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Commit 51500bde authored by Arnaud Charleroy's avatar Arnaud Charleroy
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First docker compose commit

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README.md
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# opensilex-docker-compose
This project aims to create a opensilex instance running on docker-compose stack
## Getting started
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Add your files
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
```
cd existing_repo
git remote add origin https://forgemia.inra.fr/OpenSILEX/opensilex-docker-compose.git
git branch -M main
git push -uf origin main
```
## Integrate with your tools
- [ ] [Set up project integrations](https://forgemia.inra.fr/OpenSILEX/opensilex-docker-compose/-/settings/integrations)
## Collaborate with your team
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
## Test and Deploy
Use the built-in continuous integration in GitLab.
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
Choose a self-explaining name for your project.
## Description
Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
## Badges
On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
## Visuals
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
# Minimalist opensilex docker compose environment
Docker compose environnent to deploy opensilex stack based on a previous work environment variables [opensilex-phis-igepp](https://github.com/p2m2/opensilex-phis-igepp)
- [Installation](#installation)
- [Customize hostname](#customize-hostname)
- [create an administrator user](#create-an-administrator-user)
## Installation
Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
## Usage
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
Clone this repository
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
Configure config/opensilex.yml file to configure opensilex stack
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
By default, differents services can be found at these adresses
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
Opensilex application : http://localhost/app
RDF4J Workbench : http://localhost/rdfbench
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
### Customize hostname
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
Update host parameters if needeed on docker-compose.yml and opensilex.env files
### create an administrator user
## Authors and acknowledgment
Show your appreciation to those who have contributed to the project.
docker exec -it opensilex ./bin/opensilex.sh user add --admin --email=admin@opensilex.org --lang=fr --firstName=firstName --lastName=lastName --password=admin
## License
For open source projects, say how it is licensed.
#### Acknowledgments :
## Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
Olivier Fangi & Co - [P2M2 Team](https://github.com/p2m2)
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<?xml version="1.0" encoding="UTF-8"?>
<configuration debug="false" scan="true">
<!-- configuration variables-->
<property name="log.pattern" value="%d{dd MMM yyyy;HH:mm:ss.SSS} [%thread] %-5level %logger - %msg%n" />
<property name="default.log.level" value="INFO"/>
<property name="opensilex.log.level" value="${opensilex.log.level:-INFO}"/>
<property name="log.path" value="/home/opensilex/logs"/>
<!-- output -->
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="org.opensilex.utils.LogFilter">
<!-- Default application log level (for libraries) -->
<level>${default.log.level}</level>
<!-- Log level for included and excluded patterns -->
<customLevel>${opensilex.log.level}</customLevel>
<!-- List of logger name pattern to include at custom log level -->
<include>org.opensilex</include>
<include>test.opensilex</include>
<include>opensilex.service</include>
<!-- List of classes to include at DEBUG log level -->
<!-- <debug>org.opensilex.server.Server</debug> -->
</filter>
<encoder>
<pattern>${log.pattern}</pattern>
</encoder>
</appender>
<appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
<filter class="org.opensilex.utils.LogFilter">
<!-- Default application log level (for libraries) -->
<level>${default.log.level}</level>
<!-- Log level for included and excluded patterns -->
<customLevel>${opensilex.log.level}</customLevel>
<!-- List of logger name pattern to include at custom log level -->
<include>org.opensilex</include>
<include>test.opensilex</include>
<include>opensilex.service</include>
<!-- List of classes to include at DEBUG log level -->
<!-- <debug>org.opensilex.server.Server</debug> -->
</filter>
<file>${log.path}/opensilex.log</file>
<rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
<maxHistory>30</maxHistory>
<fileNamePattern>${log.path}/opensilex.log-%d{yyyy-MM-dd}.log.zip</fileNamePattern>
</rollingPolicy>
<encoder>
<pattern>${log.pattern}</pattern>
</encoder>
</appender>
<root>
<appender-ref ref="STDOUT" />
<appender-ref ref="FILE" />
</root>
</configuration>
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#!/bin/bash
SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
CONFIG_FILE="/home/opensilex/config/opensilex.yml"
cd $SCRIPT_DIR
java -jar $SCRIPT_DIR/opensilex.jar --BASE_DIRECTORY=$SCRIPT_DIR --CONFIG_FILE=$CONFIG_FILE "$@"
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ontologies:
baseURI: http://www.opensilex.org/
baseURIAlias: os
sparql:
config:
serverURI: http://rdf4j:8080/rdf4j-server/
repository: opensilex
file-system:
fs:
config:
basePath: /home/opensilex/data
big-data:
mongodb:
config:
host: mongodb
port: 27017
database: opensilex
server:
publicURI: http://localhost/
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version: "3.5"
services:
mongo:
container_name: mongodb
image : mongo:5.0.9
restart: always
volumes:
- persist_mongo_data:/data
command: >
bash -c "
(
sleep 3 &&
mongo --eval \"rs.initiate({'_id':'opensilex','members':[{'_id':0,'host':'mongo:27017'}]})\" &&
wait
) & docker-entrypoint.sh --replSet opensilex
"
rdf4j:
container_name: rdf4j
image: eclipse/rdf4j-workbench:3.7.6
env_file: opensilex.env
volumes:
- persist_rdf4j_data:/var/rdf4j
opensilex:
container_name: opensilex
build:
context: .
args:
RELEASE_TAG: 1.0.0-rc+3
dockerfile: opensilex-build-step.docker
env_file: opensilex.env
depends_on:
- mongo
- rdf4j
volumes:
- ./config:/home/opensilex/config
- ./logs/opensilex:/home/opensilex/logs
- persist_opensilex:/home/opensilex/data
command: >
bash -c "
([ ! -f /home/opensilex/data/first_install ] && touch /home/opensilex/data/first_install && ./bin/opensilex.sh system install)
./bin/opensilex.sh server start --host=localhost --port=8081 --adminPort=4081
"
nginx:
container_name: nginx
image: nginx:1.22
env_file: opensilex.env
volumes:
- ./nginx.conf:/tmp/nginx.conf
- ./logs/nginx/log:/var/log/nginx
depends_on:
- opensilex
ports:
- "80:80"
command: /bin/bash -c "envsubst < /tmp/nginx.conf > /etc/nginx/conf.d/default.conf && nginx -g 'daemon off;'"
volumes:
persist_rdf4j_data:
persist_mongo_data:
persist_opensilex:
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resolver 127.0.0.11 valid=300s;
resolver_timeout 10s;
server {
listen ${NGINX_PORT} default_server;
listen [::]:${NGINX_PORT} default_server;
root /var/www/html;
# Add index.php to the list if you are using PHP
index index.html index.htm index.nginx-debian.html;
server_name ${NGINX_HOST};
client_body_in_file_only clean;
client_body_buffer_size 32K;
client_max_body_size 300M;
location / {
proxy_pass http://${OPENSILEX_HOST}:8081/$request_uri;
proxy_set_header X-Forwarded-Host ${NGINX_HOST};
proxy_connect_timeout 600;
proxy_send_timeout 600;
proxy_read_timeout 600;
send_timeout 600;
proxy_set_header X-Real-IP ${NGINX_HOST};
}
# uncomment to access triplestore url
location /rdf4j-server {
proxy_pass http://${RDFSTORE_HOST}:8080/rdf4j-server/;
proxy_set_header Host ${NGINX_HOST};
#rewrite ^/(.*)$ $1 permanent;
}
location /rdf4j-workbench {
proxy_pass http://${RDFSTORE_HOST}:8080/rdf4j-workbench/;
proxy_set_header Host ${NGINX_HOST};
#rewrite ^/(.*)$ $1 permanent;
}
}
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FROM tomcat:jre11-openjdk-slim
ARG RELEASE_TAG=1.0.0-rc+3
ENV RELEASE https://github.com/OpenSILEX/opensilex/releases/download/$RELEASE_TAG/opensilex-release-$RELEASE_TAG.zip
RUN apt-get -y update && apt-get install -y wget zip
RUN mkdir -p /home/opensilex
WORKDIR /home/opensilex/bin
RUN wget -nv ${RELEASE}
RUN unzip $( basename ${RELEASE} )
COPY ./bin/opensilex.sh /home/opensilex/bin/
COPY ./bin/logback.xml /home/opensilex/bin/
COPY ./config/opensilex.yml /home/opensilex/config/
WORKDIR /home/opensilex
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RDF4J_JAVA_OPTS="-Xmx1g"
RDFSTORE_SPARQL=http://rdf4j:8080/rdf4j-workbench/repositories/opensilex/query
RDFSTORE_HOST=rdf4j
MONGO_HOST=mongo
OPENSILEX_HOST=opensilex
NGINX_HOST=localhost
NGINX_PORT=80
COMPOSE_PROJECT_NAME=opensilex-stack
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