Update docker to version 1.0.0-rc+5.2

Add env file

Update docker to version 1.0.0-rc+5.2
Add env file
1661593d · Arnaud Charleroy · 195b46bd · 1661593d · 1661593d · 1661593d
Commit 1661593d authored 2 years ago by Arnaud Charleroy
--- a/.gitignore
+++ b/.gitignore
 logs/nginx/log/access.log
 logs/nginx/log/error.log
 logs/opensilex/opensilex.log
 logs/opensilex/**
\ No newline at end of file
+docker_logs/debug.log
+.gitignore
+config/opensilex.yml
--- a/README.md
+++ b/README.md
@@ -3,35 +3,58 @@
 Docker compose environnent to deploy opensilex stack based on a previous work environment variables [opensilex-phis-igepp](https://github.com/p2m2/opensilex-phis-igepp)
 - [Minimalist opensilex docker compose environment](#minimalist-opensilex-docker-compose-environment)
-  - [Installation](#installation)
+  - [Stack software name with associated versions](#stack-software-name-with-associated-versions)
-    - [Clone the Github repository](#clone-the-github-repository)
+  - [Migration steps](#migration-steps)
-    - [Run docker stack compose command](#run-docker-stack-compose-command)
+    - [From previous version before 1.0.0-rc+5.2](#from-previous-version-before-100-rc52)
-    - [Create an administrator user](#create-an-administrator-user)
+  - [Installation steps](#installation-steps)
-    - [Add a reverse proxy (Optional)](#add-a-reverse-proxy-optional)
+    - [1. Clone the Github repository](#1clone-the-github-repository)
+    - [2. Run docker stack compose command](#2-run-docker-stack-compose-command)
+    - [(First install only) Create an administrator user](#first-install-only-create-an-administrator-user)
+    - [(Optional) Add a reverse proxy](#optional-add-a-reverse-proxy)
    - [Add a gui for mongodb (Optional)](#add-a-gui-for-mongodb-optional)
    - [Test application](#test-application)
      - [Without reverse proxy](#without-reverse-proxy)
      - [With reverse proxy](#with-reverse-proxy)
    - [Debug installation](#debug-installation)
    - [Stop docker stack](#stop-docker-stack)
-    - [Stop docker stack and erase all data (Be sure to delete all data )](#stop-docker-stack-and-erase-all-data-be-sure-to-delete-all-data-)
+  - [Customize docker configuration](#customize-docker-configuration)
-    - [Customize docker port](#customize-docker-port)
-    - [Customize config file](#customize-config-file)
-    - [Customize hostname](#customize-hostname)
  - [Manage docker](#manage-docker)
+    - [Stop docker stack and erase all data (Be sure to delete all data)](#stop-docker-stack-and-erase-all-data-be-sure-to-delete-all-data)
  - [Acknowledgments](#acknowledgments)
-## Installation
+## Stack software name with associated versions
-This docker version is related to [1.0.0+rc+5.1 OpenSILEX version](https://github.com/OpenSILEX/opensilex/releases/tag/1.0.0-rc%2B5.1).
+- Mandatory softwares :
-###  Clone the Github repository
+  - RDF4J - 3.7.4
+  - MongoDB - 4.2.2
+  - OpenSILEX - 1.0.0-rc+5.2
+- Other managements softwares :
+  - mongo-express (A web based gui for mongo) - 1.0.0-alpha.4
+  - haproxy (web server used as reverse proxy) - 2.4.6
+## Migration steps
+### From previous version before 1.0.0-rc+5.2
+If you had a previous installation run the following command to remove previous docker stack :
+```bash
+docker compose --env-file opensilex.env down
+```
+## Installation steps
+This docker version is related to [1.0.0+rc+5.2 OpenSILEX version](https://github.com/OpenSILEX/opensilex/releases/tag/1.0.0-rc%2B5.2).
+### 1. Clone the Github repository
 ```bash
-git clone --branch 1.0.0-rc+5.1 https://github.com/OpenSILEX/opensilex-docker-compose
+git clone --branch 1.0.0-rc+5.2 https://github.com/OpenSILEX/opensilex-docker-compose
 ```
-### Run docker stack compose command
+### 2. Run docker stack compose command
 - Go to the following directory
@@ -42,36 +65,42 @@ cd opensilex-docker-compose
 - You must run docker compose up command to start your installation:
 ```bash
-docker-compose run --rm start_opensilex_stack
+docker compose --env-file opensilex.env run --rm start_opensilex_stack
 ```
 - Expected Output:
 ```bash
-Creating network "opensilex-docker-compose_default" with the default driver
+[+] Running 3/0
-Creating volume "opensilex-docker-compose_persist_rdf4j_data" with default driver
+ ⠿ Container rdf4jdb       Running                                                                                                                                              0.0s
-Creating volume "opensilex-docker-compose_persist_mongo_data" with default driver
+ ⠿ Container mongodb       Running                                                                                                                                              0.0s
-Creating volume "opensilex-docker-compose_persist_opensilex" with default driver
+ ⠿ Container opensilexapp  Recreated                                                                                                                                            0.0s
-Creating volume "opensilex-docker-compose_haproxy_conf" with default driver
+[+] Running 1/1
-Creating mongodb ... done
+ ⠿ Container opensilexapp  Started                                                                                                                                              0.4s
-Creating rdf4jdb ... done
-Creating opensilexapp ... done
 Waiting for mongo to listen on 27017...
 Waiting for rdf4j to listen on 8080...
-Waiting for opensilex to listen on 8081...
+Waiting for opensilex to listen on 8081..
 sleeping
-[until it stars]
+sleeping
+sleeping
+[wait until it starts]
 ```
-### Create an administrator user
+After opensilex start you will be able to access to the application on port [localhost:8081](http://localhost:8081).
+### (First install only) Create an administrator user
+Docker volumes are persistent until you remove them. You only need to create once an user.
 ```bash
 docker exec -it opensilexapp ./bin/opensilex.sh user add --admin --email=admin@opensilex.org --lang=fr --firstName=firstName --lastName=lastName --password=admin
 ```
-### Add a reverse proxy (Optional)
+### (Optional) Add a reverse proxy
+This will start the haproxy as reverse proxy for opensilex instance on port that you want to expose.
-This will start the haproxy as reverse proxy for opensilex instance on port 80
+It can be configure in the `./opensilex.env` with the variable `HAPROXY_EXPOSED_PORT` (Default to port 80 equivalent to [localhost](http://localhost).
 ```bash
 docker compose --env-file opensilex.env run --rm start_opensilex_stack_proxy
@@ -79,7 +108,7 @@ docker compose --env-file opensilex.env run --rm start_opensilex_stack_proxy
 ### Add a gui for mongodb (Optional)
-This will start the mongo express server that helps you do explore your mongo data on port 28018. You can also use your own robo3t or Mongo Compass App.
+This will start the mongo express server that helps you do explore your mongo data on port [localhost:28889](http://localhost:28889). You can also use your own robo3t or Mongo Compass App.
 ```bash
 docker compose --env-file opensilex.env run --rm start_opensilex_stack_mongogui
@@ -96,9 +125,9 @@ If you haven't installed [reverse proxy](#add-a-reverse-proxy-optional)
 - Web :
  - Opensilex web application : <http://localhost:8081/opensilex/app>
  - Opensilex API : <http://localhost:8081/opensilex/api-docs>
-  - RDF4J Workbench : <http://localhost:8080/rdf4j-workbench>
+  - RDF4J Workbench : <http://localhost:28887/rdf4j-workbench>
-  - MongoDB port : <http://localhost:27017>
+  - MongoDB port : <http://localhost:28888>
-  - MongoDB express : <http://localhost:28018>
+  - MongoDB express : <http://localhost:28889>
 ####  With reverse proxy
@@ -108,15 +137,15 @@ If you have installed [reverse proxy](#add-a-reverse-proxy-optional)
  - Opensilex web application : <http://localhost/opensilex/app>
  - Opensilex API : <http://localhost/opensilex/api-docs>
  - RDF4J Workbench : <http://localhost/rdf4j-workbench>
-  - MongoDB port : <http://localhost:27017>
+  - MongoDB port : <http://localhost:28888>
-  - MongoDB express : <http://localhost:28018>
+  - MongoDB express : <http://localhost/mongoadmin>
 ### Debug installation
 This command will give you stack trace of the docker build.
 ```bash
-docker compose --env-file opensilex.env up --build --force-recreate > debug.log
+docker compose --env-file opensilex.env build > docker_logs/debug.log
 ```
 ### Stop docker stack
@@ -127,32 +156,47 @@ This command will stop the stack.
 docker compose --env-file opensilex.env down
 ```
-### Stop docker stack and erase all data (Be sure to delete all data )
+## Customize docker configuration
-This command will give you stack trace of the docker build.
+Configure `opensilex.env` file to configure opensilex sparql config, applications ports, applciations volumes
 ```bash
-docker compose --env-file opensilex.env down --volumes
+# CAN BE MODIFIED
-```
+# SPARQL
+BASEURI=http://www.opensilex.org/
+BASEURIALIAS=opensilex
+REPOSITORIES_NAME=opensilex-docker-db
+OPENSILEX_PATH_PREFIX=opensilex
+# PORTS
+HAPROXY_EXPOSED_PORT=80
+OPENSILEX_EXPOSED_PORT=8081
+RDF4J_EXPOSED_PORT=28887
+MONGO_EXPOSED_PORT=28888
+MONGO_EXPRESS_EXPOSED_PORT=28889
+# VOLUMES  # can be a folder on host or a docker volume
+RDF4J_VOLUME="/home/charlero/test_docker"
+MONGO_VOLUME="persist_mongo_data"
+MONGO_VOLUME="persist_opensilex"
-### Customize docker port
+```
-Configure `docker-compose.yml` file to configure opensilex stack ports
 _TODO : Add exemples_
-### Customize config file
+## Manage docker
-Configure config/opensilex.yml file to configure opensilex stack
-_TODO : Add exemples_
-### Customize hostname
+In order to manage your docker stack via an web interface, we suggest you to use [Portainer CE edition](https://docs.portainer.io/start/install/server/docker/linux#deployment)
+## Danger Zone
-Update host parameters if needeed on docker-compose.yml and opensilex.env files.
+### Stop docker stack and erase all data (Be sure to delete all data)
-_TODO_
-## Manage docker
+This command will give you stack trace of the docker build.
-In order to manage your docker stack via an web interface, we suggest you to use [Portainer CE edition](https://docs.portainer.io/start/install?_ga=2.152302650.2059608137.1662022383-1714209046.1662022383)
+```bash
+docker compose --env-file opensilex.env down --volumes
+```
 ## Acknowledgments

--- a/config/opensilex.yml
+++ b/config/opensilex.yml
 ontologies:
-    baseURI: http://www.opensilex.org/
+    baseURI: $BASEURI
-    baseURIAlias: opensilex
+    baseURIAlias: $BASEURIALIAS
    sparql:
        config:
            serverURI: http://rdf4j:8080/rdf4j-server/
-            repository: opensilex
+            repository: $REPOSITORIES_NAME
 # Configuration for module: FileStorageModule (FileStorageConfig)
 file-system:
@@ -23,7 +23,7 @@ file-system:
                        host: mongodb
                        # MongoDB main host port (int)
                        port: 27017
-                        database: opensilex
+                        database: $REPOSITORIES_NAME
                local:
                    # Service implementation class for: local (FileStorageConnection)
                    implementation: org.opensilex.fs.local.LocalFileSystemConnection
@@ -36,7 +36,7 @@ big-data:
        config:
            host: mongodb
            port: 27017
-            database: opensilex
+            database: $REPOSITORIES_NAME
 server:
-    pathPrefix: /opensilex
+    pathPrefix: /$OPENSILEX_PATH_PREFIX
-    publicURI: http://localhost:$HAPROXY_PORT
+    publicURI: "http://localhost:$HAPROXY_EXPOSED_PORT"
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -5,8 +5,6 @@ services:
    container_name: haproxy
    restart: always
    env_file: opensilex.env
-    environment:
-      - HAPROXY_PORT=${HAPROXY_PORT}
    build:
      context: .
      dockerfile: haproxy-build-step.docker
@@ -16,13 +14,13 @@ services:
    volumes:
      - haproxy_conf:/usr/local/etc/haproxy
    ports:
-      - "$HAPROXY_PORT:80"
+      - "$HAPROXY_EXPOSED_PORT:80"
  mongo:
    container_name: mongodb
-    image: mongo:5.0.2
+    image: mongo:4.2.2
    restart: always
    volumes:
-      - persist_mongo_data:/data
+      - $MONGO_VOLUME:/data
    command: >
      bash -c "
      (
@@ -32,50 +30,55 @@ services:
      ) & docker-entrypoint.sh --replSet opensilex
      "
    ports:
-      - 28887:27017
+      - "$MONGO_EXPOSED_PORT:27017"
+  rdf4j:
+    container_name: rdf4jdb
+    image: eclipse/rdf4j-workbench:3.7.4
+    env_file: opensilex.env
+    volumes:
+      - $RDF4J_VOLUME:/var/rdf4j
+    ports:
+      - "$RDF4J_EXPOSED_PORT:8080"
  mongoexpress:
    image: mongo-express
    container_name: mongoexpressgui
    restart: always
    ports:
-      - "28889:8081"
+      - "$MONGO_EXPRESS_EXPOSED_PORT:8081"
    environment:
      ME_CONFIG_MONGODB_SERVER: mongodb
      ME_CONFIG_MONGODB_URL: mongo://mongodb:27017/
    depends_on:
      - mongo
-  rdf4j:
-    container_name: rdf4jdb
-    image: eclipse/rdf4j-workbench:3.7.6
-    env_file: opensilex.env
-    volumes:
-      - persist_rdf4j_data:/var/rdf4j
-    ports:
-      - "28888:8080"
  opensilex:
    container_name: opensilexapp
    build:
      context: .
      args:
-        RELEASE_TAG: 1.0.0-rc+5.2
+        RELEASE_TAG: 1.0.0-rc+5.2 # can be modify to change version
      dockerfile: opensilex-build-step.docker
    env_file: opensilex.env
    depends_on:
      - mongo
      - rdf4j
    volumes:
-      - ./config:/home/opensilex/config
+      - $OPENSILEX_CONFIG_VOLUME:/home/opensilex/config
-      - ./logs/opensilex:/home/opensilex/logs
+      - $OPENSILEX_LOGS_VOLUME:/home/opensilex/logs
-      - persist_opensilex:/home/opensilex/data
+      - $OPENSILEX_DATA_VOLUME:/home/opensilex/data
    command: >
      bash -c "
+        printenv &&
+        envsubst < /home/opensilex/config/opensilex-template.yml | more &&
+        echo 'test' &&
+        envsubst < /home/opensilex/config/opensilex-template.yml > /home/opensilex/config/opensilex.yml &&
        ([ ! -f /home/opensilex/data/first_install ] && touch /home/opensilex/data/first_install && ./bin/opensilex.sh system install --DEBUG) 
-        ./bin/opensilex.sh server start --host=localhost --port=$OPENSILEX_PORT --adminPort=4081
+        ./bin/opensilex.sh server start --host=localhost --port=8081 --adminPort=4081
      "
    ports:
-      - "$OPENSILEX_PORT:8081"
+      - "$OPENSILEX_EXPOSED_PORT:8081"
  start_opensilex_stack:
    image: dadarek/wait-for-dependencies
    depends_on:

--- a/docker_logs/.gitkeep
+++ b/docker_logs/.gitkeep
--- a/haproxy-build-step.docker
+++ b/haproxy-build-step.docker
-FROM haproxy:2.6.4
+FROM haproxy:2.6.6
 USER root
 RUN mkdir /run/haproxy  && chown haproxy:haproxy /run/haproxy && chmod 2775 /run/haproxy 
 USER haproxy

--- a/haproxy.cfg
+++ b/haproxy.cfg
@@ -48,7 +48,8 @@ frontend http-web
 	mode http
    acl is_opensilexserver path_beg /"$OPENSILEX_PATH_PREFIX"
 	acl is_rdf4jserver path_beg /"$RDFSTORE_HOST"
+	acl is_mongoadmin path_beg /"$MONGO_EXPRESS_HOST"
    acl is_css path_end css
    acl is_js path_end js 
@@ -57,9 +58,9 @@ frontend http-web
 	use_backend opensilexserver if is_opensilexserver
 	use_backend rdf4jserver if is_rdf4jserver
+	use_backend mongoadminserver if is_mongoadmin
-backend opensilexserver
+backend opensilexserver 
-	#timeout client 300s
 	timeout server 300s
 	mode http
    acl is_css path_end css
@@ -68,7 +69,9 @@ backend opensilexserver
 	http-request set-header Content-Type application/javascript if is_js
 	server app opensilex:8081/"$OPENSILEX_PATH_PREFIX" check
 backend rdf4jserver  
 	server graph rdf4j:8080 check
+backend mongoadminserver  
+	server mongoadmin mongoexpress:8081 check
--- a/opensilex-build-step.docker
+++ b/opensilex-build-step.docker
 FROM tomcat:jre11-openjdk-slim
-ARG RELEASE_TAG=1.0.0-rc+5.1 
+ARG RELEASE_TAG=1.0.0-rc+5.2 
 ENV RELEASE https://github.com/OpenSILEX/opensilex/releases/download/$RELEASE_TAG/opensilex-release-$RELEASE_TAG.zip
-RUN apt-get -y update && apt-get install -y wget zip 
+RUN apt-get -y update && apt-get install -y wget zip gettext-base
 RUN mkdir -p /home/opensilex
 WORKDIR /home/opensilex/bin
@@ -12,6 +12,5 @@ RUN unzip $( basename ${RELEASE} )
 RUN ls
 COPY ./bin/opensilex.sh /home/opensilex/bin/
 COPY ./bin/logback.xml /home/opensilex/bin/
-COPY ./config/opensilex.yml /home/opensilex/config/
+COPY ./config/opensilex-template.yml /home/opensilex/config/ 
 WORKDIR /home/opensilex
\ No newline at end of file
--- a/opensilex.env
+++ b/opensilex.env
+# MUST NOT BE MODIFIED
 COMPOSE_PROJECT_NAME=opensilex-stack
 RDF4J_JAVA_OPTS="-Xms1g -Xmx4g"
 RDFSTORE_SPARQL=http://rdf4j:8080/rdf4j-workbench/repositories/opensilex/query
@@ -7,10 +9,27 @@ MONGO_HOST=mongo
 OPENSILEX_HOST=opensilex
 OPENSILEX_PATH_PREFIX=opensilex
-MONGO_EXPRESS_HOST=mongoexpress
+MONGO_EXPRESS_HOST=mongoadmin
-OPENSILEX_PORT=8081
+OPENSILEX_CONFIG_VOLUME=./config
-HAPROXY_PORT=80
+# CAN BE MODIFIED
+# SPARQL
+BASEURI=http://www.opensilex.org/
+BASEURIALIAS=opensilex
+REPOSITORIES_NAME=opensilex-docker-db
+# customize path prefix Ex : localhost:8081/opensilex or localhost:8081/phenotyping_si
+OPENSILEX_PATH_PREFIX="opensilex"
+# PORTS
+HAPROXY_EXPOSED_PORT=80
+OPENSILEX_EXPOSED_PORT=8081
+RDF4J_EXPOSED_PORT=28887
+MONGO_EXPOSED_PORT=28888
+MONGO_EXPRESS_EXPOSED_PORT=28889
+# VOLUMES  # can be a folder on host or a docker volume by default
+RDF4J_VOLUME="/home/charlero/test_docker"
+MONGO_VOLUME="persist_mongo_data"
+OPENSILEX_DATA_VOLUME=persist_opensilex
+OPENSILEX_LOGS_VOLUME=./logs/opensilex