Feature: sync with NCBO latest version and support ruby RDF 3.0 (#28)

* Gemfile.lock update

* Gemfile.lock update; fixed ncbo/sparql-client#3

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* implemented #40 - Add incremental logging when the dictionary is being created

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Remove ffi gem version pin

* Gemfile.lock

* Gemfile.lock

* Gemfile.lock update

* pinned oj to v2.X for all projects due to an error in latest oj 3.13.1

* Gemfile.lock update

* Restore Gemfile.lock

Appears to have been accidentally deleted in the commit prior

* Pin faraday gem to 1.9

* Fix "same gem twice" parsing error

* Fix bundle install duplicate entry warnings

* Update Gemfile.lock

* Gemfile.lock update

* Update Gemfile.lock

* Update Gemfile.lock

* add docker support for unit testing

* remove wait-for-it

* add config file for testing

* Update branch specifier to develop

* remove deprecated ncbo_resource_index

* update ruby v2.6 -> 2.7

ncbo/bioportal-project#241

* ruby v2.7, bundler optimization - v2.3

* Reset branch specifier to develop

* Update Gemfile.lock

* Update Gemfile.lock

* Add Linux platform

* Update Gemfile.lock

* Fix - deprecation warning for pipelining commands on a Redis instance

Addresses #19
Pipelining commands on a Redis instance is deprecated and will be removed in Redis 5.0.0.

redis.pipelined do
  redis.get("key")
end

should be replaced by

redis.pipelined do |pipeline|
  pipeline.get("key")
end

* Remove duplicated line

* Restore branch specifier to master

* Update Gemfile.lock

* Bump tzinfo from 0.3.60 to 0.3.61

Bumps [tzinfo](https://github.com/tzinfo/tzinfo) from 0.3.60 to 0.3.61.
- [Release notes](https://github.com/tzinfo/tzinfo/releases)
- [Changelog](https://github.com/tzinfo/tzinfo/blob/master/CHANGES.md)
- [Commits](tzinfo/tzinfo@v0.3.60...v0.3.61)

---
updated-dependencies:
- dependency-name: tzinfo
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>

* Reset branch specifier to develop

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile had references to develop branch

* Gemfile.lock update

* Allow setting ruby version in the docker-compose file

* Add codecov reporting

* fixed a failing unit test, test_annotate_minsize_term

* Gemfile.lock update

* Set mgrep default port to 55556

* gem version update

* fixed #26 - annotator cache generation failure - Unsupported command argument type: RDF::URI

* Gemfile.lock update

* bundle update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* Gemfile.lock update

* resolved an issue with the Recommender query in AllegroGraph

* an improved fix to ncbo/ncbo_ontology_recommender#21

* Add AllegroGraph backend to unit test matrix

* minitest style change for troubleshooting purposes

* Gemfile.lock update

* Gemfile.lock update

* update test CI

* add lemmatizer_jar config default value

* fix annotator after updating RDF version to 3.0

* update agraph version to 8.1.0

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: mdorf <[email protected]>
Co-authored-by: Alex Skrenchuk <[email protected]>
Co-authored-by: Jennifer Vendetti <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.dockerignore

@@ -0,0 +1,13 @@
+.bundle
+.git
+.gitignore
+.github
+.DS_Store
+vendor/bundle
+# Logs
+log/*
+# Temp files
+tmp/*
+# Editor temp files
+*.swp
+*.swo

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

@@ -0,0 +1,45 @@
+name: Ruby Unit Tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        goo-slice: [ '20', '100', '500' ]
+        ruby-version: [ '2.7' ]
+        triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: create config.rb file
+        run: cp config/config.test.rb config/config.rb
+      - name: Set up solr configsets
+        run: ./test/solr/generate_ncbo_configsets.sh
+      - name: Install Dependencies
+        run: sudo apt-get update && sudo apt-get -y install raptor2-utils
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: ${{ matrix.ruby-version }}
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+      - name: Run unit tests
+        # unit tests are run inside a container
+        # http://docs.codecov.io/docs/testing-with-docker
+        run: |
+          ci_env=`bash <(curl -s https://codecov.io/env)`
+          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          flags: unittests
+          verbose: true
+          fail_ci_if_error: false # optional (default = false)

.gitignore

@@ -43,3 +43,5 @@ bin/mallet-deps.jar
 bin/CogPOTerms
 
 create_permissions.log
+
+test/data/dictionary-lem.txt

Dockerfile

@@ -0,0 +1,22 @@
+ARG RUBY_VERSION
+ARG DISTRO_NAME=bullseye
+
+FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+
+RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
+  openjdk-11-jre-headless \
+  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/
+
+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 bundle install
+COPY . /srv/ontoportal/ncbo_annotator
+CMD ["/bin/bash"]

Gemfile

@@ -1,17 +1,24 @@
 source 'https://rubygems.org'
 
+gem 'cube-ruby'
+gem 'faraday', '~> 1.9'
+gem 'ffi'
+gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'
 gem 'redis'
-gem 'minitest', '~> 4.0'
-gem 'cube-ruby', require: "cube"
 gem 'ruby-xxHash'
-gem 'ffi', '< 1.9.22'
+gem 'request_store'
+gem 'jwt'
+gem 'addressable', '~> 2.8.0'
 
-# Development
-gem 'pry', group: :development
+group :development do
+  gem 'minitest', '~> 4.0'
+  gem 'pry'
+  gem 'simplecov'
+  gem 'simplecov-cobertura' # for codecov.io
+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: 'ncbo/sparql-client', branch: 'master'
+gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
 gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'
-gem 'ncbo_resource_index', github: 'ncbo/resource_index'