toxbank-investigation 0.0.1pre-x86-linux

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Files changed (67) hide show
  1. data/.gitignore +11 -0
  2. data/Gemfile +7 -0
  3. data/Gemfile.lock +101 -0
  4. data/LICENSE +674 -0
  5. data/README +14 -0
  6. data/Rakefile +31 -0
  7. data/application.rb +246 -0
  8. data/bin/toxbank-investigation-install +76 -0
  9. data/config/production.rb +9 -0
  10. data/config.ru +5 -0
  11. data/java/config/isa_configurator/cellcount_flowcytometry.xml +1 -0
  12. data/java/config/isa_configurator/cellsorting_flowcyt.xml +5 -0
  13. data/java/config/isa_configurator/clinical_chemistry.xml +1 -0
  14. data/java/config/isa_configurator/copynumvariation_micro.xml +1 -0
  15. data/java/config/isa_configurator/dnamethylation_micro.xml +1 -0
  16. data/java/config/isa_configurator/dnamethylation_seq.xml +1 -0
  17. data/java/config/isa_configurator/envgen_survey_seq.xml +1 -0
  18. data/java/config/isa_configurator/genome_seq.xml +1 -0
  19. data/java/config/isa_configurator/hematology.xml +1 -0
  20. data/java/config/isa_configurator/heterozygosity_micro.xml +1 -0
  21. data/java/config/isa_configurator/histology.xml +1 -0
  22. data/java/config/isa_configurator/histonemodification_seq.xml +1 -0
  23. data/java/config/isa_configurator/metaboliteprofiling_ms.xml +114 -0
  24. data/java/config/isa_configurator/metaboliteprofiling_nmr.xml +114 -0
  25. data/java/config/isa_configurator/metagenome_seq.xml +1 -0
  26. data/java/config/isa_configurator/nru_assay.xml +8 -0
  27. data/java/config/isa_configurator/ppi_detection_micro.xml +1 -0
  28. data/java/config/isa_configurator/protein_dna_binding_ident_micro.xml +1 -0
  29. data/java/config/isa_configurator/protein_dna_binding_ident_seq.xml +1 -0
  30. data/java/config/isa_configurator/protein_expression_ge.xml +101 -0
  31. data/java/config/isa_configurator/protein_expression_micro.xml +1 -0
  32. data/java/config/isa_configurator/protein_expression_ms.xml +1 -0
  33. data/java/config/isa_configurator/proteinident_ms.xml +1 -0
  34. data/java/config/isa_configurator/snpanalysis_micro.xml +1 -0
  35. data/java/config/isa_configurator/studySample.xml +1 -0
  36. data/java/config/isa_configurator/tfbsident_micro.xml +1 -0
  37. data/java/config/isa_configurator/tfbsident_seq.xml +1 -0
  38. data/java/config/isa_configurator/transcription_micro.xml +1 -0
  39. data/java/config/isa_configurator/transcription_rtpcr.xml +1 -0
  40. data/java/config/isa_configurator/transcription_seq.xml +6 -0
  41. data/test/Rakefile +48 -0
  42. data/test/all.rb +3 -0
  43. data/test/authorization.rb +112 -0
  44. data/test/basic_rest.rb +98 -0
  45. data/test/data/invalid/BII-invalid.n3 +19641 -0
  46. data/test/data/invalid/a_TB-ACCUTOX-plate1.txt +97 -0
  47. data/test/data/invalid/a_TB-ACCUTOX-plate2.txt +97 -0
  48. data/test/data/invalid/a_TB-ACCUTOX-plate3.txt +97 -0
  49. data/test/data/invalid/acetaminophen-plate1-data.txt +97 -0
  50. data/test/data/invalid/acetaminophen-plate2-data.txt +97 -0
  51. data/test/data/invalid/acetaminophen-plate3-data.txt +97 -0
  52. data/test/data/invalid/i_Investigation.txt +156 -0
  53. data/test/data/invalid/ic50.txt +20 -0
  54. data/test/data/invalid/isa_TB_ACCUTOX.xls +0 -0
  55. data/test/data/invalid/isa_TB_ACCUTOX.zip +0 -0
  56. data/test/data/invalid/s_TB-ACCUTOX-acetaminophen.txt +58 -0
  57. data/test/data/valid/BII-I-1.n3 +19648 -0
  58. data/test/data/valid/BII-I-1.rdf +19648 -0
  59. data/test/data/valid/BII-I-1.zip +0 -0
  60. data/test/data/valid/isa-tab-renamed.zip +0 -0
  61. data/test/data/valid/isa_TB_BII.xls +0 -0
  62. data/test/httpd.rb +69 -0
  63. data/test/querytest.rb +42 -0
  64. data/test/upload.rb +152 -0
  65. data/test/xls_upload.rb +60 -0
  66. data/toxbank-investigation.gemspec +29 -0
  67. metadata +133 -0
data/.gitignore ADDED
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+ *.gem
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+ .bundle
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+ pkg/*
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+ tmp/*
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+ public/*
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+ investigation/*
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+ target/*
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+ java/*.jar
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+ java/logs
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+ oo_*/*
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+ *~
data/Gemfile ADDED
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+ source :gemcutter
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+ gemspec
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+ #gem 'opentox-server', :path => "~/opentox-server"
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+ #gem "opentox-client", :path => "~/opentox-client"
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+ group :test do
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+ gem "rack-test", :require => "rack/test"
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+ end
data/Gemfile.lock ADDED
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+ PATH
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+ remote: .
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+ specs:
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+ toxbank-investigation (0.0.1pre)
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+ opentox-server
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+
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+ GEM
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+ remote: http://rubygems.org/
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+ specs:
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+ addressable (2.2.7)
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+ backports (2.3.0)
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+ choice (0.1.5)
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+ emk-sinatra-url-for (0.2.1)
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+ sinatra (>= 0.9.1.1)
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+ eventmachine (0.12.10)
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+ faraday (0.7.6)
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+ addressable (~> 2.2)
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+ multipart-post (~> 1.1)
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+ rack (~> 1.1)
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+ ffi (1.0.11)
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+ google-spreadsheet-ruby (0.1.8)
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+ nokogiri (>= 1.4.3.1)
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+ oauth (>= 0.3.6)
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+ oauth2 (>= 0.5.0)
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+ kgio (2.7.2)
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+ log4r (1.1.10)
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+ mime-types (1.17.2)
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+ multi_json (1.1.0)
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+ multipart-post (1.1.5)
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+ nokogiri (1.5.2)
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+ oauth (0.4.5)
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+ oauth2 (0.5.2)
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+ faraday (~> 0.7)
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+ multi_json (~> 1.0)
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+ open4 (1.3.0)
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+ opentox-client (0.0.1pre)
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+ bundler
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+ open4
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+ rdf
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+ rdf-raptor
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+ rest-client
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+ opentox-server (0.0.1pre)
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+ emk-sinatra-url-for
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+ opentox-client
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+ rack
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+ rack-contrib
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+ roo
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+ sinatra
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+ sinatra-contrib
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+ unicorn
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+ rack (1.4.1)
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+ rack-contrib (1.1.0)
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+ rack (>= 0.9.1)
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+ rack-protection (1.2.0)
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+ rack
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+ rack-test (0.6.1)
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+ rack (>= 1.0)
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+ raindrops (0.8.0)
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+ rdf (0.3.5)
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+ addressable (>= 2.2.6)
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+ rdf-raptor (0.4.1)
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+ ffi (>= 1.0)
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+ rdf (~> 0.3.0)
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+ rest-client (1.6.7)
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+ mime-types (>= 1.16)
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+ roo (1.10.1)
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+ choice (>= 0.1.4)
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+ google-spreadsheet-ruby (>= 0.1.5)
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+ nokogiri (>= 1.5.0)
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+ rubyzip (>= 0.9.4)
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+ spreadsheet (> 0.6.4)
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+ todonotes (>= 0.1.0)
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+ ruby-ole (1.2.11.3)
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+ rubyzip (0.9.6.1)
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+ sinatra (1.3.2)
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+ rack (~> 1.3, >= 1.3.6)
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+ rack-protection (~> 1.2)
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+ tilt (~> 1.3, >= 1.3.3)
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+ sinatra-contrib (1.3.1)
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+ backports (>= 2.0)
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+ eventmachine
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+ rack-protection
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+ rack-test
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+ sinatra (~> 1.3.0)
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+ tilt (~> 1.3)
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+ spreadsheet (0.6.8)
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+ ruby-ole (>= 1.0)
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+ tilt (1.3.3)
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+ todonotes (0.1.0)
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+ log4r
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+ unicorn (4.2.0)
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+ kgio (~> 2.6)
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+ rack
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+ raindrops (~> 0.7)
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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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+ rack-test
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+ toxbank-investigation!