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.
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# 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.
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# 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
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# 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.
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# 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.
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# 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.
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# 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'
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# 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.
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# 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'.
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# 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).
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# 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 |