Class: SampleManifestExcel::Upload::Row

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

Overview

A Row relates to a row in a sample manifest spreadsheet. Each Row relates to a sample Required fields: number: Number of the row which is used for error tracking data: An array of sample data *columns: The columns which relate to the data.

Constant Summary

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(attributes = {}) ⇒ Row

Finds a sample based on the sanger_sample_id column. Must exist for row to be valid. Creates the specialised fields for updating the sample based on the passed columns



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 51

def initialize(attributes = {})
  super
  @cache ||= SampleManifestAsset
  @sanger_sample_id ||= value(:sanger_sample_id).presence if columns.present? && data.present?
end

Instance Attribute Details

#cache ⇒ Object

Returns the value of attribute cache.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 16

def cache
  @cache
end

#columns ⇒ Object

Returns the value of attribute columns.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 16

def columns
  @columns
end

#data ⇒ Object

Returns the value of attribute data.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 16

def data
  @data
end

#number ⇒ Object

Returns the value of attribute number.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 16

def number
  @number
end

#sanger_sample_id ⇒ Object (readonly)

Returns the value of attribute sanger_sample_id.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 17

def sanger_sample_id
  @sanger_sample_id
end

Instance Method Details

#aliquot ⇒ Object 



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

def aliquot
  @aliquot ||= manifest_asset.aliquot
end

#aliquot_transferred? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 174

def aliquot_transferred?
  @aliquot_transferred
end

#at(col_num) ⇒ Object

Finds the data value for a particular column. Offset by 1. Columns have numbers data is an array



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 60

def at(col_num)
  val = data[col_num - 1]
  strip_all_blanks(val)
end

#changed? ⇒ Boolean

rubocop:enable Metrics/MethodLength

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 127

def changed?
  (@sample_updated && sample.previous_changes.present?) || metadata.previous_changes.present? ||
    aliquots.any? { |a| a.previous_changes.present? }
end

#empty? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 178

def empty?
  # a row must have one of the primary column options
  primary_column_names = %w[supplier_name bioscan_supplier_name]

  # check the columns exist, are valid, and at least one of the primary column options are present
  unless columns.present? && columns.valid? &&
      primary_column_names.any? { |column_name| columns.names.include? column_name }
    return true
  end

  # it is mandatory to have a value in the primary column
  return true if primary_column_names.all? { |column_name| value(column_name).blank? }

  false
end

#first? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 76

def first?
  number == 1
end

#i5_present ⇒ Object

Ensure i5 column is not blank if it exists in the manifest



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 39

def i5_present
  return unless columns.present? && data.present? && columns.names.include?('i5') && value('i5').blank?

  warnings.add(:base, "#{row_title} i5 is blank! ")
end

#i7_present ⇒ Object

Ensure i7 column is not blank if it exists in the manifest



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 31

def i7_present
  return unless columns.present? && data.present? && columns.names.include?('i7') && value('i7').blank?

  warnings.add(:base, "#{row_title} i7 is blank! ")
end

#labware ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 194

def labware
  sample.primary_receptacle.labware
end

#metadata ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 92

def metadata
  @metadata ||= sample.sample_metadata
end

#reuploaded? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 154

def reuploaded?
  @reuploaded || false
end

#row_title ⇒ Object

Used for errors



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

def row_title
  "Row #{number} -"
end

#sample ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 158

def sample
  @sample ||= manifest_asset&.find_or_create_sample if sanger_sample_id.present? && !empty?
end

#sample_created? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 170

def sample_created?
  sample_updated? && !reuploaded?
end

#sample_skipped_or_updated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 166

def sample_skipped_or_updated?
  @sample_skipped || sample_updated?
end

#sample_updated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 162

def sample_updated?
  @sample_updated || false
end

#specialised_fields ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 96

def specialised_fields
  @specialised_fields ||= create_specialised_fields
end

#transfer_aliquot ⇒ Object

If it is a multiplexed library tube the aliquot is transferred from the library tube to a multiplexed library tube and stated set to passed.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 146

def transfer_aliquot
  return unless valid?

  asset.external_library_creation_requests.each do |request|
    @aliquot_transferred = request.passed? || request.manifest_processed!
  end
end

#update_metadata_fields ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 136

def update_metadata_fields
  columns.with_metadata_fields.each do |column|
    value = at(column.number)
    column.update_metadata(metadata, value) if value.present?
  end
end

#update_sample(tag_group, override) ⇒ Object

Updating the sample involves: Checking it is ok to update row Updating all of the specialised fields in the aliquot Updating the sample metadata Saving the asset, metadata and sample rubocop:todo Metrics/MethodLength



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 107

def update_sample(tag_group, override) # rubocop:todo Metrics/AbcSize
  return unless valid?

  @reuploaded = sample.updated_by_manifest

  if sample.updated_by_manifest && !override
    @sample_skipped = true
  else
    update_specialised_fields(tag_group)
    asset.save!
    update_metadata_fields
    metadata.save!
    sample.updated_by_manifest = true
    sample.empty_supplier_sample_name = false
    @sample_updated = sample.save
  end
end

#update_specialised_fields(tag_group) ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 132

def update_specialised_fields(tag_group)
  specialised_fields.each { |specialised_field| specialised_field.update(tag_group:) }
end

#validate_sample ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 198

def validate_sample
  check_sample_present
  sample_can_be_updated
  errors.empty?
end

#value(key) ⇒ Object

Find a value based on a column name



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 67

def value(key)
  column_number = columns.find_column_or_null(:name, key).number

  # column_number is -1 if no column found by this name (returns NullColumn object from find)
  return nil if column_number.negative?

  at(column_number)
end

#warnings ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/row.rb', line 19

def warnings
  @warnings ||= ActiveModel::Errors.new(self)
end