Fix: recommender size limit using SOLR with a GET call not a POST call

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

@@ -13,12 +13,14 @@ jobs:
       run: cp config/config.test.rb config/config.rb
     - name: Build docker compose
       run: docker compose build
-    - name: Run unit tests
+    - name: Run docker
       # unit tests are run inside a container
       # http://docs.codecov.io/docs/testing-with-docker
       run: |
         ci_env=`bash <(curl -s https://codecov.io/env)`
-        docker compose run $ci_env -e CI --rm ruby bundle exec rake test TESTOPTS='-v'
+        docker compose up
+    - name: Run unit tests
+      run : bundle exec rake test  TESTOPTS="-v"
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       with:

Gemfile

@@ -6,12 +6,14 @@ gem 'ffi'
 gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'
 gem 'redis'
+gem 'request_store'
+gem 'jwt'
 
 # NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
+gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'
+gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
 
 group :development do
   gem 'simplecov'

Gemfile.lock

@@ -1,21 +1,23 @@
 GIT
-  remote: https://github.com/ncbo/goo.git
-  revision: daea7822af9e5ca1961d6873a758735133a1b2db
-  branch: master
+  remote: https://github.com/ontoportal-lirmm/goo.git
+  revision: cd5bc312bd3acd2ff056a87a6f37b5419f3444dc
+  branch: development
   specs:
     goo (0.0.2)
-      addressable (~> 2.8)
       pry
-      rdf (= 1.0.8)
+      rdf (= 3.2.11)
+      rdf-raptor
+      rdf-rdfxml
+      rdf-vocab
       redis
       rest-client
       rsolr
       sparql-client
       uuid
 
 GIT
-  remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 04226ac5840a328e6f906f15c769ee6ee5723102
+  remote: https://github.com/ontoportal-lirmm/ncbo_annotator.git
+  revision: 57204d8e54432ba660af4c49806e2a3019a23fa2
   branch: master
   specs:
     ncbo_annotator (0.0.1)
@@ -25,9 +27,9 @@ GIT
       ruby-xxHash
 
 GIT
-  remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: a7ad210e846a390f203457be2459719214d142fe
-  branch: master
+  remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
+  revision: c9b8b42b09f9a734507965a9529809ea581ef58a
+  branch: development
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -45,8 +47,8 @@ GIT
       rubyzip
 
 GIT
-  remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
+  remote: https://github.com/ontoportal-lirmm/sparql-client.git
+  revision: aed51baf4106fd0f3d0e3f9238f0aad9406aa3f0
   branch: master
   specs:
     sparql-client (1.0.1)
@@ -63,34 +65,36 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.5)
-      public_suffix (>= 2.0.2, < 6.0)
-    base64 (0.1.1)
-    bcrypt (3.1.19)
+    base64 (0.2.0)
+    bcrypt (3.1.20)
+    bigdecimal (3.1.6)
     builder (3.2.4)
     coderay (1.1.3)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
-    date (3.3.3)
+    date (3.3.4)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
-    faraday (2.7.11)
+    domain_name (0.6.20240107)
+    faraday (2.8.1)
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-net_http (3.0.2)
     ffi (1.16.3)
+    htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
-    json_pure (2.6.3)
-    libxml-ruby (4.1.1)
-    logger (1.5.3)
+    json (2.7.1)
+    json_pure (2.7.1)
+    jwt (2.8.0)
+      base64
+    libxml-ruby (5.0.2)
+    link_header (0.0.8)
+    logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -99,42 +103,57 @@ GEM
       net-pop
       net-smtp
     method_source (1.0.0)
-    mime-types (3.5.1)
+    mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1003)
+    mime-types-data (3.2024.0206)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.7)
+    net-imap (0.4.10)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
-    net-protocol (0.2.1)
+    net-protocol (0.2.2)
       timeout
-    net-smtp (0.4.0)
+    net-smtp (0.4.0.1)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.1)
+    oj (3.16.3)
+      bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
-    rack (3.0.8)
+    rack (3.0.9.1)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (10.5.0)
-    rdf (1.0.8)
-      addressable (>= 2.2)
-    redis (5.0.8)
+    rdf (3.2.11)
+      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)
+      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)
+      rexml (~> 3.2)
+    redis (5.1.0)
       redis-client (>= 0.17.0)
-    redis-client (0.18.0)
+    redis-client (0.20.0)
       connection_pool
+    request_store (1.6.0)
+      rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -158,36 +177,32 @@ GEM
     simplecov_json_formatter (0.1.4)
     systemu (2.6.5)
     thread_safe (0.3.6)
-    timeout (0.4.0)
+    timeout (0.4.1)
     tzinfo (0.3.62)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
-  aarch64-linux
-  arm64-darwin-22
-  x86_64-darwin-18
   x86_64-darwin-21
-  x86_64-linux
+  x86_64-darwin-23
 
 DEPENDENCIES
   cube-ruby
   faraday (~> 2.0)
   ffi
   goo!
+  jwt
   minitest (~> 4.0)
   ncbo_annotator!
   oj (~> 3.0)
   ontologies_linked_data!
   pry
   rake (~> 10.0)
   redis
+  request_store
   simplecov
   simplecov-cobertura
   sparql-client!
 
 BUNDLED WITH
-   2.3.15
+   2.4.22

README.md

@@ -1,2 +1,2 @@
-ncbo_ontology_recommender
+ncbo_ontology_recommender 
 =========================

config/solr/property_search/enumsconfig.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" ?>
+<enumsConfig>
+  <enum name="ontologyType">
+    <value>ONTOLOGY</value>
+    <value>VALUE_SET_COLLECTION</value>
+  </enum>
+  <enum name="propertyType">
+    <value>ANNOTATION</value>
+    <value>DATATYPE</value>
+    <value>OBJECT</value>
+  </enum>
+</enumsConfig>