Class: Report_html

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

Instance Method Summary collapse

Constructor Details

#initialize(hash_vars, title = "report", data_from_files = false) ⇒ Report_html 



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# File 'lib/report_html/report_html.rb', line 9

def initialize(hash_vars, title = "report", data_from_files = false)
  @all_report = ""
  @title = title
  @hash_vars = hash_vars
  @data_from_files = data_from_files
  @plots_data = []
  @count_objects = 0
end

Instance Method Details

#add_header_row_names(data, options) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 92

def add_header_row_names(data, options)
  if options[:add_header_row_names] # This check if html object needs a default header/row_names or not
    if !options[:header]
      range = 0..(data.first.length - 1)
      data.unshift(range.to_a)
    end
    if !options[:row_names]
      data.each_with_index do |row, i|
        row.unshift(i) 
      end
    end
  end
end

#add_sample_attributes(data_structure, options) ⇒ Object

CANVASXPRESS METHODS



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# File 'lib/report_html/report_html.rb', line 241

def add_sample_attributes(data_structure, options)
  parsed_sample_attributes = {}
  options[:sample_attributes].each do |key, col|
    data = get_data({id: options[:id], fields: [col], text: true})
    data.shift if options[:header]
    parsed_sample_attributes[key] = data.flatten 
  end
  data_structure['x'] = parsed_sample_attributes
end

#assign_rgb(link_data) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 522

def assign_rgb(link_data)
  colors = {
    'red' => [255, 0, 0],
    'green' => [0, 255, 0],
    'black' => [0, 0, 0],
    'yellow' => [255, 255, 0],
    'blue' => [0, 0, 255],
    'gray' => [128, 128, 128],
    'orange' => [255, 165, 0],
    'cyan' => [0, 255, 255],
    'magenta' => [255, 0, 255]
  }
  link_data.each do |link|
    code = colors[link[0]]
    if !code.nil?
      link[0] = "rgb(#{code.join(',')})"
    else
      raise "Color link #{link} is not allowed. The allowed color names are: #{colors.keys.join(' ')}"
    end
  end
end

#barplot(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 373

def barplot(user_options = {}, &block)
  default_options = {
    row_names: true
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'Bar'
  end
  return html_string
end

#boxplot(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 393

def boxplot(user_options = {}, &block)
  default_options = {
    row_names: true,
    header: true
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'Boxplot'
    options[:mod_data_structure] = 'boxplot'
    if options[:extracode].nil?
      options[:extracode] = "C#{object_id}.groupSamples([\"Factor\"]);"
    end
  end
  return html_string
end

#build(template) ⇒ Object 



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

def build(template)
  renderered_template = ERB.new(template).result(binding)
  @all_report = "<HTML>\n"
  make_head
  build_body do 
    renderered_template
  end
  @all_report << "\n</HTML>"
end

#build_body ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 28

def build_body
  @all_report << "<body onload=\"initPage();\">\n#{yield}\n</body>\n"
end

#canvasXpress_main(user_options, block = nil) {|options, config, samples, vars, values, object_id| ... } ⇒ Object

Yields:

  • (options, config, samples, vars, values, object_id) 


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# File 'lib/report_html/report_html.rb', line 267

def canvasXpress_main(user_options, block = nil)
  # Handle arguments
  #------------------------------------------
  options = {
    id: nil,
    fields: [],
    data_format: 'one_axis',
    responsive: true,
    height: '600px',
    width: '600px',
    header: false,
    row_names: false,
    add_header_row_names: true,
    transpose: true,
    x_label: 'x_axis',
    title: 'Title',
    sample_attributes: {},
    config: {},
    after_render: [],
    treeBy: 's'
  }
  options.merge!(user_options)
  config = {
    'toolbarPermanent' => true,
    'xAxisTitle' => options[:x_label],
    'title' => options[:title]
  }
  if  !options[:tree].nil?
    set_tree(options, config)
  end
  config.merge!(options[:config])
  # Data manipulation
  #------------------------------------------
  no_data_string = ERB.new("<div width=\"#{options[:width]}\" height=\"#{options[:height]}\" > <p>NO DATA<p></div>").result(binding)
  data_array = get_data(options)
  return no_data_string if data_array.empty?
  block.call(data_array) if !block.nil?
  object_id = "obj_#{@count_objects}_"
  raise("ID #{options[:id]} has not data") if data_array.nil?
  row_length = data_array.first.length
  samples = data_array.shift[1..row_length]
  return no_data_string if data_array.empty?
  vars = []
  data_array.each do |row|
    vars << row.shift
  end
  values = data_array

  yield(options, config, samples, vars, values, object_id)
  # Build JSON objects and Javascript code
  #-----------------------------------------------
  @count_objects += 1
  data_structure = {
    'y' => {
      'vars' => vars,
      'smps' => samples,
      'data' => values
    }
  }
  events = false
  info = false
  afterRender = options[:after_render]
  if options[:mod_data_structure] == 'boxplot'
    data_structure['y']['smps'] = nil
    data_structure.merge!({ 'x' => {'Factor' => samples}})
  elsif options[:mod_data_structure] == 'circular'
    data_structure.merge!({ 'z' => {'Ring' => options[:ring_assignation]}})
  end
  add_sample_attributes(data_structure, options) if !options[:sample_attributes].empty?
  extracode = "#{options[:extracode]}\n"
  extracode << "C#{object_id}.groupSamples(#{options[:group_samples]})\n" if !options[:group_samples].nil?
  plot_data = "
  var data = #{data_structure.to_json};
        var conf = #{config.to_json}; 
        var events = #{events.to_json};
        var info = #{info.to_json};
        var afterRender = #{afterRender.to_json};                
        var C#{object_id} = new CanvasXpress(\"#{object_id}\", data, conf, events, info, afterRender);\n#{extracode}"
        @plots_data << plot_data
       
        responsive = ''
        responsive = "responsive='true'" if options[:responsive]
  html = "<canvas  id=\"#{object_id}\" width=\"#{options[:width]}\" height=\"#{options[:height]}\" aspectRatio='1:1' #{responsive}></canvas>"
  return ERB.new(html).result(binding)
end

#circular(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 486

def circular(user_options = {}, &block)
  default_options = {
    ring_assignation: [],
    ringsType: [],
    ringsWeight: []
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    options[:mod_data_structure] = 'circular'
    config['graphType'] = 'Circular'
    config['segregateVariablesBy'] = ['Ring']
    if default_options[:ringsType].empty?
      config['ringsType'] = Array.new(vars.length, 'heatmap')
    else
      config['ringsType'] = default_options[:ringsType]
    end
    if default_options[:ringsWeight].empty?
      size = 100/vars.length
      config['ringsWeight'] = Array.new(vars.length, size)
    else
      config['ringsWeight'] = default_options[:ringsWeight]
    end
    if default_options[:ring_assignation].empty?
      options[:ring_assignation] = Array.new(vars.length) {|index| (index + 1).to_s}
    else
      options[:ring_assignation] = default_options[:ring_assignation].map{|item| item.to_s}
    end
    if !default_options[:links].nil?
      if !@hash_vars[default_options[:links]].nil? && !@hash_vars[default_options[:links]].empty?
        link_data = get_data({id: default_options[:links], fields: [], add_header_row_names: false, text: true, transpose: false}) 
        config['connections'] = assign_rgb(link_data)
      end
    end
  end
  return html_string
end

#embed_img(img_file, img_attribs = nil) ⇒ Object

EMBED FILES



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# File 'lib/report_html/report_html.rb', line 547

def embed_img(img_file, img_attribs = nil)
  img_content = File.open(img_file).read
  img_base64 = Base64.encode64(img_content)
  format = File.basename(img_file).split('.').last
  img_string = "<img #{img_attribs} src=\"data:image/#{format};base64,#{img_base64}\">"
  return img_string
end

#embed_pdf(pdf_file, pdf_attribs = nil) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 555

def embed_pdf(pdf_file, pdf_attribs = nil)
  pdf_content = File.open(pdf_file).read
  pdf_base64 = Base64.encode64(pdf_content)
  pdf_string = "<embed #{pdf_attribs} src=\"data:application/pdf;base64,#{pdf_base64}\" type=\"application/pdf\"></embed>"
  return pdf_string
end

#extract_data(options) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 106

def extract_data(options)
  data = []
  ids = options[:id]
  fields = options[:fields]
  ids = ids.split(',') if ids.class == String && ids.include?(',') # String syntax
  if ids.class == Array
    fields = fields.split(';').map{|data_fields| data_fields.split(',').map{|fields| fields.to_i} } if fields.class == String # String syntax
    ids.each_with_index do |id, n|
      data_file = extract_fields(id, fields[n])
      if data.empty?
        data.concat(data_file)
      else
        data.each_with_index do |row, n|
          data[n] = row + data_file[n]
        end
      end
    end
  else
    fields = fields.first if fields.class == Array
    data = extract_fields(ids, options[:fields])
  end
  return data
end

#extract_fields(id, fields) ⇒ Object 



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

def extract_fields(id, fields)
  data = []
  @hash_vars[id].each do |row|
    if fields.empty?
      data << row.dup # Dup generates a array copy that avoids to modify original objects on data manipulation creating graphs
    else
      data << fields.map{|field| row[field]} #Map without bang do the same than dup
    end
  end
  return data
end

#get_cell_align(align_vector, position) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 219

def get_cell_align(align_vector, position)
  cell_align = '' 
  if !align_vector.empty? 
    align = align_vector[position]
    cell_align = "align=\"#{align}\""
  end
  return cell_align
end

#get_col_n_row_span(table) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 194

def get_col_n_row_span(table)
  colspan = []
  rowspan = []
  last_row = 0
  table.each_with_index do |row, r|
    rowspan << Array.new(row.length, 1)
    colspan << Array.new(row.length, 1)
    last_col = 0
    row.each_with_index do |col, c|
      if col == 'colspan'
        colspan[r][last_col] += 1
      else
        last_col = c
      end
      if col == 'rowspan'
        rowspan[last_row][c] += 1
      else
        last_row = r
      end
    end
  end
  return rowspan, colspan
end

#get_data(options) ⇒ Object

DATA MANIPULATION METHODS



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# File 'lib/report_html/report_html.rb', line 68

def get_data(options)
  data = []
  data = extract_data(options)
  if !data.empty?
    if @data_from_files # If data on container is loaded using html_report as lib, we don't care about data format
              # if data comes from files and is loaded as strings. We need to format correctly the data.
      rows = data.length
      cols = data.first.length
      if !options[:text]
        rows.times do |r|
          cols.times do |c|
            next if r == 0 && options[:header]
            next if c == 0 && options[:row_names]
            data[r][c] = data[r][c].to_f
          end
        end
      end
    end
    add_header_row_names(data, options)
    data = data.transpose if options[:transpose]
  end
  return data
end

#get_report ⇒ Object

return all html string



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# File 'lib/report_html/report_html.rb', line 51

def get_report #return all html string
  renderer = ERB.new(@all_report)
  return renderer.result(binding) #binding does accesible all the current ruby enviroment to erb
end

#get_span(colspan, rowspan, row, col) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 181

def get_span(colspan, rowspan, row, col)
  span = []
  colspan_value = colspan[row][col]
  rowspan_value = rowspan[row][col]
  if colspan_value > 1
    span << "colspan=\"#{colspan_value}\""
  end
  if rowspan_value > 1
    span << "rowspan=\"#{rowspan_value}\""
  end
  return span.join(' ')
end

#heatmap(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 383

def heatmap(user_options = {}, &block)
  default_options = {
    row_names: true
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'Heatmap' 
  end
  return html_string
end

#line(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 353

def line(user_options = {}, &block)
  default_options = {
    row_names: true     
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'Line'  
  end
  return html_string
end

#make_head ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 32

def make_head
  @all_report << "\t<title>#{@title}</title>
    <head>
        <meta http-equiv=\"CACHE-CONTROL\" CONTENT=\"NO-CACHE\">
        <meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />
        <meta http-equiv=\"Content-Language\" content=\"en-us\" />

        <link rel=\"stylesheet\" href=\"js/canvasXpress.css\" type=\"text/css\"/>
        <script type=\"text/javascript\" src=\"js/canvasXpress.min.js\"></script>
        <script>
        var initPage = function () {        
          <% @plots_data.each do |plot_data| %>
            <%= plot_data %>
          <% end %>
        }
      </script>
    </head>\n"
end

#pie(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 408

def pie(user_options = {}, &block) 
  default_options = {
    transpose: false
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'Pie'
    if samples.length > 1
      config['showPieGrid'] = true
      config['xAxis'] = samples 
      config['layout'] = "#{(samples.length.to_f/2).ceil}X2" if config['layout'].nil?
      config['showPieSampleLabel'] = true if config['showPieSampleLabel'].nil?
    end
  end
  return html_string
end

#prepare_table_attribs(attribs) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 228

def prepare_table_attribs(attribs)
  attribs_string = ''
  if !attribs.empty?
    attribs.each do |attrib, value|
      attribs_string << "#{attrib}= \"#{value}\" "
    end
  end
  return attribs_string
end

#scatterbubble2D(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 445

def scatterbubble2D(user_options = {}, &block)
  default_options = {
    row_names: true,
    transpose: false
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'ScatterBubble2D'
    if options[:xAxis].nil? 
      config['xAxis'] = [samples[0]]
    else
      config['xAxis'] = options[:xAxis]
    end
    if options[:yAxis].nil? 
      config['yAxis'] = [samples[1]]
    else
      config['yAxis'] = options[:yAxis]
    end
    if options[:zAxis].nil? 
      config['zAxis'] = [samples[2]]
    else
      config['zAxis'] = options[:zAxis]
    end
    if default_options[:y_label].nil?
      config['yAxisTitle'] = 'y_axis'
    else
      config['yAxisTitle'] = default_options[:y_label]
    end
    if default_options[:z_label].nil?
      config['zAxisTitle'] = 'z_axis'
    else
      config['zAxisTitle'] = default_options[:z_label]
    end
    if !options[:upper_limit].nil? && !options[:lower_limit].nil? && !options[:ranges].nil?
      diff = (options[:upper_limit] - options[:lower_limit]).to_f/options[:ranges]
      sizes = Array.new(options[:ranges]) {|index| options[:lower_limit] + index * diff}
      config['sizes'] = sizes
    end
  end
  return html_string
end

#sccater2D(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 424

def sccater2D(user_options = {}, &block)
  default_options = {
    row_names: false,
    transpose: false
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'Scatter2D'
    config['xAxis'] = [samples.first] if config['xAxis'].nil? 
    config['yAxis'] = samples[1..samples.length-1] if config['yAxis'].nil?
    if default_options[:y_label].nil?
      config['yAxisTitle'] = 'y_axis'
    else
      config['yAxisTitle'] = default_options[:y_label]
    end
    if options[:regressionLine]
      options[:extracode] = "C#{object_id}.addRegressionLine();"
    end
  end
  return html_string
end

#set_tree(options, config) ⇒ Object 



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

def set_tree(options, config)
  tree = tree_from_file(options[:tree])
  if options[:treeBy] == 's'
    config['smpDendrogramNewick'] = tree
    config['samplesClustered'] = true
  elsif options[:treeBy] == 'v'
    config['varDendrogramNewick'] = tree
    config['variablesClustered'] = true
  end
end

#stacked(user_options = {}, &block) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 363

def stacked(user_options = {}, &block)
  default_options = {
    row_names: true,
  }.merge!(user_options)
  html_string = canvasXpress_main(default_options, block) do |options, config, samples, vars, values, object_id|
    config['graphType'] = 'Stacked' 
  end
  return html_string
end

#table(user_options = {}, &block) ⇒ Object

TABLE METHODS



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# File 'lib/report_html/report_html.rb', line 144

def table(user_options = {}, &block)
  options = {
    id: nil,
    header: false,
    row_names: false,
    add_header_row_names: false,
    transpose: false,
    fields: [],
    border: 1,
    cell_align: [],
    attrib: {}
  }
  options.merge!(user_options)
  table_attr = prepare_table_attribs(options[:attrib])
  array_data = get_data(options)
  block.call(array_data) if !block.nil?
  rowspan, colspan = get_col_n_row_span(array_data)
  html = "
  <table border=\"#{options[:border]}\" #{table_attr}>
    <% array_data.each_with_index do |row, i| %>
      <tr>
        <% row.each_with_index do |cell, j|
          if cell != 'colspan' && cell != 'rowspan' 
            if i == 0 && options[:header] %>
              <th <%= get_span(colspan, rowspan, i, j) %>><%= cell %></th>
            <% else %>
              <td <%= get_cell_align(options[:cell_align], j) %> <%= get_span(colspan, rowspan, i, j) %>><%= cell %></td>
            <% end 
          end %>
        <% end %>
      </tr>
    <% end %>
  </table>
  "
  return ERB.new(html).result(binding)
end

#tree_from_file(file) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 251

def tree_from_file(file)
        string_tree = File.open(file).read.gsub("\n", '')
        return string_tree
end

#write(file) ⇒ Object 



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# File 'lib/report_html/report_html.rb', line 56

def write(file)
  dir = File.dirname(file)
  string_report = get_report
  FileUtils.cp_r(JS_FOLDER, dir) 
  File.open(file, 'w'){|f| f.puts string_report}
end