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# Application R-Shiny HowTo
# Exogenous Organic Matter visualisation tool
Ce projet template utilise un **format basic** d'une application R-Shiny.
This repository contains the R and Rshiny scripts needed to run the EOM4SOIL visualisation tool. This user-friendly software allows for the dissemination of EOM references at the national and European levels to public authorities and EOM sector partners. This interactive tool enables users to explore and analyze the diverse physicochemical properties of EOM types contained in the "Physico-chemical Characteristics of External Organic Matters" database (datapaper in progress). The software allows for dynamic filtering and visualization of data, providing users with customized graphical representations of EOM. By offering an intuitive interface, the application supports policymakers, scientists, and other stakeholders in making informed decisions by visualizing complex datasets in a clear and accessible manner.
Dans ce template on dispose de :
To cite this tool, please use the following Zenodo DOI : 10.5281/zenodo.13805742
* [ui.R](ui.R) la partie interface
* [server.R](server.R) la partie serveur
* [global.R](global.R) les définitions globals
* [www/](www/) Répertoire pour les fichiers statics
* [.gitlab-ci.yml](.gitlab-ci.yml) gère l'intégration continue pour l'application
* [.gitlab-ci-sk8.yml](.gitlab-ci-sk8.yml) intégration continue de SK8 pour l'application
* [.dockerignore](.dockerignore) fichiers ou repertoires a ne pas inclure dans l'image docker
This tool is based on the "Physico-chemical Characteristics of External Organic Matters" database, developped in the EOM4SOIL project. To cite this database, please the following Zenodo DOI : 10.5281/zenodo.13969793
## Développement de l'application.
## Architecture
Compléter/modifier/changer les fichiers ui.R, server.R et global.R .
The Shiny app is comprised of ten distinct R scripts, which are organized as follows: two support scripts, four UI scripts, three server scripts, and one global script, which serves to integrate all other components.
### Merci d'ajouter les remerciements et hébergement par SK8
c.f.: [footer.html](footer.html)
```
div(
class="footer",
includeHTML("footer.html")
)
```
Vous pouvez le modifer et/ou inclure les informations qu'il contient d'une manière qui soit plus en résonance avec votre application (merci de garder le logo à minima).
## Pour récupérer l'image docker de mon application
```
## Connection au dépôt image docker si le projet est privée.
docker login -u <uid> -t <token_gitlab> registry.forgemia.inra.fr
## Téléchargement et instantiation du container (l'application) sur sa machine.
docker run -it -p 3838:3838 registry.forgemia.inra.fr/<Chemin du projet>:latest
```
Accès à l'application:
http://localhost:3838
## Fonctionnement du pipeline d'intégration
L'accès au pipeline s'effectue via le menu de gauche (**CI/CD**).
Le dernier pipeline activé (au dernier commit and push) est le premier de la liste.
En cliquant sur le pipeline, on a accès à différentes actions.
La configuration et la construction automatique de l'image (docker) de mon application. Ainsi que des actions manuelles pour : publier et dépublier mon application, annuler la dernière publication, recevoir les logs de mon application.
## Documentations
Pour avoir plus d'information sur les modifications possibles [https://forgemia.inra.fr/sk8/sk8-conf/sk8-template-ci/](https://forgemia.inra.fr/sk8/sk8-conf/sk8-templates-ci/) et la [documentation en ligne](https://docs.sk8.inrae.fr).
## Problèmes / questions
Contact via une issue : [https://forgemia.inra.fr/sk8/sk8-support](https://forgemia.inra.fr/sk8/sk8-support/-/issues/new) de préférence.
Ou par email contact-sk8@groupes.renater.fr
The two support scripts are a configuration file (config.R) and a function file (func.R). The configuration file calls upon the necessary packages and data, while the function file contains the functions that are used throughout the software. By externalising these functionalities, we can facilitate code maintenance and improvements without compromising the overall architectural integrity.
The UI scripts encapsulate the user interface, including drop-down menus, checkboxes, buttons, and other elements. The Shiny app has four user interface scripts, which are coded separately for each of the four tabs.
The server scripts perform the back-end operations of the software. They can generate dynamic drop-down and checkbox menus, filter the database, and produce output based on the user's inputs.
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