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|
## SETUP
[ 'rubygems', 'sinatra', 'sinatra/url_for', 'dm-core', 'dm-more', 'builder', 'opentox-ruby-api-wrapper' ].each do |lib|
require lib
end
## MODELS
class Dataset
include DataMapper::Resource
property :id, Serial
property :name, String
property :finished, Boolean, :default => false
has n, :associations
end
class Association
include DataMapper::Resource
property :id, Serial
property :compound_uri, String, :size => 255
property :feature_uri, String, :size => 255
belongs_to :dataset
end
sqlite = "#{File.expand_path(File.dirname(__FILE__))}/#{Sinatra::Base.environment}.sqlite3"
DataMapper.setup(:default, "sqlite3:///#{sqlite}")
DataMapper::Logger.new(STDOUT, 0)
unless FileTest.exists?("#{sqlite}")
[Dataset, Association].each do |model|
model.auto_migrate!
end
end
## REST API
get '/?' do
Dataset.all.collect{ |d| url_for("/", :full) + d.id.to_s }.join("\n")
end
get '/:id' do
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
halt 202, dataset.to_yaml unless dataset.finished
dataset.to_yaml
=begin
builder do |xml|
xml.instruct!
xml.dataset do
xml.uri url_for("/", :full) + dataset.id.to_s
xml.name dataset.name
dataset.associations.each do |a|
xml.association do
xml.compound_uri a.compound_uri
xml.feature_uri a.feature_uri
end
end
end
end
=end
end
get '/:id/name' do
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
dataset.name
end
get '/:id/compounds' do
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
dataset.associations.collect{ |a| a.compound_uri }.uniq.join("\n")
end
get '/:id/features' do
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
dataset.associations.collect{ |a| a.feature_uri }.uniq.join("\n")
end
get '/:id/features/compounds' do
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
features = {}
dataset.associations.each do |a|
if features[a.feature_uri]
features[a.feature_uri] << a.compound_uri
else
features[a.feature_uri] = [a.compound_uri]
end
end
features.to_yaml
=begin
builder do |xml|
xml.instruct!
xml.dataset do
features.each do |feature,compounds|
xml.feature do
xml.uri feature
compounds.each do |c|
xml.compound_uri c
end
end
end
end
end
=end
end
get '/:id/compounds/features' do
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
compounds = {}
dataset.associations.each do |a|
if compounds[a.compound_uri]
compounds[a.compound_uri] << a.feature_uri
else
compounds[a.compound_uri] = [a.feature_uri]
end
end
compounds.to_yaml
=begin
builder do |xml|
xml.instruct!
xml.dataset do
compounds.each do |compound,features|
xml.compound do
xml.uri compound
features.each do |f|
xml.feature_uri f
end
end
end
end
end
=end
end
get '/:id/compound/*/features' do
compound_uri = params[:splat].first
Association.all(:dataset_id => params[:id], :compound_uri => compound_uri).collect { |a| a.feature_uri }.uniq.join("\n")
end
get '/:id/feature/*/compounds' do
feature_uri = params[:splat].first
Association.all(:dataset_id => params[:id], :feature_uri => feature_uri).collect { |a| a.compound_uri }.uniq.join("\n")
end
post '/?' do
#protected!
dataset = Dataset.create :name => params[:name]
if params[:file]
Spork.spork do
File.open(params[:file][:tempfile].path).each_line do |line|
record = line.chomp.split(/,\s*/)
compound = OpenTox::Compound.new :smiles => record[0]
feature = OpenTox::Feature.new :name => params[:name], :values => { 'classification' => record[1] }
Association.create(:compound_uri => compound.uri, :feature_uri => feature.uri, :dataset_id => dataset.id)
end
dataset.update_attributes(:finished => true)
end
=begin
elsif params[:data]
puts params[:data]
dataset = Dataset.create :name => params[:name]
#Spork.spork do
YAML.load(params[:data]).each do |record|
compound = OpenTox::Compound.new :uri => record[0]
feature = OpenTox::Feature.new :uri => record[1]
puts compound + "\t" , feature
Association.create(:compound_uri => compound.uri, :feature_uri => feature.uri, :dataset_id => dataset.id)
end
dataset.update_attributes(:finished => true)
#end
=end
end
url_for("/", :full) + dataset.id.to_s
end
put '/:id/?' do
#protected!
pass if params[:finished]
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
compound_uri = params[:compound_uri]
feature_uri = params[:feature_uri]
Association.create(:compound_uri => compound_uri.to_s, :feature_uri => feature_uri.to_s, :dataset_id => dataset.id)
url_for("/", :full) + dataset.id.to_s
end
put '/:id/?' do
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
dataset.update_attributes(:finished => true) if params[:finished] == 'true'
end
delete '/:id/?' do
# dangerous, because other datasets might refer to it
#protected!
halt 404, "Dataset #{params[:id]} not found." unless dataset = Dataset.get(params[:id])
dataset.associations.each { |a| a.destroy }
dataset.destroy
"Successfully deleted dataset #{params[:id]}."
end
|
