diff options
Diffstat (limited to 'pug.rb')
| -rw-r--r-- | pug.rb | 193 |
1 files changed, 193 insertions, 0 deletions
@@ -0,0 +1,193 @@ +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 |