Merge pull request #15 from ontoportal-lirmm/development

Merge development & upstream  (2022-12)

.github/workflows/ruby-unit-test.yml

@@ -0,0 +1,32 @@
+name: Ruby Unit Test
+
+on: [push, pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        ruby-version: ['2.7']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Install Dependencies
+      run: sudo apt-get -y install raptor2-utils
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: ${{ matrix.ruby-version }}
+        bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+    - name: Start backend services via docker-compose
+      run: docker compose up -d
+    - name: Run tests
+      run: bundle exec rake test
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+

Gemfile

@@ -2,20 +2,24 @@ source 'https://rubygems.org'
 
 gemspec
 
-gem 'rake'
-gem 'pry'
-gem 'simplecov'
-gem 'minitest', '< 5.0'
-gem 'activesupport'
+gem "activesupport"
+gem "cube-ruby", require: "cube"
+gem "faraday", '~> 1.9'
+gem "rake"
 gem "uuid"
-gem 'cube-ruby', require: "cube"
-gem 'faraday', '~> 1.9'
+
+group :test do
+  gem "minitest", '< 5.0'
+  gem "pry"
+  gem 'simplecov'
+  gem 'simplecov-cobertura' # for submitting code coverage results to codecov.io
+end
 
 group :profiling do
-  gem 'sinatra'
-  gem 'rack-accept'
-  gem 'rack-post-body-to-params'
-  gem 'thin'
+  gem "rack-accept"
+  gem "rack-post-body-to-params"
+  gem "sinatra"
+  gem "thin"
 end
 
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'

Gemfile.lock

@@ -12,14 +12,13 @@ PATH
   remote: .
   specs:
     goo (0.0.2)
-      addressable (= 2.3.5)
+      addressable (~> 2.8)
       pry
       rdf (= 1.0.8)
       redis
       rest-client
       rsolr
       sparql-client
-      systemu
       uuid
 
 GEM
@@ -31,17 +30,19 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.3.5)
+    addressable (2.8.1)
+      public_suffix (>= 2.0.2, < 6.0)
     builder (3.2.4)
     coderay (1.1.3)
-    concurrent-ruby (1.1.9)
+    concurrent-ruby (1.1.10)
+    connection_pool (2.3.0)
     cube-ruby (0.0.3)
     daemons (1.4.1)
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     eventmachine (1.2.7)
-    faraday (1.10.0)
+    faraday (1.10.2)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
       faraday-excon (~> 1.1)
@@ -57,19 +58,19 @@ GEM
     faraday-em_synchrony (1.0.0)
     faraday-excon (1.1.0)
     faraday-httpclient (1.0.1)
-    faraday-multipart (1.0.3)
-      multipart-post (>= 1.2, < 3)
+    faraday-multipart (1.0.4)
+      multipart-post (~> 2)
     faraday-net_http (1.0.1)
     faraday-net_http_persistent (1.2.0)
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
     http-accept (1.7.0)
-    http-cookie (1.0.4)
+    http-cookie (1.0.5)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json_pure (2.6.1)
+    json_pure (2.6.2)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     method_source (1.0.0)
@@ -78,30 +79,35 @@ GEM
     mime-types-data (3.2022.0105)
     minitest (4.7.5)
     multi_json (1.15.0)
-    multipart-post (2.1.1)
-    mustermann (1.1.1)
+    multipart-post (2.2.3)
+    mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
     net-http-persistent (2.9.4)
     netrc (0.11.0)
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    rack (2.2.3)
+    public_suffix (5.0.0)
+    rack (2.2.4)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-post-body-to-params (0.1.8)
       activesupport (>= 2.3)
-    rack-protection (2.2.0)
+    rack-protection (3.0.3)
       rack
     rake (13.0.6)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (4.6.0)
+    redis (5.0.5)
+      redis-client (>= 0.9.0)
+    redis-client (0.11.1)
+      connection_pool
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
+    rexml (3.2.5)
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -110,29 +116,34 @@ GEM
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
+    simplecov-cobertura (2.1.0)
+      rexml
+      simplecov (~> 0.19)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
-    sinatra (2.2.0)
-      mustermann (~> 1.0)
-      rack (~> 2.2)
-      rack-protection (= 2.2.0)
+    sinatra (3.0.3)
+      mustermann (~> 3.0)
+      rack (~> 2.2, >= 2.2.4)
+      rack-protection (= 3.0.3)
       tilt (~> 2.0)
     systemu (2.6.5)
     thin (1.8.1)
       daemons (~> 1.0, >= 1.0.9)
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
-    tilt (2.0.10)
-    tzinfo (0.3.60)
+    tilt (2.0.11)
+    tzinfo (0.3.61)
     unf (0.1.4)
       unf_ext
-    unf_ext (0.0.8.1)
+    unf_ext (0.0.8.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
-  x86_64-darwin-21
+  ruby
+  x86_64-darwin-16
+  x86_64-linux
 
 DEPENDENCIES
   activesupport
@@ -145,10 +156,11 @@ DEPENDENCIES
   rack-post-body-to-params
   rake
   simplecov
+  simplecov-cobertura
   sinatra
   sparql-client!
   thin
   uuid
 
 BUNDLED WITH
-   2.3.5
+   2.3.22

docker-compose.yml

@@ -0,0 +1,26 @@
+version: '3'
+
+services:
+  4store:
+    image: bde2020/4store
+    ports:
+      - 9000:9000
+    command: >
+      bash -c "4s-backend-setup --segments 4 ontoportal_kb
+      && 4s-backend ontoportal_kb
+      && 4s-httpd -D -s-1 -p 9000 ontoportal_kb"
+
+  redis:
+    image: redis
+    ports:
+      - 6379:6379
+    healthcheck:
+      test: redis-cli ping
+      interval: 1s
+      timeout: 3s
+      retries: 30
+
+  solr:
+    image: ontoportal/solr-ut:0.1
+    ports:
+      - 8983:8983

goo.gemspec

@@ -1,19 +1,17 @@
 Gem::Specification.new do |s|
-  s.name = 'goo'
-  s.version = '0.0.2'
-  s.date = '2012-11-21'
-  s.summary = ""
+  s.name = "goo"
+  s.version = "0.0.2"
+  s.summary = "Graph Oriented Objects (GOO) for Ruby. A RDF/SPARQL based ORM."
   s.authors = ["Manuel Salvadores", "Paul Alexander"]
-  s.email = 'manuelso@stanford.edu'
-  s.files = Dir['lib/**/*.rb']
-  s.homepage = 'http://github.com/ncbo/goo'
-  s.add_dependency("uuid")
-  s.add_dependency("systemu") # remove when https://github.com/ahoward/macaddr/pull/20 is resolved
-  s.add_dependency("rsolr")
+  s.email = "manuelso@stanford.edu"
+  s.files = Dir["lib/**/*.rb"]
+  s.homepage = "http://github.com/ncbo/goo"
+    s.add_dependency("addressable", "~> 2.8")
+  s.add_dependency("pry")
   s.add_dependency("rdf", "= 1.0.8")
-  s.add_dependency("sparql-client")
-  s.add_dependency("addressable", "= 2.3.5")
-  s.add_dependency("rest-client")
   s.add_dependency("redis")
-  s.add_dependency("pry")
+  s.add_dependency("rest-client")
+  s.add_dependency("rsolr")
+  s.add_dependency("sparql-client")
+  s.add_dependency("uuid")
 end

lib/goo/sparql/query_builder.rb

@@ -147,7 +147,7 @@ def ids_filter(ids)
         filter_id = []
 
         ids.each do |id|
-          filter_id << "?id = #{id.to_ntriples.to_s}"
+          filter_id << "?id = #{id.to_ntriples.to_s.gsub(' ', '%20')}"
         end
         filter_id_str = filter_id.join ' || '
         @query.filter filter_id_str

lib/goo/sparql/solutions_mapper.rb

@@ -316,7 +316,9 @@ def include_embed_attributes(incl_embed, objects_new)
           }.values
           unless range_objs.empty?
             range_objs.uniq!
-            attr_range.where().models(range_objs).in(@collection).include(*next_attrs).all
+            query = attr_range.where().models(range_objs).in(@collection).include(*next_attrs)
+            query = query.read_only if @read_only
+            query.all
           end
         end
       end

test/test_case.rb

@@ -1,6 +1,13 @@
-# Start simplecov if this is a coverage task
-if ENV["COVERAGE"].eql?("true")
-  require 'simplecov'
+# Start simplecov if this is a coverage task or if it is run in the CI pipeline
+if ENV["COVERAGE"] == "true" || ENV["CI"] == "true"
+  require "simplecov"
+  require "simplecov-cobertura"
+  # https://github.com/codecov/ruby-standard-2
+  # Generate HTML and Cobertura reports which can be consumed by codecov uploader
+  SimpleCov.formatters = SimpleCov::Formatter::MultiFormatter.new([
+    SimpleCov::Formatter::HTMLFormatter,
+    SimpleCov::Formatter::CoberturaFormatter
+  ])
   SimpleCov.start do
     add_filter "/test/"
     add_filter "app.rb"
@@ -34,16 +41,19 @@ def _run_suites(suites, type)
     end
 
     def _run_suite(suite, type)
-      [1,5,10,200].each do |slice_size|
+      %[1,5,10,20]
+      ret = []
+      [1,5,10,20].each do |slice_size|
         puts "\nrunning test with slice_loading_size=#{slice_size}"
         Goo.slice_loading_size=slice_size
         begin
           suite.before_suite if suite.respond_to?(:before_suite)
-          super(suite, type)
+          ret += super(suite, type)
         ensure
           suite.after_suite if suite.respond_to?(:after_suite)
         end
       end
+      return ret
     end
   end
 

test/test_model_complex.rb

@@ -10,7 +10,7 @@ class Submission < Goo::Base::Resource
 end
 
 class Term < Goo::Base::Resource
-  model :class,
+  model :term,
         namespace: :owl,
         collection: :submission,
         name_with: :id,
@@ -25,22 +25,22 @@ class Term < Goo::Base::Resource
   attribute :parents, 
             namespace: :rdfs, 
             property: lambda { |x| tree_property(x) },
-            enforce: [:list, :class]
+            enforce: [:list, :term]
 
   attribute :ancestors, 
             namespace: :rdfs, 
             property: lambda { |x| tree_property(x) },
-            enforce: [:list, :class], transitive: true
+            enforce: [:list, :term], transitive: true
 
   attribute :children, 
             namespace: :rdfs, 
             property: lambda { |x| tree_property(x) },
-            inverse: { on: :class , attribute: :parents }
+            inverse: { on: :term , attribute: :parents }
 
   attribute :descendants, 
             namespace: :rdfs, 
             property: lambda { |x| tree_property(x) },
-            inverse: { on: :class , attribute: :parents }, 
+            inverse: { on: :term , attribute: :parents },
             transitive: true
 
   def self.tree_property(*args)
@@ -482,6 +482,7 @@ def test_empty_attributes
   end
 
   def test_aggregate
+    skip "Transitive closure doesn't work yet.  AllegroGraph?"
     submission = Submission.new(name: "submission1")
     unless submission.exist?
       submission.save