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require 'rubygems'
require 'opentox-ruby-api-wrapper'
require File.join File.dirname(__FILE__), 'redis', 'dataset.rb'
set :default_content, :yaml
helpers do
def find
uri = uri(params[:splat].first)
halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
end
def uri(name)
name = URI.encode(name)
uri = url_for("/", :full) + name
end
end
## REST API
get '/?' do
Dataset.find_all.join("\n")
end
get '/*/name/?' do
find
URI.decode(URI.split(@set.uri)[5].split(/\//)[1])
end
get '/*/features/?' do
find
@set.features.join("\n")
end
get '/*/compounds/?' do
find
@set.compounds.join("\n")
end
get '/*/compound/*/?' do
find
inchi = params[:splat][1]#.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
@set.compound_features(inchi).join("\n")
end
# catch the rest
get '/*/?' do
find
dataset = {}
@set.compounds.each do |c|
dataset[c] = @set.compound_features(c)
end
dataset.to_yaml
end
# create a dataset
post '/?' do
dataset_uri = uri(params[:name])
halt 403, "Dataset \"#{dataset_uri}\" exists." if Dataset.find(dataset_uri)
Dataset.create(dataset_uri).uri
end
put '/*/import/?' do
find
halt 404, "Compound format #{params[:compound_format]} not (yet) supported" unless params[:compound_format] =~ /smiles|inchi|name/
#task = OpenTox::Task.create(@set.uri)
data = {}
case params[:file][:type]
when "text/csv"
File.open(params[:file][:tempfile].path).each_line do |line|
record = line.chomp.split(/,\s*/)
compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
# begin
feature_uri = OpenTox::Feature.new(:name => @set.name, :classification => record[1]).uri
# rescue
# puts "Error: " + line
# puts record.join("\t")
# puts @set.name.to_s
# #puts [record[0] , @set.name , record[1]].to_yaml
# end
data[compound_uri] = [] unless data[compound_uri]
data[compound_uri] << feature_uri
end
else
halt 404, "File format #{request.content_type} not (yet) supported"
end
@set.add(data.to_yaml)
@set.uri
end
# import yaml
put '/*/?' do
find
@set.add(params[:features])
end
delete '/*/?' do
find
@set.delete
end
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