neurohmmerapp 0.0.1

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Files changed (44) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +24 -0
  3. data/Gemfile +4 -0
  4. data/Gemfile.lock +81 -0
  5. data/LICENSE.txt +661 -0
  6. data/README.md +96 -0
  7. data/Rakefile +21 -0
  8. data/bin/neurohmmerapp +166 -0
  9. data/config.ru +3 -0
  10. data/lib/neurohmmerapp/config.rb +87 -0
  11. data/lib/neurohmmerapp/exceptions.rb +77 -0
  12. data/lib/neurohmmerapp/logger.rb +24 -0
  13. data/lib/neurohmmerapp/neurohmmer.rb +158 -0
  14. data/lib/neurohmmerapp/routes.rb +79 -0
  15. data/lib/neurohmmerapp/server.rb +63 -0
  16. data/lib/neurohmmerapp/version.rb +3 -0
  17. data/lib/neurohmmerapp.rb +207 -0
  18. data/neurohmmerapp.gemspec +50 -0
  19. data/public/NeuroHmmer/loading.html +12 -0
  20. data/public/src/css/bootstrap1.min.css +7 -0
  21. data/public/src/css/custom.css +189 -0
  22. data/public/src/css/custom.min.css +1 -0
  23. data/public/src/css/font-awesome.min.css +4 -0
  24. data/public/src/js/bionode-seq.min.js +1 -0
  25. data/public/src/js/bootstrap.min.js +6 -0
  26. data/public/src/js/jquery.cookie.min.js +1 -0
  27. data/public/src/js/jquery.min.js +4 -0
  28. data/public/src/js/jquery.validate.min.js +4 -0
  29. data/public/src/js/neurohmmer.js +228 -0
  30. data/public/src/js/neurohmmer.min.js +1 -0
  31. data/public/web_files/css/nh_compiled_css.min.css +14 -0
  32. data/public/web_files/fonts/FontAwesome.otf +0 -0
  33. data/public/web_files/fonts/fontawesome-webfont.eot +0 -0
  34. data/public/web_files/fonts/fontawesome-webfont.svg +504 -0
  35. data/public/web_files/fonts/fontawesome-webfont.ttf +0 -0
  36. data/public/web_files/fonts/fontawesome-webfont.woff +0 -0
  37. data/public/web_files/js/nh_compiled_js.min.js +20 -0
  38. data/spec/empty_config.yml +0 -0
  39. data/spec/route_spec.rb +72 -0
  40. data/views/500.slim +5 -0
  41. data/views/index.slim +38 -0
  42. data/views/layout.slim +74 -0
  43. data/views/results.slim +9 -0
  44. metadata +281 -0
checksums.yaml ADDED
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+ ---
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+ SHA1:
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+ metadata.gz: 0e0d520f45b1e2ecdc92c07614f43fc73f122eb7
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+ data.tar.gz: 8c7a52cf4b06e3ab3b91c46cb4ab17ef734a2fe8
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+ SHA512:
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+ metadata.gz: 7b655903472ebfb36b6748379c6e5f615ff64dc590e9faa952bf8cb9835e5185b84f71eb3b6d3cfa6cef765e7b6ea9863b2a8975945d09c0bc2d00c6aa748870
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+ data.tar.gz: c79c5df182399717389aeab2fa88fc47d5b2d327d1f64d5dbf912af3bb1dc034136e437271a79c941e95040c210ec02b315ad98cfdd043d5e87487eb68cf24c9
data/.gitignore ADDED
@@ -0,0 +1,24 @@
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+ *.gem
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+ *.rbc
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+ .bundle
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+ .config
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+ .yardoc
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+ .DS_Store
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+ Gemfile.lock
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+ InstalledFiles
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+ _yardoc
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+ coverage
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+ doc/
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+ lib/bundler/man
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+ pkg
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+ rdoc
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+ spec/reports
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+ test/tmp
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+ test/version_tmp
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+ tmp
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+ *.bundle
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+ *.so
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+ *.o
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+ *.a
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+ mkmf.log
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+ .DS_Store
data/Gemfile ADDED
@@ -0,0 +1,4 @@
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in GeneValidatorApp.gemspec
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+ gemspec
data/Gemfile.lock ADDED
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+ PATH
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+ remote: .
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+ specs:
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+ neurohmmerapp (0.0.1)
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+ bio (~> 1.4)
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+ neurohmmer (~> 0.1)
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+ sinatra (~> 1.4)
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+ sinatra-cross_origin (~> 0.3)
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+ slim (~> 3.0)
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+ slop (~> 3.6)
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+
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+ GEM
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+ remote: https://rubygems.org/
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+ specs:
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+ bio (1.5.0)
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+ bio-hmmer3_report (0.1.0)
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+ bio-logger (~> 1.0)
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+ bio-logger (1.0.1)
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+ log4r (>= 1.1.9)
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+ capybara (2.5.0)
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+ mime-types (>= 1.16)
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+ nokogiri (>= 1.3.3)
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+ rack (>= 1.0.0)
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+ rack-test (>= 0.5.4)
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+ xpath (~> 2.0)
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+ diff-lcs (1.2.5)
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+ json (1.8.3)
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+ log4r (1.1.10)
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+ mime-types (2.6.2)
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+ mini_portile (0.6.2)
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+ neurohmmer (0.1.0)
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+ bio
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+ bio-hmmer3_report
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+ slim (~> 3.0)
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+ nokogiri (1.6.6.2)
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+ mini_portile (~> 0.6.0)
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+ rack (1.6.4)
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+ rack-protection (1.5.3)
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+ rack
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+ rack-test (0.6.3)
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+ rack (>= 1.0)
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+ rake (10.4.2)
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+ rspec (2.99.0)
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+ rspec-core (~> 2.99.0)
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+ rspec-expectations (~> 2.99.0)
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+ rspec-mocks (~> 2.99.0)
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+ rspec-core (2.99.2)
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+ rspec-expectations (2.99.2)
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+ diff-lcs (>= 1.1.3, < 2.0)
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+ rspec-mocks (2.99.4)
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+ sinatra (1.4.6)
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+ rack (~> 1.4)
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+ rack-protection (~> 1.4)
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+ tilt (>= 1.3, < 3)
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+ sinatra-cross_origin (0.3.2)
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+ slim (3.0.6)
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+ temple (~> 0.7.3)
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+ tilt (>= 1.3.3, < 2.1)
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+ slop (3.6.0)
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+ temple (0.7.6)
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+ tilt (2.0.1)
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+ w3c_validators (1.2)
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+ json
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+ nokogiri
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+ xpath (2.0.0)
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+ nokogiri (~> 1.3)
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+
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+ PLATFORMS
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+ ruby
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+
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+ DEPENDENCIES
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+ bundler (~> 1.6)
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+ capybara (~> 2.4, >= 2.4.4)
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+ neurohmmerapp!
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+ rack-test (~> 0.6)
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+ rake (~> 10.3)
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+ rspec (~> 2.8, >= 2.8.0)
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+ w3c_validators (~> 1.1)
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+
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+ BUNDLED WITH
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+ 1.10.5