Important
To report bugs or suggesting enhancements, you can create a tempalted issue. For more information, CONTRIBUTING GUIDE
- Minimalist opensilex docker compose environment
- Pre-requesite softwares
- Check your installed softwares
- Stack software name with associated versions
- Contributing to the project
- Installation steps
- Run minimal opensilex docker stack compose
- Update opensilex version
- Stop opensilex docker
- Restart opensilex docker
- Stop docker stack
- Migration steps from previous versions
- Manage data
- Advanced opensilex docker stack compose configuration
Tested Operating system :
Not working operating system :
First you need to have these software installed, you can check if they are installed :
Following commands should work from everywhere in your system without errors:
git --version
docker --version
docker compose version
-
Mandatory softwares :
- RDF4J - 5.1.3
- MongoDB - 8.0.11
- OpenSILEX - 1.4.9
-
Other managements softwares :
- mongo-express (A web based gui for mongo) - 1.0.2-20
- haproxy (web server used as reverse proxy) - 3.2
If you want to contibute to the project by declaring a bug or submit a new fonctionnality, see CONTRIBUTING.md file.
This docker version is related to 1.4.9 OpenSILEX version
Clone the repository to in order to get the project.
git clone --branch 1.4.9 https://forgemia.inra.fr/OpenSILEX/opensilex-docker-compose
cd opensilex-docker-composeImportant
For migration steps from previous versions, take a look to the Migration steps from previous version section
- With a bash terminal go to the project directory (where this readme is located).
- You must run docker compose up command to start your installation:
docker compose --env-file opensilex.env build --build-arg UID=$(id -u) --build-arg GID=$(id -g)
docker compose --env-file opensilex.env up start_opensilex_stack -d- Expected Output:
WARN[0000] The "OPENSILEX_START_CMD_DEBUG" variable is not set. Defaulting to a blank string.
WARN[0000] The "OPENSILEX_START_CMD_DEBUG" variable is not set. Defaulting to a blank string.
[+] Running 4/10
⠸ Network opensilex-stack_default Created 2.3s
⠸ Volume "opensilex-stack_persist_rdf4j_logs" Created 2.2s
⠸ Volume "opensilex-stack_persist_opensilex" Created 2.2s
⠸ Volume "opensilex-stack_haproxy_conf" Created 2.2s
⠹ Volume "opensilex-stack_persist_mongo_data" Created 2.2s
⠹ Volume "opensilex-stack_persist_rdf4j_data" Created 2.2s
✔ Container opensilex-docker-mongodb Started 1.0s
✔ Container opensilex-docker-rdf4j Started 1.0s
✔ Container opensilex-docker-opensilexapp Started 1.5s
✔ Container opensilex-stack-start_opensilex_stack-1 Started - Check if opensilex is launched:
docker logs -f opensilex-docker-opensilexapp - Expected Output:
These lines must be written in the docker logs.
INFO: No Spring WebApplicationInitializer types detected on classpath
Feb 26, 2024 10:00:06 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-nio-8081"]Docker volumes are persistent until you remove them. You only need to create once an user.
docker exec -it opensilex-docker-opensilexapp ./bin/opensilex.sh user add --admin [email protected] --lang=fr --firstName=firstName --lastName=lastName --password=adminAfter opensilex start you will be able to access to the application on port localhost:28081/sandbox/app.
By default, different available services can be found at these adresses :
- OpenSILEX web application : http://localhost:28081/sandbox/app
- OpenSILEX API : http://localhost:28081/sandbox/api-docs
- MongoDB port : http://localhost:28888
- RDF4J Workbench : http://localhost:28887/rdf4j-workbench
PS: At the first connection, you will need to change rdf4j server port to 8080 (internal docker port) in order to access to rdf4j repositories.
Expected configuration :
Warning ! Before updating, if you already have a running version, please check the migration guides between releases. You can find the migration instructions in the changelog for each release (https://github.com/OpenSILEX/opensilex/tree/master/opensilex-doc/src/main/resources/release).
You can do it in two steps :
- By modifying opensilex.env file with this following configuration you will be able to change.
# Choose opensilex version.
# VERSIONS
OPENSILEX_RELEASE_TAG=1.2.0
# Ex: OPENSILEX_RELEASE_TAG=1.2.1-rdg or OPENSILEX_RELEASE_TAG=1.2.1- You will be able to restart opensilex container only by running the following command.
# construct opensilex docker container
docker compose --env-file opensilex.env build --build-arg UID=$(id -u) --build-arg GID=$(id -g) opensilex
# restart opensilex service
docker compose --env-file=opensilex.env up --force-recreate --no-Ctrl
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deps opensilex -dThis command will stop the stack.
docker stop opensilex-docker-opensilexappThis command will restart the opensilex service.
docker compose --env-file=opensilex.env up --force-recreate --no-deps opensilex -dThis command will stop the docker stack.
docker compose --env-file opensilex.env downFirst, go to the previous directory and get the actual version of the repository.
# Go inside opensilex-docker-compose directory and get the latest tag
git checkout $(git tag | sort -V | tail -1)See migration Migration versions
File system management are not shown in the the following steps because local files are manage with bind volumes or with gridfs. Other file systems are not managed in this version of opensilex docker.
This script will dumps mongodb and rdf4j data in a directory with this structure.
# Step 1
cd <opensilex-docker-compose-dir>/dump_scripts
# Example directory structure <opensilex-docker-compose-dir>/dump_scripts/dump_example_structure
# ├── mongodb
# │ └── opensilex-docker-db-2022-11-21
# └── rdf4j
# └── opensilex-docker-db-2022-11-21
sh export_data.sh <path_to_data>This script will restore mongodb and rdf4j data in a directory with this structure.
# Step 1
cd <opensilex-docker-compose-dir>/dump_scripts
# Example directory structure <opensilex-docker-compose-dir>/dump_scripts/dump_example_structure
# ├── mongodb
# │ └── opensilex-dump-db-2022-11-21
# └── rdf4j
# └── opensilex-dump-db-2022-11-21
sh import_data.sh <path_to_data>This will start the mongo express server that helps you do explore your mongo data on port localhost:28889/mongoexpress. You can also use your own robo3t or Mongo Compass App.
Before run mongoexpress, please configure admin and password of mongo-express.
ME_CONFIG_BASICAUTH_USERNAME=
ME_CONFIG_BASICAUTH_PASSWORD=
#default
#ME_CONFIG_BASICAUTH_USERNAME=adminexpress
#ME_CONFIG_BASICAUTH_PASSWORD=admindocker compose --env-file opensilex.env up --no-recreate start_opensilex_stack_mongogui -d
This will start the haproxy as reverse proxy for opensilex instance on port that you want to expose.
It can be configure in the ./opensilex.env with the variable HAPROXY_EXPOSED_PORT (Default to port 80 equivalent to http://localhost.
docker compose --env-file opensilex.env up --no-recreate start_opensilex_stack_proxy -d
If you have installed optional reverse proxy
By default, different available services can be found at these adresses. The port might be change depending on your ./opensilex.env configuration file.
- Web :
- OpenSILEX web application : http://localhost:8087/sandbox/app/
- OpenSILEX API : http://localhost:8087/sandbox/api-docs
- RDF4J Workbench : http://localhost:8087/rdf4j-workbench
Mongo express will be automatically installed (Optional) Add a gui for opensilex-docker-mongodb
- MongoDB express : http://localhost:8087/mongoexpress
Configure opensilex.env file to configure opensilex sparql config, applications ports, applications volumes
# CAN BE MODIFIED BY USER
## START COMMAND can had debug option by uncommenting the following statment
# OPENSILEX_START_CMD_DEBUG=--DEBUG
# SPARQL
BASEURI=http://opensilex.test/
BASEURIALIAS=opensilex-sandbox
# customize path prefix Ex : localhost:28081/sandbox or localhost:8081/phenotyping_si
OPENSILEX_PATH_PREFIX=sandbox
VERSION_LABEL=test-version
OPENSILEX_PUBLIC_URL=http://localhost:28081/ # public url for web api
# FILE SYSTEM
# Default value is "gridfs" - Only "gridfs" or "local" are supported
OPENSILEX_FILESYSTEM=gridfs
DATAFILE_OPENSILEX_FILESYSTEM=gridfs
DOCUMENTS_OPENSILEX_FILESYSTEM=gridfs
# If "local" file system is choosed OPENSILEX_LOCAL_FILE_SYSTEM_DIRECTORY is mandatory if you choose gridfs local will be not used
# File system configuration can be customized to opensilex-template.yml
OPENSILEX_LOCAL_FILE_SYSTEM_DIRECTORY=./opensilex_data
#Ex :
#OPENSILEX_LOCAL_FILE_SYSTEM_DIRECTORY=/home/charlero/GIT/GITLAB/opensilex-docker-compose/dump_scripts/demo_dump/publictest
# PORTS
HAPROXY_EXPOSED_PORT=8087
OPENSILEX_EXPOSED_PORT=28081
RDF4J_EXPOSED_PORT=28887
MONGO_EXPOSED_PORT=28888
MONGO_EXPRESS_EXPOSED_PORT=28889
## START COMMAND can had debug option : --DEBUG
OPENSILEX_START_CMD=./bin/opensilex.sh server start --host=localhost --port=8081 --adminPort=4081 --CONFIG_FILE=/home/opensilex/config/opensilex.yml
# VERSIONS
HAPROXY_IMAGE_VERSION=2.6.6
OPENSILEX_RELEASE_TAG=1.2.1
RDF4J_IMAGE_VERSION=3.7.7
MONGO_IMAGE_VERSION=5.0.19
MONGO_EXPRESS_IMAGE_VERSION=1.0.0-alpha.4
# # THEME
OPENSILEX_CONFIG_THEME=opensilex-front#opensilex
OPENSILEX_CONFIG_HOMECOMPONENT=opensilex-HomeView
OPENSILEX_CONFIG_LOGINCOMPONENT=opensilex-DefaultLoginComponent
OPENSILEX_CONFIG_FOOTERCOMPONENT=opensilex-DefaultFooterComponent
OPENSILEX_CONFIG_MENUCOMPONENT=opensilex-DefaultMenuComponent
OPENSILEX_CONFIG_HEADERCOMPONENT=opensilex-DefaultHeaderComponent
# Example of modification for sixtine
#OPENSILEX_CONFIG_THEME=inrae-sixtine-vigne#vigne
#OPENSILEX_CONFIG_HOMECOMPONENT=inrae-sixtine-vigne-SixtineHomeComponent
#OPENSILEX_CONFIG_LOGINCOMPONENT=inrae-sixtine-vigne-SixtineLoginComponent
#OPENSILEX_CONFIG_FOOTERCOMPONENT=inrae-sixtine-vigne-SixtineFooterComponent
#OPENSILEX_CONFIG_MENUCOMPONENT=inrae-sixtine-vigne-SixtineMenuComponent
#OPENSILEX_CONFIG_HEADERCOMPONENT=inrae-sixtine-vigne-SixtineHeaderComponentConfigure config/opensilex-custom-config.yml file to activate custom features.
Example : Activate and calculated metrics each 2 hours.
# ------------------------------------------------------------------------------
# Configuration for module: CoreModule (CoreConfig)
core:
# Metrics options (MetricsConfig)
metrics:
# Activate access metrics (boolean)
enableMetrics: true
# Metrics configs about system (SystemMetricsConfig)
system:
# First metrics for any time depending on is time unit (int)
timeBeforeFirstMetric: 1
# Delay between whole system metrics (combined with corresponding TimeUnit) (int)
delayBetweenMetrics: 2
# Default metrics units : DAYS, HOURS, MINUTES, SECONDS are authorized (String)
metricsTimeUnit: HOURS
# Metrics configs about experiments (ExperimentsMetricsConfig)
experiments:
# First metrics for any time depending on is time unit (int)
timeBeforeFirstMetric: 1
# Delay between whole system metrics (combined with corresponding TimeUnit) (int)
delayBetweenMetrics: 2
# Default metrics units : DAYS, HOURS, MINUTES, SECONDS are authorized (String)
metricsTimeUnit: HOURSOther modules can be activated by modifiyng OPENSILEX_RELEASE_TAG version (Example : RDG module).
By modifying opensilex.env file with this following configuration you will be able to activate rdg module. For more configuration, see RDG module configuration.
# Example of modification for RDG module
# VERSIONS
HAPROXY_IMAGE_VERSION=2.6.6
OPENSILEX_RELEASE_TAG=1.2.1-rdg
RDF4J_IMAGE_VERSION=3.7.7
MONGO_IMAGE_VERSION=5.0.19
MONGO_EXPRESS_IMAGE_VERSION=1.0.0-alpha.4Module (opensilex jar) can be added to "modules" directory (opensilex-docker-compose/modules) in order to be deployed in opensilex stack.
There is a module example directory working with "inrae-sixtine-vigne" module (inrae-sixtine-vigne-1.1.0.jar) that allow you to change ontology and instance front style. It is localised in opensilex-docker-compose/modules_examples/1.0.0-rc+6.5/inrae-sixtine-vigne-1.1.0.jar.
How to do it ?
- To activate your module you must copy a module example that have been compiled for a specified opensilex version in modules directory. (Ex : the module located in 1.0.0-rc+6.5/inrae-sixtine-vigne-1.1.0.jar has been compiled for opensilex version 1.0.0-rc+6.5). It's all.
By modifying opensilex.env file with this following configuration you will be able to change the theme.
OPENSILEX_CONFIG_APPLICATIONNAME=Phis
OPENSILEX_CONFIG_THEME=opensilex-phis#phis
OPENSILEX_CONFIG_HOMECOMPONENT=opensilex-HomeView
OPENSILEX_CONFIG_LOGINCOMPONENT=opensilex-phis-PhisLoginComponent
OPENSILEX_CONFIG_HEADERCOMPONENT=opensilex-phis-PhisHeaderComponent
OPENSILEX_CONFIG_FOOTERCOMPONENT=opensilex-DefaultFooterComponent
OPENSILEX_CONFIG_MENUCOMPONENT=opensilex-DefaultMenuComponentBy modifying opensilex.env file with this following configuration you will be able to change the theme.
# Example of modification for sixtine vigne module
OPENSILEX_CONFIG_THEME=inrae-sixtine-vigne#vigne
OPENSILEX_CONFIG_HOMECOMPONENT=inrae-sixtine-vigne-SixtineHomeComponent
OPENSILEX_CONFIG_LOGINCOMPONENT=inrae-sixtine-vigne-SixtineLoginComponent
OPENSILEX_CONFIG_FOOTERCOMPONENT=inrae-sixtine-vigne-SixtineFooterComponent
OPENSILEX_CONFIG_MENUCOMPONENT=inrae-sixtine-vigne-SixtineMenuComponent
OPENSILEX_CONFIG_HEADERCOMPONENT=inrae-sixtine-vigne-SixtineHeaderComponentIn order to manage your docker stack via an web interface, we suggest you to use Portainer Community edition edition
This command will give you stack trace of the docker build.
docker compose --env-file opensilex.env build --build-arg UID=$(id -u) --build-arg GID=$(id -g) > docker_logs/debug.logCaution
The following commands may produce a loss of data.
This command will stop docker stack and erase all data in your databases.
docker compose --env-file opensilex.env down --volumes
# this command will erase all the dataThis Docker compose environnent to deploy opensilex stack based on a previous work opensilex-phis-igepp.
Olivier Fangi & Co - P2M2 Team