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require "./pubchem.rb"
require 'rack/session/dalli'
require "rack/cache"
module OpenTox
class Application < Service
set :static, true
set :root, File.dirname(__FILE__)
also_reload './pubchem.rb'
@@pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
before do
#cache_control :public, :max_age => 3600
end
before '/cid/:cid/*' do
#cache_control :public, :max_age => 3600
session[:compound] = PubChemCompound.new params[:cid] unless session[:compound] and session[:compound].cid == params[:cid]
end
get '/?' do
#cache_control :public, :no_cache
haml :index
end
get '/cid/:cid/?' do
haml :compound
end
get '/search/?' do
#cache_control :public, :no_cache
begin
cids = RestClient.get(File.join(@@pug_uri,"compound","name",CGI.escape(params[:name]),"cids","TXT")).split("\n")
if cids.size == 1
session[:compound] = PubChemCompound.new cids.first
haml :compound
elsif cids.size > 1
@compounds = cids.collect{|cid| PubChemCompound.new cid }
haml :select
end
rescue
haml :not_found
end
end
get '/cid/:cid/targets/?' do
@assays = session[:compound].targets
haml :targets, :layout => false
end
get '/cid/:cid/nontargets/?' do
@assays = session[:compound].non_targets
haml :targets, :layout => false
end
get '/cid/:cid/other_active_assays/?' do
@assays = session[:compound].active_assays - session[:compound].targets
haml :assays, :layout => false
end
get '/cid/:cid/other_inactive_assays/?' do
@assays = session[:compound].inactive_assays - session[:compound].non_targets
haml :assays, :layout => false
end
get '/cid/:cid/predicted_targets/?' do
@assays = session[:compound].predicted_targets
haml :predicted_targets, :layout => false
end
get '/cid/:cid/predicted_nontargets/?' do
@assays = session[:compound].predicted_non_targets
haml :predicted_targets, :layout => false
end
get '/cid/:cid/other_predicted_active_assays/?' do
@assays = session[:compound].predicted_active_assays - session[:compound].predicted_targets
haml :predicted_assays, :layout => false
end
get '/cid/:cid/other_predicted_inactive_assays/?' do
@assays = session[:compound].predicted_inactive_assays - session[:compound].predicted_non_targets
haml :predicted_assays, :layout => false
end
get '/cid/:cid/neighbors/?' do
haml :neighbors, :layout => false
end
get '/cid/:cid/cosine/:cid2/?' do
session[:compound].cosine(PubChemCompound.new(params[:cid2])).round(3).to_s
end
=begin
get '/aid/:aid/?' do
puts File.join(@@pug_uri, "assay", "aid", params[:aid].to_s, "description", "JSON")
json = RestClient.get File.join(@@pug_uri, "assay", "aid", params[:aid].to_s, "description", "JSON")
@description = JSON.parse(json)["PC_AssayContainer"][0]["assay"]["descr"]
haml :assay_description, :layout => false
end
get '/pubchem_proxy/*' do |path|
puts path.inspect
puts "http://pubchem.ncbi.nlm.nih.gov/rest/pug/#{path}"
RestClientWrapper.get "http://pubchem.ncbi.nlm.nih.gov/rest/pug/#{path}"
end
=end
get '/fp/?' do
@fp = []
YAML.load_file("false_positives.yaml").each do |pred|
pred[:fp_targets].each do |gi,t|
@fp << {
"CID" => pred[:cid],
"Target GI" => gi,
"p_active" => t[:p][:active].first,
"p_inactive" => t[:p][:inactive].first,
:assays => t[:measured],
:neighbors => t[:neighbors]
}
end
end
@fp.sort!{|a,b| b["p_active"] <=> a["p_active"]}
haml :fp
end
end
end
|
