Class: SampleManifestExcel::Upload::Data

Inherits:
Object
  • Object
show all
Includes:
ActiveModel::Model, Enumerable, Converters
Defined in:
app/sample_manifest_excel/sample_manifest_excel/upload/data.rb

Overview

An object to store the data for a particular manifest upload. The data is split into a header row (column names) and the actual data.

Constant Summary collapse

SANGER_SAMPLE_ID_COLUMN_LABEL = 
'SANGER SAMPLE ID'

Constants included from Converters

Converters::BLANK_CHARS, Converters::BLANK_CHARS_REGEXP

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Converters

#strip_all_blanks

Constructor Details

#initialize(file) ⇒ Data

The file is opened as a Roo spreadsheet. If it is valid it is split by the start row. Start row of column headers and data put into separate rows.

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 29

def initialize(file) # rubocop:todo Metrics/MethodLength
  @file = file
  @file_errors = nil
  @sheet = read_sheet
  @start_row = find_start_row
  return if @start_row.nil?

  @header_row = sheet&.row(@start_row)
  @data = sheet&.drop(@start_row)
  @description_info = extract_description_info(sheet, @start_row)
ensure
  @header_row ||= []
  @data ||= []
end

Instance Attribute Details

#data ⇒ Object (readonly)

Returns the value of attribute data.


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 13

def data
  @data
end

#description_info ⇒ Object (readonly)

Returns the value of attribute description_info.


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 13

def description_info
  @description_info
end

#file ⇒ Object (readonly)

Returns the value of attribute file.


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 13

def file
  @file
end

#header_row ⇒ Object (readonly)

Returns the value of attribute header_row.


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 13

def header_row
  @header_row
end

#sheet ⇒ Object (readonly)

Returns the value of attribute sheet.


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 13

def sheet
  @sheet
end

#start_row ⇒ Object (readonly)

Returns the value of attribute start_row.


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 13

def start_row
  @start_row
end

Instance Method Details

#cell(row, column) ⇒ Object

Find a cell of data based on the column and row

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 56

def cell(row, column)
  val = data.try(:fetch, row - 1).try(:fetch, column - 1)
  strip_all_blanks(val)
end

#column(col_num) ⇒ Object

Return a column of data for a particular column number

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 63

def column(col_num)
  data.map do |row|
    val = row[col_num - 1]
    strip_all_blanks(val)
  end
end

#each ⇒ Object

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 44

def each(&)
  data.each(&)
end

#extract_description_info(sheet, start_row) ⇒ Object

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 100

def extract_description_info(sheet, start_row)
  # look through each row starting from from under the heading (row 2), to above the start row
  # build a hash of the value in the first column => value in second column
  # this was built to extract the tube rack barcodes, and assumes the label is in the first column and the value
  # in the second
  return nil if sheet.nil? || start_row.nil?

  output = {}
  (2..(start_row - 1)).each do |row_num|
    row = sheet.row(row_num)
    info_label = row[0]
    info_value = row[1]
    output[info_label] = info_value unless info_label.nil?
  end
  output
end

#file_errors_empty ⇒ Object

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 82

def file_errors_empty
  errors.add(:file, @file_errors) if @file_errors.present?
end

#file_extension ⇒ Object

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 48

def file_extension
  return nil if file.nil?

  File.extname(file.path)
end

#find_start_row ⇒ Object

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 90

def find_start_row
  return nil if sheet.nil?

  (0..sheet.last_row).each do |row_num|
    sheet.row(row_num).each { |cell_value| return row_num if cell_value == SANGER_SAMPLE_ID_COLUMN_LABEL }
  end

  nil
end

#inspect ⇒ Object

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 86

def inspect
  "<#{self.class}: @header_row=#{header_row}, @data=#{data}, @start_row=#{@start_row}, @file=#{file}>"
end

#read_sheet ⇒ Object

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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/data.rb', line 70

def read_sheet
  return nil if file.nil?

  Roo::Spreadsheet.open(file).sheet(0)
  # In production we see a variety of errors here, all of which indicate problems with the manifest
rescue StandardError => e
  # We store the errors in an instance variable, as otherwise they get lost on any subsequent
  # calls to #valid?
  @file_errors = "could not be read: #{e.message}"
  nil
end