Merge branch 'master' into fix/show-multiple-languages

Gemfile

@@ -19,6 +19,7 @@ gem 'rest-client'
 gem 'rsolr', '~> 1.0'
 gem 'rubyzip', '~> 1.0'
 gem 'thin'
+gem "oauth2", "~> 2.0"
 gem 'request_store'
 gem 'jwt'
 gem 'json-ld', '~> 3.0.2'

lib/ontologies_linked_data/concerns/ontology_submissions/submission_validators.rb

@@ -71,6 +71,20 @@ def is_person(inst, attr)
           enforce_agent_type(persons, 'person', attr)
         end
 
+        def is_person(inst, attr)
+          inst.bring(attr) if inst.bring?(attr)
+          persons = inst.send(attr)
+
+          Array(persons).each do |person|
+            person.bring(:agentType) if person.bring?(:agentType)
+            unless person.agentType&.eql?('person')
+              return  [:persons, "`#{attr}` must contain only agents of type Person"]
+            end
+          end
+
+          []
+        end
+
         def lexvo_language(inst, attr)
           values = Array(attr_value(inst, attr))
 

lib/ontologies_linked_data/models/identifier_request.rb

@@ -0,0 +1,59 @@
+require "ontologies_linked_data/models/users/user"
+require "ontologies_linked_data/models/ontology_submission"
+
+module LinkedData
+  module Models
+
+    class IdentifierRequestType
+      DOI_CREATE = "DOI_CREATE"
+      DOI_UPDATE = "DOI_UPDATE"
+    end
+
+    class IdentifierRequestStatus
+      PENDING = "PENDING"
+      SATISFIED = "SATISFIED"
+      CANCELED = "CANCELED"
+      REJECTED = "REJECTED"
+      ERROR = "ERROR"
+    end
+
+    class IdentifierRequest < LinkedData::Models::Base
+      # ECOPORTAL_LOGGER.debug("\n\n\nONTOLOGIES_LINKED_DATA: identifier_request.rb")
+      model :identifier_request, :name_with => :requestId
+
+      attribute :requestId, enforce: [:unique, :existence]
+      attribute :status, enforce: [:existence] #[PENDING, SATISFIED, CANCELED, REJECTED, ERROR]   
+      attribute :requestType, enforce: [:existence]  #[DOI_CREATE, DOI_UPDATE]
+      attribute :requestedBy, enforce: [:existence, :user]
+      attribute :requestDate, enforce: [:existence, :date_time]
+      attribute :processedBy, enforce: [:user]
+      attribute :processingDate, enforce: [:date_time]
+      attribute :message
+      attribute :submission, enforce: [:ontology_submission]
+      link_to LinkedData::Hypermedia::Link.new("requestedBy", lambda {|r| "identifier_requests/#{r.requestId}/requestedBy"}, LinkedData::Models::User.uri_type),
+              LinkedData::Hypermedia::Link.new("processedBy", lambda {|r| "identifier_requests/#{r.requestId}/processedBy"}, LinkedData::Models::User.uri_type),
+              LinkedData::Hypermedia::Link.new("submission", lambda {|r| "identifier_requests/#{r.requestId}/submission"}, LinkedData::Models::OntologySubmission.uri_type)
+
+      # Access control
+      #read_restriction_based_on lambda {|req| req.submission.ontology}
+      #access_control_load submission: [ontology: [:administeredBy, :acl, :viewingRestriction]]
+      #write_access submission: [ontology: [:administeredBy]]
+      #access_control_load submission: [:access_control_load_attrs]
+
+      embed :submission, :requestedBy, :processedBy
+      embed_values submission: LinkedData::Models::OntologySubmission.goo_attrs_to_load + [ontology: [:acronym,:viewingRestriction]],
+                   requestedBy: [:username, :email],
+                   processedBy: [:username, :email]
+
+      def self.identifierRequest_id_generator()
+        millis = Time.now.strftime('%s%3N')
+        return millis     
+      end
+
+    end
+
+
+
+
+  end
+end

lib/ontologies_linked_data/models/ontology.rb

@@ -10,6 +10,7 @@
 require 'ontologies_linked_data/models/skos/collection'
 require 'ontologies_linked_data/models/skos/skosxl'
 require 'ontologies_linked_data/models/notes/note'
+require 'ontologies_linked_data/models/identifier_request'
 require 'ontologies_linked_data/purl/purl_client'
 
 module LinkedData
@@ -51,7 +52,7 @@ class OntologyAnalyticsError < StandardError; end
 
       attribute :acl, enforce: [:list, :user]
 
-      attribute :viewOf, enforce: [:ontology], onUpdate: :update_submissions_has_part
+      attribute :viewOf, enforce: [:ontology]
       attribute :views, :inverse => { on: :ontology, attribute: :viewOf }
       attribute :ontologyType, enforce: [:ontology_type], default: lambda { |record| LinkedData::Models::OntologyType.find("ONTOLOGY").include(:code).first }
 
@@ -77,7 +78,8 @@ class OntologyAnalyticsError < StandardError; end
               LinkedData::Hypermedia::Link.new("download", lambda {|s| "ontologies/#{s.acronym}/download"}, self.type_uri),
               LinkedData::Hypermedia::Link.new("views", lambda {|s| "ontologies/#{s.acronym}/views"}, self.type_uri),
               LinkedData::Hypermedia::Link.new("analytics", lambda {|s| "ontologies/#{s.acronym}/analytics"}, "#{Goo.namespaces[:metadata].to_s}Analytics"),
-              LinkedData::Hypermedia::Link.new("ui", lambda {|s| "http://#{LinkedData.settings.ui_host}/ontologies/#{s.acronym}"}, self.uri_type)
+              LinkedData::Hypermedia::Link.new("ui", lambda {|s| "http://#{LinkedData.settings.ui_host}/ontologies/#{s.acronym}"}, self.uri_type),
+              LinkedData::Hypermedia::Link.new("identifier_requests", lambda {|s| "ontologies/#{s.acronym}/identifier_requests"}, LinkedData::Models::IdentifierRequest.uri_type)
 
       # Access control
       read_restriction lambda {|o| !o.viewingRestriction.eql?("public") }

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -165,13 +165,15 @@ class OntologySubmission < LinkedData::Models::Base
       # Metrics metadata
       attribute :metrics, type: :metrics
 
+
       # Configuration metadata
 
       # Internal values for parsing - not definitive
       attribute :submissionStatus, type: %i[submission_status list], default: ->(record) { [LinkedData::Models::SubmissionStatus.find("UPLOADED").first] }
       attribute :missingImports, type: :list
 
       # Link to ontology
+      attribute :identifierRequests, inverse: {on: :identifier_request, attribute: :submission}
       attribute :ontology, type: :ontology, enforce: [:existence]
 
       def self.agents_attrs
@@ -201,8 +203,8 @@ def self.embed_values_hash
 
       # Links
       links_load :submissionId, ontology: [:acronym]
-      link_to LinkedData::Hypermedia::Link.new("metrics", ->(s) { "#{self.ontology_link(s)}/submissions/#{s.submissionId}/metrics" }, self.type_uri)
-      LinkedData::Hypermedia::Link.new("download", ->(s) { "#{self.ontology_link(s)}/submissions/#{s.submissionId}/download" }, self.type_uri)
+      link_to LinkedData::Hypermedia::Link.new("metrics", ->(s) { "#{self.ontology_link(s)}/submissions/#{s.id.split('/').last}/metrics" }, self.type_uri)
+      LinkedData::Hypermedia::Link.new("download", ->(s) { "#{self.ontology_link(s)}/submissions/#{s.id.split('/').last}/download" }, self.type_uri)
 
       # HTTP Cache settings
       cache_timeout 3600

lib/ontologies_linked_data/models/users/oauth_authentication.rb

@@ -10,7 +10,7 @@ module Models
     module Users
       module OAuthAuthentication
 
-        def self.included base
+        def self.included(base)
           base.extend ClassMethods
         end
 

lib/ontologies_linked_data/models/users/user.rb

@@ -1,6 +1,7 @@
 require 'bcrypt'
 require 'securerandom'
 require 'ontologies_linked_data/models/users/authentication'
+require 'ontologies_linked_data/models/users/oauth_authentication'
 require 'ontologies_linked_data/models/users/role'
 require 'ontologies_linked_data/models/users/subscription'
 

lib/ontologies_linked_data/security/authorization.rb

@@ -1,4 +1,5 @@
 require 'set'
+require 'jwt'
 
 module LinkedData
   module Security
@@ -96,6 +97,16 @@ def find_apikey(env, params)
         cookie_apikey(env)
       end
 
+      def find_access_token(env, params)
+        access_token = nil
+        header_auth = env["HTTP_AUTHORIZATION"] || env["Authorization"]
+        if header_auth && header_auth.downcase().start_with?("bearer ")
+          access_token = header_auth.split()[1]
+        end
+        access_token
+      end
+
+
       def authorized?(apikey, env)
         return false if apikey.nil?
 

lib/ontologies_linked_data/serializer.rb

@@ -84,9 +84,7 @@ def self.response(options = {})
     end
 
     def self.serialize(type, obj, params, request)
-
-      lang = self.get_language(params)
-
+      lang = params['lang'] || Goo.main_languages.first
       only = params['display'] || []
       only = only.split(',') unless only.is_a?(Array)
       all = only[0] == 'all'
@@ -108,11 +106,5 @@ def self.print_stacktrace?
       end
     end
 
-    def self.get_language(params)
-      lang = params['lang'] || params['language'] ||  Goo.main_languages&.first.to_s || 'en'
-      lang = lang.split(',').map {|l| l.downcase.to_sym}
-      return lang.length == 1 ? lang.first : lang
-    end
-
   end
 end

lib/ontologies_linked_data/serializers/json.rb

@@ -71,7 +71,7 @@ def self.get_languages(submission, user_languages)
       def self.get_submission_languages(submission_natural_language = [])
         submission_natural_language = submission_natural_language.values.flatten if submission_natural_language.is_a?(Hash)
         submission_natural_language.map { |natural_language| natural_language.to_s['iso639'] && natural_language.to_s.split('/').last[0..1].to_sym }.compact
-      end 
+      end
 
       def self.type(current_cls, hashed_obj)
         if current_cls.respond_to?(:type_uri)

rakelib/docker_based_test.rake

@@ -54,6 +54,7 @@ namespace :test do
       ENV["GOO_PORT"]="9000"
       ENV["COMPOSE_PROFILES"]='fs'
       Rake::Task["test:docker:up"].invoke
+
       Rake::Task["test"].invoke
       Rake::Task["test:docker:down"].invoke
     end

test/models/test_class_portal_lang.rb

@@ -9,7 +9,6 @@ def self.before_suite
 
   def self.after_suite
     Goo.main_languages = @@old_main_languages
-    RequestStore.store[:requested_lang] = nil
   end
 
   def self.parse
@@ -20,7 +19,7 @@ def self.parse
   end
 
   def test_map_attribute_found
-    cls = parse_and_get_class lang: [:FR]
+    cls = parse_and_get_class lang: ['fr']
     cls.bring :unmapped
     LinkedData::Models::Class.map_attributes(cls)
     assert_equal ['entité matérielle detaillée'], cls.label
@@ -29,7 +28,7 @@ def test_map_attribute_found
   end
 
   def test_map_attribute_not_found
-    cls = parse_and_get_class lang: [:ES]
+    cls = parse_and_get_class lang: ['es']
     cls.bring :unmapped
     LinkedData::Models::Class.map_attributes(cls)
     assert_empty cls.label
@@ -38,7 +37,7 @@ def test_map_attribute_not_found
   end
 
   def test_map_attribute_secondary_lang
-    cls = parse_and_get_class lang: %i[ES FR]
+    cls = parse_and_get_class lang: %w[es fr]
     cls.bring :unmapped
     LinkedData::Models::Class.map_attributes(cls)
     assert_empty cls.label
@@ -55,7 +54,7 @@ def test_label_main_lang_fr_found
   end
 
   def test_label_main_lang_not_found
-    cls = parse_and_get_class lang: [:ES]
+    cls = parse_and_get_class lang: ['es']
 
     assert_empty cls.label
     assert_equal 'skos prefLabel rien', cls.prefLabel
@@ -73,7 +72,7 @@ def test_label_secondary_lang
   end
 
   def test_label_main_lang_en_found
-    cls = parse_and_get_class lang: [:EN]
+    cls = parse_and_get_class lang: ['en']
     assert_equal 'material detailed entity', cls.label.first
     assert_includes ['skos prefLabel en', 'skos prefLabel rien'], cls.prefLabel # TODO fix in Goo to show en in priority
     assert_equal ['entity eng', 'entite rien'].sort, cls.synonym.sort
@@ -83,18 +82,16 @@ def test_label_main_lang_en_found
   private
 
   def parse_and_get_class(lang:, klass: 'http://lirmm.fr/2015/resource/AGROOE_c_03')
-    portal_lang_set portal_languages: lang
+    lang_set lang
 
     cls = get_class(klass,'AGROOE')
     assert !cls.nil?
     cls.bring_remaining
     cls
   end
 
-
-  def portal_lang_set(portal_languages: nil)
-    Goo.main_languages = portal_languages if portal_languages
-    RequestStore.store[:requested_lang] = nil
+  def lang_set(lang)
+    Goo.main_languages = lang
   end
 
 

test/models/test_search.rb

@@ -157,7 +157,7 @@ def test_search_ontology_data
                .first[:c]
                .to_i
 
-    assert_equal count, response['response']['numFound']
+    assert_includes [count, count+1], response['response']['numFound']
 
     response = conn.search('*', fq: ' resource_id:"http://opendata.inrae.fr/thesaurusINRAE/c_10065"')