Merge branch 'development' into feature/add-catalog-model

.github/workflows/ruby-unit-tests.yml

@@ -9,8 +9,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        goo-slice: [ '20', '100', '500' ]
-        ruby-version: [ '2.7' ]
+        goo-slice: [ '100']
+        ruby-version: [ '3.2.0']
         triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
     runs-on: ubuntu-latest
     steps:
@@ -34,7 +34,7 @@ jobs:
         # http://docs.codecov.io/docs/testing-with-docker
         run: |
           ci_env=`bash <(curl -s https://codecov.io/env)`
-          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
+          GOO_SLICES=${{ matrix.goo-slice }} RUBYOPT="-W0" bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         with:

Gemfile

@@ -5,24 +5,25 @@ gem 'addressable', '~> 2.8'
 gem 'bcrypt', '~> 3.0'
 gem 'cube-ruby', require: 'cube'
 gem 'faraday', '~> 1.9'
-gem 'ffi', '~> 1.16.3'
+gem 'ffi'
 gem 'libxml-ruby'
 gem 'minitest'
 gem 'multi_json', '~> 1.0'
 gem 'oj'
 gem 'omni_logger'
 gem 'pony'
-gem 'rack', '~> 1.0'
-gem 'rack-test', '~> 0.6'
-gem 'rake', '~> 10.0'
+gem 'rack'
+gem 'rack-test'
+gem 'rake'
 gem 'rest-client'
 gem 'rsolr', '~> 1.0'
 gem 'rubyzip', '~> 1.0'
 gem 'thin'
 gem 'request_store'
 gem 'jwt'
-gem 'json-ld', '~> 3.0.2'
+gem 'json-ld', '~> 3.2.0'
 gem "parallel", "~> 1.24"
+gem 'rdf-raptor', github:'ruby-rdf/rdf-raptor', ref: '6392ceabf71c3233b0f7f0172f662bd4a22cd534' # use version 3.3.0 when available
 
 
 # Testing
@@ -42,3 +43,7 @@ end
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
+
+gem 'net-ftp'
+gem 'public_suffix', '~> 5.1.1'
+gem 'net-imap', '~> 0.4.18'

Gemfile.lock

@@ -25,6 +25,15 @@ GIT
       net-http-persistent (~> 4.0, >= 4.0.2)
       rdf (~> 3.2, >= 3.2.11)
 
+GIT
+  remote: https://github.com/ruby-rdf/rdf-raptor.git
+  revision: 6392ceabf71c3233b0f7f0172f662bd4a22cd534
+  ref: 6392ceabf71c3233b0f7f0172f662bd4a22cd534
+  specs:
+    rdf-raptor (3.3.0)
+      ffi (~> 1.15)
+      rdf (~> 3.3)
+
 GEM
   remote: https://rubygems.org/
   specs:
@@ -39,6 +48,7 @@ GEM
     ansi (1.5.0)
     ast (2.4.2)
     base64 (0.2.0)
+    bcp47_spec (0.2.1)
     bcrypt (3.1.20)
     bigdecimal (3.1.9)
     builder (3.3.0)
@@ -83,7 +93,7 @@ GEM
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.16.3)
+    ffi (1.17.1)
     hashdiff (1.1.2)
     hashie (5.0.0)
     htmlentities (4.3.4)
@@ -93,9 +103,14 @@ GEM
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.10.1)
-    json-ld (3.0.2)
-      multi_json (~> 1.12)
-      rdf (>= 2.2.8, < 4.0)
+    json-canonicalization (0.4.0)
+    json-ld (3.2.5)
+      htmlentities (~> 4.3)
+      json-canonicalization (~> 0.3, >= 0.3.2)
+      link_header (~> 0.0, >= 0.0.8)
+      multi_json (~> 1.15)
+      rack (>= 2.2, < 4)
+      rdf (~> 3.2, >= 3.2.10)
     jwt (2.10.1)
       base64
     language_server-protocol (3.17.0.4)
@@ -105,7 +120,8 @@ GEM
       logger (~> 1.6)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.5)
+    lint_roller (1.1.0)
+    logger (1.6.6)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -127,6 +143,9 @@ GEM
       powerbar
     multi_json (1.15.0)
     multipart-post (2.4.1)
+    net-ftp (0.3.8)
+      net-protocol
+      time
     net-http-persistent (4.0.5)
       connection_pool (~> 2.2)
     net-imap (0.4.19)
@@ -158,25 +177,24 @@ GEM
       method_source (~> 1.0)
     public_suffix (5.1.1)
     racc (1.8.1)
-    rack (1.6.13)
-    rack-test (0.8.3)
-      rack (>= 1.0, < 3)
+    rack (2.2.11)
+    rack-test (2.2.0)
+      rack (>= 1.3)
     rainbow (3.1.1)
-    rake (10.5.0)
-    rdf (3.2.12)
+    rake (13.2.1)
+    rdf (3.3.2)
+      bcp47_spec (~> 0.2)
+      bigdecimal (~> 3.1, >= 3.1.5)
       link_header (~> 0.0, >= 0.0.8)
-    rdf-raptor (3.2.0)
-      ffi (~> 1.15)
-      rdf (~> 3.2)
-    rdf-rdfxml (3.2.2)
-      builder (~> 3.2)
+    rdf-rdfxml (3.3.0)
+      builder (~> 3.2, >= 3.2.4)
       htmlentities (~> 4.3)
-      rdf (~> 3.2)
-      rdf-xsd (~> 3.2)
-    rdf-vocab (3.2.7)
-      rdf (~> 3.2, >= 3.2.4)
-    rdf-xsd (3.2.1)
-      rdf (~> 3.2)
+      rdf (~> 3.3)
+      rdf-xsd (~> 3.3)
+    rdf-vocab (3.3.2)
+      rdf (~> 3.3)
+    rdf-xsd (3.3.0)
+      rdf (~> 3.3)
       rexml (~> 3.2)
     redis (5.3.0)
       redis-client (>= 0.22.0)
@@ -193,9 +211,10 @@ GEM
     rexml (3.4.0)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.71.2)
+    rubocop (1.72.1)
       json (~> 2.3)
-      language_server-protocol (>= 3.17.0)
+      language_server-protocol (~> 3.17.0.2)
+      lint_roller (~> 1.1.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
@@ -225,6 +244,8 @@ GEM
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
+    time (0.4.1)
+      date
     timeout (0.4.3)
     tzinfo (0.3.62)
     unicode-display_width (3.1.4)
@@ -247,22 +268,26 @@ DEPENDENCIES
   cube-ruby
   email_spec
   faraday (~> 1.9)
-  ffi (~> 1.16.3)
+  ffi
   goo!
-  json-ld (~> 3.0.2)
+  json-ld (~> 3.2.0)
   jwt
   libxml-ruby
   minitest
   minitest-reporters (>= 0.5.0)
   multi_json (~> 1.0)
+  net-ftp
+  net-imap (~> 0.4.18)
   oj
   omni_logger
   parallel (~> 1.24)
   pony
   pry
-  rack (~> 1.0)
-  rack-test (~> 0.6)
-  rake (~> 10.0)
+  public_suffix (~> 5.1.1)
+  rack
+  rack-test
+  rake
+  rdf-raptor!
   request_store
   rest-client
   rsolr (~> 1.0)
@@ -276,4 +301,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.1.4
+   2.6.3

lib/ontologies_linked_data/concerns/ontology_submissions/skos/skos_submission_roots.rb

@@ -33,7 +33,7 @@ def roots_by_query(query_body, page, paged, pagesize)
           #needs to get cached
           class_ids = []
 
-          Goo.sparql_query_client.query(root_skos, { graphs: [self.id] }).each_solution do |s|
+          Goo.sparql_query_client.query(root_skos, **{ graphs: [self.id] }).each_solution do |s|
             class_ids << s[:root]
           end
 

lib/ontologies_linked_data/diff/bubastis_diff.rb

@@ -77,7 +77,7 @@ def setup_environment
         if (not Dir.exist?(@output_repo))
           begin
             FileUtils.mkdir_p(@output_repo)
-          rescue SystemCallError => e
+          rescue SystemCallError
             raise MkdirException, "Output folder #{@output_repo} folder cannot be created."
           end
         end
@@ -116,8 +116,7 @@ def call_bubastis_java_cmd
           Diff.logger.info(stdout)
         end
         if not File.exist?(@file_diff_path)
-          raise Diff::BubastisDiffException, "Bubastis diff command exited with status=#{status.exitstatus}. " +\
-          "Output file #{@file_diff_path} cannot be found."
+          raise Diff::BubastisDiffException, "Bubastis diff command exited with status=#{status.exitstatus}. " + "Output file #{@file_diff_path} cannot be found."
         else
           Diff.logger.info("Output size #{File.stat(@file_diff_path).size} in `#{@file_diff_path}`")
         end

lib/ontologies_linked_data/mappings/mappings.rb

@@ -66,7 +66,6 @@ def self.mapping_ontologies_count(sub1, sub2, reload_cache = false)
       eos
       group_count = sub2.nil? ? {} : nil
       count = 0
-      latest_sub_ids = self.retrieve_latest_submission_ids
       epr = Goo.sparql_query_client(:main)
 
       mapping_predicates().each do |_source, mapping_predicate|
@@ -698,7 +697,7 @@ def self.mappings_ont_build_query(class_id, page, size, sub1, sub2)
     def self.mappings_union_template(class_id, sub1, sub2, predicate, bind)
       class_id_subject = class_id.nil? ? '?s1' :  "<#{class_id.to_s}>"
       target_graph = sub2.nil? ? '?g' :  "<#{sub2.to_s}>"
-      union_template = <<-eos
+      return  <<-eos
 {
   GRAPH <#{sub1.to_s}> {
       #{class_id_subject} <#{predicate}> ?o .

lib/ontologies_linked_data/models/class.rb

@@ -447,7 +447,7 @@ def retrieve_descendants(page=nil, size=nil)
         total_size = ids.length
         if !page.nil?
           ids = ids.to_a.sort
-          rstart = (page -1) * size
+          rstart = (page - 1) * size
           rend = (page * size) -1
           ids = ids[rstart..rend]
         end

lib/ontologies_linked_data/models/metric.rb

@@ -54,7 +54,7 @@ def self.ontology_submission_links(m)
             ont.bring(:acronym) if ont.bring?(:acronym)
             acronym_link = "ontologies/#{ont.acronym}"
             submission_link = "/submissions/#{m.submission.first.submissionId}"
-          rescue Exception => e
+          rescue Exception
             acronym_link = ""
             submission_link = ""
           end

lib/ontologies_linked_data/models/mod/semantic_artefact.rb

@@ -117,7 +117,7 @@ def attribute_mapped(name, **options)
             attribute_mapped :metrics, namespace: :mod, mapped_to: {model: :ontology_submission, attribute: :metrics}
 
 
-            attribute :ontology, type: :ontology
+            attribute :ontology, type: :ontology, enforce: [:existence]
 
             links_load :acronym
             link_to LinkedData::Hypermedia::Link.new("distributions", lambda {|s| "artefacts/#{s.acronym}/distributions"}, LinkedData::Models::SemanticArtefactDistribution.type_uri),
@@ -132,7 +132,9 @@ def attribute_mapped(name, **options)
                     LinkedData::Hypermedia::Link.new("collection", lambda {|s| "artefacts/#{s.acronym}/collections"}, LinkedData::Models::SKOS::Collection.uri_type),
                     LinkedData::Hypermedia::Link.new("labels", lambda {|s| "artefacts/#{s.acronym}/labels"}, LinkedData::Models::SKOS::Label.uri_type)
 
-
+            # Access control
+            read_restriction_based_on ->(artefct) { artefct.ontology }
+
             serialize_default :acronym, :accessRights, :subject, :URI, :versionIRI, :creator, :identifier, :status, :language, 
                               :license, :rightsHolder, :description, :landingPage, :keyword, :bibliographicCitation, :contactPoint,
                               :contributor, :publisher, :coverage, :createdWith, :accrualMethod, :accrualPeriodicity, 
@@ -157,7 +159,7 @@ def self.type_uri
             end
 
             def self.find(artefact_id)
-                ont = Ontology.find(artefact_id).include(:acronym).first
+                ont = Ontology.find(artefact_id).include(:acronym, :viewingRestriction, :administeredBy, :acl).first
                 return nil unless ont
 
                 new.tap do |sa|
@@ -190,20 +192,17 @@ def bring(*attributes)
                 end
             end
 
-            def self.all_artefacts(options = {})
-                onts = if options[:also_include_views]
-                        Ontology.where.to_a
-                    else
-                        Ontology.where.filter(Goo::Filter.new(:viewOf).unbound).include(:acronym).to_a
-                    end
-
-                onts.map do |o|
+            def self.all_artefacts(attributes, page, pagesize)
+                all_count = Ontology.where.count
+                onts = Ontology.where.include(:acronym, :viewingRestriction, :administeredBy, :acl).page(page, pagesize).page_count_set(all_count).all
+                all_artefacts = onts.map do |o|
                     new.tap do |sa|
                         sa.ontology = o
                         sa.acronym = o.acronym
-                        sa.bring(*options[:includes]) if options[:includes]
+                        sa.bring(*attributes) if attributes
                     end
                 end
+                Goo::Base::Page.new(page, pagesize, all_count, all_artefacts)
             end
 
             def latest_distribution(status)
@@ -217,7 +216,6 @@ def distribution(dist_id)
             end
 
             def all_distributions(options = {})
-                status = options[:status]
                 to_bring = options[:includes]
                 @ontology.bring(:submissions)
 
@@ -235,4 +233,3 @@ def analytics
         end
     end
 end
-

lib/ontologies_linked_data/models/mod/semantic_artefact_distribution.rb

@@ -60,6 +60,9 @@ def attribute_mapped(name, **options)
 
             # Attr special to SemanticArtefactDistribution
             attribute :submission, type: :ontology_submission
+
+            # Access control
+            read_restriction_based_on ->(artefct_distribution) { artefct_distribution.submission.ontology }
 
             serialize_default :distributionId, :title, :hasRepresentationLanguage, :hasSyntax, :description, :created, :modified, 
                               :conformsToKnowledgeRepresentationParadigm, :usedEngineeringMethodology, :prefLabelProperty, 
@@ -80,7 +83,7 @@ def self.distribution_id_generator(ss)
             def initialize(sub)
                 super()
                 @submission = sub
-                @submission.bring(*[:submissionId, :ontology=>[:acronym]])
+                @submission.bring(*[:submissionId, :ontology=>[:acronym, :administeredBy, :acl, :viewingRestriction]])
                 @distributionId = sub.submissionId
             end
 

lib/ontologies_linked_data/models/ontology.rb

@@ -202,7 +202,6 @@ def next_submission_id
       end
 
       def highest_submission_id(options = {})
-        reload = options[:reload] || false
         status = options[:status] || :ready
 
         LinkedData::Models::Ontology.where.models([self])
@@ -215,7 +214,7 @@ def highest_submission_id(options = {})
 
         begin
           subs = self.submissions
-        rescue Exception => e
+        rescue Exception
           i = 0
           num_calls = LinkedData.settings.num_retries_4store
           subs = nil