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