Merge branch 'upstream' into pl/feature-instances

Author: syphax-bouazzouni

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

@@ -0,0 +1,20 @@
+name: Ruby Unit Tests
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up solr configsets
+      run: test/solr/generate_ncbo_configsets.sh
+    - name: create config.rb file
+      run: cp config/config.rb.sample config/config.rb
+    - name: Build docker-compose
+      run: docker-compose build
+    - name: Run unit tests
+      run: docker-compose up --exit-code-from unit-test
+

.gitignore

@@ -30,4 +30,8 @@ test/test_run.log
 create_permissions.log
 
 # jEnv
-.java-version
+.java-version
+
+# solr configsets, these are generated with a script
+test/solr/configsets/term_search
+test/solr/configsets/property_search

Dockerfile

@@ -0,0 +1,17 @@
+FROM ruby:2.6
+
+RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends vim openjdk-11-jre-headless raptor2-utils
+# The Gemfile Caching Trick
+RUN mkdir -p /srv/ontoportal/ontologies_linked_data
+COPY Gemfile* /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
+
+COPY . /srv/ontoportal/ontologies_linked_data
+
+# unit tests have to run with unprivileged user
+# otherwise TestOWLApi#test_command_KO_output test fails
+RUN adduser --disabled-password ontoportal
+RUN chown -R ontoportal  /srv/ontoportal/ontologies_linked_data
+USER ontoportal

Gemfile

@@ -1,12 +1,13 @@
 source 'https://rubygems.org'
 
-gem 'activesupport', '~> 4.0'
+gem 'activesupport', '~> 4'
 gem 'addressable', '= 2.3.5'
 gem 'bcrypt', '~> 3.0'
 gem 'cube-ruby', require: 'cube'
+gem 'faraday', '~> 1.9'
 gem 'ffi'
 gem 'libxml-ruby', '~> 2.0'
-gem 'minitest', '~> 4.0'
+gem 'minitest'
 gem 'multi_json', '~> 1.0'
 gem 'oj', '~> 2.0'
 gem 'omni_logger'

Gemfile.lock

@@ -54,7 +54,7 @@ GEM
     coderay (1.1.3)
     concurrent-ruby (1.1.9)
     cube-ruby (0.0.3)
-    daemons (1.4.0)
+    daemons (1.4.1)
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
@@ -70,50 +70,54 @@ GEM
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
       mail (~> 2.7)
-    ethon (0.14.0)
+    ethon (0.15.0)
       ffi (>= 1.15.0)
     eventmachine (1.2.7)
-    faraday (1.7.0)
+    faraday (1.9.3)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
       faraday-excon (~> 1.1)
-      faraday-httpclient (~> 1.0.1)
+      faraday-httpclient (~> 1.0)
+      faraday-multipart (~> 1.0)
       faraday-net_http (~> 1.0)
-      faraday-net_http_persistent (~> 1.1)
+      faraday-net_http_persistent (~> 1.0)
       faraday-patron (~> 1.0)
       faraday-rack (~> 1.0)
-      multipart-post (>= 1.2, < 3)
+      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)
-    ffi (1.15.3)
-    hashie (4.1.0)
+    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 (2.5.1)
+    json_pure (2.6.1)
     launchy (2.4.3)
       addressable (~> 2.3)
     libxml-ruby (2.9.0)
-    logger (1.4.3)
+    logger (1.5.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.7.1)
       mini_mime (>= 0.1.1)
     method_source (1.0.0)
-    mime-types (3.3.1)
+    mime-types (3.4.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2021.0704)
-    mini_mime (1.1.0)
+    mime-types-data (3.2022.0105)
+    mini_mime (1.1.2)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
       ansi
@@ -128,8 +132,8 @@ GEM
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
-    parallel (1.20.1)
-    parser (3.0.2.0)
+    parallel (1.21.0)
+    parser (3.1.0.0)
       ast (~> 2.4.1)
     pony (1.13.1)
       mail (>= 2.0)
@@ -141,13 +145,13 @@ GEM
     rack (1.6.13)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
-    rainbow (3.0.0)
+    rainbow (3.1.1)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (4.4.0)
+    redis (4.6.0)
     ref (2.0.0)
-    regexp_parser (2.1.1)
+    regexp_parser (2.2.0)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -156,22 +160,22 @@ GEM
     rexml (3.2.5)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.18.4)
+    rubocop (1.25.0)
       parallel (~> 1.10)
-      parser (>= 3.0.0.0)
+      parser (>= 3.1.0.0)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml
-      rubocop-ast (>= 1.8.0, < 2.0)
+      rubocop-ast (>= 1.15.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.9.0)
+    rubocop-ast (1.15.1)
       parser (>= 3.0.1.1)
     ruby-progressbar (1.11.0)
-    ruby-xxHash (0.4.0.1)
+    ruby-xxHash (0.4.0.2)
     ruby2_keywords (0.0.5)
     rubyzip (1.3.0)
-    sequel (5.47.0)
+    sequel (5.53.0)
     simplecov (0.21.2)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
@@ -191,25 +195,25 @@ GEM
     tzinfo (0.3.60)
     unf (0.1.4)
       unf_ext
-    unf_ext (0.0.7.7)
-    unicode-display_width (2.0.0)
+    unf_ext (0.0.8)
+    unicode-display_width (2.1.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
   ruby
-  x86_64-darwin-17
 
 DEPENDENCIES
-  activesupport (~> 4.0)
+  activesupport (~> 4)
   addressable (= 2.3.5)
   bcrypt (~> 3.0)
   cube-ruby
   email_spec
+  faraday (~> 1.9)
   ffi
   goo!
   libxml-ruby (~> 2.0)
-  minitest (~> 4.0)
+  minitest
   minitest-reporters (>= 0.5.0)
   multi_json (~> 1.0)
   ncbo_resource_index!

Rakefile

@@ -1,5 +1,7 @@
 require 'rake/testtask'
 
+task default: %w[test]
+
 Rake::TestTask.new do |t|
   t.libs = []
   t.test_files = FileList['test/**/test*.rb']

bin/owlapi-wrapper-1.3.6.jar bin/owlapi-wrapper-1.3.7.jarbin/owlapi-wrapper-1.3.6.jar renamed to bin/owlapi-wrapper-1.3.7.jar

@@ -0,0 +1,50 @@
+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'"
+    environment:
+      - GOO_BACKEND_NAME=4store
+      - GOO_PORT=9000
+      - GOO_HOST=4store
+      - GOO_PATH_QUERY=/sparql/
+      - GOO_PATH_DATA=/data/
+      - GOO_PATH_UPDATE=/update/
+      - OVERRIDE_CONNECT_GOO=true
+      - REDIS_HOST=redis
+      - REDIS_PORT=6379
+      - SOLR_HOST=solr
+    command: "bundle exec rake test TESTOPTS='-v'"
+    depends_on:
+      - solr
+      - redis
+      - 4store
+
+  redis:
+    image: redis
+
+  4store:
+    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
+    volumes:
+      - ./test/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

docker-compose.yml

@@ -13,7 +13,7 @@ class RDFFileNotGeneratedException < Parser::ParserException
 
     class OWLAPICommand
       def initialize(input_file, output_repo, opts = {})
-        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.3.6.jar"
+        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.3.7.jar"
         @input_file = input_file
         @output_repo = output_repo
         @master_file = opts[:master_file]

lib/ontologies_linked_data/parser/owlapi.rb

@@ -0,0 +1,11 @@
+#!/bin/bash
+# sample script to run unit tests with docker
+
+#generate solr configsets
+test/solr/generate_ncbo_configsets.sh
+
+# build docker env
+docker-compose build
+# start up all containers and exit with exit code from unit-test container which runs unit tests
+docker-compose up --exit-code-from unit-test
+#docker-compose run --rm ont_ld bundle exec rake test TESTOPTS='-v'