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# SETUP
[ 'rubygems', 'redis', 'opentox-ruby-api-wrapper' ].each do |lib|
require lib
end
case ENV['RACK_ENV']
when 'production'
@@redis = Redis.new :db => 0
when 'development'
@@redis = Redis.new :db => 1
when 'test'
@@redis = Redis.new :db => 2
@@redis.flush_db
end
load File.join(File.dirname(__FILE__), 'dataset.rb')
set :default_content, :yaml
helpers do
def find
# + charges are dropped
uri = uri(params[:splat].first.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
#puts uri
halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
end
def uri(name)
=begin
if name =~ /InChI/
name = URI.encode(name,/[^#{URI::PATTERN::UNRESERVED}]/)
else
name = URI.encode(name)
end
=end
name = URI.encode(name)
uri = url_for("/dataset/", :full) + name
end
end
## REST API
load 'compound.rb'
load 'feature.rb'
get '/datasets/?' do
Dataset.find_all.join("\n")
end
get '/algorithm/tanimoto/dataset/*/dataset/*/?' do
find
@set.tanimoto(uri(params[:splat][1]))
end
get '/algorithm/weighted_tanimoto/dataset/*/dataset/*/?' do
find
@set.weighted_tanimoto(uri(params[:splat][1]))
end
get '/dataset/*/name/?' do
find
URI.decode @set.name
end
get '/dataset/*/features/?' do
find
@set.features.join("\n")
end
# catch the rest
get '/dataset/*/?' do
find
@set.members.join("\n")
end
# create a dataset
post '/datasets/?' do
dataset_uri = uri(params[:name])
halt 403, "Dataset \"#{dataset_uri}\" exists." if Dataset.find(dataset_uri)
@set = Dataset.create(dataset_uri)
@set.add Dataset.create(File.join(dataset_uri, "compounds")).uri
@set.add Dataset.create(File.join(dataset_uri, "features")).uri
@set.uri
end
load 'import.rb'
# import yaml
post '/dataset/*/?' do
find
@compounds_set = Dataset.find File.join(@set.uri, "compounds")
@features_set = Dataset.find File.join(@set.uri, "features")
YAML.load(params[:features]).each do |compound_uri,feature_uris|
# key: /dataset/:dataset/compound/:inchi
@compound_features = Dataset.find_or_create File.join(@set.uri,'compound',OpenTox::Compound.new(:uri => compound_uri).inchi)
feature_uris.each do |feature_uri|
@compounds_set.add compound_uri
@features_set.add feature_uri
@compound_features.add feature_uri
end
end
@set.uri
end
delete '/dataset/*/?' do
find
@set.members.each{|m| Dataset.find(m).delete} if @set.members
@set.delete
end
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