Class: AccessionService
- Inherits:
-
Object
- Object
- AccessionService
- 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'
Direct Known Subclasses
EgaAccessionService, EnaAccessionService, NoAccessionService, UnsuitableAccessionService
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
- #accession_dac_xml(study) ⇒ Object
- #accession_policy_xml(study) ⇒ Object
- #accession_sample_xml(sample) ⇒ Object
- #accession_study_xml(study) ⇒ Object
- #dac_visibility(_study) ⇒ Object
- #policy_visibility(_study) ⇒ Object
- #private? ⇒ Boolean
- #provider ⇒ Object
- #sample_visibility(_sample) ⇒ Object
- #study_visibility(_study) ⇒ Object
-
#submit(user, *accessionables) ⇒ Object
rubocop:todo Metrics/CyclomaticComplexity.
- #submit_dac_for_user(_study, _user) ⇒ Object
- #submit_sample_for_user(sample, user) ⇒ Object
- #submit_study_for_user(study, user) ⇒ Object
Instance Method Details
#accession_dac_xml(study) ⇒ Object
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# File 'app/models/accession_service.rb', line 160 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 155 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 151 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 147 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 176 def dac_visibility(_study) Protect end |
#policy_visibility(_study) ⇒ Object
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# File 'app/models/accession_service.rb', line 172 def policy_visibility(_study) Protect end |
#private? ⇒ Boolean
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# File 'app/models/accession_service.rb', line 180 def private? false end |
#provider ⇒ Object
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# File 'app/models/accession_service.rb', line 36 def provider; end |
#sample_visibility(_sample) ⇒ Object
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# File 'app/models/accession_service.rb', line 164 def sample_visibility(_sample) Protect end |
#study_visibility(_study) ⇒ Object
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# File 'app/models/accession_service.rb', line 168 def study_visibility(_study) Protect end |
#submit(user, *accessionables) ⇒ Object
rubocop:todo Metrics/CyclomaticComplexity
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# File 'app/models/accession_service.rb', line 56 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: #{$!} #{errors.map do |e| "\n - #{e}" end }" else raise AccessionServiceError, "Could not get accession number. Error in submitted data: #{$!}" end ensure files.each(&:close) # not really necessary but recommended end return accessionables.map(&:accession_number) end end |
#submit_dac_for_user(_study, _user) ⇒ Object
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# File 'app/models/accession_service.rb', line 143 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 122 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
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# File 'app/models/accession_service.rb', line 131 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 |