Merge pull request #4 from ontoportal-lirmm/feature/create-a-script-t…

…o-ontoportal-docker-api-ui

Feature: create a script to ontoportal docker api UI

.env.sample

@@ -1,26 +1,39 @@
-BUNDLE_PATH="/srv/ontoportal/bundle"
-# default bundle config resolves to /usr/local/bundle/config inside of the container
-# we are setting it to local app directory if we need to use 'bundle config local'
-BUNDLE_APP_CONFIG="/srv/ontoportal/.bundle"
-# API/NCBO configs
-REDIS_GOO_CACHE_HOST="redis"
-REDIS_HTTP_CACHE_HOST="redis"
-REDIS_PERSISTENT_HOST="redis"
-REPOSITORY_FOLDER="/srv/ontoportal/data/repository"
-REPORT_PATH="/srv/ontoportal/data/reports/ontologies_report.json"
-SOLR_TERM_SEARCH_URL="http://solr:8983/solr"
-SOLR_PROP_SEARCH_URL="http://solr:8983/solr"
-MGREP_HOST="mgrep"
-MGREP_PORT="55556"
-GOO_PORT=9000
-GOO_HOST="4store"
+##################### General configuration ####################
+ORGANIZATION_NAME=ontoportal-lirmm
+COMPOSE_API_FILE_PATH=/ontologies_api/master/docker-compose.yml
+COMPOSE_UI_FILE_PATH=/bioportal_web_ui/master/docker-compose.yml
+SERVICE=ontoportal
 
-# AllegroGraph related settings
-AGRAPH_SUPER_USER="test"
-AGRAPH_SUPER_PASSWORD="xyzzy"
+##################### API configuration ####################
+API_URL=http://localhost:9393
+REDIS_GOO_CACHE_HOST=redis-ut
+REDIS_HTTP_CACHE_HOST=redis-ut
+REDIS_PERSISTENT_HOST=redis-ut
 
+##################### UI configuration ####################
+RAILS_ENV=development
+SITE=Ontoportal
+ORG_URL=http://www.lirmm.fr
+UI_URL=http://localhost:3000
+API_KEY=72c72cba-ad45-4785-b94e-483fa55cdddb
+UI_THEME=ontoportal
+FAIRNESS_DISABLED=false
+NCBO_ANNOTATORPLUS_ENABLED=false
+SUPPORT_EMAIL=sifrportal-support@lirmm.fr
+RELEASE_VERSION="OntoPortal Appliance 3.0.1"
+USE_RECAPTCHA=false
+ANNOTATOR_URL=""
+
+##################### CRON configuration #####################
+OP_API_URL=https://data.bioontology.org
+OP_APIKEY=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
+STARTER_ONTOLOGY=STY
 IMAGE_REPOSITORY=bioportal
 IMAGE_TAG=latest
-OP_APIKEY=<YOUR ONTOPORTAL API KEY>
-OP_API_URL="https://data.bioontology.org"
-STARTER_ONTOLOGY="STY"
+
+##################### KAMAL configuration ####################
+IMAGE_NAME=
+SERVER_IP=
+DOCKER_REGISTRY_NAME=
+KAMAL_REGISTRY_PASSWORD=
+SSH_USER=

.github/workflows/tests.yml

@@ -0,0 +1,17 @@
+name: "Run docker scripts tests CI"
+
+on:
+  push:
+  pull_request:
+    types: [opened, reopened]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          submodules: "recursive" # Make sure submodules are fetched recursively
+
+      - name: Run OntoPortal Docker tests
+        run: test/run_tests.sh

.gitignore

@@ -3,4 +3,12 @@ dip.override.yml
 /ontologies_linked_data/
 /.idea/
 
-ontologies_linked_data
+
+.kamal/hooks/
+
+docker-compose_api.yml
+
+docker-compose_ui.yml
+
+*.iml
+/config/deploy.yml

.gitmodules

@@ -0,0 +1,9 @@
+[submodule "test/bats"]
+	path = test/bats
+	url = https://github.com/bats-core/bats-core.git
+[submodule "test/test_helper/bats-support"]
+	path = test/test_helper/bats-support
+	url = https://github.com/bats-core/bats-support.git
+[submodule "test/test_helper/bats-assert"]
+	path = test/test_helper/bats-assert
+	url = https://github.com/bats-core/bats-assert.git

Dockerfile

@@ -0,0 +1,21 @@
+FROM alpine:latest
+
+ENV TERM xterm-256color
+RUN apk --update --no-cache add \
+    bash \
+    curl \
+    docker \
+    docker-compose \
+    git \
+    iproute2 \ 
+    busybox \
+    ncurses \
+    bind-tools
+
+COPY . /app
+RUN chmod +x /app/ontoportal
+RUN chmod +x /app/bin/*
+RUN chmod +x /app/utils/*
+WORKDIR /app
+
+CMD ["/bin/sh", "-c", "/app/ontoportal start --no-provision"]

README.md

@@ -1,16 +1,93 @@
-# OntoPortal docker  environment
-See help 
+# OntoPortal docker
+OntoPortal Docker is a comprehensive collection of scripts designed to facilitate the running, testing, and deployment of ontoPortal using Docker.
+
+With this project, you can quickly spin up a fully functional ontoPortal instance with minimal setup by leveraging docker's containerization technology. This allows you to test its features and deploy the instance using Kamal.
+
+## Features
+- Start ontoportal instance (with or without parsing ontology)
+- Start specific services (API/UI)
+- Build docker image for this project and push it to your repository 
+- Deploy the instance to server
+
+## Project architecture
+- **bin**: directory contains essential scripts for deploying and running various components of the ontoPortal system
+- **config**: contains deploy.yml file which contains settings and parameters required for deployment using kamal deployment tool
+- **test**: testing-related files and scripts using bats testing framework
+- **utils**: utility and additional scripts for various purposes
+- **.env.sample**: sample file contains configuration of the ontoportal instance (will be copied to .env when running)
+- **Dockerfile**: defines configurations to build the docker image for the project
+- **ontoportal**: the main script to run the ontoportal, it includes the entry point and main execution logic for the ontoPortal services
+- **run**: This file is used to set up environment for tests (it will be deleted).
+## Prerequisites
+- [git](https://git-scm.com/downloads)
+- [Docker](https://docs.docker.com/engine/install/)
+- [Docker Compose](https://docs.docker.com/compose/install/)
+- [Kamal deploy tool](https://kamal-deploy.org/docs/installation/) (if you plan to use the deploy feature)
+
+## Installation
 ```
-./run  -h    
+~> git clone https://github.com/ontoportal-lirmm/ontoportal_docker.git
+~> cd ontoportal-docker
 ```
+## Usage
+### General Command Structure
+```
+./ontoportal <command> [arguments]
+```
+### Commands
+- **Start**
+    - start ontoportal instance
+    ```
+    ./ontoportal start [--no-provision]
+    ```
+    - start specific services (API or UI)
+    ```
+    ./ontoportal start [api|ui] [--no-provision]
+    ```
+    - `--no-provision`: Start the appliance without any data (an empty appliance).
 
-to know how to run an ontoportal API docker instance
+- **Deploy**
+    - build and push image to repository (by default docker hub)
+    ```
+    ./ontoportal deploy push
+    ```
+    - Deploy ontoportal instance to server (or just specific services mentioned in the arguments)
+    ```
+    ./ontoportal deploy [api|ui]
+    ```
+- **Stop**: stop the OntoPortal API and UI services.
+    ```
+    ./ontoportal stop [api|ui]
+    ```
+- **Clean**: clean up the server. This removes all data, Docker Compose files, and containers
+    ```
+    ./ontoportal clean [-f]
+    ```
+    - `-f` : for force clean
 
-```                                                                                                 
-Usage: ./run [-k API_KEY] [-u API_URL] [-r IMAGE_REPOSITORY] [-t IMAGE_TAG] [-s STARTER_ONTOLOGY] [--no-provision]
-```
+- **Help**: display the help message.
+    ```
+    ./ontoportal help
+    ```
 
-Example
-```bash
-./run  -k <apikey>-r agroportal -t master  -s STY -u "https://data.bioontology.org"
-```
+### Additional Notes
+- You can provide your own `.env` file to customize parameters. Place the .env file in the project directory.
+- `.env` file contains 5 parts:
+    - **General configuration**: where you can specify:
+    ```yml
+    ORGANIZATION_NAME: github organization from where script will fetch docker compose files
+    COMPOSE_API_FILE_PATH: docker compose file of the UI 
+    COMPOSE_UI_FILE_PATH: docker compose file of the UI 
+    SERVICE: specify the service you want to run (script will handle this)
+    ```
+    - **API Configurations:** contains settings for api service
+    - **UI Configurations:** contains settings for ui service
+    - **Cron Configurations:** contains settings for cron service
+    - **Kamal configurations**: for build and deployment of the ontoportal instance:
+    ```yml
+    IMAGE_NAME: the name of the image to build and push to docker hub
+    SERVER_IP: the ip server where you want to deploy the instance 
+    DOCKER_REGISTRY_NAME: the name of account in docker hub of another repository
+    KAMAL_REGISTRY_PASSWORD: password of token to access the repository
+    SSH_USER: the user that will be used when deploying into the server
+    ```

bin/deploy.sh

@@ -0,0 +1,54 @@
+#!/usr/bin/env bash
+deploy() {
+	local env_path='.env'
+
+	if [ -f "$env_path" ]; then
+		echo "[+] Env file exist"
+	else
+		echo "[+] Env file does not exist"
+		cp .env.sample .env
+	fi
+
+	if [ -z "$1" ]; then
+		SERVICE="ontoportal"
+	else
+		SERVICE="$1"
+	fi
+
+	# Update SERVICE variable in .env file without using sed
+	awk -v SERVICE="$SERVICE" '/^SERVICE=/{sub(/=.*/, "=" SERVICE)} 1' .env >temp && mv temp .env
+
+	echo "[+] Checking for env variables"
+	source .env
+
+	variables=("IMAGE_NAME" "SERVER_IP" "DOCKER_REGISTRY_NAME" "KAMAL_REGISTRY_PASSWORD" "SSH_USER")
+
+	for variable in "${variables[@]}"; do
+		if [ -z "${!variable}" ]; then
+			echo "[-] Error: $variable is not set."
+			exit
+		fi
+	done
+
+	echo "[+] Changing kamal deploy.yml file"
+	echo "" > config/deploy.yml
+	echo "service: ontoportal_docker" > config/deploy.yml
+	echo "image: ${IMAGE_NAME}" >> config/deploy.yml
+	echo -e "servers:\n  - ${SERVER_IP}" >> config/deploy.yml
+	echo "run_directory: /root/app" >> config/deploy.yml
+	echo -e "registry:\n  username:\n    - ${DOCKER_REGISTRY_NAME}\n  password:\n    - ${KAMAL_REGISTRY_PASSWORD}" >>config/deploy.yml
+	echo -e "ssh:\n  user: ${SSH_USER}" >> config/deploy.yml
+	echo -e "volumes:\n  - /var/run/docker.sock:/var/run/docker.sock" >> config/deploy.yml
+	echo -e "traefik:\n  host_port: 4000" >> config/deploy.yml
+	echo -e "healthcheck:\n  cmd: /bin/true" >> config/deploy.yml
+	if [ -z "$1" ]; then
+	    echo "[+] Starting the deployment"
+    	kamal setup -vv
+	elif [ "$1" == "push" ]; then
+    	echo "[+] Pushing image to Docker Hub without deploying to server"
+    	kamal build push -vv
+	fi
+
+}
+
+deploy "$1"