Class: Accession::Sample

Inherits:
Object
  • Object
show all
Includes:
Accessionable, ActiveModel::Model
Defined in:
lib/accession/sample.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Accessionable

#date, #ebi_alias_datestamped, #filename, #schema_type, #to_file, #to_xml

Constructor Details

#initialize(standard_tags, sample) ⇒ Sample

Returns a new instance of Sample.



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# File 'lib/accession/sample.rb', line 26

def initialize(standard_tags, sample)
  @standard_tags = standard_tags
  @sample = sample
  @tags = standard_tags.extract(sample.sample_metadata)
  @service = Service.new(sample.study_for_accessioning&.data_release_strategy)
end

Instance Attribute Details

#sample ⇒ Object (readonly)

Returns the value of attribute sample.



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# File 'lib/accession/sample.rb', line 22

def sample
  @sample
end

#service ⇒ Object (readonly)

Returns the value of attribute service.



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# File 'lib/accession/sample.rb', line 22

def service
  @service
end

#standard_tags ⇒ Object (readonly)

Returns the value of attribute standard_tags.



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# File 'lib/accession/sample.rb', line 22

def standard_tags
  @standard_tags
end

#tags ⇒ Object (readonly)

Returns the value of attribute tags.



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# File 'lib/accession/sample.rb', line 22

def tags
  @tags
end

Instance Method Details

#accessioned? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/accession/sample.rb', line 105

def accessioned?
  ebi_accession_number.present?
end

#build_xml(xml) ⇒ Object

rubocop:disable Metrics/AbcSize,Metrics/MethodLength



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# File 'lib/accession/sample.rb', line 60

def build_xml(xml) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
  tag_groups = tags.by_group

  xml.SAMPLE_SET(XML_NAMESPACE) do # rubocop:disable Metrics/BlockLength
    xml.SAMPLE(alias: ebi_alias) do
      xml.TITLE title if title.present?
      xml.SAMPLE_NAME do
        tag_groups[:sample_name].each { |_k, tag| xml.tag!(tag.label.tr(' ', '_').upcase, tag.value) }
      end
      xml.SAMPLE_ATTRIBUTES do
        tag_groups[:sample_attributes].each do |_k, tag|
          xml.SAMPLE_ATTRIBUTE do
            xml.TAG tag.label
            if tag.label == 'gender'
              xml.VALUE tag.value.downcase
            else
              xml.VALUE tag.value
            end
          end
        end
        if service.ena?
          tag_groups[:array_express].each do |_k, tag|
            xml.SAMPLE_ATTRIBUTE do
              xml.TAG tag.array_express_label
              xml.VALUE tag.value
            end
          end
        end
      end
    end
  end
end

#ebi_alias ⇒ Object 



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# File 'lib/accession/sample.rb', line 93

def ebi_alias
  sample.uuid
end

#name ⇒ Object 



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# File 'lib/accession/sample.rb', line 33

def name
  @name ||= (sample.sample_metadata.sample_public_name || sample.name).sanitize
end

#title ⇒ Object 



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# File 'lib/accession/sample.rb', line 37

def title
  @title ||= sample.sample_metadata.sample_public_name || sample.sanger_sample_id
end

#update_accession_number(accession_number, event_user) ⇒ Object

Updates the accession number, saving the sample and adding an event to the events table for viewing under sample history.



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# File 'lib/accession/sample.rb', line 99

def update_accession_number(accession_number, event_user)
  sample.sample_metadata.sample_ebi_accession_number = accession_number
  sample.sample_metadata.save # prevent an infinite loop due to after_save callbacks on sample.save
  sample.events.assigned_accession_number!('sample', accession_number, event_user)
end

#validate! ⇒ Object

Validates the sample for accessioning.

If the sample is valid, the method returns silently. If the sample is invalid, logs an error message and raisesAccession::InternalValidationError with details of the validation errors.

Raises:



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# File 'lib/accession/sample.rb', line 48

def validate!
  return if valid?

  # Add errors from the accession sample to the underlying sample for user feedback
  @sample.errors.add(:base, errors.full_messages.join(', '))

  # Add sample context to the error message for logging
  error_message = "Sample '#{sample.name}' cannot be accessioned: #{errors.full_messages.join(', ')}"
  Rails.logger.error(error_message)
  raise Accession::InternalValidationError, error_message
end