From b111a1d5b61d112ad6752f17d3ad94c9c3cf69db Mon Sep 17 00:00:00 2001
From: mdorf <mdorf@stanford.edu>
Date: Tue, 27 Feb 2024 16:09:40 -0800
Subject: [PATCH 01/11] Gemfile.lock update

---
 Gemfile.lock | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 412e9f9b..681ff4e0 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: db2b330fb6c5fd4ea9ee17d5b58ca997f304a340
+  revision: 4ad4db41216ab9a0e328d4c08cd4a27c82e9b917
   branch: develop
   specs:
     goo (0.0.2)
@@ -15,7 +15,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 4b6b7f42882b9ad815ff5e90c354212aca085fda
+  revision: 4cdcf8d96d9e525aecb8110f02656bd45520b133
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -55,10 +55,10 @@ GEM
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.5)
+    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 (3.3.4)
@@ -107,13 +107,13 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1205)
+    mime-types-data (3.2024.0206)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
-    multipart-post (2.3.0)
+    multipart-post (2.4.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.9.1)
+    net-imap (0.3.7)
       date
       net-protocol
     net-pop (0.1.2)
@@ -133,15 +133,15 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.4)
-    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)
+    redis (5.1.0)
       redis-client (>= 0.17.0)
-    redis-client (0.19.1)
+    redis-client (0.20.0)
       connection_pool
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -192,4 +192,4 @@ DEPENDENCIES
   sparql-client!
 
 BUNDLED WITH
-   2.4.22
+   2.3.15

From fe0783c542479ed0a12da5663ef28e1673e80eba Mon Sep 17 00:00:00 2001
From: mdorf <mdorf@stanford.edu>
Date: Sat, 2 Mar 2024 11:54:50 -0800
Subject: [PATCH 02/11] Gemfile.lock update

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 681ff4e0..d09be353 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 4ad4db41216ab9a0e328d4c08cd4a27c82e9b917
+  revision: 4ea0e70a4361fc694700e11f1012129452278c7d
   branch: develop
   specs:
     goo (0.0.2)
@@ -15,7 +15,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 4cdcf8d96d9e525aecb8110f02656bd45520b133
+  revision: 2575a6ecf62f6f1161f103429fc278939630ad87
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)

From 2527ee6d1f8662aa052ab9e4a236ca66ecbd8d0c Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Mon, 4 Mar 2024 20:45:58 -0800
Subject: [PATCH 03/11] update ruby v3.0

---
 Dockerfile         | 11 +++++----
 Gemfile            |  2 +-
 Gemfile.lock       | 42 ++++++++++------------------------
 dip.yml            | 56 +++++++++++++++++++++++++++++++++++++++++++++
 docker-compose.yml | 57 +++++++++++++++++++++++++---------------------
 run-unit-tests.sh  |  6 ++---
 6 files changed, 109 insertions(+), 65 deletions(-)
 create mode 100644 dip.yml

diff --git a/Dockerfile b/Dockerfile
index 5016faa1..8911c31d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,15 +8,16 @@ RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
   raptor2-utils \
   && rm -rf /var/lib/apt/lists/*
 
-# The Gemfile Caching Trick
 RUN mkdir -p /srv/ontoportal/ncbo_annotator
-COPY *.gemspec Gemfile* /srv/ontoportal/ncbo_annotator/
+RUN mkdir -p /srv/ontoportal/bundle
+COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_annotator/
 
 WORKDIR /srv/ontoportal/ncbo_annotator
 
-# set bundler to v2.4.22 which is the last version supported by ruby 2.7
-RUN gem install bundler -v 2.4.22
-ENV BUNDLE_PATH /bundle
+RUN gem update --system
+RUN gem install bundler
+ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install
+
 COPY . /srv/ontoportal/ncbo_annotator
 CMD ["/bin/bash"]
diff --git a/Gemfile b/Gemfile
index 11eea763..09d65eda 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 
 gem 'cube-ruby'
-gem 'faraday', '~> 1.9'
+gem 'faraday'
 gem 'ffi'
 gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'
diff --git a/Gemfile.lock b/Gemfile.lock
index d09be353..442260e5 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -15,7 +15,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 2575a6ecf62f6f1161f103429fc278939630ad87
+  revision: b78284bac1a2d9c7b04245e55f3708de5dfe591e
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -64,29 +64,10 @@ GEM
     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)
-      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)
+    faraday (2.9.0)
+      faraday-net_http (>= 2.0, < 3.2)
+    faraday-net_http (3.1.0)
+      net-http
     ffi (1.16.3)
     http-accept (1.7.0)
     http-cookie (1.0.5)
@@ -111,9 +92,10 @@ GEM
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
-    multipart-post (2.4.0)
+    net-http (0.4.1)
+      uri
     net-http-persistent (2.9.4)
-    net-imap (0.3.7)
+    net-imap (0.4.10)
       date
       net-protocol
     net-pop (0.1.2)
@@ -141,7 +123,7 @@ GEM
       addressable (>= 2.2)
     redis (5.1.0)
       redis-client (>= 0.17.0)
-    redis-client (0.20.0)
+    redis-client (0.21.0)
       connection_pool
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -153,7 +135,6 @@ GEM
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
     ruby-xxHash (0.4.0.2)
-    ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
     simplecov (0.22.0)
       docile (~> 1.1)
@@ -168,6 +149,7 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.1)
     tzinfo (0.3.62)
+    uri (0.13.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
@@ -177,7 +159,7 @@ PLATFORMS
 
 DEPENDENCIES
   cube-ruby
-  faraday (~> 1.9)
+  faraday
   ffi
   goo!
   minitest (~> 4.0)
@@ -192,4 +174,4 @@ DEPENDENCIES
   sparql-client!
 
 BUNDLED WITH
-   2.3.15
+   2.4.22
diff --git a/dip.yml b/dip.yml
new file mode 100644
index 00000000..46b9bc08
--- /dev/null
+++ b/dip.yml
@@ -0,0 +1,56 @@
+version: '7.1'
+
+# Define default environment variables to pass
+# to Docker Compose
+#environment:
+#  RAILS_ENV: development
+
+compose:
+  files:
+    - docker-compose.yml
+      #  project_name: ncbo_annotator
+
+interaction:
+  # This command spins up a ontologies_api container with the required dependencies (solr, 4store, etc),
+  # and opens a terminal within it.
+  runner:
+    description: Open a Bash shell within a ontologies_api container (with dependencies up)
+    service: ruby
+    command: /bin/bash
+
+  # Run a Rails container without any dependent services (useful for non-Rails scripts)
+  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
+
+  test-ag:
+    description: Run minitest unit tests
+    service: ruby-ag
+    command: bundle exec rake test
+
+
+  'redis-cli':
+    description: Run Redis console
+    service: redis-ut
+    command: redis-cli -h redis-ut
+
+#provision:
+  #- dip compose down --volumes
+  #- dip compose up -d solr 4store
+  #- dip bundle install
+  #- dip bash -c bin/setup
diff --git a/docker-compose.yml b/docker-compose.yml
index 3b343882..7f831884 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,30 +1,35 @@
 version: '3.8'
 
 x-app: &app
-    build:
-      context: .
-      args:
-        RUBY_VERSION: '2.7'
-    environment: &env
-      COVERAGE: 'true' # enable simplecov code coverage
-      REDIS_HOST: redis-ut
-      REDIS_PORT: 6379
-      MGREP_HOST: mgrep-ut
-      MGREP_PORT: 55556
-      SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr/term_search_core1
-      SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr/prop_search_core1
-    volumes:
-      - .:/srv/ontoportal/ncbo_annotator
-    stdin_open: true
-    tty: true
-    command: "bundle exec rake test TESTOPTS='-v'"
-    depends_on: &depends_on
-      solr-ut:
-        condition: service_healthy
-      redis-ut:
-        condition: service_healthy
-      mgrep-ut:
-        condition: service_healthy
+  image: ncbo_annotator:0.0.1
+  build:
+    context: .
+    args:
+      RUBY_VERSION: '3.0'
+  environment: &env
+    BUNDLE_PATH: /srv/ontoportal/bundle
+    # default bundle config resolves to /usr/local/bundle/config inside of the container
+    # we are setting it to local app directory if we need to use 'bundle config local'
+    BUNDLE_APP_CONFIG: /srv/ontoportal/ncbo_annotator/.bundle
+    COVERAGE: 'true' # enable simplecov code coverage
+    REDIS_HOST: redis-ut
+    REDIS_PORT: 6379
+    MGREP_HOST: mgrep-ut
+    MGREP_PORT: 55556
+    SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr/term_search_core1
+    SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr/prop_search_core1
+  volumes:
+    - .:/srv/ontoportal/ncbo_annotator
+  stdin_open: true
+  tty: true
+  command: "bundle exec rake test TESTOPTS='-v'"
+  depends_on: &depends_on
+    solr-ut:
+      condition: service_healthy
+    redis-ut:
+      condition: service_healthy
+    mgrep-ut:
+      condition: service_healthy
 
 services:
   ruby:
@@ -59,7 +64,7 @@ services:
       - agraph
 
   solr-ut:
-    image: ontoportal/solr-ut:0.0.2
+    image: ontoportal/solr-ut:0.1.0
     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
@@ -96,7 +101,7 @@ services:
       - 4store
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.0
+    image: franzinc/agraph:v8.1.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test
diff --git a/run-unit-tests.sh b/run-unit-tests.sh
index 476c2b83..e25a7a8b 100755
--- a/run-unit-tests.sh
+++ b/run-unit-tests.sh
@@ -5,6 +5,6 @@
 [ -f config/config.rb ] || cp config/config.test.rb config/config.rb
 docker-compose build
 
-docker-compose run --rm ruby bundle exec rake test TESTOPTS='-v'
-#docker-compose run --rm ruby-agraph bundle exec rake test TESTOPTS='-v'
-docker-compose --profile agraph --profile 4store kill
+docker compose run --rm ruby bundle exec rake test TESTOPTS='-v'
+#docker compose run --rm ruby-agraph bundle exec rake test TESTOPTS='-v'
+docker compose --profile agraph --profile 4store stop

From a427ff3719f88f887e04ac695a002ef24ce3afb8 Mon Sep 17 00:00:00 2001
From: mdorf <mdorf@stanford.edu>
Date: Wed, 24 Apr 2024 12:39:36 -0700
Subject: [PATCH 04/11] Gemfile.lock update

---
 Gemfile.lock | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index d09be353..bbe0b98c 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 4ea0e70a4361fc694700e11f1012129452278c7d
+  revision: c7ee4a6a44cdf69c8186decc5da0c80887af1b11
   branch: develop
   specs:
     goo (0.0.2)
@@ -15,7 +15,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 2575a6ecf62f6f1161f103429fc278939630ad87
+  revision: d885010c4dcb79a71fd161988a8feceb77331b58
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -35,7 +35,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
   branch: develop
   specs:
     sparql-client (1.0.1)
@@ -55,7 +55,7 @@ GEM
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.6)
+    bigdecimal (3.1.7)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
@@ -93,9 +93,9 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.7.1)
-    json_pure (2.7.1)
-    libxml-ruby (5.0.2)
+    json (2.7.2)
+    json_pure (2.7.2)
+    libxml-ruby (5.0.3)
     logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
@@ -104,10 +104,10 @@ GEM
       net-imap
       net-pop
       net-smtp
-    method_source (1.0.0)
+    method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0206)
+    mime-types-data (3.2024.0305)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
@@ -120,7 +120,7 @@ GEM
       net-protocol
     net-protocol (0.2.2)
       timeout
-    net-smtp (0.4.0.1)
+    net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
     oj (3.16.3)
@@ -132,16 +132,16 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.4)
-    rack (3.0.9.1)
+    public_suffix (5.0.5)
+    rack (3.0.10)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.1.0)
-      redis-client (>= 0.17.0)
-    redis-client (0.20.0)
+    redis (5.2.0)
+      redis-client (>= 0.22.0)
+    redis-client (0.22.1)
       connection_pool
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -149,7 +149,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     rexml (3.2.6)
-    rsolr (2.5.0)
+    rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
     ruby-xxHash (0.4.0.2)

From 36125bdaafd36f394263b9495af96d21a81b1217 Mon Sep 17 00:00:00 2001
From: mdorf <mdorf@stanford.edu>
Date: Wed, 24 Apr 2024 14:19:04 -0700
Subject: [PATCH 05/11] Gemfile.lock update after merging pull request #150

---
 Gemfile.lock | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index bbe0b98c..6ec4e9e4 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: c7ee4a6a44cdf69c8186decc5da0c80887af1b11
+  revision: 563a47fa4329ffb8a774731be210f44a054726c0
   branch: develop
   specs:
     goo (0.0.2)
@@ -8,6 +8,7 @@ GIT
       pry
       rdf (= 1.0.8)
       redis
+      request_store
       rest-client
       rsolr
       sparql-client
@@ -15,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: d885010c4dcb79a71fd161988a8feceb77331b58
+  revision: ab7b2f0eb6c4256ff1a01ace55b5a966c040e1ca
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -113,7 +114,7 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.4.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.7)
+    net-imap (0.4.10)
       date
       net-protocol
     net-pop (0.1.2)
@@ -143,6 +144,8 @@ GEM
       redis-client (>= 0.22.0)
     redis-client (0.22.1)
       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)
@@ -192,4 +195,4 @@ DEPENDENCIES
   sparql-client!
 
 BUNDLED WITH
-   2.3.15
+   2.4.22

From f9a1be204e81d72f408927b8f60c0be208611929 Mon Sep 17 00:00:00 2001
From: mdorf <mdorf@stanford.edu>
Date: Wed, 24 Apr 2024 14:32:04 -0700
Subject: [PATCH 06/11] Gemfile.lock update

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 6ec4e9e4..4eb16011 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 563a47fa4329ffb8a774731be210f44a054726c0
+  revision: 5d911f587f22059581ae3e713e5fe9bde9de82e7
   branch: develop
   specs:
     goo (0.0.2)
@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: ab7b2f0eb6c4256ff1a01ace55b5a966c040e1ca
+  revision: cf8100e47090be1bfb79e7ea642eb6a528013efa
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)

From 7531e10ad55ac66e925c099d7fc05a5a3ceae67e Mon Sep 17 00:00:00 2001
From: mdorf <mdorf@stanford.edu>
Date: Tue, 30 Apr 2024 15:54:12 -0700
Subject: [PATCH 07/11] Gemfile.lock update

---
 Gemfile.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 4eb16011..eb64cba5 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 5d911f587f22059581ae3e713e5fe9bde9de82e7
+  revision: 33583fd1c1d72b449cd6bb91815e3422b8448983
   branch: develop
   specs:
     goo (0.0.2)
@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: cf8100e47090be1bfb79e7ea642eb6a528013efa
+  revision: da1642ed8f9f04db2e427e35d88f235a55138d03
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)

From b75f425f83aa10468a30dc4e8982749d4b959f55 Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Wed, 3 Jul 2024 13:30:29 -0700
Subject: [PATCH 08/11] fix failing unit tests

---
 Gemfile               |  4 ---
 Gemfile.lock          | 69 +++++++++++++++----------------------------
 dip.yml               | 44 +++++++++++++++++++++++++++
 docker-compose.yml    | 21 +++++++------
 lib/ncbo_annotator.rb |  4 +--
 test/test_case.rb     |  4 +--
 6 files changed, 82 insertions(+), 64 deletions(-)
 create mode 100644 dip.yml

diff --git a/Gemfile b/Gemfile
index 11eea763..f1d18c01 100644
--- a/Gemfile
+++ b/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
diff --git a/Gemfile.lock b/Gemfile.lock
index eb64cba5..225ea490 100644
--- a/Gemfile.lock
+++ b/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
@@ -133,8 +114,8 @@ 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)
@@ -142,16 +123,17 @@ GEM
       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
diff --git a/dip.yml b/dip.yml
new file mode 100644
index 00000000..8bf3a609
--- /dev/null
+++ b/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
diff --git a/docker-compose.yml b/docker-compose.yml
index 3b343882..1e7e22a4 100644
--- a/docker-compose.yml
+++ b/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
@@ -96,7 +95,7 @@ services:
       - 4store
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.0
+    image: franzinc/agraph:v8.2.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test
@@ -104,12 +103,12 @@ services:
     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
diff --git a/lib/ncbo_annotator.rb b/lib/ncbo_annotator.rb
index 4631b53a..e1e76c3b 100644
--- a/lib/ncbo_annotator.rb
+++ b/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)
diff --git a/test/test_case.rb b/test/test_case.rb
index 52476b5d..aa9817f2 100644
--- a/test/test_case.rb
+++ b/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)

From c766e2ad136d846d28f0b4020a62f86d2fd4e64b Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Mon, 23 Sep 2024 17:07:13 -0700
Subject: [PATCH 09/11] Fix intermittent unit test failures by adding sleep(1)

fix for #21
---
 test/test_annotator.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/test_annotator.rb b/test/test_annotator.rb
index 755c99c1..f63e0235 100644
--- a/test/test_annotator.rb
+++ b/test/test_annotator.rb
@@ -71,6 +71,7 @@ def test_all_classes_in_cache
 
   def test_generate_dictionary_file
     start_timestamp = Time.now
+    sleep(1)
     ontologies = AnnotatorUnit.ontologies.dup
     class_pages = TestAnnotator.all_classes(ontologies)
     assert class_pages.length > 100, "No classes in system ???"

From d776b5c456870c9c7a95bf47181a02f4ec8eb87c Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Mon, 23 Sep 2024 17:13:36 -0700
Subject: [PATCH 10/11] use docker compose instead of docker-compose

---
 .github/workflows/ruby-unit-tests.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
index c4268d19..aefeb2c0 100644
--- a/.github/workflows/ruby-unit-tests.yml
+++ b/.github/workflows/ruby-unit-tests.yml
@@ -12,19 +12,19 @@ jobs:
       matrix:
         backend: ['ruby', 'ruby-agraph'] # api runs tests with 4store backend and api-agraph runs with AllegroGraph backend
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: copy config file
       run: cp config/config.test.rb config/config.rb
-    - name: Build docker-compose
-      run: docker-compose build
+    - name: Build docker compose
+      run: docker compose build
     - name: Run unit tests
       # 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 ${{ matrix.backend }} bundle exec rake test TESTOPTS='-v'
+        docker compose run $ci_env -e CI ${{ matrix.backend }} bundle exec rake test TESTOPTS='-v'
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         flags: unittests
         verbose: true

From d46d667ec1b2343fbcdab587f1a70e763b894133 Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Mon, 7 Oct 2024 18:03:41 -0700
Subject: [PATCH 11/11] reset branch specifier to master

---
 Gemfile      |  6 +++---
 Gemfile.lock | 19 ++++++++++---------
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/Gemfile b/Gemfile
index f45945cb..8e5b5a40 100644
--- a/Gemfile
+++ b/Gemfile
@@ -15,6 +15,6 @@ group :development do
 end
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'develop'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'master'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
diff --git a/Gemfile.lock b/Gemfile.lock
index f706d744..d430872b 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
-  branch: develop
+  revision: f943ac33e87c55c88131c32d826ed5d39c89302c
+  branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: c30887ee907acd39500cae6c12f45edb06fe0802
-  branch: develop
+  revision: 9ab4be437ed84f5a480e7f0d8799824fcea310ae
+  branch: master
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -36,8 +36,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
-  branch: develop
+  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
+  branch: master
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -89,9 +89,10 @@ GEM
       net-pop
       net-smtp
     method_source (1.1.0)
-    mime-types (3.5.2)
+    mime-types (3.6.0)
+      logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0903)
+    mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
@@ -135,7 +136,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.7)
+    rexml (3.3.8)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)