Merge branch 'master' into ecoportal-ontoportal-reset

Gemfile.lock

@@ -54,6 +54,7 @@ GEM
 
 PLATFORMS
   x86_64-darwin-21
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
@@ -63,4 +64,4 @@ DEPENDENCIES
   test-unit
 
 BUNDLED WITH
-   2.3.23
+   2.4.21

lib/ontologies_api_client/collection.rb

@@ -25,7 +25,7 @@ def method_missing(meth, *args, &block)
         ##
         # Get all top-level links for the API
         def top_level_links
-          HTTP.get(LinkedData::Client.settings.rest_url)
+          @top_level_links||= HTTP.get(LinkedData::Client.settings.rest_url)
         end
 
         ##
@@ -75,16 +75,16 @@ def where(params = {}, &block)
 
         ##
         # Find a resource by id
+        # @deprecated replace with "get"
         def find(id, params = {})
-          found = where do |obj|
-            obj.id.eql?(id)
-          end
-          found.first
+          [get(id, params)]
         end
 
         ##
         # Get a resource by id (this will retrieve it from the REST service)
         def get(id, params = {})
+          path = collection_path
+          id = "#{path}/#{id}" unless id.include?(path)
           HTTP.get(id, params)
         end
 

lib/ontologies_api_client/http.rb

@@ -2,7 +2,7 @@
 require 'multi_json'
 require 'digest'
 require 'ostruct'
-
+require 'benchmark'
 ##
 # This monkeypatch makes OpenStruct act like Struct objects
 class OpenStruct
@@ -58,20 +58,20 @@ def self.get(path, params = {}, options = {})
         raw = options[:raw] || false # return the unparsed body of the request
         params = params.delete_if { |k, v| v == nil || v.to_s.empty? }
         params[:ncbo_cache_buster] = Time.now.to_f if raw # raw requests don't get cached to ensure body is available
-        invalidate_cache = params.delete(:invalidate_cache) || false
-
+        invalidate_cache = params.delete(:invalidate_cache) || $API_CLIENT_INVALIDATE_CACHE || false
         begin
-          puts "Getting: #{path} with #{params}" if $DEBUG
-
-          # LOGGER.debug("\n\n RUBY API - LinkedData::Client::HTTP ->Get: #{path} with:\n    > params:#{params.inspect}\n    > options:#{options.inspect}  ")
           begin
-            response = conn.get do |req|
-              req.url path
-              req.params = params.dup
-              req.options[:timeout] = 60
-              req.headers.merge(headers)
-              req.headers[:invalidate_cache] = invalidate_cache
+            response = nil
+            time = Benchmark.realtime do
+              response = conn.get do |req|
+                req.url path
+                req.params = params.dup
+                req.options[:timeout] = 60
+                req.headers.merge(headers)
+                req.headers[:invalidate_cache] = invalidate_cache
+              end
             end
+            puts "Getting: #{path} with #{params} (#{time}s)" if $DEBUG_API_CLIENT
           rescue Exception => e
             params = Faraday::Utils.build_query(params)
             path << "?" unless params.empty? || path.include?("?")
@@ -89,7 +89,7 @@ def self.get(path, params = {}, options = {})
             obj = recursive_struct(load_json(response.body))
           end
         rescue StandardError => e
-          puts "Problem getting #{path}" if $DEBUG
+          puts "Problem getting #{path}" if $DEBUG_API_CLIENT
           raise e
         end
         obj
@@ -146,7 +146,7 @@ def self.patch(path, obj)
       end
 
       def self.delete(id)
-        puts "Deleting #{id}" if $DEBUG
+        puts "Deleting #{id}" if $DEBUG_API_CLIENT
         response = conn.delete id
         raise StandardError, response.body if response.status >= 500
 

lib/ontologies_api_client/models/class.rb

@@ -14,12 +14,12 @@ class Class < LinkedData::Client::Base
 
         # triple store predicate is <http://www.w3.org/2002/07/owl#deprecated>
         def obsolete?
-          self.obsolete
+          self.obsolete && self.obsolete.to_s.eql?("true")
         end
 
         def prefLabel(options = {})
           if options[:use_html]
-            if self.obsolete
+            if obsolete?
               return "<span class='obsolete_class' title='obsolete class'>#{@prefLabel}</span>"
             else
               return "<span class='prefLabel'>#{@prefLabel}</span>"

lib/ontologies_api_client/models/identifier.rb

@@ -0,0 +1,14 @@
+require_relative "../base"
+
+module LinkedData
+  module Client
+    module Models
+      class Identifier < LinkedData::Client::Base
+        include LinkedData::Client::Collection
+        include LinkedData::Client::ReadWrite
+
+        @media_type = "http://www.w3.org/ns/adms#Identifier"
+      end
+    end
+  end
+end

lib/ontologies_api_client/models/ontology.rb

@@ -52,10 +52,6 @@ def admin?(user)
           return administeredBy.any? {|u| u == user.id}
         end
 
-        def invalidate_cache(cache_refresh_all = true)
-          self.class.all(invalidate_cache: true, include_views: true)
-          super(cache_refresh_all)
-        end
 
         # ACL with administrators
         def full_acl
@@ -108,7 +104,7 @@ def self.find_by(attrs, *args)
         # Override to search for views as well by default
         # Views get hidden on the REST service unless the `include_views`
         # parameter is set to `true`
-        def find(id, params = {})
+        def self.find(id, params = {})
           params[:include_views] = params[:include_views] || true
           super(id, params)
         end
@@ -119,6 +115,9 @@ def self.include_params
           "acronym,administeredBy,group,hasDomain,name,notes,projects,reviews,summaryOnly,viewingRestriction"
         end
 
+        def self.find_by_acronym(acronym, params = {})
+          [find(acronym, params)]
+        end
       end
     end
   end

lib/ontologies_api_client/read_write.rb

@@ -137,7 +137,7 @@ def invalidate_cache(cache_refresh_all = true)
         HTTP.get(self.id, invalidate_cache: true) if self.id
         session = Thread.current[:session]
         session[:last_updated] = Time.now.to_f if session
-        refresh_cache
+        # refresh_cache
       end
 
       def refresh_cache