define and test associations between dois and events #388

app/models/concerns/indexable.rb

@@ -4,12 +4,28 @@ module Indexable
   require 'aws-sdk-sqs'
 
   included do
-    after_commit on: [:create, :update] do
+    after_commit on: [:create] do
       # use index_document instead of update_document to also update virtual attributes
       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? || %w(crossref medra kisti jalc op).include?(client.symbol.downcase.split(".").first))
+        send_import_message(self.to_jsonapi) if aasm_state == "findable" && !Rails.env.test? && !%w(crossref medra kisti jalc op).include?(client.symbol.downcase.split(".").first)
+      elsif self.class.name == "Event"
+        # reindex dois associated with Event
+        @source_doi = Doi.where(doi: source_doi).first if source_doi
+        IndexJob.perform_later(@source_doi) if @source_doi
+
+        @target_doi = Doi.where(doi: target_doi).first if target_doi
+        IndexJob.perform_later(@target_doi) if @target_doi
+      end
+    end
+
+    after_commit on: [:update] do
+      # use index_document instead of update_document to also update virtual attributes
+      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" && !Rails.env.test? && !%w(crossref medra kisti jalc op).include?(client.symbol.downcase.split(".").first)
       end
     end
 

app/models/doi.rb

@@ -75,8 +75,12 @@ class Doi < ActiveRecord::Base
   has_many :views, -> { where target_relation_type_id: "views" }, class_name: "Event", primary_key: :doi, foreign_key: :target_doi, dependent: :destroy
   has_many :downloads, -> { where target_relation_type_id: "downloads" }, class_name: "Event", primary_key: :doi, foreign_key: :target_doi, dependent: :destroy
   has_many :references, -> { where source_relation_type_id: "references" }, class_name: "Event", primary_key: :doi, foreign_key: :source_doi, dependent: :destroy
-  has_many :citations, -> { where target_relation_type_id: "references" }, class_name: "Event", primary_key: :doi, foreign_key: :source_doi, dependent: :destroy
-
+  has_many :citations, -> { where target_relation_type_id: "citations" }, class_name: "Event", primary_key: :doi, foreign_key: :target_doi, dependent: :destroy
+  has_many :parts, -> { where source_relation_type_id: "parts" }, class_name: "Event", primary_key: :doi, foreign_key: :source_doi, dependent: :destroy
+  has_many :part_of, -> { where target_relation_type_id: "part_of" }, class_name: "Event", primary_key: :doi, foreign_key: :target_doi, dependent: :destroy
+  has_many :versions, -> { where source_relation_type_id: "versions" }, class_name: "Event", primary_key: :doi, foreign_key: :source_doi, dependent: :destroy
+  has_many :version_of, -> { where target_relation_type_id: "version_of" }, class_name: "Event", primary_key: :doi, foreign_key: :target_doi, dependent: :destroy
+
   delegate :provider, to: :client, allow_nil: true
   delegate :consortium_id, to: :provider, allow_nil: true
 
@@ -366,17 +370,17 @@ class Doi < ActiveRecord::Base
         technical_contact: { type: :object, properties: {
           email: { type: :text },
           given_name: { type: :text},
-          family_name: { type: :text }
+          family_name: { type: :text },
         } },
         secondary_technical_contact: { type: :object, properties: {
           email: { type: :text },
           given_name: { type: :text},
-          family_name: { type: :text }
+          family_name: { type: :text },
         } },
         billing_contact: { type: :object, properties: {
           email: { type: :text },
           given_name: { type: :text},
-          family_name: { type: :text }
+          family_name: { type: :text },
         } },
         secondary_billing_contact: { type: :object, properties: {
           email: { type: :text },
@@ -410,8 +414,24 @@ class Doi < ActiveRecord::Base
       indexes :download_count, type: :integer
       indexes :reference_count, type: :integer
       indexes :citation_count, type: :integer
+      indexes :part_count, type: :integer
+      indexes :part_of_count, type: :integer
+      indexes :version_count, type: :integer
+      indexes :version_of_count, type: :integer
       indexes :views_over_time, type: :object
       indexes :downloads_over_time, type: :object
+      indexes :reference_ids, type: :keyword
+      indexes :citation_ids, type: :keyword
+      indexes :part_ids, type: :keyword
+      indexes :part_of_ids, type: :keyword
+      indexes :version_ids, type: :keyword
+      indexes :version_of_ids, type: :keyword
+      indexes :references, type: :object
+      indexes :citations, type: :object
+      indexes :parts, type: :object
+      indexes :part_of, type: :object
+      indexes :versions, type: :object
+      indexes :version_of, type: :object
     end
   end
 
@@ -433,16 +453,22 @@ def as_indexed_json(options={})
       "consortium_id" => consortium_id,
       "resource_type_id" => resource_type_id,
       "media_ids" => media_ids,
-      "view_ids" => view_ids,
       "view_count" => view_count,
       "views_over_time" => views_over_time,
-      "download_ids" => download_ids,
       "download_count" => download_count,
       "downloads_over_time" => downloads_over_time,
       "reference_ids" => reference_ids,
       "reference_count" => reference_count,
       "citation_ids" => citation_ids,
       "citation_count" => citation_count,
+      "part_ids" => part_ids,
+      "part_count" => part_count,
+      "part_of_ids" => part_of_ids,
+      "part_of_count" => part_of_count,
+      "version_ids" => version_ids,
+      "version_count" => version_count,
+      "version_of_ids" => version_of_ids,
+      "version_of_count" => version_of_count,
       "prefix" => prefix,
       "suffix" => suffix,
       "types" => types,
@@ -478,8 +504,12 @@ def as_indexed_json(options={})
       "provider" => provider.try(:as_indexed_json),
       "resource_type" => resource_type.try(:as_indexed_json),
       "media" => media.map { |m| m.try(:as_indexed_json) },
-      # "views" => views.map { |m| m.try(:as_indexed_json) },
-      # "downloads" => downloads.map { |m| m.try(:as_indexed_json) }
+      "references" => references.map { |m| m.try(:as_indexed_json) },
+      "citations" => citations.map { |m| m.try(:as_indexed_json) },
+      "parts" => parts.map { |m| m.try(:as_indexed_json) },
+      "part_of" => part_of.map { |m| m.try(:as_indexed_json) },
+      "versions" => versions.map { |m| m.try(:as_indexed_json) },
+      "version_of" => version_of.map { |m| m.try(:as_indexed_json) },
     }
   end
 
@@ -871,10 +901,6 @@ def media_ids
     media.pluck(:id).map { |m| Base32::URL.encode(m, split: 4, length: 16) }.compact
   end
 
-  def view_ids
-    views.pluck(:uuid)
-  end
-
   def view_count
     views.pluck(:total).inject(:+).to_i
   end
@@ -883,10 +909,6 @@ def views_over_time
     views.pluck(:occurred_at, :total).map { |v| { year_month: v[0].present? ? v[0].utc.iso8601[0..6] : nil, total: v[1] } }
   end
 
-  def download_ids
-    downloads.pluck(:uuid)
-  end
-
   def download_count
     downloads.pluck(:total).inject(:+).to_i
   end
@@ -911,6 +933,38 @@ def citation_count
     citations.count
   end
 
+  def part_ids
+    parts.pluck(:uuid)
+  end
+
+  def part_count
+    parts.count
+  end
+
+  def part_of_ids
+    part_of.pluck(:uuid)
+  end
+
+  def part_of_count
+    part_of.count
+  end
+
+  def version_ids
+    versions.pluck(:uuid)
+  end
+
+  def version_count
+    versions.count
+  end
+
+  def version_of_ids
+    version_of.pluck(:uuid)
+  end
+
+  def version_of_count
+    version_of.count
+  end
+
   def xml_encoded
     Base64.strict_encode64(xml) if xml.present?
   rescue ArgumentError

app/models/event.rb

@@ -21,7 +21,7 @@ class Event < ActiveRecord::Base
   before_validation :set_defaults
   before_create :set_source_and_target_doi
 
-  validates :uuid, format: { with: /\A[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\z/i }
+  validate :uuid_format
 
   # include state machine
   include AASM
@@ -552,6 +552,10 @@ def issn
     nil
   end
 
+  def uuid_format
+    errors.add(:uuid, "#{uuid} is not a valid UUID") unless UUID.validate(uuid)
+  end
+
   def registrant_id
     [subj["registrant_id"], obj["registrant_id"], subj["provider_id"], obj["provider_id"]].compact
   end
@@ -621,10 +625,10 @@ def set_source_and_target_doi
       self.source_relation_type_id = "references"
       self.target_relation_type_id = "citations"
     when *PASSIVE_RELATION_TYPES
-      self.source_doi = doi_from_url(subj_id)
-      self.target_doi = doi_from_url(obj_id)
-      self.source_relation_type_id = "citations"
-      self.target_relation_type_id = "references"
+      self.source_doi = doi_from_url(obj_id)
+      self.target_doi = doi_from_url(subj_id)
+      self.source_relation_type_id = "references"
+      self.target_relation_type_id = "citations"
     when "unique-dataset-investigations-regular"
       self.target_doi = doi_from_url(obj_id)
       self.target_relation_type_id = "views"

app/serializers/doi_serializer.rb

@@ -7,7 +7,7 @@ class DoiSerializer
   set_id :uid
   # don't cache dois, as works are cached using the doi model
 
-  attributes :doi, :prefix, :suffix, :identifiers, :creators, :titles, :publisher, :container, :publication_year, :subjects, :contributors, :dates, :language, :types, :related_identifiers, :sizes, :formats, :version, :rights_list, :descriptions, :geo_locations, :funding_references, :xml, :url, :content_url, :metadata_version, :schema_version, :source, :is_active, :state, :reason, :landing_page, :view_count, :download_count, :reference_count, :citation_count, :views_over_time, :downloads_over_time, :created, :registered, :published, :updated, :citations
+  attributes :doi, :prefix, :suffix, :identifiers, :creators, :titles, :publisher, :container, :publication_year, :subjects, :contributors, :dates, :language, :types, :related_identifiers, :sizes, :formats, :version, :rights_list, :descriptions, :geo_locations, :funding_references, :xml, :url, :content_url, :metadata_version, :schema_version, :source, :is_active, :state, :reason, :landing_page, :view_count, :download_count, :reference_count, :citation_count, :part_count, :part_of_count, :version_count, :version_of_count, :views_over_time, :downloads_over_time, :created, :registered, :published, :updated, :citations
   attributes :prefix, :suffix, if: Proc.new { |object, params| params && params[:detail] }
 
   belongs_to :client, record_type: :clients

spec/factories/default.rb

@@ -335,12 +335,30 @@
       relation_type_id { "references" }
     end
 
+    factory :event_for_datacite_parts do
+      source_id { "datacite_related" }
+      source_token { "datacite_related_123" }
+      subj_id { "http://doi.org/10.5061/DRYAD.47SD5" }
+      subj { { "datePublished" => "2006-06-13T16:14:19Z" } }
+      sequence(:obj_id) { |n| "http://doi.org/10.5061/DRYAD.47SD5/#{n}" }
+      relation_type_id { "has-part" }
+    end
+
+    factory :event_for_datacite_part_of do
+      source_id { "datacite_related" }
+      source_token { "datacite_related_123" }
+      subj_id { "http://doi.org/10.5061/DRYAD.47SD5/1" }
+      subj { { "datePublished" => "2006-06-13T16:14:19Z" } }
+      obj_id { "http://doi.org/10.5061/DRYAD.47SD5" }
+      relation_type_id { "is-part-of" }
+    end
+
     factory :event_for_datacite_crossref do
       source_id { "datacite_crossref" }
       source_token { "datacite_crossref_123" }
-      subj_id { "https://doi.org/10.5061/DRYAD.47SD5e" }
+      sequence(:subj_id) { |n| "https://doi.org/10.5061/DRYAD.47SD5e/#{n}" }
       subj { { "datePublished" => "2006-06-13T16:14:19Z" } }
-      sequence(:obj_id) { |n| "https://doi.org/10.1371/journal.pbio.200141#{n}" }
+      obj_id { "https://doi.org/10.1371/journal.pbio.2001414" }
       relation_type_id { "is-referenced-by" }
     end
 

spec/models/doi_spec.rb

@@ -552,7 +552,6 @@
 
     it "has views" do
       expect(doi.views.count).to eq(3)
-      expect(doi.view_ids.count).to eq(3)
       expect(doi.view_count).to eq(75)
       expect(doi.views_over_time.first).to eq(:total=>25, :year_month=>"2015-06")
 
@@ -574,7 +573,6 @@
 
     it "has downloads" do
       expect(doi.downloads.count).to eq(3)
-      expect(doi.download_ids.count).to eq(3)
       expect(doi.download_count).to eq(30)
       expect(doi.downloads_over_time.first).to eq(:total=>10, :year_month=>"2015-06")
 
@@ -608,24 +606,108 @@
   describe "citations", elasticsearch: true do
     let(:client) { create(:client) }
     let(:doi) { create(:doi, client: client, aasm_state: "findable") }
-    let!(:citations) { create_list(:event_for_datacite_crossref, 3, subj_id: "https://doi.org/#{doi.doi}", relation_type_id: "is-referenced-by") }
+    let!(:citations) { create_list(:event_for_datacite_crossref, 1, subj_id: "https://doi.org/#{doi.doi}", relation_type_id: "is-referenced-by") }
 
     before do
       Doi.import
       sleep 1
     end
 
     it "has citations" do
-      expect(doi.citations.count).to eq(3)
-      expect(doi.citation_ids.count).to eq(3)
-      expect(doi.citation_count).to eq(3)
+      expect(doi.citations.count).to eq(1)
+      expect(doi.citation_ids.count).to eq(1)
+      expect(doi.citation_count).to eq(1)
 
       citation = doi.citations.first
-      expect(citation.source_doi).to eq(doi.uid)
+      expect(citation.target_doi).to eq(doi.uid)
       expect(citation.total).to eq(1)
     end
   end
 
+  describe "parts", elasticsearch: true do
+    let(:client) { create(:client) }
+    let(:doi) { create(:doi, client: client, aasm_state: "findable") }
+    let!(:parts) { create_list(:event_for_datacite_parts, 3, subj_id: "https://doi.org/#{doi.doi}", relation_type_id: "has-part") }
+
+    before do
+      Doi.import
+      sleep 1
+    end
+
+    it "has parts" do
+      expect(doi.parts.count).to eq(3)
+      expect(doi.part_ids.count).to eq(3)
+      expect(doi.part_count).to eq(3)
+
+      part = doi.parts.first
+      expect(part.source_doi).to eq(doi.uid)
+      expect(part.total).to eq(1)
+    end
+  end
+
+  describe "part of", elasticsearch: true do
+    let(:client) { create(:client) }
+    let(:doi) { create(:doi, client: client, aasm_state: "findable") }
+    let!(:part_of) { create_list(:event_for_datacite_part_of, 1, subj_id: "https://doi.org/#{doi.doi}", relation_type_id: "is-part-of") }
+
+    before do
+      Doi.import
+      sleep 1
+    end
+
+    it "has part of" do
+      expect(doi.part_of.count).to eq(1)
+      expect(doi.part_of_ids.count).to eq(1)
+      expect(doi.part_of_count).to eq(1)
+
+      part_of = doi.part_of.first
+      expect(part_of.target_doi).to eq(doi.uid)
+      expect(part_of.total).to eq(1)
+    end
+  end
+
+  describe "versions", elasticsearch: true do
+    let(:client) { create(:client) }
+    let(:doi) { create(:doi, client: client, aasm_state: "findable") }
+    let!(:versions) { create_list(:event_for_datacite_parts, 3, subj_id: "https://doi.org/#{doi.doi}", relation_type_id: "has-version") }
+
+    before do
+      Doi.import
+      sleep 1
+    end
+
+    it "has versions" do
+      expect(doi.versions.count).to eq(3)
+      expect(doi.version_ids.count).to eq(3)
+      expect(doi.version_count).to eq(3)
+
+      version = doi.versions.first
+      expect(version.source_doi).to eq(doi.uid)
+      expect(version.total).to eq(1)
+    end
+  end
+
+  describe "version of", elasticsearch: true do
+    let(:client) { create(:client) }
+    let(:doi) { create(:doi, client: client, aasm_state: "findable") }
+    let!(:part_of) { create_list(:event_for_datacite_part_of, 1, subj_id: "https://doi.org/#{doi.doi}", relation_type_id: "is-version-of") }
+
+    before do
+      Doi.import
+      sleep 1
+    end
+
+    it "has version of" do
+      expect(doi.version_of.count).to eq(1)
+      expect(doi.version_of_ids.count).to eq(1)
+      expect(doi.version_of_count).to eq(1)
+
+      version_of = doi.version_of.first
+      expect(version_of.target_doi).to eq(doi.uid)
+      expect(version_of.total).to eq(1)
+    end
+  end
+
   describe "convert_affiliations" do
     let(:doi) { create(:doi)}