Module: AccessionService

Defined in:
app/models/accession_service.rb

Overview

The EBI operates two key AccessionServices

ENAService: Mostly non-human data, provides open access to uploaded data EGAService: 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::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 fully migrated to 'a separate accession library'

See Also:

Defined Under Namespace

Classes: BaseService, EGAService, ENAService, NoService

Constant Summary collapse

AccessionServiceError =

Define custom error classes for the AccessionService

Class.new(StandardError)
AccessionValidationFailed = 
Class.new(AccessionServiceError)
NumberNotRequired = 
Class.new(AccessionServiceError)
NumberNotGenerated = 
Class.new(AccessionServiceError)
CENTER_NAME =

TODO: [xxx] use confing file

'SC'
PROTECT = 
'protect'
HOLD = 
'hold'

Class Method Summary collapse

Class Method Details

.select_for_study(study) ⇒ AccessionService::BaseService

Returns an instance of the appropriate accession service for a study based on its data release strategy. Open studies use ENA, managed studies use EGA, and others use NoService.

Parameters:

  • study (Study) —

    The study for which to select the accession service.

Returns:



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# File 'app/models/accession_service.rb', line 42

def self.select_for_study(study)
  case study.data_release_strategy
  when 'open'
    AccessionService::ENAService.new
  when 'managed'
    AccessionService::EGAService.new
  else
    AccessionService::NoService.new(study)
  end
end