Module: ClassyFireAPI + + + +
+ +-
+
+
+
+
+
+
+
+
+
- Defined in: +
- lib/classyfire_api.rb + +
Constant Summary
+ +-
+
+
- URL = + + +
'http://classyfire.wishartlab.com'
+
+
+ Class Method Summary + (collapse) +
+ +-
+
+
-
+
+
+ + (Text) get_entity_classification(inchikey, format = "json")
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Retrieves the classification results for a given entity.
+
+
+
+ -
+
+
+ + (Text) get_query(query_id, format = "json")
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Retrieves the classification results for a given query.
+
+
+
+ -
+
+
+ + (String) query_status(query_id)
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Retrieves the status of a query.
+
+
+
+ -
+
+
+ + (String) retrieve_classification(input, output)
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Reads a tab separated file, and use the structure representation to +retrieve the strutcure's classification from ClassyFire.
+
+
+
+ -
+
+
+ + (String) retrieve_entities_json(input, output)
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Reads a tab separated file, and use the structure representation to +retrieve the strutcure's classification from ClassyFire in a JSON +format.
+
+
+
+ -
+
+
+ + (String) retrieve_entities_sdf(input, output)
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Reads a tab separated file, and use the structure representation to +retrieve the strutcure's classification from ClassyFire in a SDF +format.
+
+
+
+ -
+
+
+ + (Object) submit_queries_from_directory(folder, slice_length, type = "STRUCTURE")
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Takes each file in a folder, and submit the contained structures in bluks +of a given size.
+
+
+
+ -
+
+
+ + (Hash) submit_query(label, input, type = 'STRUCTURE')
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Submits a ClassyFire query, which should be returned in a specific format.
+
+
+
+ -
+
+
+ + (Object) submit_query_input_in_chunks(input_file, slice_length, start, type = 'STRUCTURE')
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Takes a tab-separated file and submit the contained structures in bulks of +a given size.
+
+
+
+ -
+
+
+ + (Object) submit_random_subset_of_query_input_in_chunks(tab_separated_input_file, size, type = 'STRUCTURE')
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ++ +
Takes a tab-separated file and submit randomly selected structures in bulks +of a given size.
+
+
+
+
+
+
+Class Method Details
+ + +
+
+
+
+
+ + + + (Text) get_entity_classification(inchikey, format = "json") + + + + + +
+
+
+
+
+Retrieves the classification results for a given entity.
+ + +
+ + + +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80+ |
+
+ # File 'lib/classyfire_api.rb', line 61 + +def ClassyFireAPI.get_entity_classification(inchikey,format="json") + inchikey_id = inchikey.to_s.gsub('InChIKey=','') + begin + if format == "json" + RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :json + elsif format == "sdf" + RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :sdf + elsif format == "csv" + RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :csv + end + rescue RestClient::ResourceNotFound => e + e.response + rescue RestClient::InternalServerError => e + e.response + rescue RestClient::GatewayTimeout => e + e.response + rescue RestClient::RequestTimeout => e + e.response + end +end+ |
+
+
+
+
+
+ + + + (Text) get_query(query_id, format = "json") + + + + + +
+
+
+
+
+Retrieves the classification results for a given query.
+ +the query's entities in the specified format.
+ + +
+ + + +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54+ |
+
+ # File 'lib/classyfire_api.rb', line 36 + +def ClassyFireAPI.get_query(query_id,format="json") + begin + if format == "json" + RestClient.get "#{URL}/queries/#{query_id}.json", :accept => :json + elsif format == "sdf" + RestClient.get "#{URL}/queries/#{query_id}.sdf", :accept => :sdf + elsif format == "csv" + RestClient.get "#{URL}/queries/#{query_id}.csv", :accept => :csv + end + rescue RestClient::ResourceNotFound => e + e.response + rescue RestClient::InternalServerError => e + e.response + rescue RestClient::GatewayTimeout => e + e.response + rescue RestClient::RequestTimeout => e + e.response + end +end+ |
+
+
+
+
+
+ + + + (String) query_status(query_id) + + + + + +
+
+
+
+
+Retrieves the status of a query
+ + +
+ + + +85 +86 +87 +88 +89 +90 +91 +92+ |
+
+ # File 'lib/classyfire_api.rb', line 85 + +def ClassyFireAPI.query_status(query_id) + begin + RestClient.get "#{URL}/queries/#{query_id}/status.json", :accept => :json + rescue Exception=>e + $stderr.puts e. + nil + end +end+ |
+
+
+
+
+
+ + + + (String) retrieve_classification(input, output) + + + + + +
+
+
+
+
+Reads a tab separated file, and use the structure representation to +retrieve the strutcure's classification from ClassyFire.
+ + +
+ + + +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328+ |
+
+ # File 'lib/classyfire_api.rb', line 266 + +def ClassyFireAPI.retrieve_classification(input,output) + absolute_path = File.(input) + f_input = File.open(absolute_path, 'r') + h = Hash.new + directory = absolute_path.split('/')[0...-1].join("/") + f_output = File.new(output, 'w') + res = String.new + + + res += "{" + res += '"id": 1,' + res += '"label":"' + output + '",' + '"classification_status":"Done",' + '"entities":[' + + f_input.each_line do |line| + sline = line.strip.split("\t") + if sline.length == 1 + h[sline[0]] = sline[0] + elsif sline.length == 2 + h[sline[0]] = line.strip + end + end + + puts h.keys.uniq.length + if h.keys.length > 0 + i = 1 + h.keys.uniq[0..-1].each do |key| + puts i + + puts "#{key} :: #{h[key]}" + begin + qs = submit_query(key,h[key]) + + qs_decoded = JSON.parse(qs) + qr = JSON.parse(get_query(qs_decoded["id"],format="json")) + + res += qr["entities"][0].to_json + res += "," + i += 1 + rescue Exception => e + e. + end + + end + key = h.keys[-1] + puts "#{key} :: #{h[key]}" + begin + qs = submit_query(key,h[key]) + sleep(0.2) + qs_decoded = JSON.parse(qs) + qr = JSON.parse(get_query(qs_decoded["id"],format="json")) + # puts qr["entities"] + # sleep(0.2) + # f_output.print qr["entities"][0],"\n" + res += qr["entities"][0].to_json + # res += "," + rescue Exception => e + e. + end + end + + res += "]}" + f_output.print res +end+ |
+
+
+
+
+
+ + + + (String) retrieve_entities_json(input, output) + + + + + +
+
+
+
+
+Reads a tab separated file, and use the structure representation to +retrieve the strutcure's classification from ClassyFire in a JSON +format.
+ + +
+ + + +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388+ |
+
+ # File 'lib/classyfire_api.rb', line 335 + +def ClassyFireAPI.retrieve_entities_json(input,output) + absolute_path = File.(input) + f_input = File.open(absolute_path, 'r') + h = Hash.new + directory = absolute_path.split('/')[0...-1].join("/") + f_output = File.new(output, 'w') + puts + res = String.new + + res += "{" + res += '"id": 1,' + res += '"label":"' + output + '",' + '"classification_status":"Done",' + '"entities":[' + + f_input.each_line do |line| + sline = line.strip.split("\t") + h[sline[0]] = sline[-1] + end + + puts h.keys.uniq.length + if h.keys.length > 0 + i = 1 + h.keys.uniq[0...-1].each do |key| + puts i + # puts "#{key} :: #{h[key]}" + begin + inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip + # puts inchikey + qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json")) + qr['identifier'] = key + res += qr.to_json + res += "," + puts "#{key} :: RETURN NIL" if qr.nil? || qr['direct_parent']['name'].nil? + rescue Exception => e + e. + end + i += 1 + end + key = h.keys[-1] + # puts "#{key} :: #{h[key]}" + begin + inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip + # puts inchikey + qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json")) + qr['identifier'] = key + res += qr.to_json + puts "#{key} :: RETURN NIL" if qr.nil? || qr['direct_parent']['name'].nil? + # res += "," + rescue Exception => e + e. + end + end + res += "]}" + f_output.print res +end+ |
+
+
+
+
+
+ + + + (String) retrieve_entities_sdf(input, output) + + + + + +
+
+
+
+
+Reads a tab separated file, and use the structure representation to +retrieve the strutcure's classification from ClassyFire in a SDF +format.
+ + +
+ + + +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431 +432 +433 +434 +435 +436 +437 +438 +439 +440 +441 +442 +443 +444 +445 +446 +447 +448 +449 +450 +451 +452 +453 +454 +455 +456+ |
+
+ # File 'lib/classyfire_api.rb', line 397 + +def ClassyFireAPI.retrieve_entities_sdf(input,output) + absolute_path = File.(input) + f_input = File.open(absolute_path, 'r') + h = Hash.new + directory = absolute_path.split('/')[0...-1].join("/") + f_output = File.new(output, 'w') + res = String.new + + f_input.each_line do |line| + sline = line.strip.split("\t") + h[sline[0]] = sline[-1] + end + + puts h.keys.uniq.length + if h.keys.length > 0 + i = 1 + h.keys.uniq[0...-1].each do |key| + puts i + # puts "#{key} :: #{h[key]}" + begin + inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip + # puts inchikey + qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf") + if qr.include?("The page you were looking for doesn't exist") + puts "The page you were looking for doesn't exist" + elsif qr.empty? + + else + input = qr.split("\n")[1..-1].join("\n") + puts input + f_output.puts "#{key}\n" + f_output.puts input + end + rescue Exception => e + e. + end + i += 1 + end + key = h.keys[-1] + # puts "#{key} :: #{h[key]}" + begin + inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip + # puts inchikey + qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf") + if qr.include?("The page you were looking for doesn't exist") + puts "The page you were looking for doesn't exist" + elsif qr.empty? + + else + input = qr.split("\n")[1..-1].join("\n") + puts input + f_output.puts "#{key}\n" + f_output.puts input + end + rescue Exception => e + e. + end + end + # f_output.print res +end+ |
+
+
+
+
+
+ + + + (Object) submit_queries_from_directory(folder, slice_length, type = "STRUCTURE") + + + + + +
+
+
+
+
+Takes each file in a folder, and submit the contained structures in bluks +of a given size.
+ +For 'STRUCTURE' or 'IUPAC_NAME'query types, each line must +contain either
+ +1) Only a structural represenation: SMILES, InChI for the 'STRUCTURE' query_type or a IUPAC name
+ for the 'IUPAC NAME' query type.
+2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
+ 'STRUCTURE' query_type or a IUPAC name for the 'IUPAC NAME' query type.For 'FASTA' query type, just submit the query as a standard FASTA +text. @param: input_file [String] The path to the folder. @param: +slice_length [Integer] The maximum number of entries for each query input +(each file is fragmented into n part of #slice_length entries each), +'integer'
+ + +
+ + + +184 +185 +186 +187 +188 +189 +190 +191 +192 +193+ |
+
+ # File 'lib/classyfire_api.rb', line 184 + +def ClassyFireAPI.submit_queries_from_directory(folder,slice_length,type="STRUCTURE") + if File.directory?(folder) + Dir.foreach(folder) do |filename| + puts "Filename: #{filename}" + ClassyFireAPI.submit_query_input_in_chunks(folder+"/"+filename,slice_length, type) unless filename == "." || filename == ".." || filename == ".DS_Store" + end + else + $stderr.puts "#{folder} is not a folder." + end +end+ |
+
+
+
+
+
+ + + + (Hash) submit_query(label, input, type = 'STRUCTURE') + + + + + +
+
+
+
+
+Submits a ClassyFire query, which should be returned in a specific format.
+ +if there is an error.
+ + +
+ + + +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28+ |
+
+ # File 'lib/classyfire_api.rb', line 13 + +def ClassyFireAPI.submit_query(label,input, type='STRUCTURE') + begin + q = RestClient.post URL+'/queries', {:label => label, :query_input => input, :query_type => type}.to_json, :accept => :json, :content_type => :json + rescue RestClient::BadRequest => e + e.response + rescue RestClient::InternalServerError => e + e.response + rescue RestClient::GatewayTimeout => e + e.response + rescue RestClient::RequestTimeout => e + e.response + rescue RestClient::UnprocessableEntity => e + e.response + end + q +end+ |
+
+
+
+
+
+ + + + (Object) submit_query_input_in_chunks(input_file, slice_length, start, type = 'STRUCTURE') + + + + + +
+
+
+
+
+Takes a tab-separated file and submit the contained structures in bulks of +a given size
+ +For 'STRUCTURE' or 'IUPAC_NAME'query types, each line must +contain either
+ +1) Only a structural represenation: SMILES, InChI for the 'STRUCTURE' query_type or a IUPAC name
+ for the 'IUPAC NAME' query type.
+2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
+ 'STRUCTURE' query_type or a IUPAC name for the 'IUPAC NAME' query type.For 'FASTA' query type, just submit the query as a standard FASTA +text. @param: slice_length [Integer] The maximum number of entries for each +query input (the whole file is fragmented into n part of #slice_length +entries each). @param: start [Integer] The starting index. Submit +framgments from the index 'start'.
+ + +
+ + + +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169+ |
+
+ # File 'lib/classyfire_api.rb', line 107 + +def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length, start, type='STRUCTURE') + @start_time = Time.now + absolute_path = File.(input_file) + f = File.open(absolute_path, 'r') + input = [] + + lines = File.readlines(absolute_path) + + lines.uniq.each do |line| + sline = line.strip.split("\t") + if sline.length == 1 + input <<"#{sline[0]}" + elsif sline.length >= 2 + input <<"#{sline[0]}\t#{sline[2]}" + end + end + + query_ids = [] + subdivised_groups = input.uniq.each_slice(slice_length).to_a + puts "nr of subdivised_groups: #{subdivised_groups.length}" + puts subdivised_groups[0] + sleeping_time = 120 + initial_nr_of_jobs = 60 + i = start + + while i < initial_nr_of_jobs + title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}" + + begin + puts "submitting #{title}" + q = submit_query(title,subdivised_groups[i-1].join("\n"),type) + query_ids << JSON.parse(q)['id'] + rescue Exception => e + puts e. + puts e.backtrace.inspect + end + i = i + 1 + end + + puts "Going to sleep at #{Time.now - @start_time} for #{sleeping_time} s." + sleep(sleeping_time) + puts "Waking up at #{Time.now - @start_time}" + + while i < subdivised_groups.length + k = 0 + for k in (i..(i+80)) + title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{k}" + i = i + 1 + begin + puts "submitting #{title}" + q = submit_query(title,subdivised_groups[k-1].join("\n"),type) + rescue Exception => e + puts e. + puts e.backtrace.inspect + end + + end + i = k + puts "Going to sleep at #{Time.now - @start_time} for #{sleeping_time} s." + sleep(sleeping_time) + puts "Waking up at #{Time.now - @start_time}" + end +end+ |
+
+
+
+
+
+ + + + (Object) submit_random_subset_of_query_input_in_chunks(tab_separated_input_file, size, type = 'STRUCTURE') + + + + + +
+
+
+
+
+Takes a tab-separated file and submit randomly selected structures in bulks +of a given size.
+ +For 'STRUCTURE' or 'IUPAC_NAME'query types, each line must +contain either
+ +1) Only a structural represenation: SMILES, InChI for the 'STRUCTURE' query_type or a IUPAC name
+ for the 'IUPAC NAME' query type.
+2) a tab-separated pair of an ID and the corresponding sructure representation: SMILES, InChI for the
+ 'STRUCTURE' query_type or a IUPAC name for the 'IUPAC NAME' query type.For 'FASTA' query type, just submit the query as a standard FASTA +text. is fragmented into n part of #slice_length entries each).
+ + +
+ + + +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259+ |
+
+ # File 'lib/classyfire_api.rb', line 209 + +def ClassyFireAPI.submit_random_subset_of_query_input_in_chunks(tab_separated_input_file,size, type='STRUCTURE') + @start_time = Time.now + absolute_path = File.(tab_separated_input_file) + f = File.open(absolute_path, 'r') + input = [] + + f.each_line do |line| + + sline = line.strip.split("\t") + if sline.length == 1 + input <<"#{sline[0]}" + elsif sline.length == 2 + input <<"#{sline[0]}\t#{sline[1]}" + end + end + + query_ids = [] + indexes = [] + r = 1 + while r <= (size) + s = rand(0..(input.length - 1)) + unless indexes.include?(s) + indexes<<s + r += 1 + end + end + + random_subset = indexes.map{|x| input[x]} + subdivised_groups = random_subset.each_slice(100).to_a + sleeping_time = 120 + + i = 0 + while i < subdivised_groups.length + k = 0 + for k in (i..(i + 5)) + title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{k+1}" + i = i + 1 + begin + puts "submitting #{title}" + q = submit_query(title,subdivised_groups[k].join("\n"),type) + rescue Exception => e + puts e. + puts e.backtrace.inspect + end + end + i = k + puts "Going to sleep at #{Time.now - @start_time} for #{sleeping_time} s." + sleep(sleeping_time) + puts "Waking up at #{Time.now - @start_time}" + end +end+ |
+