Merge pull request #6 from ncbo/master

Sync: merge releases 2.2.3 and onward from ncbo

.github/workflows/ruby.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        ruby-version: ['2.7', '3.0']
+        ruby-version: ['3.0', '3.1']
     steps:
     - uses: actions/checkout@v3
     - name: Set up Ruby
@@ -34,4 +34,4 @@ jobs:
     - name: Run tests
       env:
         UT_APIKEY: ${{ secrets.UT_APIKEY }}
-      run: bundle exec rake test
+      run: bundle exec rake test TESTOPTS="-v"

Gemfile

@@ -1,8 +1,9 @@
+# frozen_string_literal: true
+
 source 'https://rubygems.org'
 
 gemspec
 
+gem 'pry'
 gem 'rake'
 gem 'rubocop', '~> 1.43'
-gem 'pry'
-gem 'test-unit'

Gemfile.lock

@@ -1,8 +1,8 @@
 PATH
   remote: .
   specs:
-    ontologies_api_client (2.2.2)
-      activesupport (= 6.1.7.3)
+    ontologies_api_client (2.4.0)
+      activesupport (= 7.0.8)
       addressable (~> 2.8)
       excon
       faraday
@@ -11,74 +11,83 @@ PATH
       lz4-ruby
       multi_json
       oj
-      spawnling (= 2.1.5)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.1.7.3)
+    activesupport (7.0.8)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
       tzinfo (~> 2.0)
-      zeitwerk (~> 2.3)
-    addressable (2.8.4)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     ast (2.4.2)
+    bigdecimal (3.1.8)
     coderay (1.1.3)
-    concurrent-ruby (1.2.2)
-    excon (0.100.0)
-    faraday (2.7.6)
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
+    concurrent-ruby (1.3.3)
+    excon (0.111.0)
+    faraday (2.10.0)
+      faraday-net_http (>= 2.0, < 3.2)
+      logger
     faraday-excon (2.1.0)
       excon (>= 0.27.4)
       faraday (~> 2.0)
+    faraday-follow_redirects (0.3.0)
+      faraday (>= 1, < 3)
     faraday-multipart (1.0.4)
       multipart-post (~> 2)
-    faraday-net_http (3.0.2)
-    i18n (1.14.1)
+    faraday-net_http (3.1.0)
+      net-http
+    i18n (1.14.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
+    json (2.7.2)
+    language_server-protocol (3.17.0.3)
+    logger (1.6.0)
     lz4-ruby (0.3.3)
-    method_source (1.0.0)
-    minitest (5.18.1)
+    method_source (1.1.0)
+    minitest (5.25.1)
+    minitest-hooks (1.5.1)
+      minitest (> 5.3)
     multi_json (1.15.0)
-    multipart-post (2.3.0)
-    oj (3.15.0)
-    parallel (1.22.1)
-    parser (3.2.0.0)
+    multipart-post (2.4.1)
+    net-http (0.4.1)
+      uri
+    oj (3.16.4)
+      bigdecimal (>= 3.0)
+    parallel (1.25.1)
+    parser (3.3.4.0)
       ast (~> 2.4.1)
-    power_assert (2.0.3)
+      racc
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.1)
+    public_suffix (6.0.0)
+    racc (1.8.0)
     rainbow (3.1.1)
-    rake (13.0.6)
-    regexp_parser (2.6.2)
-    rexml (3.2.5)
-    rubocop (1.44.1)
+    rake (13.2.1)
+    regexp_parser (2.9.2)
+    rexml (3.3.2)
+      strscan
+    rubocop (1.65.0)
       json (~> 2.3)
+      language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.0.0)
+      parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.8, < 3.0)
+      regexp_parser (>= 2.4, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.24.1, < 2.0)
+      rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.24.1)
-      parser (>= 3.1.1.0)
-    ruby-progressbar (1.11.0)
-    ruby2_keywords (0.0.5)
-    spawnling (2.1.5)
-    test-unit (3.5.7)
-      power_assert
+    rubocop-ast (1.31.3)
+      parser (>= 3.3.1.0)
+    ruby-progressbar (1.13.0)
+    strscan (3.1.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.4.2)
-    zeitwerk (2.6.8)
+    unicode-display_width (2.5.0)
+    uri (0.13.0)
 
 PLATFORMS
   ruby
@@ -87,11 +96,13 @@ PLATFORMS
   x86_64-linux
 
 DEPENDENCIES
+  faraday-follow_redirects (~> 0.3)
+  minitest (~> 5.25)
+  minitest-hooks (~> 1.5)
   ontologies_api_client!
   pry
   rake
   rubocop (~> 1.43)
-  test-unit
 
 BUNDLED WITH
-   2.3.22
+   2.4.18

README.md

@@ -1,10 +1,11 @@
 # ontologies_api_client
 
-Models and serializers for ontologies and related artifacts backed by a [4store](https://github.com/4store/4store) 
-RDF database. This library can be used for interacting with a 4store instance that stores 
-[BioPortal](https://bioportal.bioontology.org/) ontology data. Models in the library are based on 
-[Graph Oriented Objects for Ruby (Goo)](https://github.com/ncbo/goo). Serializers support RDF serialization as 
-Rack Middleware and automatic generation of hypermedia links.
+Models and serializers for ontologies and related artifacts backed by an 
+[AllegroGraph](https://allegrograph.com/products/allegrograph/) or a [4store](https://github.com/4store/4store) 
+database. This library can be used for interacting with an AllegroGraph or a 4store instance that 
+stores [BioPortal](https://bioportal.bioontology.org/) ontology data. Models in the library are based on 
+[Graph Oriented Objects for Ruby (Goo)](https://github.com/ncbo/goo). Serializers support RDF serialization as Rack Middleware and automatic 
+generation of hypermedia links.
 
 ## Install
 
@@ -152,7 +153,7 @@ For questions please email [[email protected]]([email protected].)
 
 ## License
 
-Copyright (c) 2021, The Board of Trustees of Leland Stanford Junior University All rights reserved.
+Copyright (c) 2024, The Board of Trustees of Leland Stanford Junior University All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

config/config.test.rb

@@ -1,13 +1,17 @@
+# frozen_string_literal: true
+
 # config.rb is required for testing
 # unit test makes calls to bioportal api so it needs a valid API key which can
 # be set via ENV variable UT_APIKEY
 abort('UT_APIKEY env variable is not set. Canceling tests') unless ENV.include?('UT_APIKEY')
 abort('UT_APIKEY env variable is set to an empty value. Canceling tests') unless ENV['UT_APIKEY'].size > 5
 
 LinkedData::Client.config do |config|
-  config.rest_url   = 'https://data.bioontology.org'
-  config.apikey     = ENV['UT_APIKEY']
-#  config.apikey     = 'xxxxx-xxxxx-xxxxxxxxxx'
-  config.links_attr = 'links'
-  config.cache      = false
+  config.rest_url    = 'https://data.bioontology.org'
+  config.apikey      = ENV['UT_APIKEY']
+  # config.apikey    = 'xxxxx-xxxxx-xxxxxxxxxx'
+  config.links_attr  = 'links'
+  config.purl_host   = 'purl.bioontology.org'
+  config.purl_prefix = 'https://purl.bioontology.org/ontology'
+  config.cache       = false
 end

lib/ontologies_api_client.rb

@@ -1,6 +1,5 @@
 require 'oj'
 require 'multi_json'
-require 'spawnling'
 
 require_relative 'ontologies_api_client/config'
 require_relative 'ontologies_api_client/http'
@@ -9,6 +8,7 @@
 require_relative 'ontologies_api_client/collection'
 require_relative 'ontologies_api_client/read_write'
 require_relative 'ontologies_api_client/analytics'
+require_relative 'ontologies_api_client/version'
 
 # Models
 curr_dir = File.expand_path("../ontologies_api_client",  __FILE__)

lib/ontologies_api_client/base.rb

@@ -6,7 +6,15 @@ class Base
       attr_accessor :context, :links
 
       class << self
-        attr_accessor :media_type, :act_as_media_type, :include_attrs, :include_attrs_full, :attrs_always_present
+        attr_accessor :act_as_media_type, :include_attrs, :include_attrs_full, :attrs_always_present
+        def media_types
+          Array(@media_type)
+        end
+
+        def media_type
+          media_types.first
+        end
+
       end
 
       ##
@@ -31,8 +39,11 @@ def self.map_classes
         map = {}
         classes = LinkedData::Client::Models.constants.map {|c| LinkedData::Client::Models.const_get(c)}
         classes.each do |media_type_cls|
-          next if map[media_type_cls] || !media_type_cls.respond_to?(:media_type) || !media_type_cls.ancestors.include?(LinkedData::Client::Base)
-          map[media_type_cls.media_type] = media_type_cls
+          next if map[media_type_cls] || !media_type_cls.respond_to?(:media_types) || !media_type_cls.ancestors.include?(LinkedData::Client::Base)
+          media_type_cls.media_types.each do |type|
+            next if map[type]
+            map[type] = media_type_cls
+          end
           media_type_cls.act_as_media_type.each {|mt| map[mt] = media_type_cls} if media_type_cls.act_as_media_type
         end
         return map

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
 
         ##
@@ -73,18 +73,18 @@ def where(params = {}, &block)
           end
         end
 
-        ##
         # Find a resource by id
+        #
+        # @deprecated Use {#get} instead
         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/config.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require 'ostruct'
 require 'faraday'
 require 'faraday/excon'
@@ -16,27 +18,30 @@ module Client
 
     def config(&block)
       return if @settings_run
+
       @settings_run = true
 
       yield @settings if block_given?
 
       # Set defaults
-      @settings.rest_url                ||= "http://stagedata.bioontology.org"
-      @settings.apikey                  ||= "4ea81d74-8960-4525-810b-fa1baab576ff"
-      @settings.links_attr              ||= "links"
+      @settings.rest_url                ||= 'http://stagedata.bioontology.org'
+      @settings.apikey                  ||= '4ea81d74-8960-4525-810b-fa1baab576ff'
+      @settings.links_attr              ||= 'links'
       @settings.cache                   ||= false
       @settings.enable_long_request_log ||= false
-      @settings.purl_prefix             ||= "http://purl.example.org"
+      @settings.purl_prefix             ||= 'http://purl.example.org'
+      @settings.purl_host               ||= 'purl.example.org'
 
       # Remove trailing slash
-      @settings.rest_url    = @settings.rest_url.chomp("/")
-      @settings.purl_prefix = @settings.purl_prefix.chomp("/")
+      @settings.rest_url    = @settings.rest_url.chomp('/')
+      @settings.purl_prefix = @settings.purl_prefix.chomp('/')
 
       @settings_run = true
     end
 
     def config_connection(options = {})
       return if @settings_run_connection
+
       store = options[:cache_store]
       @settings.conn = Faraday.new(@settings.rest_url) do |faraday|
         if @settings.enable_long_request_log
@@ -57,20 +62,20 @@ def config_connection(options = {})
           begin
             require_relative 'middleware/faraday-object-cache'
             faraday.use :object_cache, store: store
-            puts "=> faraday caching enabled"
+            puts '=> faraday caching enabled'
             puts "=> faraday cache store: #{store.class}"
           rescue LoadError
-            puts "=> WARNING: faraday http cache gem is not available, caching disabled"
+            puts '=> WARNING: faraday http cache gem is not available, caching disabled'
           end
         end
 
         faraday.request :multipart
         faraday.request :url_encoded
         faraday.adapter :excon
         faraday.headers = {
-          "Accept" => "application/json",
-          "Authorization" => "apikey token=#{@settings.apikey}",
-          "User-Agent" => "NCBO API Ruby Client v0.1.0"
+          'Accept' => 'application/json',
+          'Authorization' => "apikey token=#{@settings.apikey}",
+          'User-Agent' => "NCBO API Ruby Client v#{LinkedData::Client::VERSION}"
         }
       end
       @settings_run_connection = true
@@ -80,4 +85,4 @@ def connection_configured?
       @settings_run_connection
     end
   end
-end
+end