fix failing unit tests

Gemfile

@@ -1,11 +1,7 @@
 source 'https://rubygems.org'
 
 gem 'cube-ruby'
-gem 'faraday', '~> 1.9'
-gem 'ffi'
-gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'
-gem 'redis'
 gem 'ruby-xxHash'
 
 group :development do

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 33583fd1c1d72b449cd6bb91815e3422b8448983
+  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
   branch: develop
   specs:
     goo (0.0.2)
@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: da1642ed8f9f04db2e427e35d88f235a55138d03
+  revision: 013a322440b4cfd899908d15ff605799acf8e6ef
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -53,44 +53,26 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
+    base64 (0.2.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.7)
-    builder (3.2.4)
+    bigdecimal (3.1.8)
+    builder (3.3.0)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.3)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     date (3.3.4)
     docile (1.4.0)
     domain_name (0.6.20240107)
-    faraday (1.10.3)
-      faraday-em_http (~> 1.0)
-      faraday-em_synchrony (~> 1.0)
-      faraday-excon (~> 1.1)
-      faraday-httpclient (~> 1.0)
-      faraday-multipart (~> 1.0)
-      faraday-net_http (~> 1.0)
-      faraday-net_http_persistent (~> 1.0)
-      faraday-patron (~> 1.0)
-      faraday-rack (~> 1.0)
-      faraday-retry (~> 1.0)
+    faraday (2.8.1)
+      base64
+      faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
-    faraday-em_http (1.0.0)
-    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-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)
-    ffi (1.16.3)
+    faraday-net_http (3.0.2)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.6)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
@@ -108,13 +90,12 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0702)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
-    multipart-post (2.4.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.10)
+    net-imap (0.4.14)
       date
       net-protocol
     net-pop (0.1.2)
@@ -124,7 +105,7 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.3)
+    oj (3.16.4)
       bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
@@ -133,25 +114,26 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.5)
-    rack (3.0.10)
+    public_suffix (5.1.1)
+    rack (3.1.6)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
     redis (5.2.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.1)
+    redis-client (0.22.2)
       connection_pool
-    request_store (1.6.0)
+    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 (3.2.6)
+    rexml (3.3.1)
+      strscan
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -167,6 +149,7 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
+    strscan (3.1.0)
     systemu (2.6.5)
     thread_safe (0.3.6)
     timeout (0.4.1)
@@ -175,20 +158,16 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  ruby
+  aarch64-linux
   x86_64-linux
 
 DEPENDENCIES
   cube-ruby
-  faraday (~> 1.9)
-  ffi
   goo!
   minitest (~> 4.0)
-  oj (~> 3.0)
   ontologies_linked_data!
   pry
   rake (~> 10.0)
-  redis
   ruby-xxHash
   simplecov
   simplecov-cobertura

dip.yml

@@ -0,0 +1,44 @@
+version: '7.1'
+
+# Define default environment variables to pass
+# to Docker Compose
+#environment:
+#  RAILS_ENV: development
+
+interaction:
+  # This command spins up a container with the required dependencies (solr, 4store, etc),
+  # and opens a terminal within it.
+  runner:
+    description: Open a Bash shell within a ncbo_annotator container (with dependencies up)
+    service: ruby
+    command: /bin/bash
+
+  # Run a container without any dependent services
+  bash:
+    description: Run an arbitrary script within a container (or open a shell without deps)
+    service: ruby
+    command: /bin/bash
+    compose_run_options: [ no-deps ]
+
+  # A shortcut to run Bundler commands
+  bundle:
+    description: Run Bundler commands
+    service: ruby
+    command: bundle
+    compose_run_options: [ no-deps ]
+
+  # A shortcut to run unit tests
+  test:
+    description: Run minitest unit tests
+    service: ruby
+    command: bundle exec rake test TESTOPTS='-v'
+
+  test-agraph:
+    description: Run minitest unit tests
+    service: ruby-agraph
+    command: bundle exec rake test TESTOPTS='-v'
+
+  'redis-cli':
+    description: Run Redis console
+    service: redis-ut
+    command: redis-cli -h redis-ut

docker-compose.yml

@@ -1,5 +1,3 @@
-version: '3.8'
-
 x-app: &app
     build:
       context: .
@@ -15,6 +13,7 @@ x-app: &app
       SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr/prop_search_core1
     volumes:
       - .:/srv/ontoportal/ncbo_annotator
+      - bundle:/bundle
     stdin_open: true
     tty: true
     command: "bundle exec rake test TESTOPTS='-v'"
@@ -48,9 +47,9 @@ services:
       GOO_BACKEND_NAME: ag
       GOO_PORT: 10035
       GOO_HOST: agraph-ut
-      GOO_PATH_QUERY: /repositories/bioportal_test
-      GOO_PATH_DATA: /repositories/bioportal_test/statements
-      GOO_PATH_UPDATE: /repositories/bioportal_test/statements
+      GOO_PATH_QUERY: /repositories/ontoportal_test
+      GOO_PATH_DATA: /repositories/ontoportal_test/statements
+      GOO_PATH_UPDATE: /repositories/ontoportal_test/statements
     depends_on:
       <<: *depends_on
       agraph-ut:
@@ -59,7 +58,7 @@ services:
       - agraph
 
   solr-ut:
-    image: ontoportal/solr-ut:0.0.2
+    image: ontoportal/solr-ut:0.2.0
     healthcheck:
       test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"]
       start_period: 3s
@@ -79,7 +78,7 @@ services:
     image: ontoportal/mgrep:0.0.2
     platform: linux/amd64
     healthcheck:
-      test: ["CMD", "nc", "-z", "-v", "localhost", "55556"]
+      test: ["CMD", "nc", "-z", "-v", "127.0.0.1", "55556"]
       start_period: 3s
       interval: 10s
       timeout: 5s
@@ -96,20 +95,20 @@ services:
       - 4store
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.0
+    image: franzinc/agraph:v8.2.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test
       - AGRAPH_SUPER_PASSWORD=xyzzy
     shm_size: 1g
     command: >
        bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start
-       ; agtool repos create bioportal_test
+       ; agtool repos create --supersede ontoportal_test
        ; agtool users add anonymous
-       ; agtool users grant anonymous root:bioportal_test:rw
+       ; agtool users grant anonymous root:ontoportal_test:rw
        ; tail -f /agraph/data/agraph.log"
     healthcheck:
-      test: ["CMD-SHELL", "agtool storage-report bioportal_test || exit 1"]
+      test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"]
       start_period: 30s
       interval: 10s
       timeout: 5s

lib/ncbo_annotator.rb

@@ -142,10 +142,10 @@ def generate_dictionary_file()
           end
 
           outFile.close
-          redis_mgrep_dict_refresh_timestamp()
+          redis_mgrep_dict_refresh_timestamp
         end
 
-        @logger.info("Completed generating a dictionary file in #{(time/60).round(1)} minutes.")
+        @logger.info("Completed generating a dictionary file in #{time.round(2)} seconds.")
       end
 
       def create_term_cache_from_ontologies(ontologies, delete_cache=false, redis_prefix=nil)

test/test_case.rb

@@ -48,8 +48,8 @@ def self.ontologies
   def before_suites
     # code to run before the very first test
     LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
-    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies
-    @@sty = LinkedData::SampleData::Ontology.load_semantic_types_ontology
+    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true)
+    @@sty = LinkedData::SampleData::Ontology.load_semantic_types_ontology(process_submission: true)
     annotator = Annotator::Models::NcboAnnotator.new
     annotator.init_redis_for_tests
     annotator.create_term_cache_from_ontologies(@@ontologies, true)