Merge pull request #253 from ncbo/develop

Develop to master merge, release v6.5.0

Author: alexskr

bin/owlapi-wrapper-1.5.0.jar

@@ -40,7 +40,7 @@ interaction:
 
   test-ag:
     description: Run minitest unit tests
-    service: ruby-ag
+    service: ruby-agraph
     command: bundle exec rake test
 
 

dip.yml

@@ -52,7 +52,7 @@
 end
 
 # We need to require deterministic - that is why we have the sort.
-models = Dir.glob("#{project_root}/ontologies_linked_data/models/concerns//**/*.rb").sort
+models = Dir.glob("#{project_root}/ontologies_linked_data/models/concerns/**/*.rb").sort
 models.each do |m|
   require m
 end

lib/ontologies_linked_data.rb

@@ -0,0 +1,25 @@
+module LinkedData
+  module Concerns
+    module Concept
+      module InCollection
+        def self.included(base)
+          base.serialize_methods :isInActiveCollection
+        end
+
+        def isInActiveCollection
+          @isInActiveCollection
+        end
+
+        def inCollection?(collection)
+          self.memberOf.include?(collection)
+        end
+
+        def load_is_in_collection(collections = [])
+          included = collections.select { |s| inCollection?(s) }
+          @isInActiveCollection = included
+        end
+
+      end
+    end
+  end
+end

lib/ontologies_linked_data/concerns/concepts/concept_in_collection.rb

@@ -0,0 +1,26 @@
+module LinkedData
+  module Concerns
+    module Concept
+      module InScheme
+        def self.included(base)
+          base.serialize_methods :isInActiveScheme
+        end
+
+        def isInActiveScheme
+          @isInActiveScheme
+        end
+
+        def inScheme?(scheme)
+          self.inScheme.include?(scheme)
+        end
+
+        def load_is_in_scheme(schemes = [])
+          included = schemes.select { |s| inScheme?(s) }
+          included = [self.submission.get_main_concept_scheme] if included.empty? && schemes&.empty?
+          @isInActiveScheme = included
+        end
+
+      end
+    end
+  end
+end

lib/ontologies_linked_data/concerns/concepts/concept_in_scheme.rb

@@ -0,0 +1,55 @@
+module LinkedData
+  module Concerns
+    module Concept
+      module Sort
+        module ClassMethods
+          def compare_classes(class_a, class_b)
+            label_a = ""
+            label_b = ""
+            class_a.bring(:prefLabel) if class_a.bring?(:prefLabel)
+            class_b.bring(:prefLabel) if class_b.bring?(:prefLabel)
+
+            begin
+              label_a = class_a.prefLabel unless (class_a.prefLabel.nil? || class_a.prefLabel.empty?)
+            rescue Goo::Base::AttributeNotLoaded
+              label_a = ""
+            end
+
+            begin
+              label_b = class_b.prefLabel unless (class_b.prefLabel.nil? || class_b.prefLabel.empty?)
+            rescue Goo::Base::AttributeNotLoaded
+              label_b = ""
+            end
+
+            label_a = class_a.id if label_a.empty?
+            label_b = class_b.id if label_b.empty?
+
+            [label_a.downcase] <=> [label_b.downcase]
+          end
+
+          def sort_classes(classes)
+            classes.sort { |class_a, class_b| compare_classes(class_a, class_b) }
+          end
+
+          def sort_tree_children(root_node)
+            sort_classes!(root_node.children)
+            root_node.children.each { |ch| sort_tree_children(ch) }
+          end
+
+          private
+
+
+
+          def sort_classes!(classes)
+            classes.sort! { |class_a, class_b| LinkedData::Models::Class.compare_classes(class_a, class_b) }
+            classes
+          end
+        end
+
+        def self.included(base)
+          base.extend(ClassMethods)
+        end
+      end
+    end
+  end
+end

lib/ontologies_linked_data/concerns/concepts/concept_sort.rb

@@ -0,0 +1,139 @@
+module LinkedData
+  module Concerns
+    module Concept
+      module Tree
+        def tree(concept_schemes: [], concept_collections: [], roots: nil)
+          bring(parents: [:prefLabel]) if bring?(:parents)
+          return self if parents.nil? || parents.empty?
+          extra_include = [:hasChildren, :isInActiveScheme, :isInActiveCollection]
+          roots = self.submission.roots( extra_include, concept_schemes:concept_schemes) if roots.nil?
+          path = path_to_root(roots)
+          threshold = 99
+
+          return self if path.nil?
+
+          attrs_to_load = %i[prefLabel synonym obsolete]
+          attrs_to_load << :subClassOf if submission.hasOntologyLanguage.obo?
+          attrs_to_load += self.class.concept_is_in_attributes if submission.skos?
+          self.class.in(submission)
+              .models(path)
+              .include(attrs_to_load).all
+          load_children(path, threshold: threshold)
+
+          path.reverse!
+          path.last.instance_variable_set("@children", [])
+
+          childrens_hash = {}
+          path.each do |m|
+            next if m.id.to_s["#Thing"]
+            m.children.each do |c|
+              childrens_hash[c.id.to_s] = c
+              c.load_computed_attributes(to_load:extra_include ,
+                                         options: {schemes: concept_schemes, collections: concept_collections})
+            end
+            m.load_computed_attributes(to_load:extra_include ,
+                                       options: {schemes: concept_schemes, collections: concept_collections})
+          end
+
+          load_children(childrens_hash.values, threshold: threshold)
+
+          build_tree(path)
+        end
+
+        def tree_sorted(concept_schemes: [], concept_collections: [], roots: nil)
+          tr = tree(concept_schemes: concept_schemes, concept_collections: concept_collections, roots: roots)
+          self.class.sort_tree_children(tr)
+          tr
+        end
+
+        def paths_to_root(tree: false, roots: nil)
+          bring(parents: [:prefLabel, :synonym, :definition]) if bring?(:parents)
+          return [] if parents.nil? || parents.empty?
+
+          paths = [[self]]
+          traverse_path_to_root(self.parents.dup, paths, 0, tree, roots) unless tree_root?(self, roots)
+          paths.each do |p|
+            p.reverse!
+          end
+          paths
+        end
+
+        def path_to_root(roots)
+          paths = [[self]]
+          paths = paths_to_root(tree: true, roots: roots)
+          #select one path that gets to root
+          path = nil
+          paths.each do |p|
+            p.reverse!
+            unless (p.map { |x| x.id.to_s } & roots.map { |x| x.id.to_s }).empty?
+              path = p
+              break
+            end
+          end
+
+          if path.nil?
+            # do one more check for root classes that don't get returned by the submission.roots call
+            paths.each do |p|
+              root_node = p.last
+              root_parents = root_node.parents
+
+              if root_parents.empty?
+                path = p
+                break
+              end
+            end
+          end
+
+          path
+        end
+
+        def tree_root?(concept, roots)
+          (roots &&roots.map{|r| r.id}.include?(concept.id)) || concept.id.to_s["#Thing"]
+        end
+        
+        private
+
+        def load_children(concepts, threshold: 99)
+          LinkedData::Models::Class
+            .partially_load_children(concepts, threshold, submission)
+        end
+
+        def build_tree(path)
+          root_node = path.first
+          tree_node = path.first
+          path.delete_at(0)
+          while tree_node &&
+            !tree_node.id.to_s["#Thing"] &&
+            !tree_node.children.empty? && (!path.empty?) do
+            next_tree_node = nil
+            tree_node.load_has_children
+            tree_node.children.each_index do |i|
+              if tree_node.children[i].id.to_s == path.first.id.to_s
+                next_tree_node = path.first
+                children = tree_node.children.dup
+                children[i] = path.first
+                tree_node.instance_variable_set("@children", children)
+                children.each do |c|
+                  c.load_has_children
+                end
+              else
+                tree_node.children[i].instance_variable_set("@children", [])
+              end
+            end
+
+            if !path.empty? && next_tree_node.nil?
+              tree_node.children << path.shift
+            end
+            tree_node = next_tree_node
+            path.delete_at(0)
+          end
+
+          root_node
+        end
+
+      end
+    end
+
+  end
+end
+

lib/ontologies_linked_data/concerns/concepts/concept_tree.rb

@@ -0,0 +1,99 @@
+module LinkedData
+  module Models
+    module SKOS
+      module RootsFetcher
+
+        def skos_roots(concept_schemes, page, paged, pagesize)
+          classes = []
+          class_ids, count = roots_by_has_top_concept(concept_schemes, page, paged, pagesize)
+
+          class_ids, count = roots_by_top_concept_of(concept_schemes, page, paged, pagesize) if class_ids.empty?
+
+          class_ids.each do |id|
+            classes << LinkedData::Models::Class.find(id).in(self).disable_rules.first
+          end
+
+          classes = Goo::Base::Page.new(page, pagesize, count, classes) if paged
+          classes
+        end
+
+        private
+
+        def roots_by_query(query_body, page, paged, pagesize)
+          root_skos = <<-eos
+              SELECT DISTINCT ?root WHERE {
+              GRAPH #{self.id.to_ntriples} {
+                #{query_body}
+              }}
+          eos
+          count = 0
+
+          count, root_skos = add_pagination(query_body, page, pagesize, root_skos) if paged
+
+          #needs to get cached
+          class_ids = []
+
+          Goo.sparql_query_client.query(root_skos, { graphs: [self.id] }).each_solution do |s|
+            class_ids << s[:root]
+          end
+
+          [class_ids, count]
+        end
+
+        def roots_by_has_top_concept(concept_schemes, page, paged, pagesize)
+          query_body = <<-eos
+            ?x #{RDF::SKOS[:hasTopConcept].to_ntriples} ?root .
+            #{concept_schemes_filter(concept_schemes)}
+          eos
+          roots_by_query query_body, page, paged, pagesize
+        end
+
+        def roots_by_top_concept_of(concept_schemes, page, paged, pagesize)
+          query_body = <<-eos
+            ?root #{RDF::SKOS[:topConceptOf].to_ntriples}  ?x.
+            #{concept_schemes_filter(concept_schemes)}
+          eos
+          roots_by_query query_body, page, paged, pagesize
+        end
+
+        def add_pagination(query_body, page, pagesize, root_skos)
+          count = count_roots(query_body)
+
+          offset = (page - 1) * pagesize
+          root_skos = "#{root_skos} LIMIT #{pagesize} OFFSET #{offset}"
+          [count, root_skos]
+        end
+
+        def count_roots(query_body)
+          query = <<-eos
+            SELECT (COUNT(?x) as ?count) WHERE {
+            GRAPH #{self.id.to_ntriples} {
+              #{query_body}
+            }}
+          eos
+          rs = Goo.sparql_query_client.query(query)
+          count = 0
+          rs.each do |sol|
+            count = sol[:count].object
+          end
+          count
+        end
+
+        def concept_schemes_filter(concept_schemes)
+          concept_schemes = current_schemes(concept_schemes)
+          concept_schemes = concept_schemes.map { |x| RDF::URI.new(x.to_s).to_ntriples }
+          concept_schemes.empty? ? '' : "FILTER (?x IN (#{concept_schemes.join(',')}))"
+        end
+
+        def current_schemes(concept_schemes)
+          if concept_schemes.nil? || concept_schemes.empty?
+            main_concept_scheme = get_main_concept_scheme
+            concept_schemes = main_concept_scheme ? [main_concept_scheme] : []
+          end
+          concept_schemes
+        end
+
+      end
+    end
+  end
+end

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

@@ -0,0 +1,20 @@
+module LinkedData
+  module Models
+    module SKOS
+      module ConceptSchemes
+        def get_main_concept_scheme(default_return: ontology_uri)
+          all = all_concepts_schemes
+          unless all.nil?
+            all = all.map { |x| x.id }
+            return  default_return if all.include?(ontology_uri)
+          end
+        end
+
+        def all_concepts_schemes
+          LinkedData::Models::SKOS::Scheme.in(self).all
+        end
+      end
+    end
+  end
+end
+