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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
set :default_content, :yaml
class Dataset
include OpenTox::Utils
attr_reader :uri, :name
def initialize(uri)
@name = File.basename(uri)
@uri = uri
end
def self.create(uri)
dataset = Dataset.new(uri)
dataset.save
dataset
end
def self.find(uri)
if @@redis.set_member? "datasets", uri
Dataset.new(uri)
else
nil
end
end
def self.exists?(uri)
@@redis.set_member? "datasets", uri
end
def self.find_all_uris
@@redis.set_members("datasets")
end
def save
@@redis.set_add "datasets", uri
end
def destroy
@@redis.set_members(@uri + '::compounds').each do |compound_uri|
@@redis.delete @uri + '::' + compound_uri
end
@@redis.delete @uri + '::compounds'
@@redis.set_members(@uri + '::features').each do |feature_uri|
@@redis.delete @uri + '::' + feature_uri
end
@@redis.delete @uri + '::features'
@@redis.set_delete "datasets", @uri
end
def add(compound_uri,feature_uri)
@@redis.set_add @uri + '::compounds', compound_uri
@@redis.set_add @uri + '::features', feature_uri
@@redis.set_add @uri + '::' + compound_uri + '::features', feature_uri
@@redis.set_add @uri + '::' + feature_uri + '::compounds', compound_uri
end
def compound_uris
@@redis.set_members(@uri + "::compounds")
end
def feature_uris
@@redis.set_members(@uri + "::features")
end
def feature_uris_for_compound(compound_uri)
@@redis.set_members(@uri + '::' + compound_uri + '::features')
end
def compound_uris_for_feature(feature_uri)
@@redis.set_members(@uri + '::' + feature_uri + '::compounds')
end
def tanimoto(compound_uris)
raise "Exactly 2 compounds are needed for similarity calculations" unless compound_uris.size == 2
compound_keys = compound_uris.collect{ |c| @uri + '::' + c + "::features" }
union_size = @@redis.set_union(compound_keys[0], compound_keys[1]).size
intersect_size = @@redis.set_intersect(compound_keys[0], compound_keys[1]).size
intersect_size.to_f/union_size.to_f
end
def weighted_tanimoto(compound_uris)
raise "Exactly 2 compounds are needed for similarity calculations" unless compound_uris.size == 2
compound_keys = compound_uris.collect{ |c| @uri + '::' + c + "::features" }
union = @@redis.set_union(compound_keys[0], compound_keys[1])
intersect = @@redis.set_intersect(compound_keys[0], compound_keys[1])
p_sum_union = 0.0
p_sum_intersect = 0.0
union.each{ |f| p_sum_union += gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
intersect.each{ |f| p_sum_intersect += gauss(OpenTox::Feature.new(:uri => f).value('p_value').to_f) }
"#{p_sum_intersect/p_sum_union}"
end
end
helpers do
def not_found?
halt 404, "Dataset \"#{params[:name]}\" not found." unless Dataset.exists? uri(params[:name])
end
def uri(name)
uri = url_for("/", :full) + name.gsub(/\s|\n/,'_')
end
end
## REST API
get '/?' do
Dataset.find_all_uris.join("\n")
end
get '/:name' do
not_found?
@dataset = Dataset.find(uri params[:name])
respond_to do |format|
format.yaml { @dataset.to_yaml }
format.xml { builder :dataset }
end
end
get '/:name/name' do
not_found?
URI.decode(params[:name])
end
get '/:name/compounds' do
not_found?
Dataset.find(uri params[:name]).compound_uris.join("\n")
end
get '/:name/features' do
not_found?
Dataset.find(uri params[:name]).feature_uris.join("\n")
end
get '/:name/compound/*/features' do
not_found?
compound_uri = params[:splat].first.gsub(/ /,'+')
Dataset.find(uri params[:name]).feature_uris_for_compound(compound_uri).join("\n")
end
get '/:name/feature/*/compounds' do
not_found?
Dataset.find(uri params[:name]).compound_uris_for_feature(params[:splat].first).join("\n")
end
get '/:name/tanimoto/compound/*/compound/*/?' do
not_found?
compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
"#{Dataset.find(uri params[:name]).tanimoto(compound_uris)}"
end
get '/:name/weighted_tanimoto/compound/*/compound/*/?' do
not_found?
compound_uris = params[:splat].collect{ |c| c.gsub(/ /,'+') }
Dataset.find(uri params[:name]).weighted_tanimoto(compound_uris)
end
post '/?' do
#protected!
halt 403, "Dataset \"#{name}\" exists - please choose another name." if Dataset.exists?(uri params[:name])
dataset = Dataset.create(uri params[:name])
if params[:file]
File.open(params[:file][:tempfile].path).each_line do |line|
record = line.chomp.split(/,\s*/)
compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
feature_uri = OpenTox::Feature.new(:name => params[:name], :values => {:classification => record[1]}).uri
dataset.add(compound_uri, feature_uri)
end
end
dataset.uri
end
put '/:name/?' do
#protected!
not_found?
dataset = Dataset.find(uri params[:name])
dataset.add(params[:compound_uri],params[:feature_uri])
dataset.uri + " sucessfully updated."
end
delete '/:name/?' do
# dangerous, because other datasets might refer to it
#protected!
not_found?
Dataset.find(uri params[:name]).destroy
"Successfully deleted dataset \"#{params[:name]}\"."
end
|
