Class: DeterminationsComparison::Comparison

Inherits:
Object
  • Object
show all
Defined in:
lib/determinations_comparison.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filepath_baseline, filepath_undertest, opts = {}) ⇒ Comparison

Returns a new instance of Comparison.



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# File 'lib/determinations_comparison.rb', line 20

def initialize(filepath_baseline,filepath_undertest,opts={})

  @filepath_comparedeterminations = opts[:filepath_comparedeterminations]
  @filepath_cpplogreader =          opts[:filepath_cpplogreader]

  hashPropertyThresholds = opts[:hashPropertyThresholds] || {:area=>0,:apex_time=>0,:apex_intensity=>0}

  @folderpath_with_log = opts[:folderpath_with_log] || File.dirname(filepath_undertest)

  @filepath_baseline_origin = filepath_baseline
  @filepath_undertest_origin = filepath_undertest

  @filepath_keymapping = File.join( LIB_FOLDER,'..','config','key_mapping.yaml')

  @uuid = UUIDTools::UUID.random_create

  $log_detercomp = Logger.new File.join(LIB_FOLDER,'..',"log.txt")

  @hashDiffs = Hash.new
  differences 'Compound', hashCompoundUnderTest, hashCompoundBaseLine, @hashDiffs
  differences_extrapolated

  @hashCategory = categorize hashPropertyThresholds

end

Instance Attribute Details

#baseline_filepath ⇒ Object

Returns the value of attribute baseline_filepath.



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# File 'lib/determinations_comparison.rb', line 18

def baseline_filepath
  @baseline_filepath
end

#filepath_baseline_origin ⇒ Object

Returns the value of attribute filepath_baseline_origin.



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# File 'lib/determinations_comparison.rb', line 18

def filepath_baseline_origin
  @filepath_baseline_origin
end

#filepath_undertest_origin ⇒ Object

Returns the value of attribute filepath_undertest_origin.



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# File 'lib/determinations_comparison.rb', line 18

def filepath_undertest_origin
  @filepath_undertest_origin
end

#hashCategory ⇒ Object

Returns the value of attribute hashCategory.



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# File 'lib/determinations_comparison.rb', line 18

def hashCategory
  @hashCategory
end

#hashStd ⇒ Object

Returns the value of attribute hashStd.



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# File 'lib/determinations_comparison.rb', line 18

def hashStd
  @hashStd
end

#hashTgt ⇒ Object

Returns the value of attribute hashTgt.



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# File 'lib/determinations_comparison.rb', line 18

def hashTgt
  @hashTgt
end

#html_filepath ⇒ Object

Returns the value of attribute html_filepath.



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# File 'lib/determinations_comparison.rb', line 18

def html_filepath
  @html_filepath
end

#png_filepath ⇒ Object

Returns the value of attribute png_filepath.



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# File 'lib/determinations_comparison.rb', line 18

def png_filepath
  @png_filepath
end

#undertest_filepath ⇒ Object

Returns the value of attribute undertest_filepath.



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# File 'lib/determinations_comparison.rb', line 18

def undertest_filepath
  @undertest_filepath
end

Instance Method Details

#as_hash ⇒ Object 



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# File 'lib/determinations_comparison.rb', line 167

def as_hash
  @hashDiffs
end

#to_html(folderpath_output) ⇒ Object 



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# File 'lib/determinations_comparison.rb', line 46

def to_html(folderpath_output)

  FileUtils.mkdir_p folderpath_output

  html_filepath = File.join      folderpath_output, "#{@uuid}.html"
  png_filepath = File.join       folderpath_output, "#{@uuid}.png"
  baseline_filepath = File.join  folderpath_output, "#{@uuid}_baseline.json"
  undertest_filepath = File.join folderpath_output, "#{@uuid}_undertest.json"

  # these are necessary for cpplogreader
  @sample_index = hashCompoundBaseLine['Sample_Index']
  @analyte_name = hashCompoundBaseLine['Analyte']

  begin

    #coder = HTMLEntities.new

    FileUtils.copy_file @filepath_baseline_origin, baseline_filepath
    FileUtils.copy_file @filepath_undertest_origin, undertest_filepath

    # html for file links
      strFiles = "<p>baseline file: <a href=#{File.basename(baseline_filepath)}>#{File.basename(@filepath_baseline_origin)}</a></p>"
      strFiles += "<p>undertest file: <a href=#{File.basename(undertest_filepath)}>#{File.basename(@filepath_undertest_origin)}</a></p>"

    # html for plot
      strPlot = nil
      @plotter = Exe_CompareDeterminations.new @filepath_baseline_origin, @filepath_undertest_origin, @filepath_comparedeterminations
      retcodePNG,rundetailsPNG = @plotter.generate_png png_filepath
      if retcodePNG
        strPlot = "<img src='#{File.basename(png_filepath)}' alt='chromatogram' height='500' width='800' align='top'>"
      end

    # html for peak picking logs
      hashChromHTML = Hash.new

      @hashDiffs.each_pair do |k,v|

        chrom_type = k

        ht = HTML_Table_of_Peak_Picking_Log.new(@folderpath_with_log,@sample_index,@analyte_name,k)
        str_pp = ht.render
        unless str_pp.nil?

          peak_picked = "unknown"
          arrPP = v.select { |h| h['peak_picked'] }
          unless arrPP.empty?
            peak_picked = "#{arrPP.first[0]} #{arrPP.first[1]}"
          end

          strChrom = "<p><b>#{chrom_type}</b> - #{peak_picked}</p>"
          strChrom += str_pp
        end

        hashChromHTML[k] = strChrom

      end

    # html for property differences
      arr = Array.new

      @hashDiffs.each_pair do |k,v|

        chrom_type = k

        v.each_pair do |k,v|
          if k == 'peak'
            v.each_pair do |k,v|
              arr << property_diff_to_hash(chrom_type,k,v)
            end
          else
            unless k == 'peak_picked'
              arr << property_diff_to_hash(chrom_type,k,v)
            end
          end

        end

      end

    strProps = nil

    ht = HTML_Table_of_Property_Differences.new(arr)
    str_p = ht.render
    unless str_p.nil?
      strProps = str_p
    end

    strFull = strFiles
    strFull += strPlot unless strPlot.nil?

    hashGroups = Hash.new
    hashGroups['Properties'] = strProps
    hashChromHTML.each_pair do |k,v|
      hashGroups["Pick Log - #{k.to_s}"] = v
    end

    jt = Jquery_Tabs.new hashGroups
    strFull += jt.render


    File.open(html_filepath, "w") do |f|
      f.write(strFull)
    end

    retcode = true

  rescue Exception => e
    retcode = false
    $log_detercomp.error "unable to render html"
  end

  @html_filepath = html_filepath
  @png_filepath = png_filepath
  @baseline_filepath = baseline_filepath
  @undertest_filepath = undertest_filepath


  return retcode

end