Module: Submission::ValidationsByTemplateName

Included in:
BulkSubmission
Defined in:
app/models/submission/validations_by_template_name.rb

Constant Summary collapse

SCRNA_CORE_CDNA_PREP_GEM_X_5P =

Template names

'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p'
HEADER_TEMPLATE_NAME =

Column headers

'template name'
HEADER_STUDY_NAME = 
'study name'
HEADER_PROJECT_NAME = 
'project name'
HEADER_NUM_SAMPLES = 
'scrna core number of samples per pool'
HEADER_CELLS_PER_CHIP_WELL = 
'scrna core cells per chip well'

Instance Method Summary collapse

Instance Method Details

#apply_additional_validations_by_template_name ⇒ void

This method returns an undefined value.

Applies additional validations based on the submission template type.

This method determines the submission template type from the CSV data and calls the appropriate validation methods based on the template type. It assumes that all rows in the CSV have the same submission template name. If no match is found for the submission template name, no additional validations are performed.

Uses the following instance variables: csv_data_rows [Array<Array<String>>] The CSV data rows, where each row is an array of strings. headers [Array<String>] The headers of the CSV file, used to find the index of specific columns. errors [ActiveModel::Errors] The errors object to which validation errors are added.



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# File 'app/models/submission/validations_by_template_name.rb', line 26

def apply_additional_validations_by_template_name
  # depending on the submission template type, call additional validations
  # NB. assumption that all rows in the csv have the same submission template name
  index_of_template_name = headers.index(HEADER_TEMPLATE_NAME)
  submission_template_name = csv_data_rows.first[index_of_template_name]

  case submission_template_name
  # this validation is for the scRNA pipeline cDNA submission
  when SCRNA_CORE_CDNA_PREP_GEM_X_5P
    validate_consistent_column_value(HEADER_NUM_SAMPLES)
    validate_consistent_column_value(HEADER_CELLS_PER_CHIP_WELL)
  end
end

#validate_consistent_column_value(column_header) ⇒ void

This method returns an undefined value.

Validates that the specified column is consistent for all rows with the same study and project name.

This method groups the rows in the CSV data by the study name and project name, and checks if the specified column has the same value for all rows within each group. If inconsistencies are found, an error is added to the errors collection.

rubocop:disable Metrics/MethodLength,Metrics/AbcSize

Parameters:

  • column_header (String) —

    The header of the column to validate.



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# File 'app/models/submission/validations_by_template_name.rb', line 49

def validate_consistent_column_value(column_header)
  index_of_study_name = headers.index(HEADER_STUDY_NAME)
  index_of_project_name = headers.index(HEADER_PROJECT_NAME)
  index_of_column = headers.index(column_header)

  grouped_rows = csv_data_rows.group_by { |row| [row[index_of_study_name], row[index_of_project_name]] }

  grouped_rows.each do |study_project, rows|
    unique_values = rows.pluck(index_of_column).uniq

    next unless unique_values.size > 1
    errors.add(
      :spreadsheet,
      "Inconsistent values for column '#{column_header}' for Study name '#{study_project[0]}' and Project name " \
        "'#{study_project[1]}', " \
        'all rows for a specific study and project must have the same value'
    )
  end
end