Class: AccessionService

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

Overview

The EBI operates two key AccessionServices ENA: Mostly non-human data, provides open access to uploaded data EGA: Mostly for human data, provides managed access to uploaded data We also submit information to ArrayExpress, but this happens indirectly via the accession services above. Accessioning involves submitting metadata to an external database as XML files. This data receives a unique ‘accession number’ which we store in the database. These accession numbers can then be used in publications to allow external researchers access to the metadata.

Accessionables

Accessionable::Sample Represents information about the sample, maps to a Sequencescape Sample. Accessionable::Study Represents information about the study. Indicates WHY the samples have been sequenced. Maps to a Sequencescape Study. Accessionable::Submission Wrapper object required by the submission service. We use one per accessionable. The following are associated with EGA studies. Accessionable::Dac Data access committee. Information about who to contact to gain access to the data. (EGA) Accessionable::Policy Details about how the data may be used. (EGA)

Accessioning of samples has been partially migrated to ‘a separate accession library’

See Also:

Defined Under Namespace

Classes: AccessionedFile

Constant Summary collapse

AccessionServiceError = 
Class.new(StandardError)
NumberNotRequired = 
Class.new(AccessionServiceError)
NumberNotGenerated = 
Class.new(AccessionServiceError)
CenterName =

TODO: [xxx] use confing file

'SC'
Protect = 
'protect'
Hold = 
'hold'

Instance Method Summary collapse

Instance Method Details

#accession_dac_xml(study) ⇒ Object 



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# File 'app/models/accession_service.rb', line 168

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.rb', line 163

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.rb', line 159

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.rb', line 155

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

#dac_visibility(_study) ⇒ Object 



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# File 'app/models/accession_service.rb', line 184

def dac_visibility(_study)
  Protect
end

#policy_visibility(_study) ⇒ Object 



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# File 'app/models/accession_service.rb', line 180

def policy_visibility(_study)
  Protect
end

#private? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/accession_service.rb', line 188

def private?
  false
end

#provider ⇒ Object 



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# File 'app/models/accession_service.rb', line 37

def provider
end

#sample_visibility(_sample) ⇒ Object 



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# File 'app/models/accession_service.rb', line 172

def sample_visibility(_sample)
  Protect
end

#study_visibility(_study) ⇒ Object 



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# File 'app/models/accession_service.rb', line 176

def study_visibility(_study)
  Protect
end

#submit(user, *accessionables) ⇒ Object

rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/BlockLength, Metrics/AbcSize



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# File 'app/models/accession_service.rb', line 61

def submit(user, *accessionables) # rubocop:todo Metrics/CyclomaticComplexity
  ActiveRecord::Base.transaction do
    submission = Accessionable::Submission.new(self, user, *accessionables)

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

    raise 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 AccessionServiceError, "EBI Server Error. Couldnt 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 NumberNotGenerated, 'Service gave no numbers back' unless number_generated
      when 'false'
        errors = xmldoc.root.elements.to_a('//ERROR').map(&:text)
        raise AccessionServiceError,
              "Could not get accession number. Error in submitted data: #{$!} #{errors.map { |e| "\n  - #{e}" }}"
      else
        raise AccessionServiceError, "Could not get accession number. Error in submitted data: #{$!}"
      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.rb', line 151

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

#submit_sample_for_user(sample, user) ⇒ Object

rubocop:enable Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/BlockLength, Metrics/AbcSize



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# File 'app/models/accession_service.rb', line 132

def submit_sample_for_user(sample, user)
  ebi_accession_number = sample.sample_metadata.sample_ebi_accession_number

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

#submit_study_for_user(study, user) ⇒ Object

Raises:



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# File 'app/models/accession_service.rb', line 138

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

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

  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