ontoportal · syphax-bouazzouni · Mar 7, 2023 · Mar 7, 2023 · Mar 7, 2023 · Mar 8, 2023
diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
@@ -9,7 +9,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        backend: ['ruby', 'ruby-agraph'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
+        goo-slice: [ '20', '100', '500' ]
+        ruby-version: [ '2.7' ]
+        triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4

diff --git a/Dockerfile b/Dockerfile
@@ -14,7 +14,7 @@ COPY Gemfile* /srv/ontoportal/ontologies_linked_data/
 
 WORKDIR /srv/ontoportal/ontologies_linked_data
 
-RUN gem update --system
+RUN gem update --system 3.4.22 # the 3.4.22 can be removed if we support Ruby version > 3.0
 RUN gem install bundler
 ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install

diff --git a/Gemfile b/Gemfile
@@ -34,5 +34,5 @@ group :development do
   gem 'rubocop', require: false
 end
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
+gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -6,7 +6,10 @@ GIT
     goo (0.0.2)
       addressable (~> 2.8)
       pry
-      rdf (= 1.0.8)
+      rdf (= 3.2.11)
+      rdf-raptor
+      rdf-rdfxml
+      rdf-vocab
       redis
       request_store
       rest-client
@@ -19,10 +22,9 @@ GIT
   revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
   branch: master
   specs:
-    sparql-client (1.0.1)
-      json_pure (>= 1.4)
-      net-http-persistent (= 2.9.4)
-      rdf (>= 1.0)
+    sparql-client (3.2.2)
+      net-http-persistent (~> 4.0, >= 4.0.2)
+      rdf (~> 3.2, >= 3.2.11)
 
 GEM
   remote: https://rubygems.org/
@@ -37,7 +39,6 @@ GEM
       public_suffix (>= 2.0.2, < 7.0)
     ansi (1.5.0)
     ast (2.4.2)
-    base64 (0.2.0)
     bcrypt (3.1.20)
     bigdecimal (3.1.8)
     builder (3.3.0)
@@ -48,35 +49,37 @@ GEM
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     daemons (1.4.1)
-    date (3.4.0)
+    date (3.4.1)
     docile (1.4.1)
     domain_name (0.6.20240107)
     email_spec (2.3.0)
       htmlentities (~> 4.3.3)
       launchy (>= 2.1, < 4.0)
       mail (~> 2.7)
     eventmachine (1.2.7)
-    faraday (2.8.1)
-      base64
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
-    faraday-net_http (3.0.2)
+    faraday (2.12.2)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
     ffi (1.17.0)
+    ffi (1.17.0-arm64-darwin)
     hashie (5.0.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.7)
+    http-cookie (1.0.8)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.8.2)
+    json (2.9.0)
     json_pure (2.8.1)
     language_server-protocol (3.17.0.3)
     launchy (3.0.1)
       addressable (~> 2.8)
       childprocess (~> 5.0)
     libxml-ruby (5.0.3)
-    logger (1.6.1)
+    logger (1.6.2)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -88,7 +91,7 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1105)
+    mime-types-data (3.2024.1203)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -97,6 +100,8 @@ GEM
       minitest (>= 2.12, < 5.0)
       powerbar
     multi_json (1.15.0)
+    net-http (0.6.0)
+      uri
     net-http-persistent (2.9.4)
     net-imap (0.4.18)
       date
@@ -125,7 +130,7 @@ GEM
     pry (0.15.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.1.1)
+    public_suffix (6.0.1)
     racc (1.8.1)
     rack (2.2.10)
     rack-test (0.8.3)
@@ -136,9 +141,9 @@ GEM
       addressable (>= 2.2)
     redis (5.3.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.2)
+    redis-client (0.23.0)
       connection_pool
-    regexp_parser (2.9.2)
+    regexp_parser (2.9.3)
     request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
@@ -150,20 +155,19 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.68.0)
+    rubocop (1.69.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 2.4, < 3.0)
-      rubocop-ast (>= 1.32.2, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.36.2, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.36.1)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.36.2)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
-    ruby2_keywords (0.0.5)
     rubyzip (1.3.0)
     simplecov (0.22.0)
       docile (~> 1.1)
@@ -182,9 +186,16 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.2)
     tzinfo (0.3.62)
-    unicode-display_width (2.6.0)
+    unicode-display_width (3.1.2)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
+    uri (1.0.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webmock (3.24.0)
+      addressable (>= 2.8.0)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
   aarch64-linux
@@ -206,6 +217,7 @@ DEPENDENCIES
   multi_json (~> 1.0)
   oj (~> 3.0)
   omni_logger
+  parallel (~> 1.24)
   pony
   pry
   rack
@@ -220,6 +232,7 @@ DEPENDENCIES
   simplecov-cobertura
   sparql-client!
   thin
+  webmock
 
 BUNDLED WITH
-   2.4.22
+   2.5.11
diff --git a/README.md b/README.md
@@ -1,8 +1,69 @@
 ontologies_linked_data
 ======================
 
+## TODO
+
+DONE: Quand ces champs ne sont pas remplis, faut mettre les valeurs par défaut (skos:prefLabel, skos:altLabel)
+```ruby
+"prefLabelProperty": null,
+"definitionProperty": null,
+"synonymProperty": null,
+"authorProperty": null,
+"hierarchyProperty": null,
+"obsoleteProperty": null,
+"obsoleteParent": null
+```
+
+On pourrait aussi peupler seul exampleIdentifier (on prend l'URI d'une classe au pif dans l'ontology)
+
+On pourrait générer également useImports avec les URI des owl:imports
+
+uriregexpattern: uri de l'ontology (où on vire la fin et on met sous forme de regex)
+
+### Not valid property names
+
+Property names with - in it are not valid.
+
+Causing the following error:
+
+```
+NameError - `@bug-database' is not allowed as an instance variable name:
+  /usr/local/rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/bundler/gems/goo-7bbbb557d9f2/lib/goo/base/resource.rb:203:in `instance_variable_set'
+  /usr/local/rbenv/versions/2.1.5/lib/ruby/gems/2.1.0/bundler/gems/goo-7bbbb557d9f2/lib/goo/base/resource.rb:203:in `block in bring'
+```
+
+
+## Unit test status
+
+Unit test status:
+ - master branch:   [![Build Status](https://bmir-jenkins.stanford.edu/buildStatus/icon?job=NCBO_OntLD_MasterTest)](https://bmir-jenkins.stanford.edu/job/NCBO_OntLD_MasterTest/)
+ - staging branch:  [![Build Status](https://bmir-jenkins.stanford.edu/buildStatus/icon?job=NCBO_OntLD_StagingTest)](https://bmir-jenkins.stanford.edu/job/NCBO_OntLD_StagingTest/)
 
 Models and serializers for ontologies and related artifacts backed by 4store
 
 This is a component of the NCBO [ontologies_api](https://github.com/ncbo/ontologies_api).
 
+
+## Add a new namespace in GOO for properties
+
+To add new namespaces used in the `Goo.vocabulary` go to `lib/ontologies_linked_data/config/config.rb`
+
+And use the GOO `add_namespace` method. For example:
+
+```ruby
+Goo.configure do |conf|
+  conf.add_namespace(:omv, RDF::Vocabulary.new("http://omv.ontoware.org/2005/05/ontology#"))
+end
+```
+
+* To iterate other the namespaces
+```ruby
+Goo.namespaces.each do |prefix,uri|
+  puts "#{prefix}: #{uri}"
+end
+```
+
+* To resolve a namespace
+```ruby
+Goo.vocabulary(:omv).to_s
+```
diff --git a/bin/bubastis-1.4.0.jar b/bin/bubastis-1.4.0.jar
diff --git a/bin/bubastis.jar b/bin/bubastis.jar
diff --git a/bin/bubastis.jar b/bin/bubastis.jar
@@ -0,0 +1 @@
+./bubastis-1.4.0.jar
diff --git a/bin/bubastis_1_3.jar b/bin/bubastis_1_3.jar
diff --git a/bin/bubastis_readme.txt b/bin/bubastis_readme.txt
@@ -6,7 +6,7 @@ Bubastis is an ontology change tool which is able to analyse two ontologies (typ
 
 
 Usage:
-java -jar bubastis_1_2.jar parameters:
+java -jar bubastis.jar parameters:
 (required)  -ontology1 location of ontology 1 either a URL for an ontology on the web or a local file location in obo or owl format. Typically the older version of the ontologies being compared
 (required)  -ontology2 location of ontology 2 either a URL or local file location of an obo or owl format ontology. Typically the newer version of the ontologies being compared.
 (optional)  -output location of output file to send results, default is to console.
@@ -15,10 +15,10 @@ java -jar bubastis_1_2.jar parameters:
 
 Examples:
 Loading two files locally and outputting results to console:
-java -jar bubastis_1_2.jar -ontology1 "H://obi_nov_08.owl" -ontology2 "H://obi_jan_09.owl"
+java -jar bubastis.jar -ontology1 "H://obi_nov_08.owl" -ontology2 "H://obi_jan_09.owl"
 
 Loading two files locally and output results to xml file with an xslt location inserted into header
-java -jar bubastis_1_2.jar -1 "H://obi_nov_08.owl" -2 "H://obi_jan_09.owl" -output "H://OBIdiff.xml" -format xml -xslt "./stylesheets/bubastis.xslt"
+java -jar bubastis.jar -1 "H://obi_nov_08.owl" -2 "H://obi_jan_09.owl" -output "H://OBIdiff.xml" -format xml -xslt "./stylesheets/bubastis.xslt"
 
 Loading one file locally and one from the web and outputting results to plain text:
-java -jar bubastis_1_2.jar -ontology1 "H://disease_ontology_version_1.owl" -ontology2 "http://www.disease.org/diseaseontology_latest.owl" -output "C://my_diff.txt" 
+java -jar bubastis.jar -ontology1 "H://disease_ontology_version_1.owl" -ontology2 "http://www.disease.org/diseaseontology_latest.owl" -output "C://my_diff.txt"