Class: Parsers::BioanalysisCsvParser

Inherits:
Object
  • Object
show all
Defined in:
app/models/parsers/bioanalysis_csv_parser.rb

Overview

rubocop:todo Style/Documentation

Defined Under Namespace

Classes: InvalidFile

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(content) ⇒ BioanalysisCsvParser

Returns a new instance of BioanalysisCsvParser.


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 13

def initialize(content)
  @content = content
end

Instance Attribute Details

#content ⇒ Object (readonly)

Returns the value of attribute content


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 11

def content
  @content
end

Class Method Details

.parses?(content) ⇒ Boolean

Returns:

  • (Boolean) 

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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 155

def self.parses?(content)
  # We don't go through the whole file
  content[0..10].detect do |line|
    /Version Created/ === line[0] && /^B.*/ === line[1]
  end.present?
end

Instance Method Details

#build_range(range) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 48

def build_range(range)
  range = if range == nil
            [0, content.length - 1]
          else
            range.dup
          end
  range.push(content.length - 1) if (range.length == 1)
  range
end

#concentration(plate_position) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 24

def concentration(plate_position)
  get_parsed_attribute(plate_position, field_name_for(:concentration))
end

#each_well_and_parameters ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 146

def each_well_and_parameters
  parsed_content.each do |well, values|
    yield(well, {
      'concentration' => Unit.new(values[:peak_table][field_name_for(:concentration)], 'ng/ul'),
      'molarity' => Unit.new(values[:peak_table][field_name_for(:molarity)], 'nmol/l')
    })
  end
end

#field_name_for(sym_name) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 17

def field_name_for(sym_name)
  {
    concentration: 'Conc. [ng/µl]',
    molarity: 'Molarity [nmol/l]'
  }[sym_name]
end

#get_group_content(group) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 88

def get_group_content(group)
  content.slice(group[0], group[1] - group[0] + 1)
end

#get_groups(regexp, range = nil) ⇒ Object

Finds groups of lines by range in which the beginning of the range contains the matching regexp as text in the first column and the end of the range is an empty line

  • regexp -> Regular expression to be matched in the first column as beginning of range

  • range -> In case it is specified, restricts the searching process to this range of lines

instead of using all the content of the CSV file


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 63

def get_groups(regexp, range = nil)
  groups = []
  group = []
  range = build_range(range)

  group_contents = get_group_content(range)

  group_contents.each_with_index do |line, pos|
    if line[0].present? && line[0].match(regexp) && group.empty?
      group.push(pos)
    elsif (line.empty? && group.one?)
      group.push(pos - 1)
    end

    if group.length == 2
      groups.push [group[0] + range[0], group[1] + range[0]]
      group = []
    end
    if ((group.length == 1) && (pos == (group_contents.length - 1)))
      groups.push [group[0] + range[0], pos + range[0]]
    end
  end
  groups
end

#get_parsed_attribute(plate_position, field) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 140

def get_parsed_attribute(plate_position, field)
  return nil if parsed_content.nil? || parsed_content[plate_position].nil?

  parsed_content[plate_position][:peak_table][field]
end

#molarity(plate_position) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 28

def molarity(plate_position)
  get_parsed_attribute(plate_position, field_name_for(:molarity))
end

#parse_cell(group) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 105

def parse_cell(group)
  get_group_content(group)[0][1]
end

#parse_overall(group) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 100

def parse_overall(group)
  # Number of peaks
  get_group_content(get_groups(/Overall.*/m, group)[0])[1][1]
end

#parse_peak_table(group) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 92

def parse_peak_table(group)
  table_content_hash(get_groups(/Peak Table/m, group)[0])
end

#parse_region_table(group) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 96

def parse_region_table(group)
  table_content_hash(get_groups(/Region Table/m, group)[0])
end

#parse_sample(group) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 109

def parse_sample(group)
  {
    parse_cell(group) => {
      peak_table: parse_peak_table(group),
      region_table: parse_region_table(group),
      overall: parse_overall(group)
    }
  }
end

#parse_samples ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 119

def parse_samples
  groups = get_groups(/Sample Name/)

  groups.each_with_index.map do |group, pos|
    next_index = if (pos == (groups.length - 1))
                   @content.length - 1
                 else
                   groups[pos + 1][0] - 1
                 end
    [group[0], next_index]
  end.reduce({}) do |memo, group|
    memo.merge(parse_sample group)
  end
end

#parsed_content ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 134

def parsed_content
  @parsed_content ||= parse_samples
rescue NoMethodError => e # Ugh! I want to catch these where they happen
  raise InvalidFile
end

#table_content_hash(group) ⇒ Object 


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# File 'app/models/parsers/bioanalysis_csv_parser.rb', line 32

def table_content_hash(group)
  content_hash = {}
  starting_line = group[0]
  ending_line = group[1]
  type = content[starting_line][0]
  fields = content[starting_line + 1]

  ((starting_line + 2)..(ending_line)).each do |pos|
    values = content[pos]
    unless values.nil? && (values.length != fields.length)
      content_hash.merge!(fields.zip(values).to_h)
    end
  end
  content_hash
end