gistfile1.rb

  def concentration_value(c)
        unit = ""
        conc = c.conc_value
        mean = 0
        error = 0
        
        if (conc.nil?)
          return ""
        elsif(conc == "Detected")
          mean = -1
        elsif(conc == "not detected" || conc == "NA" || conc == "Not Detected")
          return ""
        else
          conc = conc.strip
        end
        
        if (conc =~/^([\+\-\d\.Ee]+)$/)
          mean = $1.to_f
          error = 0
        elsif (conc =~/^<?([\d\.]+)\s*\-\s*([\d\.]+)$/)
          mean = ($1.to_f + $2.to_f)/2
          error = ($2.to_f - $1.to_f)/2
        elsif (conc =~/^([\d\.]+)\s*\+\/\-\s*([\d\.]+)\s*/)
          mean = $1.to_f
          error = $2.to_f
        elsif (conc =~/^\>=?\s*([\d\.]+)$/)
          mean = $1.to_f
          error = 0
        elsif (conc =~/^\<=?\s*([\d\.]+)$/)
          mean = $1.to_f/2
          error = $1.to_f/2
        elsif (conc =~/^([\+\-\d\.Ee]+)\s+\+\/\-\s*([\+\-\d\.Ee]+)$/)
          mean = $1.to_f
          error = $2.to_f
        elsif (conc =~/^([\d\.]+)\s*\(\s*([\d\.]+)\s*[^\s\d\.\+]\s*([\d\.]+)\s*\)$/)
          mean = $1.to_f
          error = ($3.to_f - $2.to_f)/2
        else
#          puts "cannot parse concentration: '#{conc}' id: #{c.id}"
          #
        end
        
        
        if (c.biofluid_source == "Blood")
          if (c.conc_unit == "uM")
            
          else
 #           puts "ERROR: unusually unit for blood concentration: #{c.conc_unit} id: #{c.id}"
            #
          end
#          puts "#{record.hmdb_id}\t#{c.patient_status}\t#{c.conc_condition}\t#{c.biofluid_source}\t#{mean}\t#{error}\t#{c.age}\t#{c.sex}\t#{c.id}"
        elsif (c.biofluid_source == "Urine")
          if (c.conc_unit == "uM")
            # assume this is right (i.e. = umol/mmol_creatinine)
          elsif (c.conc_unit == "umol/mmol_creatinine" || c.conc_unit == "umol/mmol creatinine")
            
          elsif (c.conc_unit == "nmol/mmol_creatinine" || c.conc_unit == "nmol/mmol creatinine")
            mean = mean * 1000
            error = error * 1000
          else
#            puts "ERROR: unusually unit for urine concentration: #{c.conc_unit} id: #{c.id}"
            #
          end
#          puts "#{record.hmdb_id}\t#{c.patient_status}\t#{c.conc_condition}\t#{c.biofluid_source}\t#{mean}\t#{error}\t#{c.age}\t#{c.sex}\t#{c.id}"
        else
          #
        end
        
       return "data-value=#{mean} data-error=#{error} data-type=#{c.biofluid_source}" 
      end