Sync with BioPortal release 2.6.0

Gemfile.lock

@@ -100,7 +100,7 @@ GEM
     unicode-display_width (3.1.4)
       unicode-emoji (~> 4.0, >= 4.0.4)
     unicode-emoji (4.0.4)
-    uri (1.0.2)
+    uri (1.0.3)
 
 PLATFORMS
   arm64-darwin-24

lib/ontologies_api_client/base.rb

@@ -66,6 +66,13 @@ def type
         @type
       end
 
+      def self.explore(id)
+         path = self.respond_to?(:collection_path) ? collection_path : ''
+         id = "#{path}/#{id}" unless id.include?(path)
+         inst = self.new(values: {id: id})
+         LinkedData::Client::LinkExplorer.new({}, inst)
+      end
+
       ##
       # Retrieve a set of data using a link provided on an object
       # This instantiates an instance of this class and uses
@@ -132,11 +139,16 @@ def create_attributes(attributes)
           attr_exists = self.public_methods(false).include?(attr)
           unless attr_exists
             self.class.class_eval do
-              define_method attr.to_sym do
-                instance_variable_get("@#{attr}")
+              unless method_defined?(attr.to_sym)
+                define_method attr.to_sym do
+                  instance_variable_get("@#{attr}")
+                end
               end
-              define_method "#{attr}=" do |val|
-                instance_variable_set("@#{attr}", val)
+
+              unless method_defined?("#{attr}=".to_sym)
+                define_method "#{attr}=" do |val|
+                  instance_variable_set("@#{attr}", val)
+                end
               end
             end
           end

lib/ontologies_api_client/collection.rb

@@ -24,15 +24,16 @@ def method_missing(meth, *args, &block)
 
         ##
         # Get all top-level links for the API
-        def top_level_links
-          @top_level_links ||= HTTP.get(LinkedData::Client.settings.rest_url)
+        def top_level_links(link = LinkedData::Client.settings.rest_url)
+          @top_level_links ||= {}
+          @top_level_links[link] ||= HTTP.get(link)
         end
 
-        ##
+        #
         # Return a link given an object (with links) and a media type
         def uri_from_context(object, media_type)
           object.links.each do |type, link|
-            return link if link.media_type && link.media_type.downcase.eql?(media_type.downcase)
+            return link.dup if link.media_type && link.media_type.downcase.eql?(media_type.downcase)
           end
         end
 

lib/ontologies_api_client/link_explorer.rb

@@ -11,11 +11,17 @@ def initialize(links, instance)
         @instance = instance
       end
 
+      def get(params = {})
+        get_link(@instance.id, params)
+      end
+
       def method_missing(meth, *args, &block)
         if combined_links.key?(meth.to_s)
           explore_link(meth, *args)
         elsif meth == :batch
           explore_link(args)
+        elsif !@instance.id.blank?
+          forward_explore(meth, *args)
         else
           super
         end
@@ -43,10 +49,7 @@ def explore_link(*args)
           ids = link.map {|l| l.to_s}
           value_cls.where {|o| ids.include?(o.id)}
         else
-          url = replace_template_elements(link.to_s, replacements)
-          value_cls = LinkedData::Client::Base.class_for_type(link.media_type)
-          params[:include] ||= value_cls.attributes(full_attributes)
-          HTTP.get(url, params)
+          get_link(link, params, replacements, full_attributes)
         end
       end
 
@@ -56,6 +59,23 @@ def combined_links
 
       private
 
+      def forward_explore(meth, *args)
+        sub_id = Array(args).find { |x| x.is_a?(String) } || ''
+        escaped_sub_id = Addressable::URI.encode_component(sub_id, Addressable::URI::CharacterClasses::UNRESERVED)
+        link = "#{@instance.id}/#{meth}/#{escaped_sub_id}".chomp('/')
+        @instance.id = link
+        LinkExplorer.new(@links, @instance)
+      end
+
+      def get_link(link, params, replacements = [], full_attributes = {})
+        url = replace_template_elements(link.to_s, replacements)
+        if link.respond_to? :media_type
+          value_cls = LinkedData::Client::Base.class_for_type(link.media_type)
+          params[:include] ||= value_cls.attributes(full_attributes)
+        end
+        HTTP.get(url, params)
+      end
+
       def replace_template_elements(url, values = [])
         return url if values.nil? || values.empty?
 
@@ -95,4 +115,4 @@ def linkable_attributes
       end
     end
   end
-end
+end

lib/ontologies_api_client/models/class.rb

@@ -8,9 +8,9 @@ module Models
       class Class < LinkedData::Client::Base
         HTTP = LinkedData::Client::HTTP
         @media_type = %w[http://www.w3.org/2002/07/owl#Class http://www.w3.org/2004/02/skos/core#Concept]
-        @include_attrs = "prefLabel,definition,synonym,obsolete,hasChildren"
-        @include_attrs_full = "prefLabel,definition,synonym,obsolete,properties,hasChildren,children"
-        @attrs_always_present = :prefLabel, :definition, :synonym, :obsolete, :properties, :hasChildren, :children
+        @include_attrs = "prefLabel,definition,synonym,obsolete,hasChildren,inScheme,memberOf"
+        @include_attrs_full = "prefLabel,definition,synonym,obsolete,properties,hasChildren,childre,inScheme,memberOf"
+        @attrs_always_present = :prefLabel, :definition, :synonym, :obsolete, :properties, :hasChildren, :children, :inScheme, :memberOf
 
         alias :fullId :id
 

lib/ontologies_api_client/models/collection.rb

@@ -0,0 +1,12 @@
+require_relative "../base"
+
+module LinkedData
+  module Client
+    module Models
+      class Collection < LinkedData::Client::Base
+        include LinkedData::Client::Collection
+        @media_type =  "http://www.w3.org/2004/02/skos/core#Collection"
+      end
+    end
+  end
+end

lib/ontologies_api_client/models/scheme.rb

@@ -0,0 +1,12 @@
+require_relative "../base"
+
+module LinkedData
+  module Client
+    module Models
+      class Scheme < LinkedData::Client::Base
+        include LinkedData::Client::Collection
+        @media_type = "http://www.w3.org/2004/02/skos/core#ConceptScheme"
+      end
+    end
+  end
+end

lib/ontologies_api_client/models/skos_xl_label.rb

@@ -0,0 +1,12 @@
+require_relative "../base"
+
+module LinkedData
+  module Client
+    module Models
+      class Label < LinkedData::Client::Base
+        include LinkedData::Client::Collection
+        @media_type = "http://www.w3.org/2008/05/skos-xl#Label"
+      end
+    end
+  end
+end

test/models/test_class.rb

@@ -1,9 +1,10 @@
 # frozen_string_literal: true
 
-require 'faraday/follow_redirects'
 require_relative '../test_case'
 
 class ClassTest < LinkedData::Client::TestCase
+  @@purl_prefix = LinkedData::Client.settings.purl_prefix
+
   def test_find
     id = 'http://bioontology.org/ontologies/Activity.owl#Activity'
     ontology = 'https://data.bioontology.org/ontologies/BRO'
@@ -24,12 +25,13 @@ def test_purl_owl
       'https://data.bioontology.org/ontologies/BRO'
     )
     refute_nil cls
+    expected_purl = "#{@@purl_prefix}/BRO?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity"
+    assert_equal expected_purl, cls.purl
 
     res = fetch_response(cls.purl)
-    assert_equal 200, res.status
-    assert_equal 'https://bioportal.bioontology.org/ontologies/BRO'\
-                 '?p=classes&conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity',
-                 res.env[:url].to_s
+    assert_equal 302, res.status
+    assert_equal 'https://bioportal.bioontology.org/ontologies/BRO/classes?conceptid=http%3A%2F%2Fbioontology.org%2Fontologies%2FActivity.owl%23Activity',
+                 res.headers['location']
   end
 
   # Test PURL generation for a class in a UMLS format ontology
@@ -40,10 +42,13 @@ def test_purl_umls
     )
     refute_nil cls
 
+    # The ID already contains the PURL host, so .purl should return it as-is
+    assert_equal cls.id, cls.purl
+
     res = fetch_response(cls.purl)
-    assert_equal 200, res.status
-    assert_equal 'https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=64572001',
-                 res.env[:url].to_s
+    assert_equal 302, res.status
+    assert_equal 'https://bioportal.bioontology.org/ontologies/SNOMEDCT/classes/64572001',
+                 res.headers['location']
   end
 
   # Test PURL generation for a class in an OBO format ontology
@@ -54,20 +59,20 @@ def test_purl_obo
     )
     refute_nil cls
 
+    expected_purl = "#{@@purl_prefix}/DOID?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_4"
+    assert_equal expected_purl, cls.purl
+
     res = fetch_response(cls.purl)
-    assert_equal 200, res.status
-    assert_equal 'https://bioportal.bioontology.org/ontologies/DOID'\
-                 '?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_4',
-                 res.env[:url].to_s
+    assert_equal 302, res.status
+    assert_equal 'https://bioportal.bioontology.org/ontologies/DOID/classes?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_4',
+                 res.headers['location']
   end
 
   private
 
   def fetch_response(url)
-    conn = Faraday.new do |f|
-      f.response :follow_redirects
+    Faraday.new do |f|
       f.adapter Faraday.default_adapter
-    end
-    conn.get(url)
+    end.get(url)
   end
 end

test/models/test_explore.rb

@@ -0,0 +1,50 @@
+require_relative '../test_case'
+require 'pry'
+
+module Models
+  def self.method_missing
+    binding.pry
+  end
+end
+
+class LinkExploreTest < LinkedData::Client::TestCase
+  def test_explore
+    sub_direct_explore = LinkedData::Client::Models::Ontology.explore('MEDDRA')
+                                                             .latest_submission
+                                                             .get(include: 'all')
+
+    sub_indirect_explore = LinkedData::Client::Models::Ontology.find('MEDDRA').explore.latest_submission
+
+    refute_nil sub_direct_explore
+    refute_nil sub_indirect_explore
+
+    sub_direct_explore.to_hash.each do |key, value|
+      value_to_compare = sub_indirect_explore.to_hash[key]
+      if value.class.ancestors.include?(LinkedData::Client::Base)
+        value = value.to_hash
+        value_to_compare = value_to_compare.to_hash
+      end
+      # assert_equal value_to_compare, value, "Mismatch for key #{key}"
+      assert value == value_to_compare, "Mismatch for key #{key}: #{value.inspect} != #{value_to_compare.inspect}"
+    end
+  end
+
+  def test_explore_class
+
+    id = 'http://purl.org/sig/ont/fma/fma62955'
+    cls = LinkedData::Client::Models::Ontology.explore('FMA')
+                                              .classes(id)
+                                              .children
+                                              .get
+
+    refute_empty cls.collection
+
+    cls = LinkedData::Client::Models::Ontology.explore('FMA')
+                                              .classes(id)
+                                              .children
+                                              .get(include: 'prefLabel')
+
+    refute_empty cls.collection
+  end
+
+end