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#['rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'crack/xml', 'dm-core', 'spork'].each do |lib|
['rubygems', 'sinatra', 'rest_client', 'sinatra/url_for', 'crack/xml', 'dm-core', 'builder', 'logger'].each do |lib|
require lib
end
DataMapper.setup(:default, "sqlite3://#{Dir.pwd}/lazar.sqlite3")
class Model
include DataMapper::Resource
property :id, Serial
property :name, String
property :feature_dataset_uri, String
property :training_dataset_uri, String
end
Model.auto_migrate! unless File.exists?("lazar.sqlite3")
COMPOUNDS_URI = 'http://webservices.in-silico.ch/compounds/'
FEATURES_URI = 'http://webservices.in-silico.ch/features/'
DATASET_URI = 'http://localhost:4567/'
FEATURE_GENERATION_URI = 'http://localhost:9394/'
@similarity_prediction = RestClient::Resource.new 'http://webservices.in-silico.ch/weighted_similarity_classification'
get '/?' do # get index of models
Model.all.collect{ |m| url_for("/", :full) + m.id.to_s }.join("\n")
end
get '/:id' do
@model = Model.get(params[:id])
builder :model
end
get '/:id/:inchikey' do # show prediction
@prediction = Prediction.first(:model_id => params[:id], :compound_uri => params[:compound_uri])
builder :prediction
end
post '/:id' do # create prediction
unless prediction = Prediction.first(:model_id => params[:id], :compound_uri => params[:compound_uri])
Spork.spork do
Prediction.create(@similarity_prediction.post, :compound_uri => params[:compound_uri], :feature_dataset_uri => Model.get(params[:id]).feature_dataset_uri)
end
end
inchikey = @compounds.get "#{params[:compound_uri]}.inchikey"
# or redirect?
url_for("/#{params[:id]}/#{inchikey}", :full)
end
post '/' do # create model
training_dataset_uri = RestClient.post DATASET_URI, :name => params[:name]
dataset = RestClient::Resource.new training_dataset_uri
model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset_uri)
#Spork.spork do
pid = fork do
# create model from a tab delimited file
File.open(params[:file][:tempfile].path).each_line do |line|
items = line.split(/\s+/)
begin
compound_uri = COMPOUNDS_URI + URI.encode(items[0])
#compound_uri = RestClient.post COMPOUNDS_URI, :smiles => items[0]
rescue
puts "Failed to get InChI key for #{items[0]}"
end
feature_uri = RestClient.post FEATURES_URI, :name => params[:name], :value => items[1]
dataset.put :compound_uri => compound_uri, :feature_uri => feature_uri
model.training_dataset_uri = training_dataset_uri
model.save
#rescue
#puts "Creation of feature #{params[:name]}:#{items[1]} for compound #{items[0]} failed."
#end
end
feature_dataset_uri = RestClient.post FEATURE_GENERATION_URI, :dataset_uri => training_dataset_uri
model.feature_dataset_uri = feature_dataset_uri.chomp
model.save
# create features
#feature_dataset_uri = @feature_generation.post :dataset_uri => params[:dataset_uri]
#model = Model.create(:name => params[:name], :training_dataset_uri => training_dataset_uri, :feature_dataset_uri => feature_dataset_uri)
#model.save
# validate
# or redirect?
end
Process.detach(pid)
url_for("/", :full) + model.id.to_s
end
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