Merge branch 'development' into stage

.env.sample

@@ -0,0 +1 @@
+API_URL=http://localhost:9393

.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

@@ -12,6 +12,8 @@ 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

.gitignore

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

Gemfile.lock

@@ -53,7 +53,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 7d16b7b1ecc4da8bfd93db2a106737b06d84d6ff
+  revision: 4c7dfa80a8bb4a7d8cfb7ad1fc8a1a88e420e59e
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -109,7 +109,7 @@ GEM
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.24.1)
     base64 (0.2.0)
-    bcrypt (3.1.19)
+    bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
@@ -134,8 +134,7 @@ GEM
     date (3.3.4)
     declarative (0.0.20)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     ed25519 (1.3.0)
     faraday (1.10.3)
       faraday-em_http (~> 1.0)
@@ -217,7 +216,7 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.4)
+    net-imap (0.4.6)
       date
       net-protocol
     net-pop (0.1.2)
@@ -242,7 +241,7 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -321,7 +320,7 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.21.5)
+    sshkit (1.21.6)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
@@ -332,9 +331,6 @@ GEM
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)

README.md

@@ -2,7 +2,53 @@
 
 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.
+
+
+```
+### Configuration
+```
+cp .env.sample .env 
+```
+
+### 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 +65,7 @@ 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 +92,22 @@ 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 +119,7 @@ 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 +133,7 @@ Execute the suite of tests from the command line:
 $ bundle exec rake test 
 ```
 
-### Run the application
+#### Run the application
 
 ```
 $ bundle exec rackup --port 9393