Class: Accessionable::Sample

Inherits:
Base
  • Object
show all
Defined in:
app/models/accessionable/sample.rb

Constant Summary collapse

ARRAY_EXPRESS_FIELDS = 
%w[
  genotype
  phenotype
  strain_or_line
  developmental_stage
  sex
  cell_type
  disease_state
  compound
  dose
  immunoprecipitate
  growth_condition
  rnai
  organism_part
  species
  time_point
  age
  treatment
].freeze

Constants inherited from Base

Base::InvalidData

Instance Attribute Summary collapse

Attributes inherited from Base

#accession_number, #date, #date_short, #name

Instance Method Summary collapse

Methods inherited from Base

#center_name, #errors, #extract_accession_number, #extract_array_express_accession_number, #file_name, #label_scope, #released?, #schema_type, #update_array_express_accession_number!

Constructor Details

#initialize(sample) ⇒ Sample

rubocop:todo Metrics/MethodLength, Metrics/AbcSize



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# File 'app/models/accessionable/sample.rb', line 29

def initialize(sample) # rubocop:todo Metrics/CyclomaticComplexity
  @sample = sample
  super(sample.ebi_accession_number)

  sampname = sample.sample_metadata.sample_public_name
  @name = sampname.presence || sample.name
  @name = @name.gsub(/[^a-z\d]/i, '_') if @name.present?

  @common_name = sample.sample_metadata.sample_common_name
  @taxon_id = sample.sample_metadata.sample_taxon_id

  # Tags from the 'ENA attributes' property group
  # NOTE[xxx]: This used to also look for 'ENA links' and push them to the 'data[:links]' value, but group was empty
  @links = []
  @tags =
    sample.tags.map { |datum| Tag.new(label_scope, datum.name, sample.sample_metadata[datum.tag], datum.downcase) }

  # TODO: maybe unify this with the previous loop
  # Don't send managed AE data to SRA
  accession_service = AccessionService.select_for_sample(sample)
  unless accession_service.private?
    ARRAY_EXPRESS_FIELDS.each do |datum|
      value = sample.sample_metadata.send(datum)
      next if value.blank?

      @tags << ArrayExpressTag.new(label_scope, datum, value)
    end
  end

  sample_hold = sample.sample_metadata.sample_sra_hold
  @hold = sample_hold.presence || 'hold'
end

Instance Attribute Details

#common_name ⇒ Object (readonly)

Returns the value of attribute common_name.



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# File 'app/models/accessionable/sample.rb', line 26

def common_name
  @common_name
end

#links ⇒ Object (readonly)

Returns the value of attribute links.



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# File 'app/models/accessionable/sample.rb', line 26

def links
  @links
end

#tags ⇒ Object (readonly)

Returns the value of attribute tags.



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# File 'app/models/accessionable/sample.rb', line 26

def tags
  @tags
end

#taxon_id ⇒ Object (readonly)

Returns the value of attribute taxon_id.



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# File 'app/models/accessionable/sample.rb', line 26

def taxon_id
  @taxon_id
end

Instance Method Details

#accessionable_id ⇒ Object

rubocop:enable Metrics/AbcSize, Metrics/MethodLength



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# File 'app/models/accessionable/sample.rb', line 64

def accessionable_id
  @sample.id
end

#alias ⇒ Object 



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# File 'app/models/accessionable/sample.rb', line 68

def alias
  @sample.uuid
end

#protect?(service) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/accessionable/sample.rb', line 109

def protect?(service)
  service.sample_visibility(@sample) == AccessionService::PROTECT
end

#sample_element_attributes ⇒ Object 



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# File 'app/models/accessionable/sample.rb', line 76

def sample_element_attributes
  # In case the accession number is defined, we won't send the alias
  { alias: self.alias, accession: accession_number }.tap { |obj| obj.delete(:alias) if accession_number.present? }
end

#title ⇒ Object 



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# File 'app/models/accessionable/sample.rb', line 72

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

#update_accession_number!(user, accession_number) ⇒ Object

rubocop:enable Metrics/MethodLength



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# File 'app/models/accessionable/sample.rb', line 102

def update_accession_number!(user, accession_number)
  @accession_number = accession_number
  @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, user)
end

#xml ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/models/accessionable/sample.rb', line 82

def xml # rubocop:todo Metrics/AbcSize
  xml = Builder::XmlMarkup.new
  xml.instruct!
  xml.SAMPLE_SET('xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance') do
    xml.SAMPLE(sample_element_attributes) do
      xml.TITLE title unless title.nil?
      xml.SAMPLE_NAME do
        xml.COMMON_NAME common_name
        xml.TAXON_ID taxon_id
      end
      xml.SAMPLE_ATTRIBUTES { tags.each { |tag| xml.SAMPLE_ATTRIBUTE { tag.build(xml) } } } if tags.present?

      xml.SAMPLE_LINKS {} if links.present?
    end
  end
  xml.target!
end