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'

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'.freeze
Protect =
'protect'.freeze
Hold =
'hold'.freeze

Instance Method Summary collapse

Instance Method Details

#accession_dac_xml(study) ⇒ Object


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# File 'app/models/accession_service.rb', line 154

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 149

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 145

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 141

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 170

def dac_visibility(_study)
  Protect
end

#policy_visibility(_study) ⇒ Object


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# File 'app/models/accession_service.rb', line 166

def policy_visibility(_study)
  Protect
end

#private?Boolean


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# File 'app/models/accession_service.rb', line 174

def private?
  false
end

#providerObject


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# File 'app/models/accession_service.rb', line 35

def provider; end

#sample_visibility(_sample) ⇒ Object


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# File 'app/models/accession_service.rb', line 158

def sample_visibility(_sample)
  Protect
end

#study_visibility(_study) ⇒ Object


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# File 'app/models/accession_service.rb', line 162

def study_visibility(_study)
  Protect
end

#submit(user, *accessionables) ⇒ Object


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# File 'app/models/accession_service.rb', line 55

def submit(user, *accessionables)
  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 }
      raise AccessionServiceError, "EBI Server Error. Couldnt get accession number: #{xml_result}" if xml_result.match?(/(Server error|Auth required|Login failed)/)

      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
      if success == '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

      elsif success == '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 { |f| f.close } # not really necessary but recommended
    end

    return accessionables.map(&:accession_number)
  end
end

#submit_dac_for_user(_study, _user) ⇒ Object

Raises:


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# File 'app/models/accession_service.rb', line 137

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

#submit_sample_for_user(sample, user) ⇒ Object


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# File 'app/models/accession_service.rb', line 116

def submit_sample_for_user(sample, user)
  # raise NumberNotRequired, 'Does not require an accession number' unless sample.studies.first.ena_accession_required?

  ebi_accession_number = sample..sample_ebi_accession_number
  # raise NumberNotGenerated, 'No need to' if not ebi_accession_number.blank? and not /ERS/.match(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 125

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

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

  ebi_accession_number = study..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