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require "json"
require 'base64'
require 'sinatra/base'
require "sinatra/reloader"
require "rest-client"
require 'memcache'
class Application < Sinatra::Base
# doc @ http://pubchem.ncbi.nlm.nih.gov/pug_rest/
@@pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
@@similarity_threshold = 90
@@max_neighbors = 100
CACHE = MemCache.new 'localhost:11211'
helpers do
def local route
status, headers, body = call env.merge("PATH_INFO" => route)
begin
Float body[0]
rescue
JSON.parse body[0]
end
end
def pubchem_search url
attempts = 0
begin
attempts += 1
puts url
json = RestClient.get url, :timeout => 90000000
JSON.parse json
rescue
if $!.message =~ /Timeout/i and attempts < 4
sleep 2
retry
elsif $!.message =~ /Timeout/i and attempts >= 4
File.open("timeouts","a+"){|f| f.puts url}
puts url
puts $!.message
nil
elsif $!.message.match /404/
nil
else
puts url
puts $!.message
nil
end
end
end
def fingerprint cid
local("/cid/#{cid}/fingerprint")
end
def neighbors cid
local "/cid/#{cid}/neighbors"
end
def assays cid
local "/cid/#{cid}/assays"
end
def similarity cid1, cid2
local("/cid/#{cid1}/cosine/#{cid2}")
end
def cosine fp1, fp2
if fp1 and fp2
m11 = 0.0
m01 = 0.0
m10 = 0.0
m00 = 0.0
fp1.each_index do |i|
m11 += 1 if (fp1[i] and fp2[i])
m01 += 1 if (!fp1[i] and fp2[i])
m10 += 1 if (fp1[i] and !fp2[i])
m00 += 1 if (!fp1[i] and !fp2[i])
end
m11/((m01+m11)*(m10+m11))**0.5
end
end
end
before do
@result = CACHE.get request.path
halt 200, @result unless @result.nil? # should be 304, but this does not work with local()
end
after do
CACHE.add request.path, @result, 7200
end
get '/cid/:cid/name' do
@result = RestClient.get(File.join(@@pug_uri, "compound", "cid", params[:cid], "property", "IUPACName","TXT")).chomp
end
get '/cid/:cid/fingerprint' do
# ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt
# it seems that only SDF formats contain fingerprints
sdf_lines = RestClient.get(File.join(@@pug_uri, "compound", "cid", params[:cid], "SDF")).split("\n")
index = sdf_lines.index(sdf_lines.grep(/PUBCHEM_CACTVS_SUBSKEYS/).first)
@result = Base64.decode64(sdf_lines[index+1])[4..-1].unpack("B*").first[0..-8].split(//).collect{|c| c == "1"}.to_json
end
get '/cid/:cid/assays' do
assays = []
result = pubchem_search File.join(@@pug_uri, "compound", "cid", params[:cid], "assaysummary", "JSON")
if result and result["Table"]
columns = result["Table"]["Columns"]["Column"]
result["Table"]["Row"].collect{|cell| cell.values.flatten}.each do |row|
assay = {}
row.each_with_index do |cell,i|
assay[columns[i]] = cell unless cell.empty? or columns[i] == "CID"
end
assays << assay unless assay.empty?
end
end
@result = assays.to_json
end
get '/cid/:cid/neighbors' do
result = pubchem_search File.join(@@pug_uri, "compound", "similarity", "cid", params[:cid], "JSON")+"?Threshold=#{@@similarity_threshold}&MaxRecords=#{@@max_neighbors}"
while result["Waiting"] do
sleep 2
listkey = result["Waiting"]["ListKey"]
result = pubchem_search File.join(@@pug_uri, "compound", "listkey", listkey, "cids", "JSON")
end
result["IdentifierList"]["CID"].delete params[:cid].to_i
@result = result["IdentifierList"]["CID"].to_json
end
get '/name/:name' do
@result = RestClient.get(File.join(@@pug_uri,"compound","name",CGI.escape(params[:name]),"cids","TXT")).split("\n").to_json
end
get '/cid/:cid/image' do
@result = RestClient.get File.join(@@pug_uri, "compound", "cid", params[:cid], "PNG")
end
get '/cid/:cid1/cosine/:cid2' do
fp1 = fingerprint params[:cid1]
fp2 = fingerprint params[:cid2]
@result = cosine(fp1, fp2).to_json
end
get '/cid/:cid/predictions' do
assays = {}
assay_details = {}
neighbors(params[:cid]).each do |cid|
neighbor_assays = assays cid
unless neighbor_assays.empty?
neighbor_assays.each do |assay|
if assay["Activity Outcome"] == "active" or assay["Activity Outcome"] == "inactive"
assays[assay["AID"]] ||= []
assays[assay["AID"]] << [cid,similarity(params[:cid],cid),assay["Activity Outcome"]]
assay_details[assay["AID"]] ||= {}
["Target GI", "Target Name", "Assay Name"].each do |d|
assay_details[assay["AID"]][d] = assay[d] #if assay[d]
end
end
end
end
end
predictions = []
assays.each do |aid,neighbors|
prediction = {"AID" => aid}
neighbors.each do |neighbor|
cid = neighbor[0]
sim = neighbor[1]
activity = neighbor[2]
if activity == "active"
prediction[:p_active] ? prediction[:p_active] = prediction[:p_active]*sim : prediction[:p_active] = sim
prediction[:p_inactive] ? prediction[:p_inactive] = prediction[:p_inactive]*(1-sim) : prediction[:p_inactive] = 1-sim
elsif activity == "inactive"
prediction[:p_active] ? prediction[:p_active] = prediction[:p_active]*(1-sim) : prediction[:p_active] = 1-sim
prediction[:p_inactive] ? prediction[:p_inactive] = prediction[:p_inactive]*sim : prediction[:p_inactive] = sim
end
["Target GI", "Target Name", "Assay Name"].each do |d|
prediction[d] = assay_details[aid][d] if assay_details[aid][d]
end
end
predictions << prediction
end
@result = predictions.to_json
end
# get '/*' do |path|
# RestClient.get File.join(@@pug_uri,path), params
# end
end
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