Module: SampleManifestExcel::Tags::ClashesFinder

Included in:
Pooling::TagClashReport, Validator::Uniqueness
Defined in:
app/sample_manifest_excel/sample_manifest_excel/tags/clashes_finder.rb

Overview

ClashesFinder

Instance Method Summary collapse

Instance Method Details

#create_tags_clashes_message(duplicated_tags_combinations_with_indexes, first_row = 0) ⇒ Object

This method takes a hash of not unique tags combinations with indexes, i.e 'TT'] => [0, 3], ['CC', 'GG'] => [1, 5] and returns a message, in this example: 'Same tags 'AA', 'TT' are used on rows 1, 4.
Same tags 'CC', 'GG' are used on rows 2, 6.'' It is also possible to pass in the first row number (if tags combinations do not start on row 1)



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# File 'app/sample_manifest_excel/sample_manifest_excel/tags/clashes_finder.rb', line 27

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#find_tags_clash(tag_and_tag2_oligos_combinations) ⇒ Object

This method takes an array of tags combinations, i.e. [['AA', 'TT'], ['CC', 'GG'], ['ACG', 'CGT'], ['AA', 'TT'], ['A', 'TCG'], ['CC', 'GG']] and returns a hash, indicating the indexes of tags clahses, in this example 'TT'] => [0, 3], ['CC', 'GG'] => [1, 5]



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# File 'app/sample_manifest_excel/sample_manifest_excel/tags/clashes_finder.rb', line 13

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end