Class: Accessionable::Dac

Inherits:
Base
  • Object
show all
Defined in:
app/models/accessionable/dac.rb

Overview

Represents a Data Access Committee who co-ordinate access to managed (EGA) studies. Should ideally be a completely separate record from Study but currently just a group of attributes in the Study::Metadata

Constant Summary

Constants inherited from Base

Base::InvalidData

Instance Attribute Summary collapse

Attributes inherited from Base

#accession_number, #date, #date_short, #name

Instance Method Summary collapse

Methods inherited from Base

#add_updated_event, #alias, #center_name, #extract_accession_number, #extract_array_express_accession_number, #file_name, #label_scope, #released?, #schema_type, #update_array_express_accession_number!

Constructor Details

#initialize(study) ⇒ Dac

Returns a new instance of Dac.



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# File 'app/models/accessionable/dac.rb', line 8

def initialize(study)
  @study = study
  @name = study.dac_refname
  @contacts =
    study.data_access_contacts.map do |contact|
      { email: contact.email, name: contact.name, organisation: AccessionService::CenterName }
    end

  super(study.dac_accession_number)
end

Instance Attribute Details

#contacts ⇒ Object (readonly)

Returns the value of attribute contacts.



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# File 'app/models/accessionable/dac.rb', line 6

def contacts
  @contacts
end

Instance Method Details

#accessionable_id ⇒ Object 



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# File 'app/models/accessionable/dac.rb', line 49

def accessionable_id
  @study.id
end

#errors ⇒ Object 



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# File 'app/models/accessionable/dac.rb', line 19

def errors
  [].tap { |errors| errors << 'Data Access Contacts Empty. Please add a contact' if @contacts.empty? }
end

#protect?(service) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/accessionable/dac.rb', line 45

def protect?(service)
  service.dac_visibility(@study) == AccessionService::Protect
end

#update_accession_number!(user, accession_number) ⇒ Object 



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# File 'app/models/accessionable/dac.rb', line 38

def update_accession_number!(user, accession_number)
  @accession_number = accession_number
  add_updated_event(user, "DAC for Study #{@study.id}", @study) if @accession_number
  @study.study_metadata.ega_dac_accession_number = accession_number
  @study.save!
end

#xml ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/models/accessionable/dac.rb', line 23

def xml # rubocop:todo Metrics/MethodLength
  xml = Builder::XmlMarkup.new
  xml.instruct!
  xml.DAC_SET('xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance') do
    xml.DAC(alias: self.alias, accession: accession_number, center_name: center_name) do
      xml.CONTACTS do
        contacts.each do |contact|
          xml.CONTACT(name: contact[:name], email: contact[:email], organisation: contact[:organisation])
        end
      end
    end
  end
  xml.target!
end