Onto Viewer

Onto Viewer is an open-source project that is hosted by EDM Council. The project started in May 2019. Onto Viewer is a Java application that is specifically designed to access both the ontology structure and its content in the easiest possible way. Onto Viewer servers REST API.

Onto website

Onto viewer is used in the ontology view in html-pages.

https://github.com/edmcouncil/html-pages

How to run Onto Viewer

Running locally

To run the Onto Viewer locally:

Download the file named "onto-viewer.zip" from the latest release.
Unzip the file.
In the command prompt of your operating system run the following command in the folder with the last release:

java -jar app-v-LAST_VERSION_NUMBER.war

e.g.,

java -jar app-v-0.1.0.war

Run with docker

Requirements:

git (install)
docker - install:
- Docker Desktop or ...
- Docker Engine with Docker Compose plugin

... with FIBO

How to start: Clone the edmcouncil/onto-viewer repository to the onto-viewer directory, go to the onto-viewer directory (run all subsequent commands inside this directory), then build the images (or pull from the registry if available) and run the containers:

# clone the repository
git clone https://github.com/edmcouncil/onto-viewer onto-viewer

# got to the onto-viewer directory
cd onto-viewer

# build images
docker compose build
# alternatively pull images from registry if available
#docker compose pull --ignore-pull-failures

# run the containers
docker compose up -d

After some time, check the status of running containers:

docker compose ps

if they work correctly, the following message will appear:

NAME                        IMAGE                           COMMAND                  SERVICE             CREATED             STATUS                   PORTS
onto-viewer-fibo-pages-1    edmcouncil/fibo-pages:latest    "docker-entrypoint.s…"   fibo-pages          7 minutes ago       Up 6 minutes (healthy)   
onto-viewer-fibo-strapi-1   edmcouncil/fibo-strapi:latest   "docker-entrypoint.s…"   fibo-strapi         7 minutes ago       Up 6 minutes (healthy)   
onto-viewer-fibo-viewer-1   edmcouncil/onto-viewer:latest   "sh entrypoint.sh"       fibo-viewer         7 minutes ago       Up 6 minutes (healthy)   
onto-viewer-spec-1          edmcouncil/spec:latest          "/docker-entrypoint.…"   spec                7 minutes ago       Up 6 minutes (healthy)   0.0.0.0:8080->80/tcp, :::8080->80/tcp

The services provide endpoints at the following URLs:

http://localhost:8080 :- html-pages home page
http://localhost:8080/fibo :- html-pages general template for FIBO ontology
http://localhost:8080/fibo/ontology :- onto-viewer for FIBO ontology
http://localhost:8080/fibo/strapi/admin :- Strapi admin panel for for FIBO ontology (Email: edmc-strapi@dev.com, Password: devDBonly1)

It is also possible to build (or pull from the registry, if available) Docker images with tag names other than the default develop - use environment variables:

VIEWER_BRANCH for edmcouncil/onto-viewer, e.g. for edmcouncil/onto-viewer:build-dev:
```
echo VIEWER_BRANCH=build-dev >> .env
```
HTML_BRANCH for edmcouncil/html-pages, e.g. for edmcouncil/html-pages:build-dev:
```
echo HTML_BRANCH=build-dev >> .env
```

... with an ontology of your choice

It is possible to run containers with any ontology (instead of FIBO):

place the ontology files of your choice in the onto-viewer-web-app/ontologies subdirectory and the config files in the onto-viewer-web-app/config subdirectory
using the docker-compose.dev.yaml compose file (instead of the default docker-compose.yaml), build the images,then run the containers:
```
echo COMPOSE_FILE=docker-compose.dev.yaml >> .env
docker compose build
docker compose up -d
```
once all services are up and running, onto-viewer with your ontology will be available at http://localhost:8080/dev/ontology

If you want to see the logs use:

# to view continuous log output for <SERVICE>=dev-viewer
docker compose logs --follow dev-viewer

# to view *100* latest log lines for <SERVICE>=dev-viewer
docker compose logs --tail 100 dev-viewer

Stop the services with the command:

docker compose down

Remove all images and volumes with the command:

docker compose down --rmi all -v

Contributing

Please read CONTRIBUTING.md and CODE_OF_CONDUCT.md for details on our code of conduct, and the process for submitting pull requests to us.

Development

To run integration tests, use the following command:

mvn -P integration-tests verify

sasjonge/onto-viewer