Class: AccessionService::BaseService

Inherits:
Object
  • Object
show all
Includes:
REXML
Defined in:
app/models/accession_service/base_service.rb

Direct Known Subclasses

EGAService, ENAService, NoService, UnsuitableService

Defined Under Namespace

Classes: AccessionedFile

Instance Method Summary collapse

Instance Method Details

#accession_dac_xml(study) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 153

def accession_dac_xml(study)
  Accessionable::Dac.new(study).xml
end

#accession_policy_xml(study) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 148

def accession_policy_xml(study)
  policy = Accessionable::Policy.new(study)
  policy.xml
end

#accession_sample_xml(sample) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 144

def accession_sample_xml(sample)
  Accessionable::Sample.new(sample).xml
end

#accession_study_xml(study) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 140

def accession_study_xml(study)
  Accessionable::Study.new(study).xml
end

#dac_visibility(_study) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 169

def dac_visibility(_study)
  AccessionService::PROTECT
end

#policy_visibility(_study) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 165

def policy_visibility(_study)
  AccessionService::PROTECT
end

#private? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/accession_service/base_service.rb', line 173

def private?
  false
end

#provider ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 9

def provider
end

#sample_visibility(_sample) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 157

def sample_visibility(_sample)
  AccessionService::PROTECT
end

#study_visibility(_study) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 161

def study_visibility(_study)
  AccessionService::PROTECT
end

#submit(user, *accessionables) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 32

def submit(user, *accessionables)
  ActiveRecord::Base.transaction do
    submission = Accessionable::Submission.new(self, user, *accessionables)

    errors = submission.all_accessionables.map(&:errors).flatten

    raise AccessionService::AccessionServiceError, errors.join("\n") unless errors.empty?

    files = [] # maybe not necessary, but just to be sure that the tempfile still exists when they are sent
    begin
      xml_result =
        post_files(
          submission.all_accessionables.map do |acc|
            file = Tempfile.open("#{acc.schema_type}_file")
            files << file
            file.puts(acc.xml)
            file.open # reopen for read

            Rails.logger.debug { file.each_line.to_a.join("\n") }

            { name: acc.schema_type.upcase, local_name: file.path, remote_name: acc.file_name }
          end
        )
      Rails.logger.debug { xml_result }
      if xml_result.match?(/(Server error|Auth required|Login failed)/)
        raise AccessionService::AccessionServiceError,
              "EBI Server Error. Could not get accession number: #{xml_result}"
      end

      xmldoc = Document.new(xml_result)
      success = xmldoc.root.attributes['success']
      accession_numbers = []

      # for some reasons, ebi doesn't give us back a accession number for the submission if it's a MODIFY action
      # therefore, we should be ready to get one or not
      number_generated = true
      case success
      when 'true'
        # extract and update accession numbers
        accession_number =
          submission.all_accessionables.each do |acc|
            accession_number = acc.extract_accession_number(xmldoc)
            if accession_number
              acc.update_accession_number!(user, accession_number)
              accession_numbers << accession_number
            else
              # error only, if one of the expected accessionable didn't get a AN
              # We don't care about the submission
              number_generated = false if accessionables.include?(acc)
            end
            ae_an = acc.extract_array_express_accession_number(xmldoc)
            acc.update_array_express_accession_number!(ae_an) if ae_an
          end

        raise AccessionService::NumberNotGenerated, 'Service gave no numbers back' unless number_generated
      when 'false'
        errors = xmldoc.root.elements.to_a('//ERROR').map(&:text)
        current_error = errors.first
        message = "Current error is: '#{current_error}'"
        more_messages = "There are #{errors.length - 1} more errors." if errors.many?
        raise AccessionService::AccessionServiceError,
              ['Could not get accession number. Error in submitted data:', $!.to_s, message,
               more_messages].compact.join(' ')
      else
        raise AccessionService::AccessionServiceError,
              "Could not get accession number. Error in submitted data: #{$!}"
      end
    ensure
      files.each(&:close) # not really necessary but recommended
    end
  end

  accessionables.map(&:accession_number)
end

#submit_dac_for_user(_study, _user) ⇒ Object

Raises:



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# File 'app/models/accession_service/base_service.rb', line 136

def submit_dac_for_user(_study, _user)
  raise AccessionService::NumberNotRequired, 'No need to'
end

#submit_sample_for_user(sample, user) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 107

def submit_sample_for_user(sample, user)
  # TODO: commented out line as not used without error handling
  # ebi_accession_number = sample.sample_metadata.sample_ebi_accession_number

  submit(user, Accessionable::Sample.new(sample))
end

#submit_study_for_user(study, user) ⇒ Object 



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# File 'app/models/accession_service/base_service.rb', line 114

def submit_study_for_user(study, user)
  unless study.accession_required?
    raise AccessionService::NumberNotRequired,
          'An accession number is not required for this study'
  end

  # Flag set in the deployment project to allow per-environment enabling of accessioning
  unless configatron.accession_samples
    raise AccessionService::AccessioningDisabledError, 'Accessioning is not enabled in this environment.'
  end

  # TODO: check error
  # raise AccessionServiceError, "Cannot generate accession number: #{ sampledata[:error] }" if sampledata[:error]

  # TODO: commented as not used without error handling
  # ebi_accession_number = study.study_metadata.study_ebi_accession_number

  # raise NumberNotGenerated, 'No need to' if not ebi_accession_number.blank? and not /ER/.match(ebi_accession_number)

  submit(user, Accessionable::Study.new(study))
end