Class: Pipeline::BSI::Importer::AddBatch

Inherits:
DataEntryBatch show all
Defined in:
lib/bsi-pipeline/importer.rb

Instance Attribute Summary collapse

Attributes inherited from DataEntryBatch

#client, #id, #properties, #specimens

Instance Method Summary collapse

Constructor Details

#initialize(client, batch_properties) ⇒ AddBatch

Returns a new instance of AddBatch.



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# File 'lib/bsi-pipeline/importer.rb', line 19

def initialize(client, batch_properties)
  super client, 'A', batch_properties
end

Instance Attribute Details

#seminal_parents ⇒ Object

Returns the value of attribute seminal_parents.



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# File 'lib/bsi-pipeline/importer.rb', line 17

def seminal_parents
  @seminal_parents
end

Instance Method Details

#add_specimens(specimens) ⇒ Object 



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# File 'lib/bsi-pipeline/importer.rb', line 27

def add_specimens(specimens)
  @specimens = specimens
  format
  @bsi.batch.addVials( @id, @specimens.map{ |s| s.to_bfh } )
  nil
end

#commit ⇒ Object 



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# File 'lib/bsi-pipeline/importer.rb', line 76

def commit
  @bsi.batch.commit(@id)
end

#format ⇒ Object 



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# File 'lib/bsi-pipeline/importer.rb', line 34

def format
  # Find out how many seminal parents there are

  # Old way of estimating number of seminal parents, different now that we import in groups.
  # num_seminal_parents = @specimens.select{|s| ['N/A', ''].include?( s.parent_id.to_s )}.length

  num_seminal_parents = @specimens.map{|s| [s.date_drawn, s.specimen_type]}.uniq.length

  fails = 0
  begin
  # Reserve Sample ID's for all the seminal parent's
  # Returns and array of strings with both the sampleID and the sequence number in the format: AAA000000 0000
    # Only keep first 6 characters which represent the sample id's (remove the sequence suffix)
    @sample_id_pool = @bsi.batch.reserveAvailableBsiIds( @id, 'LAA000000', num_seminal_parents ).map{|i| i[0..-6]} if num_seminal_parents > 0
  # Not sure why I've been getting this error periodically, but it happens
  rescue NoMethodError
    fails += 1
    retry if fails < 3
  end

  collection_dates = @specimens.map{|s| s.date_drawn}.uniq
  specimen_types   = @specimens.map{|s| s.specimen_type}.uniq
  collection_dates.each do |date|
    specimen_types.each do |type|
      specimen_family = @specimens.select{|s| s.date_drawn == date && s.specimen_type == type}
      family_sample_id = @sample_id_pool.pop
      specimen_family.each_with_index do |spec, i|
        # Assign sample and sequence numbers
        spec.sample_id  = family_sample_id
        unless specimen_family.length == 1
          spec.sequence   = i+1
        else
          spec.sequence   = 0
        end
      end
    end
  end
end

#perform_edit_checks ⇒ Object 



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# File 'lib/bsi-pipeline/importer.rb', line 73

def perform_edit_checks
end

#type ⇒ Object 



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# File 'lib/bsi-pipeline/importer.rb', line 23

def type
  'Add'
end