diff options
-rw-r--r-- | Rakefile | 2 | ||||
-rw-r--r-- | lib/algorithm.rb | 7 | ||||
-rw-r--r-- | lib/config/config_ru.rb | 5 | ||||
-rw-r--r-- | lib/environment.rb | 5 | ||||
-rw-r--r-- | lib/validation.rb | 10 | ||||
-rw-r--r-- | opentox-ruby-api-wrapper.gemspec | 9 |
6 files changed, 27 insertions, 11 deletions
@@ -13,7 +13,7 @@ begin ["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep| gem.add_dependency dep end - ['cucumber','jeweler', "thin"].each do |dep| + ['cucumber','jeweler'].each do |dep| gem.add_development_dependency dep end gem.files = FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore'] diff --git a/lib/algorithm.rb b/lib/algorithm.rb index 7a25408..b573ea3 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -21,8 +21,11 @@ module OpenTox def self.create_model(params) LOGGER.debug params LOGGER.debug File.basename(__FILE__) + ": creating model" - resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "text/x-yaml") - @uri = resource.post(:dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).chomp + LOGGER.debug File.join(@@config[:services]["opentox-algorithm"], "lazar") + #resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "text/x-yaml") + resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml") + #@uri = resource.post(:dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).chomp + @uri = resource.post(:dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).body.chomp end def self.uri diff --git a/lib/config/config_ru.rb b/lib/config/config_ru.rb index 1d32c7e..8470f0e 100644 --- a/lib/config/config_ru.rb +++ b/lib/config/config_ru.rb @@ -18,3 +18,8 @@ set :raise_errors, true end use Rack::ShowExceptions +#use Rack::MailExceptions do |mail| +# mail.to '...@example.com' +# mail.subject '[ERROR] %s' +# mail.smtp MAIL +#end diff --git a/lib/environment.rb b/lib/environment.rb index f89a758..44efd6e 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -40,13 +40,16 @@ if @@config[:database] end end +# mail +#load File.join config_dir,"mail.rb" + # hack: store sinatra in global var to make url_for and halt methods accessible before {$sinatra = self unless $sinatra} class Sinatra::Base # overwriting halt to log halts (!= 202) def halt(*response) - LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response.first >= 300 + LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response and response.first and response.first >= 300 # orig sinatra code: response = response.first if response.length == 1 throw :halt, response diff --git a/lib/validation.rb b/lib/validation.rb index 6fd5704..97aafc4 100644 --- a/lib/validation.rb +++ b/lib/validation.rb @@ -4,8 +4,14 @@ module OpenTox attr_accessor :uri def initialize(params) - resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]) - @uri = resource.post(params).to_s + #resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]) + #@uri = resource.post(params).to_s + call = "curl -X POST " + params.each do |k,v| + call += " -d "+k.to_s+"=\""+v.to_s+"\"" unless k == :uri + end + call += " "+params[:uri] + LOGGER.debug call end def self.crossvalidation(params) diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec index 258ee09..e30b56f 100644 --- a/opentox-ruby-api-wrapper.gemspec +++ b/opentox-ruby-api-wrapper.gemspec @@ -9,10 +9,10 @@ Gem::Specification.new do |s| s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= s.authors = ["Christoph Helma"] - s.date = %q{2010-03-18} + s.date = %q{2010-05-04} s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)} s.email = %q{helma@in-silico.ch} - s.executables = ["opentox-install-ubuntu.sh", "opentox-install-debian.sh", "yaml2owl.rb"] + s.executables = ["opentox-install-ubuntu.sh", "yaml2owl.rb", "opentox-install-debian.sh"] s.extra_rdoc_files = [ "LICENSE", "README.rdoc" @@ -31,11 +31,13 @@ Gem::Specification.new do |s| "lib/config/config_ru.rb", "lib/dataset.rb", "lib/environment.rb", + "lib/features.rb", "lib/helper.rb", "lib/model.rb", "lib/opentox-ruby-api-wrapper.rb", "lib/opentox.owl", "lib/owl.rb", + "lib/rest_client_wrapper.rb", "lib/spork.rb", "lib/task.rb", "lib/tasks/opentox.rb", @@ -67,7 +69,6 @@ Gem::Specification.new do |s| s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"]) s.add_development_dependency(%q<cucumber>, [">= 0"]) s.add_development_dependency(%q<jeweler>, [">= 0"]) - s.add_development_dependency(%q<thin>, [">= 0"]) else s.add_dependency(%q<sinatra>, [">= 0"]) s.add_dependency(%q<rest-client>, [">= 0"]) @@ -81,7 +82,6 @@ Gem::Specification.new do |s| s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) s.add_dependency(%q<cucumber>, [">= 0"]) s.add_dependency(%q<jeweler>, [">= 0"]) - s.add_dependency(%q<thin>, [">= 0"]) end else s.add_dependency(%q<sinatra>, [">= 0"]) @@ -96,7 +96,6 @@ Gem::Specification.new do |s| s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) s.add_dependency(%q<cucumber>, [">= 0"]) s.add_dependency(%q<jeweler>, [">= 0"]) - s.add_dependency(%q<thin>, [">= 0"]) end end |