include medra dois in dois index. #303

Gemfile.lock

@@ -106,7 +106,7 @@ GEM
       latex-decode (~> 0.0)
     binding_of_caller (0.8.0)
       debug_inspector (>= 0.0.1)
-    bolognese (1.2.3)
+    bolognese (1.2.4)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

app/controllers/dois_controller.rb

@@ -397,7 +397,7 @@ def random
   def get_url
     authorize! :get_url, @doi
 
-    if !@doi.is_registered_or_findable? || %w(europ crossref).include?(@doi.provider_id) || %w(Crossref).include?(@doi.agency)
+    if !@doi.is_registered_or_findable? || %w(europ crossref medra).include?(@doi.provider_id) || %w(Crossref mEDRA).include?(@doi.agency)
       url = @doi.url
       head :no_content and return unless url.present?
     else

app/jobs/crossref_doi_by_id_job.rb

@@ -19,8 +19,14 @@ def perform(id, options={})
       return {} unless result.blank?
     end
 
-    # otherwise store Crossref metadata with DataCite 
-    # using client crossref.citations and DataCite XML
+    # otherwise store DOI metadata with DataCite 
+    # check DOI registration agency as Crossref also indexes DOIs from other RAs
+    # using client crossref.citations, medra.citations, etc. and DataCite XML
+    ra = get_doi_ra(id).downcase
+    return {} unless ra.present?
+
+    client_id = ra.downcase + ".citations"
+
     xml = Base64.strict_encode64(id)
     attributes = {
       "xml" => xml,
@@ -35,7 +41,7 @@ def perform(id, options={})
           "client" =>  {
             "data" => {
               "type" => "clients",
-              "id" => "crossref.citations"
+              "id" => client_id
             }
           }
         }
@@ -54,7 +60,7 @@ def perform(id, options={})
     elsif response.status == 200
       logger.info "DOI #{doi} record updated."
     else
-      logger.error "[Error parsing Crossref DOI #{doi}]: " + response.body["errors"].inspect
+      logger.error "[Error parsing #{ra} DOI #{doi}]: " + response.body["errors"].inspect
     end
   end
 
@@ -64,4 +70,18 @@ def doi_from_url(url)
       uri.path.gsub(/^\//, '').downcase
     end
   end
+
+  def get_doi_ra(doi)
+    prefix = validate_prefix(doi)
+    return nil if prefix.blank?
+
+    url = "https://doi.org/ra/#{prefix}"
+    result = Maremma.get(url)
+
+    result.body.dig("data", 0, "RA")
+  end
+
+  def validate_prefix(doi)
+    Array(/\A(?:(http|https):\/(\/)?(dx\.)?(doi.org|handle.test.datacite.org)\/)?(doi:)?(10\.\d{4,5}).*\z/.match(doi)).last
+  end
 end

app/jobs/url_job.rb

@@ -14,13 +14,13 @@ def perform(doi_id)
       response = Doi.get_doi(doi: doi.doi, agency: doi.agency)
       url = response.body.dig('data', 'values', 0, 'data', 'value')
       if url.present?
-        if (doi.is_registered_or_findable? || %w(europ crossref).include?(doi.provider_id)) && doi.minted.blank?
+        if (doi.is_registered_or_findable? || %w(europ crossref medra).include?(doi.provider_id)) && doi.minted.blank?
           doi.update_attributes(url: url, minted: Time.zone.now)
         else
           doi.update_attributes(url: url)
         end
 
-        doi.update_attributes(aasm_state: "findable") if %w(europ crossref).include?(doi.provider_id)
+        doi.update_attributes(aasm_state: "findable") if %w(europ crossref medra).include?(doi.provider_id)
 
         doi.__elasticsearch__.index_document
 

app/models/ability.rb

@@ -12,7 +12,7 @@ def initialize(user)
     if user.role_id == "staff_admin"
       can :manage, :all
       cannot [:new, :create], Doi do |doi|
-        doi.client.blank? || !(doi.client.prefixes.where(prefix: doi.prefix).first || doi.client.symbol.downcase.start_with?("crossref."))
+        doi.client.blank? || !(doi.client.prefixes.where(prefix: doi.prefix).first || doi.client.symbol.downcase.start_with?("crossref.") || doi.client.symbol.downcase.start_with?("medra.")
       end
     elsif user.role_id == "staff_user"
       can :read, :all
@@ -65,7 +65,7 @@ def initialize(user)
 
       can [:read, :destroy, :update, :register_url, :validate, :undo, :get_url, :get_urls, :read_landing_page_results], Doi, :client_id => user.client_id
       can [:new, :create], Doi do |doi| 
-        doi.client.prefixes.where(prefix: doi.prefix).present? || doi.client.symbol.downcase.start_with?("crossref.")
+        doi.client.prefixes.where(prefix: doi.prefix).present? || doi.client.symbol.downcase.start_with?("crossref.") || doi.client.symbol.downcase.start_with?("medra.")
       end
       can [:read], Doi do |doi|
         doi.findable?

app/models/concerns/indexable.rb

@@ -9,7 +9,7 @@ module Indexable
       IndexJob.perform_later(self)
       if self.class.name == "Doi"
         update_column(:indexed, Time.zone.now)
-        send_import_message(self.to_jsonapi) if aasm_state == "findable" unless (Rails.env.test? || client_id == "crossref.citations")
+        send_import_message(self.to_jsonapi) if aasm_state == "findable" unless (Rails.env.test? || client_id == "crossref.citations" || client_id == "medra.citations")
       end
     end
 
@@ -183,12 +183,12 @@ def query(query, options={})
         must << { terms: { "software.raw" => options[:software].split(",") }} if options[:software].present?
         must << { term: { repository_id: options[:repository_id].gsub("/", '\/') }} if options[:repository_id].present?
         must_not << { exists: { field: "deleted_at" }} unless options[:include_deleted]
-        must_not << { terms: { provider_id: ["crossref"] }} if options[:exclude_registration_agencies]
+        must_not << { terms: { provider_id: ["crossref", "medra"] }} if options[:exclude_registration_agencies]
       elsif self.name == "Doi"
         must << { terms: { aasm_state: options[:state].to_s.split(",") }} if options[:state].present?
         must << { range: { registered: { gte: "#{options[:registered].split(",").min}||/y", lte: "#{options[:registered].split(",").max}||/y", format: "yyyy" }}} if options[:registered].present?
         must << { term: { "client.repository_id" => options[:repository_id].upcase.gsub("/", '\/') }} if options[:repository_id].present?
-        must_not << { terms: { provider_id: ["crossref"] }} if options[:exclude_registration_agencies]
+        must_not << { terms: { provider_id: ["crossref", "medra"] }} if options[:exclude_registration_agencies]
       elsif self.name == "Event"
         must << { term: { subj_id: options[:subj_id] }} if options[:subj_id].present?
         must << { term: { obj_id: options[:obj_id] }} if options[:obj_id].present?

app/models/doi.rb

@@ -580,7 +580,7 @@ def registerable?
   # end
 
   def is_registered_or_findable?
-    %w(registered findable).include?(aasm_state) || %w(crossref).include?(provider_id)
+    %w(registered findable).include?(aasm_state) || %w(crossref medra).include?(provider_id)
   end
 
   def validatable?

app/models/event.rb

@@ -331,6 +331,34 @@ def self.update_datacite_crossref(options={})
     response.results.total
   end
 
+  def self.update_datacite_medra(options={})
+    logger = Logger.new(STDOUT)
+
+    size = (options[:size] || 1000).to_i
+    cursor = (options[:cursor] || 0).to_i
+
+    response = Event.query(nil, source_id: "datacite-medra", page: { size: 1, cursor: cursor })
+    logger.info "[Update] #{response.results.total} events for source datacite-medra."
+
+    # walk through results using cursor
+    if response.results.total > 0
+      while response.results.results.length > 0 do
+        response = Event.query(nil, source_id: "datacite-medra", page: { size: size, cursor: cursor })
+        break unless response.results.results.length > 0
+
+        logger.info "[Update] Updating #{response.results.results.length} datacite-medra events starting with _id #{cursor + 1}."
+        cursor = response.results.to_a.last[:sort].first.to_i
+
+        dois = response.results.results.map(&:obj_id).uniq
+
+        # use same jobs as for crossref dois
+        CrossrefDoiJob.perform_later(dois, options)
+      end
+    end
+
+    response.results.total
+  end
+
   def self.update_datacite_orcid_auto_update(options={})
     logger = Logger.new(STDOUT)
 

lib/tasks/event.rake

@@ -41,6 +41,15 @@ namespace :datacite_crossref do
   end
 end
 
+namespace :datacite_medra do
+  desc 'Import medra dois for all events'
+  task :import_doi => :environment do
+    cursor = (ENV['CURSOR'] || Event.minimum(:id)).to_i
+
+    Event.update_datacite_medra(cursor: cursor, refresh: ENV['REFRESH'], size: ENV['SIZE'])
+  end
+end
+
 namespace :datacite_orcid_auto_update do
   desc 'Import orcid ids for all events'
   task :import_orcid => :environment do