Module: ClassyFireAPI

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# File 'lib/classyfire_api.rb', line 105

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

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# File 'lib/classyfire_api.rb', line 38

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

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# File 'lib/classyfire_api.rb', line 84

def ClassyFireAPI.get_sequence_classification(fingerprint,format="json")
  begin
    if format == "json"
      RestClient.get "#{URL}/entities/#{fingerprint}.#{format}", :accept => :json
    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

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# File 'lib/classyfire_api.rb', line 130

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

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# File 'lib/classyfire_api.rb', line 256

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

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# File 'lib/classyfire_api.rb', line 324

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(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0] 
        # 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(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
      # 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

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# File 'lib/classyfire_api.rb', line 386

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(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
        # 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]
    begin
      inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
      # 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
end

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# File 'lib/classyfire_api.rb', line 239

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

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# File 'lib/classyfire_api.rb', line 15

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

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# File 'lib/classyfire_api.rb', line 152

def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length=1000, start=1, 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)
  i = 0
  lines.uniq.each do |line|
    i += 1
    sline = line.strip.split("\t")
    if sline.length == 1
      input <<"#{sline[0]}"
    elsif sline.length == 2
      #ID\tSMILES (OR INCHI, OR VALID IUPAC NAME)
      input <<"#{sline[0]}\t#{sline[1]}"
    end
    input <<"#{sline[0]}"
  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 = 240
  initial_nr_of_jobs = 30
  i = start

  while i <  initial_nr_of_jobs

    title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}"

    if i <= subdivised_groups.length
      puts "\n\n\n\n---------------------- -----------"
      # begin
        puts "submitting #{title}"
        puts subdivised_groups[i-1].join("\n")
        q       = submit_query(title,subdivised_groups[i-1].join("\n"),type)
        # puts q
        query_ids << JSON.parse(q)['id']
      # rescue Exception => e  
        # puts e.message  
        # puts e.backtrace.inspect
      # end
      i = i + 1
    else
      break
    end
  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 >= initial_nr_of_jobs && i < subdivised_groups.length
    k = 0
    for k in (i..(i + initial_nr_of_jobs))
      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