
-      if hsp.sframe > 0
-        hsp.sstart.should be <= hsp.send
-      else
-        hsp.sstart.should be >= hsp.send
-      end
-    end
-  end
-
-  describe 'BLASTP' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.2.30/blastp'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      hsp.qframe.should eql(0)
-      hsp.sframe.should eql(0)
-    end
-
-    it 'have correct qstart, qend, sstart, send values' do
-      hsp.qstart.should be <= hsp.qend
-      hsp.sstart.should be <= hsp.send
-    end
-
-  end
-
-  describe 'BLASTX' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.2.30/blastx'))
-
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      hsp.qframe.should_not eql(0)
-      hsp.sframe.should eql(0)
-    end
-
-    it 'have correct qstart, qend, sstart, send' do
-      hsp.qstart.should be <= hsp.qend
-      hsp.sstart.should be <= hsp.send
-    end
-  end
-
-  describe 'TBLASTX' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.2.30/tblastx'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      hsp.qframe.should_not eql(0)
-      hsp.sframe.should_not eql(0)
-    end
-
-    it 'have correct qstart, qend, sstart, send' do
-      hsp.qstart.should be <= hsp.qend
-      hsp.sstart.should be <= hsp.send
-    end
-  end
-
-  describe 'TBLASTN' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.2.30/tblastn'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      hsp.qframe.should eql(0)
-      hsp.sframe.should_not eql(0)
-    end
-
-    it 'have correct qstart, qend, sstart, send' do
-      hsp.qstart.should be <= hsp.qend
-      hsp.sstart.should be <= hsp.send
-    end
-  end
-end