Class: Parsers::PlateReaderParser

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

Overview

rubocop:todo Style/Documentation

Defined Under Namespace

Classes: InvalidFile

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(content) ⇒ PlateReaderParser

Returns a new instance of PlateReaderParser.


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# File 'app/models/parsers/plate_reader_parser.rb', line 57

def initialize(content)
  @content = content
end

Class Method Details

.parses?(content) ⇒ Boolean

Returns:

  • (Boolean) 

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# File 'app/models/parsers/plate_reader_parser.rb', line 50

def self.parses?(content)
  parser = Parsers::PlateReaderParser.new(content)
  %i[row col content raw_data concentration].each_with_index.map do |sym, pos|
    parser.get_column_for_header(sym) == pos
  end.all?
end

Instance Method Details

#concentration(location) ⇒ Object 


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# File 'app/models/parsers/plate_reader_parser.rb', line 25

def concentration(location)
  get_row(location)[get_column_for_header(:concentration)]
rescue NoMethodError # Ugh! I want to catch these where they happen
  raise InvalidFile
end

#each_well_and_parameters ⇒ Object 


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# File 'app/models/parsers/plate_reader_parser.rb', line 65

def each_well_and_parameters
  locations.each do |location_name|
    yield(location_name, { 'concentration' => Unit.new(concentration(location_name), 'ng/ul') })
  end
end

#get_column_for_header(sym) ⇒ Object 


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# File 'app/models/parsers/plate_reader_parser.rb', line 31

def get_column_for_header(sym)
  headers.each_with_index do |h, pos|
    name = get_name_for_header(sym)
    return pos if h.squish == name.squish unless name.nil? || h.nil?
  end
end

#get_name_for_header(sym_name) ⇒ Object 


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# File 'app/models/parsers/plate_reader_parser.rb', line 38

def get_name_for_header(sym_name)
  {
    row: 'Well Row',
    col: 'Well Col',
    content: 'Content',
    raw_data: 'Raw Data (485/520)',
    concentration: 'Linear regression fit based on Raw Data (485/520)'
  }[
    sym_name
  ]
end

#get_row(location) ⇒ Object 


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# File 'app/models/parsers/plate_reader_parser.rb', line 19

def get_row(location)
  letter = location[0].chr
  num = location.slice(1, location.length)
  table.detect { |row| row[0] == letter && row[1] == num }
end

#headers ⇒ Object 


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

def headers
  @content[0]
end

#locations ⇒ Object 


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# File 'app/models/parsers/plate_reader_parser.rb', line 61

def locations
  table.sort { |a, b| a[0] <=> b[0] && a[1].to_i <=> b[1].to_i }.map { |l| l[0] + l[1] }
end

#table ⇒ Object 


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# File 'app/models/parsers/plate_reader_parser.rb', line 15

def table
  @content.slice(1, @content.length)
end