Merge to master: Release 2.6.0

Gemfile

@@ -5,4 +5,4 @@ gemspec
 gem 'rake'
 gem 'pry'
 gem 'test-unit'
-gem 'webmock', require: false
+gem 'webmock', require: false

Gemfile.lock

@@ -17,16 +17,16 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.0.8.6)
+    activesupport (7.0.8.7)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
       tzinfo (~> 2.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
-    bigdecimal (3.1.8)
+    bigdecimal (3.1.9)
     coderay (1.1.3)
-    concurrent-ruby (1.3.4)
+    concurrent-ruby (1.3.5)
     crack (1.0.0)
       bigdecimal
       rexml
@@ -37,35 +37,35 @@ GEM
     faraday-excon (2.0.0)
       excon (>= 0.27.4)
       faraday (~> 2.0.0.alpha.pre.2)
-    faraday-multipart (1.0.4)
-      multipart-post (~> 2)
+    faraday-multipart (1.1.0)
+      multipart-post (~> 2.0)
     faraday-net_http (2.1.0)
-    hashdiff (1.1.1)
-    i18n (1.14.6)
+    hashdiff (1.1.2)
+    i18n (1.14.7)
       concurrent-ruby (~> 1.0)
     lz4-ruby (0.3.3)
     method_source (1.1.0)
-    minitest (5.25.1)
+    minitest (5.25.4)
     multi_json (1.15.0)
     multipart-post (2.4.1)
-    oj (3.16.6)
+    oj (3.16.9)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
-    ostruct (0.6.0)
+    ostruct (0.6.1)
     parallel (1.26.3)
-    power_assert (2.0.4)
-    pry (0.14.2)
+    power_assert (2.0.5)
+    pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
-    rack (3.1.8)
+    rack (3.1.9)
     rake (13.2.1)
     request_store (1.7.0)
       rack (>= 1.4)
-    rexml (3.3.9)
+    rexml (3.4.0)
     ruby2_keywords (0.0.5)
     spawnling (2.1.5)
-    test-unit (3.6.2)
+    test-unit (3.6.7)
       power_assert
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)

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

lib/ontologies_api_client/collection.rb

@@ -29,14 +29,15 @@ def method_missing(meth, *args, &block)
         ##
         # Get all top-level links for the API
         def top_level_links(link = LinkedData::Client.settings.rest_url)
-          HTTP.get(link)
+          @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/http.rb

@@ -72,7 +72,7 @@ def self.get(path, params = {}, options = {})
               response = connection.get do |req|
                 req.url path
                 req.params = params.dup
-                req.options[:timeout] = 60
+                req.options[:timeout] = 30
                 req.headers.merge(headers)
                 req.headers[:invalidate_cache] = invalidate_cache
               end

lib/ontologies_api_client/link_explorer.rb

@@ -11,11 +11,18 @@ 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 +50,7 @@ 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 +60,22 @@ def combined_links
 
       private
 
+      def forward_explore(meth, *args)
+        sub_id = Array(args).find { |x| x.is_a?(String) } || ''
+        link = "#{@instance.id}/#{meth}/#{CGI.escape(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?
         values = values.dup
@@ -94,4 +114,4 @@ def linkable_attributes
       end
     end
   end
-end
+end

lib/ontologies_api_client/request_federation.rb

@@ -14,10 +14,22 @@ def federated_get(params = {}, &link)
           main_thread_locals = Thread.current.keys.map { |key| [key, Thread.current[key]] }.to_h
 
           connections = Parallel.map(portals, in_threads: portals.size) do |conn|
+            portal_name = portal_name_from_id(conn.url_prefix.to_s)
+            portal_status = true
+
+            unless Rails.cache.read("federation_portal_up_#{portal_name}").nil?
+              portal_status = Rails.cache.read("federation_portal_up_#{portal_name}")
+            end
+
+            unless portal_status
+              next [OpenStruct.new(errors: "Problem retrieving #{portal_name}")]
+            end
+
             main_thread_locals.each { |key, value| Thread.current[key] = value }
             begin
               HTTP.get(link.call(conn.url_prefix.to_s.chomp('/')), params, connection: conn)
             rescue Exception => e
+              Rails.cache.write("federation_portal_up_#{portal_name}", false, expires_in: 10.minutes)
               [OpenStruct.new(errors: "Problem retrieving #{link.call(conn.url_prefix.to_s.chomp('/')) || conn.url_prefix}")]
             end
           end
@@ -42,6 +54,11 @@ def request_portals(params = {})
 
           portals
         end
+
+
+        def portal_name_from_id(id)
+          LinkedData::Client::HTTP.federated_conn.find { |_, value| value.url_prefix.to_s.eql?(id) }&.first || ''
+        end
       end
 
     end

mise.toml

@@ -0,0 +1,2 @@
+[tools]
+ruby = "2.7.8"

test/models/test_explore.rb

@@ -0,0 +1,45 @@
+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
+    sub_direct_explore.to_hash.each do |key, value|
+      value_to_compare = sub_indirect_explore[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, value_to_compare
+    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
+
+    assert_not_empty cls.collection
+
+    cls = LinkedData::Client::Models::Ontology.explore('FMA')
+                                              .classes(id)
+                                              .children
+                                              .get(include: 'prefLabel')
+
+    assert_not_empty cls.collection
+  end
+
+end

test/models/test_federation.rb

@@ -23,7 +23,7 @@ def test_federated_ontologies_all
 
     refute_equal ontologies.length, ontologies_federate_all.length
 
-    ontologies_federate_all.group_by{|x| x.id.split('/')[0..-2].join('/')}.each do |portal, onts|
+    ontologies_federate_all.reject{|x| x.errors}.group_by{|x| x.id.split('/')[0..-2].join('/')}.each do |portal, onts|
       puts "#{portal} ontologies: #{onts.length}"
     end
 
@@ -45,10 +45,6 @@ def test_federated_ontologies_all
     puts "Federated ontologies  with two portal only with cache: #{ontologies_federate_two.length} in #{time2}s"
 
     refute_equal ontologies_federate_two.size, ontologies_federate_all.size
-
-    federated_portals =  ontologies_federate_two.map{|x| x.id.split('/')[0..-2].join('/')}.uniq
-    assert_equal 3, federated_portals.size
-    assert %w[bioontology ecoportal biodivportal].all? { |p| federated_portals.any?{|id| id[p]}  }
   end
 
   def test_federated_submissions_all
@@ -68,7 +64,7 @@ def test_federated_submissions_all
 
     refute_equal onts.length, onts_federate.length
 
-    onts_federate.group_by{|x| x.id.split('/')[0..-4].join('/')}.each do |portal, onts|
+    onts_federate.reject{|x| x.errors}.group_by{|x| x.id.split('/')[0..-4].join('/')}.each do |portal, onts|
       puts "#{portal} submissions: #{onts.length}"
     end
 

test/test_case.rb

@@ -1,9 +1,21 @@
 require 'test-unit'
+require 'logger'
+require 'active_support'
+require 'active_support/logger'
+require 'active_support/cache'
 require_relative '../lib/ontologies_api_client'
 require_relative '../config/config'
 require 'webmock'
 
 WebMock.allow_net_connect!
+
+Logger = ::Logger unless defined?(Logger)
+module Rails
+  def self.cache
+    @cache ||= ActiveSupport::Cache::MemoryStore.new
+  end
+end
+
 module LinkedData
   module Client
     class TestCase < Test::Unit::TestCase