Merge MOD-API release from AgroPortal + Projects

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

@@ -9,8 +9,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        goo-slice: [ '20', '100', '500' ]
-        ruby-version: [ '2.7' ]
+        goo-slice: [ '100']
+        ruby-version: [ '3.2.0']
         triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
     runs-on: ubuntu-latest
     steps:
@@ -34,7 +34,7 @@ jobs:
         # http://docs.codecov.io/docs/testing-with-docker
         run: |
           ci_env=`bash <(curl -s https://codecov.io/env)`
-          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
+          GOO_SLICES=${{ matrix.goo-slice }} RUBYOPT="-W0" bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         with:

.gitignore

@@ -36,3 +36,4 @@ create_permissions.log
 # solr configsets, these are generated with a script
 test/solr/configsets/term_search
 test/solr/configsets/property_search
+.qodo

Gemfile

@@ -5,24 +5,25 @@ gem 'addressable', '~> 2.8'
 gem 'bcrypt', '~> 3.0'
 gem 'cube-ruby', require: 'cube'
 gem 'faraday', '~> 1.9'
-gem 'ffi', '~> 1.16.3'
-gem 'libxml-ruby', '~> 2.0'
+gem 'ffi'
+gem 'libxml-ruby'
 gem 'minitest'
 gem 'multi_json', '~> 1.0'
 gem 'oj'
 gem 'omni_logger'
 gem 'pony'
-gem 'rack', '~> 1.0'
-gem 'rack-test', '~> 0.6'
-gem 'rake', '~> 10.0'
+gem 'rack'
+gem 'rack-test'
+gem 'rake'
 gem 'rest-client'
 gem 'rsolr', '~> 1.0'
 gem 'rubyzip', '~> 1.0'
 gem 'thin'
 gem 'request_store'
 gem 'jwt'
-gem 'json-ld', '~> 3.0.2'
+gem 'json-ld', '~> 3.2.0'
 gem "parallel", "~> 1.24"
+gem 'rdf-raptor', github:'ruby-rdf/rdf-raptor', ref: '6392ceabf71c3233b0f7f0172f662bd4a22cd534' # use version 3.3.0 when available
 
 
 # Testing
@@ -42,3 +43,7 @@ end
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
+
+gem 'net-ftp'
+gem 'public_suffix', '~> 5.1.1'
+gem 'net-imap', '~> 0.4.18'

Gemfile.lock

@@ -1,12 +1,12 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: f8ac7b00e8d8b46d1eea04de014175525c1cdd83
+  revision: e48a2d13a65cc2dd1c12d116cfc9da9061106861
   branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
       pry
-      rdf (= 3.2.11)
+      rdf
       rdf-raptor
       rdf-rdfxml
       rdf-vocab
@@ -18,13 +18,22 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/sparql-client.git
-  revision: 59251e59346c9a69a67c88552ba55a1244eec602
+  revision: 736b7650e28db3ce5e3e49511ac30f958a29e8f1
   branch: development
   specs:
     sparql-client (3.2.2)
       net-http-persistent (~> 4.0, >= 4.0.2)
       rdf (~> 3.2, >= 3.2.11)
 
+GIT
+  remote: https://github.com/ruby-rdf/rdf-raptor.git
+  revision: 6392ceabf71c3233b0f7f0172f662bd4a22cd534
+  ref: 6392ceabf71c3233b0f7f0172f662bd4a22cd534
+  specs:
+    rdf-raptor (3.3.0)
+      ffi (~> 1.15)
+      rdf (~> 3.3)
+
 GEM
   remote: https://rubygems.org/
   specs:
@@ -39,20 +48,21 @@ GEM
     ansi (1.5.0)
     ast (2.4.2)
     base64 (0.2.0)
+    bcp47_spec (0.2.1)
     bcrypt (3.1.20)
-    bigdecimal (3.1.8)
+    bigdecimal (3.1.9)
     builder (3.3.0)
     childprocess (5.1.0)
       logger (~> 1.5)
     coderay (1.1.3)
-    concurrent-ruby (1.3.4)
-    connection_pool (2.4.1)
+    concurrent-ruby (1.3.5)
+    connection_pool (2.5.0)
     crack (1.0.0)
       bigdecimal
       rexml
     cube-ruby (0.0.3)
     daemons (1.4.1)
-    date (3.3.4)
+    date (3.4.1)
     docile (1.4.1)
     domain_name (0.6.20240107)
     email_spec (2.3.0)
@@ -76,35 +86,42 @@ GEM
     faraday-em_synchrony (1.0.0)
     faraday-excon (1.1.0)
     faraday-httpclient (1.0.1)
-    faraday-multipart (1.0.4)
-      multipart-post (~> 2)
+    faraday-multipart (1.1.0)
+      multipart-post (~> 2.0)
     faraday-net_http (1.0.2)
     faraday-net_http_persistent (1.2.0)
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.16.3)
-    hashdiff (1.1.1)
+    ffi (1.17.1)
+    hashdiff (1.1.2)
     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 (2.7.2)
-    json-ld (3.0.2)
-      multi_json (~> 1.12)
-      rdf (>= 2.2.8, < 4.0)
-    jwt (2.9.3)
+    json (2.10.1)
+    json-canonicalization (0.4.0)
+    json-ld (3.2.5)
+      htmlentities (~> 4.3)
+      json-canonicalization (~> 0.3, >= 0.3.2)
+      link_header (~> 0.0, >= 0.0.8)
+      multi_json (~> 1.15)
+      rack (>= 2.2, < 4)
+      rdf (~> 3.2, >= 3.2.10)
+    jwt (2.10.1)
       base64
-    language_server-protocol (3.17.0.3)
-    launchy (3.0.1)
+    language_server-protocol (3.17.0.4)
+    launchy (3.1.0)
       addressable (~> 2.8)
       childprocess (~> 5.0)
-    libxml-ruby (2.9.0)
+      logger (~> 1.6)
+    libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.1)
+    lint_roller (1.1.0)
+    logger (1.6.6)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -116,7 +133,7 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1001)
+    mime-types-data (3.2025.0204)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -126,83 +143,86 @@ GEM
       powerbar
     multi_json (1.15.0)
     multipart-post (2.4.1)
-    net-http-persistent (4.0.4)
+    net-ftp (0.3.8)
+      net-protocol
+      time
+    net-http-persistent (4.0.5)
       connection_pool (~> 2.2)
-    net-imap (0.4.17)
+    net-imap (0.4.19)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
     net-protocol (0.2.2)
       timeout
-    net-smtp (0.5.0)
+    net-smtp (0.5.1)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.6)
+    oj (3.16.9)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
-    ostruct (0.6.0)
+    ostruct (0.6.1)
     parallel (1.26.3)
-    parser (3.3.5.0)
+    parser (3.3.7.1)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
       mail (>= 2.0)
     powerbar (2.0.1)
       hashie (>= 1.1.0)
-    pry (0.14.2)
+    pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
     racc (1.8.1)
-    rack (1.6.13)
-    rack-test (0.8.3)
-      rack (>= 1.0, < 3)
+    rack (2.2.11)
+    rack-test (2.2.0)
+      rack (>= 1.3)
     rainbow (3.1.1)
-    rake (10.5.0)
-    rdf (3.2.11)
+    rake (13.2.1)
+    rdf (3.3.2)
+      bcp47_spec (~> 0.2)
+      bigdecimal (~> 3.1, >= 3.1.5)
       link_header (~> 0.0, >= 0.0.8)
-    rdf-raptor (3.2.0)
-      ffi (~> 1.15)
-      rdf (~> 3.2)
-    rdf-rdfxml (3.2.2)
-      builder (~> 3.2)
+    rdf-rdfxml (3.3.0)
+      builder (~> 3.2, >= 3.2.4)
       htmlentities (~> 4.3)
-      rdf (~> 3.2)
-      rdf-xsd (~> 3.2)
-    rdf-vocab (3.2.7)
-      rdf (~> 3.2, >= 3.2.4)
-    rdf-xsd (3.2.1)
-      rdf (~> 3.2)
+      rdf (~> 3.3)
+      rdf-xsd (~> 3.3)
+    rdf-vocab (3.3.2)
+      rdf (~> 3.3)
+    rdf-xsd (3.3.0)
+      rdf (~> 3.3)
       rexml (~> 3.2)
     redis (5.3.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.2)
+    redis-client (0.23.2)
       connection_pool
-    regexp_parser (2.9.2)
+    regexp_parser (2.10.0)
     request_store (1.7.0)
       rack (>= 1.4)
     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 (3.3.8)
+    rexml (3.4.0)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.67.0)
+    rubocop (1.72.1)
       json (~> 2.3)
-      language_server-protocol (>= 3.17.0)
+      language_server-protocol (~> 3.17.0.2)
+      lint_roller (~> 1.1.0)
       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 (>= 1.38.0, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.32.3)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.38.0)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -224,12 +244,16 @@ GEM
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
-    timeout (0.4.1)
+    time (0.4.1)
+      date
+    timeout (0.4.3)
     tzinfo (0.3.62)
-    unicode-display_width (2.6.0)
+    unicode-display_width (3.1.4)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
     uuid (2.3.9)
       macaddr (~> 1.0)
-    webmock (3.24.0)
+    webmock (3.25.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -244,22 +268,26 @@ DEPENDENCIES
   cube-ruby
   email_spec
   faraday (~> 1.9)
-  ffi (~> 1.16.3)
+  ffi
   goo!
-  json-ld (~> 3.0.2)
+  json-ld (~> 3.2.0)
   jwt
-  libxml-ruby (~> 2.0)
+  libxml-ruby
   minitest
   minitest-reporters (>= 0.5.0)
   multi_json (~> 1.0)
+  net-ftp
+  net-imap (~> 0.4.18)
   oj
   omni_logger
   parallel (~> 1.24)
   pony
   pry
-  rack (~> 1.0)
-  rack-test (~> 0.6)
-  rake (~> 10.0)
+  public_suffix (~> 5.1.1)
+  rack
+  rack-test
+  rake
+  rdf-raptor!
   request_store
   rest-client
   rsolr (~> 1.0)
@@ -273,4 +301,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.1.4
+   2.6.3