Class: SampleManifestExcel::Upload::Processor::Base

Inherits:
Object
  • Object
show all
Includes:
ActiveModel::Model, SequencescapeExcel::SubclassChecker
Defined in:
app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb

Overview

rubocop:disable Metrics/ClassLength

Uploads will be processed slightly differently based on the manifest type.

Constant Summary collapse

MANDATORY_FIELDS = 
%w[country_of_origin date_of_sample_collection].freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(upload) ⇒ Base

Returns a new instance of Base.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 24

def initialize(upload)
  @upload = upload
end

Instance Attribute Details

#upload ⇒ Object (readonly)

Returns the value of attribute upload.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 17

def upload
  @upload
end

Instance Method Details

#aliquots_updated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 99

def aliquots_updated?
  downstream_aliquots_updated? || no_substitutions? ||
    log_error_and_return_false('Could not update tags in other assets.')
end

#create_samples_if_not_present ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 44

def create_samples_if_not_present
  upload.rows.each(&:sample)
end

#downstream_aliquots_updated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 95

def downstream_aliquots_updated?
  @downstream_aliquots_updated
end

#processed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 73

def processed?
  samples_updated? && sample_manifest_updated? && aliquots_updated?
end

#run(tag_group) ⇒ Object

If the processor is valid the samples and manifest are updated.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 30

def run(tag_group)
  return unless valid?

  # find or create samples
  create_samples_if_not_present

  # run the validation (some depends on samples being present)
  return unless samples_valid?

  # update the metadata and specialised fields
  update_samples_and_aliquots(tag_group)
  update_sample_manifest
end

#sample_manifest_updated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 83

def sample_manifest_updated?
  @sample_manifest_updated
end

#samples_updated? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 69

def samples_updated?
  upload.rows.all?(&:sample_skipped_or_updated?) || log_error_and_return_false('Could not update samples')
end

#samples_valid? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 48

def samples_valid?
  all_valid = true

  upload.rows.each do |row|
    unless row.validate_sample
      upload.errors.add(:base, row.errors.full_messages.join(', ').to_s)
      all_valid = false
    end
  end

  all_valid
end

#substitutions ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 91

def substitutions
  @substitutions ||= []
end

#type ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 87

def type
  self.class.to_s
end

#update_sample_manifest ⇒ Object

Override the sample manifest with the raw uploaded data.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 79

def update_sample_manifest
  @sample_manifest_updated = upload.sample_manifest.update(uploaded: upload.file)
end

#update_samples_and_aliquots(tag_group) ⇒ Object 



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb', line 61

def update_samples_and_aliquots(tag_group)
  upload.rows.each do |row|
    row.update_sample(tag_group, upload.override)
    substitutions.concat(row.aliquots.filter_map(&:substitution_hash)) if row.reuploaded?
  end
  update_downstream_aliquots unless no_substitutions?
end