Merge branch 'develop' into pr/sync-agroportal-bioportal

Gemfile

@@ -42,11 +42,11 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
-gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
+gem 'ncbo_annotator', git: 'https://github.com/ncbo/ncbo_annotator.git', branch: 'master'
+gem 'ncbo_cron', git: 'https://github.com/ncbo/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
-gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'pr/sync-agroportal-bioportal'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'pr/sync-agroportal-bioportal'
 gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'pr/sync-agroportal-ncbo'
 
 group :development do

Gemfile.lock

@@ -1,3 +1,30 @@
+GIT
+  remote: https://github.com/ncbo/ncbo_annotator.git
+  revision: 63c986880aa88c9384043e6611a682434a14aba7
+  branch: master
+  specs:
+    ncbo_annotator (0.0.1)
+      goo
+      ontologies_linked_data
+      redis
+      ruby-xxHash
+
+GIT
+  remote: https://github.com/ncbo/ncbo_cron.git
+  revision: f239b34230131cd7cfb9eec5b34068ba990b698b
+  branch: master
+  specs:
+    ncbo_cron (0.0.1)
+      dante
+      goo
+      google-analytics-data
+      mlanett-redis-lock
+      multi_json
+      ncbo_annotator
+      ontologies_linked_data
+      redis
+      rufus-scheduler (~> 2.0.24)
+
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
   revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
@@ -35,37 +62,9 @@ GIT
       sparql-client
       uuid
 
-GIT
-  remote: https://github.com/ontoportal-lirmm/ncbo_annotator.git
-  revision: 1eb751b65d10ae23d45c74e0516c78754a8419f0
-  branch: development
-  specs:
-    ncbo_annotator (0.0.1)
-      goo
-      ontologies_linked_data
-      redis
-      ruby-xxHash
-
-GIT
-  remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: 9ec0147203007cc368a5119ffe1a019fa8701c14
-  branch: master
-  specs:
-    ncbo_cron (0.0.1)
-      dante
-      goo
-      google-analytics-data
-      google-apis-analytics_v3
-      mlanett-redis-lock
-      multi_json
-      ncbo_annotator
-      ontologies_linked_data
-      redis
-      rufus-scheduler (~> 2.0.24)
-
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: f70abe981c6fb3533b7785d58b7234855bcd5cf2
+  revision: fc48343ad7a3f1867821c173be900cf16506b4b7
   branch: pr/sync-agroportal-ncbo
   specs:
     ontologies_linked_data (0.0.1)
@@ -137,7 +136,6 @@ GEM
     cube-ruby (0.0.3)
     dante (0.2.0)
     date (3.3.4)
-    declarative (0.0.20)
     docile (1.4.0)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
@@ -165,16 +163,6 @@ GEM
     google-analytics-data-v1beta (0.12.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
-    google-apis-analytics_v3 (0.15.0)
-      google-apis-core (>= 0.14.0, < 2.a)
-    google-apis-core (0.14.1)
-      addressable (~> 2.5, >= 2.5.1)
-      googleauth (~> 1.9)
-      httpclient (>= 2.8.1, < 3.a)
-      mini_mime (~> 1.0)
-      representable (~> 3.0)
-      retriable (>= 2.0, < 4.a)
-      rexml
     google-cloud-core (1.7.0)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
@@ -213,12 +201,9 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
-    httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.7.2)
-    json-ld (1.1.1)
-      rdf (>= 1.0.8)
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.7.2)
@@ -311,18 +296,13 @@ GEM
     redis-store (1.10.0)
       redis (>= 4, < 6)
     regexp_parser (2.9.0)
-    representable (3.2.0)
-      declarative (< 0.1.0)
-      trailblazer-option (>= 0.1.1, < 0.2.0)
-      uber (< 0.2.0)
     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)
-    retriable (3.1.2)
     rexml (3.2.6)
     rsolr (2.6.0)
       builder (>= 2.1.2)
@@ -383,10 +363,8 @@ GEM
     temple (0.10.3)
     tilt (2.3.0)
     timeout (0.4.1)
-    trailblazer-option (0.1.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    uber (0.1.0)
     unicode-display_width (2.5.0)
     unicorn (6.1.0)
       kgio (~> 2.6)
@@ -403,6 +381,7 @@ GEM
 
 PLATFORMS
   arm64-darwin-22
+  arm64-darwin-23
   x86_64-darwin-18
   x86_64-darwin-23
   x86_64-linux
@@ -420,7 +399,6 @@ DEPENDENCIES
   ffi
   goo!
   haml (~> 5.2.2)
-  json-ld
   json-schema (~> 2.0)
   minitest (~> 4.0)
   minitest-stub_any_instance
@@ -431,7 +409,6 @@ DEPENDENCIES
   newrelic_rpm
   oj (~> 3.0)
   ontologies_linked_data!
-  parallel
   parseconfig
   rack
   rack-accept (~> 0.4)

test/controllers/test_search_controller.rb

@@ -265,27 +265,31 @@ def test_search_obo_id
       assert_equal ogms_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[0]["links"]["ontology"])
       assert_equal cno_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[1]["links"]["ontology"])
       assert_equal ncit_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[2]["links"]["ontology"])
+
       assert_equal 'realization', docs[1]["prefLabel"].first
       assert_equal 'realization', docs[2]["prefLabel"].first
       assert docs[3]["prefLabel"].first.upcase.include?('OGMS ')
       assert docs[4]["prefLabel"].first.upcase.include?('OGMS ')
       assert docs[5]["prefLabel"].first.upcase.include?('OGMS ')
 
+
       get "/search?q=CNO:0000002"
       assert last_response.ok?
       results = MultiJson.load(last_response.body)
       docs = results["collection"]
       assert_equal 7, docs.size
       assert_equal cno_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[0]["links"]["ontology"])
       acr_1 = LinkedData::Utils::Triples.last_iri_fragment(docs[1]["links"]["ontology"])
-      assert acr_1 === ncit_acronym || acr_1 === ogms_acronym
+      assert_includes [ncit_acronym, ogms_acronym], acr_1
       acr_2= LinkedData::Utils::Triples.last_iri_fragment(docs[2]["links"]["ontology"])
+
       assert acr_2 === ncit_acronym || acr_2 === ogms_acronym
       assert docs[3]["prefLabel"].first.upcase.include?('CNO ')
       assert docs[4]["prefLabel"].first.upcase.include?('CNO ')
       assert docs[5]["prefLabel"].first.upcase.include?('CNO ')
       assert docs[6]["prefLabel"].first.upcase.include?('CNO ')
 
+
       # mdorf, 3/2/2024, when the : is followed by a LETTER, as in NCIT:C20480,
       # then Solr does not split the query on the tokens,
       # but when the : is followed by a number, as in OGMS:0000071,
@@ -315,17 +319,17 @@ def test_search_obo_id
       ont = LinkedData::Models::Ontology.find(ncit_acronym).first
       ont.delete if ont
       ont = LinkedData::Models::Ontology.find(ncit_acronym).first
-      assert ont.nil?
+      assert_nil ont
 
       ont = LinkedData::Models::Ontology.find(ogms_acronym).first
       ont.delete if ont
       ont = LinkedData::Models::Ontology.find(ogms_acronym).first
-      assert ont.nil?
+      assert_nil ont
 
       ont = LinkedData::Models::Ontology.find(cno_acronym).first
       ont.delete if ont
       ont = LinkedData::Models::Ontology.find(cno_acronym).first
-      assert ont.nil?
+      assert_nil ont
     end
   end