https://github.com/edmcouncil/onto-viewer
OntoViewer is an open-source project that is hosted by EDM Council. The project started in May 2019. OntoViewer is a JAVA application that is specifically designed to access both the ontology structure and its content in the easiest possible way. OntoViewer servers both as a web application and REST API.
https://github.com/edmcouncil/onto-viewer
auto-viewer fibo-viewer java java-application onto-viewer ontology-documentation ontology-search
Last synced: 6 months ago
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OntoViewer is an open-source project that is hosted by EDM Council. The project started in May 2019. OntoViewer is a JAVA application that is specifically designed to access both the ontology structure and its content in the easiest possible way. OntoViewer servers both as a web application and REST API.
- Host: GitHub
- URL: https://github.com/edmcouncil/onto-viewer
- Owner: edmcouncil
- License: mit
- Created: 2019-09-04T09:17:53.000Z (almost 7 years ago)
- Default Branch: develop
- Last Pushed: 2024-12-13T09:46:50.000Z (over 1 year ago)
- Last Synced: 2024-12-13T10:41:04.780Z (over 1 year ago)
- Topics: auto-viewer, fibo-viewer, java, java-application, onto-viewer, ontology-documentation, ontology-search
- Language: Java
- Homepage: https://spec.edmcouncil.org/fibo/ontology
- Size: 6.34 MB
- Stars: 29
- Watchers: 9
- Forks: 10
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# onto-viewer
onto-viewer is an open-source Java application that provides a number of REST API endpoints to access the content of OWL ontologies. If run together with [html-pages frontend](https://github.com/edmcouncil/html-pages), it will visualise them as a web application.
# Table of contents
* [How to run onto-viewer](#how-to-run-onto-viewer)
* [How to customise your ontology to be properly displayed by onto-viewer](#how-to-customise-ontologies)
* [How to run it locally](#how-to-run-locally)
* [How to run it using docker](#how-to-run-docker)
* [Contributing](#contributing)
* [Development](#development)
* [License](#license)
# How to run onto-viewer
## How to customise your ontology to be properly displayed by onto-viewer
1. We require each _ontology IRI_ to follow the convention described in [Vocabularies that use a 'slash namespace'](https://www.w3.org/TR/swbp-vocab-pub/#slash), i.e. end with a forward slash character `/` (e.g., `https://www.omg.org/spec/Commons/Classifiers/`).
1. We require that all ontologies are "registered" in the meta file(s), which store the relevant metadata, in particular allow for custom modularisation - see https://github.com/edmcouncil/idmp/blob/master/ISO/MetadataISO.rdf for an example of such file.
1. We recommend that all imported ontologies and locally cached and their local references are listed in catalog-v001.xml file.
## How to run it locally
To run the onto-viewer locally:
* Download the file named "onto-viewer.zip" from the [latest release](https://github.com/edmcouncil/onto-viewer/releases).
* 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
```
## How to run it using docker
Requirements:
- [git](https://git-scm.com/) ([install](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git))
- [docker](https://www.docker.com/) - install:
* [Docker Desktop](https://docs.docker.com/desktop/) or ...
* [Docker Engine](https://docs.docker.com/engine/) with [Docker Compose plugin](https://docs.docker.com/compose/)
### ... with FIBO
How to start:
Clone the [edmcouncil/onto-viewer](https://github.com/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:
```bash
# 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](http://localhost:8080) :- [html-pages home page](https://github.com/edmcouncil/html-pages/blob/develop/home/README.md)
- [http://localhost:8080/fibo](http://localhost:8080/fibo) :- [html-pages general template](https://github.com/edmcouncil/html-pages/tree/develop/general) for [FIBO](https://github.com/edmcouncil/fibo) ontology
- [http://localhost:8080/fibo/ontology](http://localhost:8080/fibo/ontology) :- onto-viewer for [FIBO](https://github.com/edmcouncil/fibo) ontology
- [http://localhost:8080/fibo/strapi/admin](http://localhost:8080/fibo/strapi/admin) :- [Strapi admin panel](https://docs.strapi.io/user-docs/intro#accessing-the-admin-panel) for for [FIBO](https://github.com/edmcouncil/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](https://github.com/edmcouncil/onto-viewer/tree/build-dev):
```bash
echo VIEWER_BRANCH=build-dev >> .env
```
- `HTML_BRANCH` for `edmcouncil/html-pages`, e.g. for [edmcouncil/html-pages:build-dev](https://github.com/edmcouncil/html-pages/tree/build-dev):
```bash
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:
```bash
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:
```bash
# to view continuous log output for =dev-viewer
docker compose logs --follow dev-viewer
# to view *100* latest log lines for =dev-viewer
docker compose logs --tail 100 dev-viewer
```
Stop the services with the command:
```bash
docker compose down
```
Remove all images and volumes with the command:
```bash
docker compose down --rmi all -v
```
# Contributing
Please read [CONTRIBUTING.md](CONTRIBUTING.md) and [CODE_OF_CONDUCT.md](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:
```shell
mvn -P integration-tests verify
```
# License
[](LICENSE)