Class: Import::SequenceRelationships::PrimersInterpreter

Inherits:
BatchLoad::Import
  • Object
show all
Defined in:
lib/batch_load/import/sequence_relationships/primers_interpreter.rb

Instance Method Summary collapse

Constructor Details

#initialize(**args) ⇒ PrimersInterpreter

Returns a new instance of PrimersInterpreter.

Parameters:

  • args (Hash) 


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# File 'lib/batch_load/import/sequence_relationships/primers_interpreter.rb', line 5

def initialize(**args)
  @sequence_relationships = {}
  super(**args)
end

Instance Method Details

#build ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/batch_load/import/sequence_relationships/primers_interpreter.rb', line 87

def build
  if valid?
    build_sequence_relationships
    @processed = true
  end
end

#build_sequence_relationships ⇒ Integer

Returns:

  • (Integer) 


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# File 'lib/batch_load/import/sequence_relationships/primers_interpreter.rb', line 11

def build_sequence_relationships
  @total_data_lines = 0
  i = 0
  gene_descriptors = {}
  gene_attributes = {}

  # loop through rows
  csv.each do |row|
    i += 1

    parse_result = BatchLoad::RowParse.new
    parse_result.objects[:sequence_relationship] = []
    parse_result.objects[:gene_descriptor] = []
    parse_result.objects[:gene_attribute] = []

    @processed_rows[i] = parse_result

    begin # processing
      # gene descriptor
      gene_name = row['gene_name']
      gene_descriptor = gene_descriptors[gene_name]

      if !gene_descriptor
        gene_descriptor = Descriptor::Gene.new(name: gene_name)
        gene_descriptors[gene_name] = gene_descriptor
        parse_result.objects[:gene_descriptor].push(gene_descriptor)
      end

      # sequence relationships/gene attributes
      sequence_id = row['identifier']
      sequence = Sequence.with_namespaced_identifier('DRMSequenceId', sequence_id).take
      next if sequence.blank?
      created_sequence_relationship = false

      ['forward_primers', 'reverse_primers'].each do |primer_type|
        primers = row[primer_type]
        next if primers.blank?
        sequence_relationship_type = 'SequenceRelationship::' + primer_type.singularize.camelize

        primers.split(', ').each do |primer_name|
          primer_sequence = Sequence.with_any_value_for(:name, primer_name).take
          next if primer_sequence.blank?

          sequence_relationship = SequenceRelationship.new({
            subject_sequence: primer_sequence,
            object_sequence: sequence,
            type: sequence_relationship_type
          })

          parse_result.objects[:sequence_relationship].push(sequence_relationship)
          created_sequence_relationship = true

          gene_attribute_props = {
            descriptor: gene_descriptor,
            sequence: primer_sequence,
            sequence_relationship_type: sequence_relationship_type
          }

          if !gene_attributes.key?(gene_attribute_props)
            gene_attributes[gene_attribute_props] = true
            parse_result.objects[:gene_attribute].push(GeneAttribute.new(gene_attribute_props))
          end
        end
      end

      if created_sequence_relationship
        @total_data_lines += 1
      end
    # rescue
    end
  end

  @total_lines = i
end