Merge to master - Release 2.3.6 - add Docker image (#35)

* add request_lang middleware

* pin redis gem version to 4.8.1

* update Gemfile.lock

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* update Gemfile to use ontologies_linked_data new metadata branch

* update TestOntologySubmissionsController to be adapted to the new model

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* in submission_metadata rename display with category

* add to submission_metadata description and example fields

* add the option to do pagination for the submission endpoint

* extract retrieve_latest_submissions method to submission helper

* implement apply_filters to submissions endpoint using SPARQL FILTERs

* add test for submissions endpoint pagination

* [ontoportal-bot] Gemfile.lock update

* fix private only submission filter

* add hasFormalityLevel filter for submissions endpoint

* add  for ontology: reviews, notes, projects on the submissions endpoints

* bring submission metrics for submissions  endpoints

* bring all contact attributes if asked in the submissions endpoints

* refactor submissions endpoint filters by extracting some methods

* add ontology acronym or name filters for submissions endpoints

* add submissions endpoint order_by option

* [ontoportal-bot] Gemfile.lock update

* fix including ontology and contacts in the submissions endpoints

* fix list admin filter_access control (e.g for submissions  endpoints)

* [ontoportal-bot] Gemfile.lock update

* check access of ontologies in /ontologies/:acronym/submissions endpoint

* include ontology viewOf attribute in the submission endpoints

* make apply_filters helper generic for any of model attributes

* add Agents controller

* add pagination to agents index endpoint if asked

* make agents routes work for /Agent and /agent

* handle agent indentifiers and affiliations attributes  save and update

* make agent controller work for affiliations attribute

* add agent controller tests

* don't update affiliations if only 'id' sent in params

* bring identifier attributes when we update an agent

* update agent test to work with the new Agent validators

* bring the agent attributes on display all of the submissions endpoints

* handle exception for  class attribute but aren't in populate_from_params

* update Gemfile to use development branch of OLD

* refactor user controller to extract reset password helpers

* remove the send notification on user creation, now handled by user.save

* add access token authentication

* fix test after enforcing the uniqueness of user emails

* fix search test

* add oauth_authentication test

* bring the correct attributes when the oauth_authenticate is used

* Feature: Add support of multilingual search (#40)

* update get_term_search_query to support multilanguages search

* rename var

* fix search lang suffix to use underscore not @

* add multilangual search test

---------

Co-authored-by: Syphax Bouazzouni <[email protected]>

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* update Goo version and add submissions filters test

* Fix: display contact for get submissions  (#45)

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* Fix: Submissions filters with order_by  for the same attribute  (#46)

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* update Goo version and add submissions filters test

* make the ontology submissions endpoint include views

* include all metrics attribues in the submissions endpoints (#53)

* add ontology submissions filter by status (#56)

* add agent usage attribute tests (#55)

* Fix: optimize fetching all agents usages query by batch loading them (#57)

* add agent usage attribute tests

* optimize fetching all agents usages query by batch loading them

* Feature: Add ontologies_api docker image build CI  (#58)

* add docker build CI

* Feature: add ontoportal bash script (#59)

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* Feature: add ontoportal bash script (#59)

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* fix date list properties population helper

* Feature: update ontoportal bash script to handle local gems binding   (#61)

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* update ontoportal script to handle local gems bindq

* update ontoportal script to handle binding to local gem for development

* fixing the test runner after the new changes in the ontoportal script

* add description filter to the submissions endpoint (#62)

---------

Co-authored-by: OntoPortal Bot <[email protected]>
Co-authored-by: HADDAD Zineddine <[email protected]>

.env.sample

@@ -0,0 +1,4 @@
+API_URL=http://localhost:9393
+ONTOLOGIES_LINKED_DATA_PATH=
+GOO_PATH=
+SPARQL_CLIENT_PATH=

.github/workflows/docker-image.yml

@@ -0,0 +1,55 @@
+name: Docker branch Images build
+
+on:
+  push:
+    branches:
+      - development
+      - stage
+      - test
+  release:
+    types: [ published ]
+jobs:
+  push_to_registry:
+    name: Push Docker branch image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: |
+            agroportal/ontologies_api
+            ghcr.io/${{ github.repository }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          build-args: |
+            RUBY_VERSION=2.7.8
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

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

@@ -12,13 +12,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
+    - name: copy-env-config
+      run: cp .env.sample .env
     - name: Build docker-compose
       run: docker-compose --profile 4store build #profile flag is set in order to build all containers in this step
     - 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 --rm ${{ matrix.backend }} wait-for-it solr-ut:8983 -- bundle install 
         docker-compose run $ci_env -e CI --rm ${{ matrix.backend }} wait-for-it solr-ut:8983 -- bundle exec rake test TESTOPTS='-v'
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3

.gitignore

@@ -71,3 +71,5 @@ test/data/ontology_files/catalog-v001.xml
 create_permissions.log
 
 ontologies_api.iml
+
+.env

Dockerfile

@@ -21,6 +21,7 @@ ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install
 
 COPY . /srv/ontoportal/ontologies_api
+RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
 
 EXPOSE 9393
-CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]
+CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]

Gemfile

@@ -1,6 +1,6 @@
 source 'https://rubygems.org'
 
-gem 'activesupport', '~> 3.1'
+gem 'activesupport', '~> 3.2'
 # see https://github.com/ncbo/ontologies_api/issues/69
 gem 'bigdecimal', '1.4.2'
 gem 'faraday', '~> 1.9'
@@ -44,12 +44,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'master'
+gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'development'
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'master'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
@@ -63,6 +63,7 @@ group :development do
   gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo'
 end
 
+
 group :profiling do
   gem 'rack-mini-profiler'
 end

Gemfile.lock

@@ -11,8 +11,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 74ea47defc7f6260b045a6c6997bbe6a59c7bf62
-  branch: master
+  revision: 5979402d5138850fb9bdb34edfa350e9af1b5d22
+  branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 80a331d053ea04397a903452288c2186822c340c
-  branch: master
+  revision: a199eff007f5d7f18205d61194f3823445aa6460
+  branch: development
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -216,7 +216,7 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.7)
+    net-imap (0.4.6)
       date
       net-protocol
     net-pop (0.1.2)
@@ -247,7 +247,7 @@ GEM
       rack (>= 0.4)
     rack-attack (6.6.1)
       rack (>= 1.0, < 3)
-    rack-cache (1.14.0)
+    rack-cache (1.13.0)
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
@@ -270,8 +270,8 @@ GEM
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
-    redis-store (1.9.2)
-      redis (>= 4, < 6)
+    redis-store (1.9.1)
+      redis (>= 4, < 5)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
@@ -346,12 +346,11 @@ GEM
     webrick (1.8.1)
 
 PLATFORMS
-  x86_64-darwin-21
   x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
-  activesupport (~> 3.1)
+  activesupport (~> 3.2)
   bcrypt_pbkdf (>= 1.0, < 2.0)
   bigdecimal (= 1.4.2)
   capistrano (~> 3)

README.md

@@ -2,7 +2,50 @@
 
 ontologies_api provides a RESTful interface for accessing [BioPortal](https://bioportal.bioontology.org/) (an open repository of biomedical ontologies). Supported services include downloads, search, access to terms and concepts, text annotation, and much more.
 
-## Prerequisites
+# Run ontologies_api
+
+## Using OntoPortal api utilities script 
+### See help
+
+```bash 
+bin/ontoportal help
+```
+
+```
+Usage: bin/ontoportal {dev|test|run|help} [--reset-cache] [--api-url API_URL] [--api-key API_KEY]
+  dev            : Start the Ontoportal API development server.
+                  Example: bin/ontoportal dev --api-url http://localhost:9393
+                  Use --reset-cache to remove volumes: bin/ontoportal dev --reset-cache
+  test           : Run tests.
+  run            : Run a command in the Ontoportal API Docker container.
+  help           : Show this help message.
+
+Description:
+  This script provides convenient commands for managing an Ontoportal API
+  application using Docker Compose. It includes options for starting the development server,
+  running tests, and executing commands within the Ontoportal API Docker container.
+
+Goals:
+  - Simplify common tasks related to Ontoportal API development using Docker.
+  - Provide a consistent and easy-to-use interface for common actions.
+
+
+```
+
+
+### Run dev
+```bash 
+bin/ontoportal dev 
+```
+
+### Run test with a local OntoPortal API
+```bash 
+bin/ontoportal test 
+```
+
+
+## Manually 
+### Prerequisites
 
 - [Ruby 2.x](http://www.ruby-lang.org/en/downloads/) (most recent patch level)
 - [rbenv](https://github.com/sstephenson/rbenv) and [ruby-build](https://github.com/sstephenson/ruby-build) (optional)
@@ -19,7 +62,7 @@ ontologies_api provides a RESTful interface for accessing [BioPortal](https://bi
 - [Solr](http://lucene.apache.org/solr/)
     - BioPortal indexes ontology class and property content using Solr (a Lucene-based server)
 
-## Configuring Solr
+### Configuring Solr
 
 To configure Solr for ontologies_api usage, modify the example project included with Solr by doing the following:
 
@@ -46,22 +89,22 @@ To configure Solr for ontologies_api usage, modify the example project included
     # Edit the ontologieS_api/config/environments/{env}.rb file to point to your running instance:
     # http://localhost:8983/solr/NCBO1
 
-## Installing
+### Installing
 
-### Clone the repository
+#### Clone the repository
 
 ```
 $ git clone [email protected]:ncbo/ontologies_api.git
 $ cd ontologies_api
 ```
 
-### Install the dependencies
+#### Install the dependencies
 
 ```
 $ bundle install
 ```
 
-### Create an environment configuration file
+#### Create an environment configuration file
 
 ```
 $ cp config/environments/config.rb.sample config/environments/development.rb
@@ -73,7 +116,7 @@ production.rb<br />
 development.rb<br />
 test.rb
 
-### Run the unit tests (optional)
+#### Run the unit tests (optional)
 
 Requires a configuration file for the test environment:
 
@@ -87,7 +130,7 @@ Execute the suite of tests from the command line:
 $ bundle exec rake test 
 ```
 
-### Run the application
+#### Run the application
 
 ```
 $ bundle exec rackup --port 9393