merge to upstream v5.22.3

.dockerignore

@@ -0,0 +1,11 @@
+# Git
+.git
+.gitignore
+# Logs
+log/*
+# Temp files
+tmp/*
+# Editor temp files
+*.swp
+*.swo
+test/solr

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

@@ -10,11 +10,14 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up solr configsets
-      run: test/solr/generate_ncbo_configsets.sh
+      working-directory: ./test
+      run: solr/generate_ncbo_configsets.sh
     - name: create config.rb file
       run: cp config/config.rb.sample config/config.rb
     - name: Build docker-compose
+      working-directory: ./test
       run: docker-compose build
     - name: Run unit tests
-      run: docker-compose up --exit-code-from unit-test
+      working-directory: ./test
+      run: docker-compose run ld-unit-test wait-for-it ld-solr-ut:8983 -- bundle exec rake test TESTOPTS='-v'
 

Dockerfile

@@ -1,12 +1,12 @@
 FROM ruby:2.6
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends vim openjdk-11-jre-headless raptor2-utils
+RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends openjdk-11-jre-headless raptor2-utils wait-for-it
 # The Gemfile Caching Trick
 RUN mkdir -p /srv/ontoportal/ontologies_linked_data
-COPY Gemfile* /srv/ontoportal/ontologies_linked_data/
+COPY Gemfile* *.gemspec /srv/ontoportal/ontologies_linked_data/
 WORKDIR /srv/ontoportal/ontologies_linked_data
 RUN gem install bundler -v "$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1)"
-RUN bundle install --binstubs
+RUN bundle install
 
 COPY . /srv/ontoportal/ontologies_linked_data
 

Gemfile.lock

@@ -0,0 +1,237 @@
+GIT
+  remote: https://github.com/ncbo/resource_index.git
+  revision: 24a7f14a6da4f4a0eaba1016ca5a378dfccd7441
+  specs:
+    ncbo_resource_index (0.0.1)
+      elasticsearch (= 2.0.0)
+      mysql2 (= 0.5.2)
+      pony
+      ref
+      ruby-xxHash
+      sequel
+      typhoeus
+
+GIT
+  remote: https://github.com/ncbo/sparql-client.git
+  revision: fb4a89b420f8eb6dda5190a126b6c62e32c4c0c9
+  branch: master
+  specs:
+    sparql-client (1.0.1)
+      json_pure (>= 1.4)
+      net-http-persistent (= 2.9.4)
+      rdf (>= 1.0)
+
+GIT
+  remote: https://github.com/ontoportal-lirmm/goo.git
+  revision: dd9681d91873341850df5b49a0e7b8dd87a3d252
+  branch: development
+  specs:
+    goo (0.0.2)
+      addressable (= 2.3.5)
+      pry
+      rdf (= 1.0.8)
+      redis
+      rest-client
+      rsolr
+      sparql-client
+      systemu
+      uuid
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (4.0.13)
+      i18n (~> 0.6, >= 0.6.9)
+      minitest (~> 4.2)
+      multi_json (~> 1.3)
+      thread_safe (~> 0.1)
+      tzinfo (~> 0.3.37)
+    addressable (2.3.5)
+    ansi (1.5.0)
+    ast (2.4.2)
+    bcrypt (3.1.17)
+    builder (3.2.4)
+    coderay (1.1.3)
+    concurrent-ruby (1.1.10)
+    cube-ruby (0.0.3)
+    daemons (1.4.1)
+    docile (1.4.0)
+    domain_name (0.5.20190701)
+      unf (>= 0.0.5, < 1.0.0)
+    elasticsearch (2.0.0)
+      elasticsearch-api (= 2.0.0)
+      elasticsearch-transport (= 2.0.0)
+    elasticsearch-api (2.0.0)
+      multi_json
+    elasticsearch-transport (2.0.0)
+      faraday
+      multi_json
+    email_spec (2.2.0)
+      htmlentities (~> 4.3.3)
+      launchy (~> 2.1)
+      mail (~> 2.7)
+    ethon (0.15.0)
+      ffi (>= 1.15.0)
+    eventmachine (1.2.7)
+    faraday (1.10.0)
+      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 (1.0.3)
+      multipart-post (>= 1.2, < 3)
+    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 (1.15.5)
+    hashie (5.0.0)
+    htmlentities (4.3.4)
+    http-accept (1.7.0)
+    http-cookie (1.0.4)
+      domain_name (~> 0.5)
+    i18n (0.9.5)
+      concurrent-ruby (~> 1.0)
+    json_pure (2.6.1)
+    launchy (2.4.3)
+      addressable (~> 2.3)
+    libxml-ruby (2.9.0)
+    logger (1.5.1)
+    macaddr (1.7.2)
+      systemu (~> 2.6.5)
+    mail (2.7.1)
+      mini_mime (>= 0.1.1)
+    method_source (1.0.0)
+    mime-types (3.4.1)
+      mime-types-data (~> 3.2015)
+    mime-types-data (3.2022.0105)
+    mini_mime (1.1.2)
+    minitest (4.7.5)
+    minitest-reporters (0.14.24)
+      ansi
+      builder
+      minitest (>= 2.12, < 5.0)
+      powerbar
+    multi_json (1.15.0)
+    multipart-post (2.1.1)
+    mysql2 (0.5.2)
+    net-http-persistent (2.9.4)
+    netrc (0.11.0)
+    oj (2.18.5)
+    omni_logger (0.1.4)
+      logger
+    parallel (1.22.1)
+    parser (3.1.2.0)
+      ast (~> 2.4.1)
+    pony (1.13.1)
+      mail (>= 2.0)
+    powerbar (2.0.1)
+      hashie (>= 1.1.0)
+    pry (0.14.1)
+      coderay (~> 1.1)
+      method_source (~> 1.0)
+    rack (1.6.13)
+    rack-test (0.8.3)
+      rack (>= 1.0, < 3)
+    rainbow (3.1.1)
+    rake (10.5.0)
+    rdf (1.0.8)
+      addressable (>= 2.2)
+    redis (4.6.0)
+    ref (2.0.0)
+    regexp_parser (2.4.0)
+    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 (3.2.5)
+    rsolr (1.1.2)
+      builder (>= 2.1.2)
+    rubocop (1.29.0)
+      parallel (~> 1.10)
+      parser (>= 3.1.0.0)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8, < 3.0)
+      rexml (>= 3.2.5, < 4.0)
+      rubocop-ast (>= 1.17.0, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 1.4.0, < 3.0)
+    rubocop-ast (1.17.0)
+      parser (>= 3.1.1.0)
+    ruby-progressbar (1.11.0)
+    ruby-xxHash (0.4.0.2)
+    ruby2_keywords (0.0.5)
+    rubyzip (1.3.0)
+    sequel (5.56.0)
+    simplecov (0.21.2)
+      docile (~> 1.1)
+      simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
+    simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.4)
+    systemu (2.6.5)
+    test-unit-minitest (0.9.1)
+      minitest (~> 4.7)
+    thin (1.8.1)
+      daemons (~> 1.0, >= 1.0.9)
+      eventmachine (~> 1.0, >= 1.0.4)
+      rack (>= 1, < 3)
+    thread_safe (0.3.6)
+    typhoeus (1.4.0)
+      ethon (>= 0.9.0)
+    tzinfo (0.3.60)
+    unf (0.1.4)
+      unf_ext
+    unf_ext (0.0.8.1)
+    unicode-display_width (2.1.0)
+    uuid (2.3.9)
+      macaddr (~> 1.0)
+
+PLATFORMS
+  x86_64-darwin-21
+
+DEPENDENCIES
+  activesupport (~> 4)
+  addressable (= 2.3.5)
+  bcrypt (~> 3.0)
+  cube-ruby
+  email_spec
+  faraday (~> 1.9)
+  ffi
+  goo!
+  libxml-ruby (~> 2.0)
+  minitest
+  minitest-reporters (>= 0.5.0)
+  multi_json (~> 1.0)
+  ncbo_resource_index!
+  oj (~> 2.0)
+  omni_logger
+  pony
+  pry
+  rack (~> 1.0)
+  rack-test (~> 0.6)
+  rake (~> 10.0)
+  rest-client
+  rsolr (~> 1.0)
+  rubocop
+  rubyzip (~> 1.0)
+  simplecov
+  sparql-client!
+  test-unit-minitest
+  thin
+
+BUNDLED WITH
+   2.3.7

bin/owlapi-wrapper.jar

@@ -1 +1 @@
-owlapi-wrapper-1.3.7-SNAPSHOT.jar
+owlapi-wrapper-1.3.8.jar

docker-compose.yml → test/docker-compose.yml

@@ -1,50 +1,42 @@
 version: '3'
 
 services:
-  unit-test:
-    # volumes:
-    #  - .:/srv/ontoportal/ontologies_linked_data
-    build: .
-    #command: "bundle exec rake test TESTOPTS='-v' TEST='./test/parser/test_owl_api_command.rb'"
+  ld-unit-test:
+    build: ../.
     environment:
+      - OVERRIDE_CONNECT_GOO=true
       - GOO_BACKEND_NAME=4store
       - GOO_PORT=9000
-      - GOO_HOST=4store
+      - GOO_HOST=4store-ut
       - GOO_PATH_QUERY=/sparql/
       - GOO_PATH_DATA=/data/
       - GOO_PATH_UPDATE=/update/
-      - OVERRIDE_CONNECT_GOO=true
-      - REDIS_HOST=redis
+      - REDIS_HOST=redis-ut
       - REDIS_PORT=6379
-      - SOLR_HOST=solr
-    command: "bundle exec rake test TESTOPTS='-v'"
+      - SOLR_HOST=ld-solr-ut
+    command: "rake test TESTOPTS='-v'"
     depends_on:
-      - solr
-      - redis
-      - 4store
+      - ld-solr-ut
+      - redis-ut
+      - 4store-ut
 
-  redis:
+  redis-ut:
     image: redis
 
-  4store:
+  4store-ut:
     image: bde2020/4store
-    ports:
-        - "9000:9000"
     command: >
       bash -c "4s-backend-setup --segments 4 ontoportal_kb
       && 4s-backend ontoportal_kb
       && 4s-httpd -D -s-1 -p 9000 ontoportal_kb"
 
-  solr:
-    image: solr:8.8
+  ld-solr-ut:
+    image: solr:8
     volumes:
-      - ./test/solr/configsets:/configsets:ro
-    ports:
-      - "8983:8983"
+      - ./solr/configsets:/configsets:ro
+    #ports:
+    #  - "8983:8983"
     command: >
       bash -c "precreate-core term_search_core1 /configsets/term_search
       && precreate-core prop_search_core1 /configsets/property_search
       && solr-foreground"
-
-#  mgrep:
-#    image: ontoportal/mgrep-ncbo:0.1

test/run-unit-tests.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+# sample script to run unit tests with docker
+
+# add config for unit testing
+[ -f ../config/config.rb ] || cp ../config/config.rb.sample ../config/config.rb
+
+#generate solr configsets for solr container
+solr/generate_ncbo_configsets.sh
+
+# build docker containers
+docker-compose build
+
+#docker-compose up --exit-code-from unit-test
+docker-compose run --rm ld-unit-test wait-for-it ld-solr-ut:8983 -- bundle exec rake test TESTOPTS='-v'
+