classyfire_api/lib/classyfire_api.rb

require 'JSON'
require 'csv'

module ClassyFireAPI
  URL = 'http://classyfire.wishartlab.com'

  # Submits a ClassyFire query, which should be returned in a specific format.
  #
  # @param label [String] the label of the query.
  # @param input[String] the input of the query.
  # @return [Hash] A Ruby Hash with the id (and other attributes) of the Query or nil
  # if there is an error.
  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

  # Retrieves the classification results for a given query.
  #
  # @param query_id [Integer] the ID of the query.
  # @param format [String] the format of the query (either JSON, CSV, or SDF)
  # @return [Text] A text file displaying the classification results for 
  # the query's entities in the specified format.
  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

  # Retrieves the classification results for a given entity.
  #
  # @param inchikey [String] the ID of the query.
  # @param format [String] the format of the query, 'text' (either JSON, CSV, or SDF)
  # @return [Text] A text file displaying the classification results for the entity in the specified format.
  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

  # Retrieves the status of a query
  # @param query_id [Integer] the ID of the query
  # @return [String] the query status, 'Done' or 'In progress', 'string'
  def ClassyFireAPI.query_status(query_id)
    begin
      RestClient.get "#{URL}/queries/#{query_id}/status.json", :accept => :json
    rescue Exception=>e
      $stderr.puts e.message
      nil
    end
  end

  # 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 input_file [Text] The path to the input file.
  # @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'.
  def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length, start, type='STRUCTURE')
    @start_time = Time.now
    absolute_path = File.expand_path(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.message  
        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.message  
          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

  # 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'  
  # @param type [String] the query_type 'STRUCTURE' (default) or 'IUPAC_NAME' or 'FASTA'
  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


  # 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.
  # @param tab_separated_input_file [Text] The path to the input file.
  # @param size [Integer] The maximum number of entries for each query input (the whole file 
  # is fragmented into n part of #slice_length entries each).
  # @param type [String] The query_type, 'STRUCTURE' (default) or 'IUPAC_NAME' or 'FASTA'.
  def ClassyFireAPI.submit_random_subset_of_query_input_in_chunks(tab_separated_input_file,size, type='STRUCTURE')
    @start_time = Time.now
    absolute_path = File.expand_path(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.message  
          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

  # Reads a tab separated file, and use the structure representation 
  #to retrieve the strutcure's classification from ClassyFire.
  #
  # @param input [String] path to the input file.
  # @return [String] path to the output file.
  def ClassyFireAPI.retrieve_classification(input,output)
    absolute_path = File.expand_path(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.message
        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.message
      end        
    end

    res += "]}"
    f_output.print res
  end

  # Reads a tab separated file, and use the structure representation
  # to retrieve the strutcure's classification from ClassyFire in a JSON format.
  #
  # @param input [String] path to the input file
  # @return [String] path to the output file
  def ClassyFireAPI.retrieve_entities_json(input,output)
    absolute_path = File.expand_path(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.message
        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.message
      end        
    end
    res += "]}"
    f_output.print res
  end



  # Reads a tab separated file, and use the structure representation
  # to retrieve the strutcure's classification from ClassyFire in a SDF format.
  #
  # @param input [String] path to the input file
  # @return [String] path to the output file
  def ClassyFireAPI.retrieve_entities_sdf(input,output)
    absolute_path = File.expand_path(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.message
        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.message
      end        
    end
    # f_output.print res
  end
end