MetaboHUB - Forum Library

Metadata

• authors: [email protected], [email protected]
• creation date: 2023-01-20
• main usage: Vue.js webcomponent use for Forum Web-Applications.

Description

FORUM is an open knowledge network aiming at supporting metabolomics results interpretation in biomedical sciences and automated reasoning. Containing more than 8 billion statements, it federate data from several life-science resources such as PubMed, ChEBI and PubChem. Leveraging the bridges in this linked dataset, we automatically extract associations between compound and biomedical concepts, using literature metadata enrichment.

Features

• :pencil: build Forvm queries: provides a web-GUI to create your requests
• :rocket: send these queries to the Forvm API: submit your requests to the API and fetch results
• :eyes: show / browse Forvm results: display your results in a nice web-GUI
• :floppy_disk: download Forvm results: download your results in a CSV file

Getting Started

This WebComponent library is compatible with projects using Vue.js 3 and TypeScript. This project is based on Vue.js, Vite and Vuetify frameworks.

Prerequisites

Before you begin, ensure you have met the following requirements:

• Programming Language: NodeJS version 20.19+ and npm version 11.7 or higher
• Frameworks: Vue.js version 3.4+, Vuetify.js version 3.5+

Installing

Note: this section is for developers who want to implement and use this library into their own project(s). To add the library to your Node.js project, please enter the following commands: npm i @metabohub/forum-library

Then you must import the library in your src/main.ts file:

// import the library and its styles
import { MetabohubForumLibrary } from '@metabohub/forum-library';
import '@metabohub/forum-library/dist/src/components/main.css';

const app = createApp(App);
registerPlugins(app); // <= import your plugin like vuetify, ...
app.use(MetabohubForumLibrary); // <= add this line!
app.mount('#app');

Finally you can add our WebComponent in you own Vue components:

<!-- Template -->
<template>
  <div class="find-associations">
    <mth-forum-form-finder @search-query="onSearchQuery" />
    <mth-forum-results-display :search-results="dataSearchResults" />
  </div>
</template>
<!-- Code -->
<script lang="ts">
// from Vue core
import { ref } from "vue";
// forum - core services and mappers
import { //
  ChebiApi, ChemontApi, PubchemApi,//
  EndpointSearchQuery, EndpointSearchResults//
} from "@metabohub/forum-library";
// main
export default {
  name: "Demo",
  components: {},
  setup() {
    return {
      dataSearchResults: ref(new EndpointSearchResults(new ChebiApi(), new ChemontApi(), new PubchemApi()))
    };
  },
  methods: {
    onSearchQuery(data: EndpointSearchQuery): void {
      // Create new query results
      this.dataSearchResults = new EndpointSearchResults(new ChebiApi(), new ChemontApi(), new PubchemApi());
      // Apply the query emitted
      this.dataSearchResults.searchQuery = data;
    },
  },
};
</script>
<!-- Style -->
<style lang="scss">
form {
  fieldset {
    padding: 5px;

    legend {
      padding: 5px;
      margin-left: 20px;
    }
  }
}
</style>

Running the tests

Upcoming.

Deployment

Edit Forum endpoint connection

If you edit src/assets/doc_forum-openapi.json file, you must re-generate the endpoint client code thanks npm run openapi-generator code.

Library build and publish

Build and publish the library

# install node modules listed into 'package.json' / 'package-lock.json' files
npm install
# build the library
npm run build:lib
npm pack
# publish the library
npm publish

Notes:

• the publication registry is set into these files:
  • .npmrc.
  • package.json - key "publishConfig".
• the publication is automatic during CI/CD process; see .gitlab-ci.yml file.
• during the GitLab CI/CD pipeline, the previous package with the same version identifier is removed thanks:
  • curl commands - to get all published packages in targeted GitLab packages registry and remove a specific one
    (it require a GitLab API token with correct authorizations)

You can use non-stable version of the library using the GitLab npm package registry:

# if you already have installed the library, you must remove the previous one:
npm remove @metabohub/forum-library
# config GitLab npm registry
npm config set -- //forge.inrae.fr/api/v4/projects/11325/packages/npm/:_authToken=__YOUR_GITLAB_TOKEN_HERE__
npm config set @metabohub:registry https://forge.inrae.fr/api/v4/projects/11325/packages/npm/
# to install the library in your current Node.js project:
npm i --save \
  --registry=https://forge.inrae.fr/api/v4/projects/11325/packages/npm/ \
  @metabohub/forum-library;

Standalone showcase build

Build the standalone version with these commands

# install node modules listed into 'package.json' / 'package-lock.json' files
npm install
# either build the DEV standalone version
npm run build:dev
# or build the PROD standalone version
npm run build:prod

Please refer to .env, .env.development and .env.production files to see changes between PROD and DEV versions.

Note: you can run the standalone version into "dev mode" thanks npm run dev command.

Contributing

We welcome contributions! Please follow these steps:

Development Guidelines

Please read Development Guidelines for details on our code of conduct, and the process for submitting pull requests to us.

Code Style

• Use Visual Studio Code IDE
• Use ESLint for JavaScript
• Use Prettier for code formatting
• Run npm run lint before committing

Changelog

All notable changes to this project will be documented in CHANGELOG.md. For the versions available, see the tags on this repository.

Authors

• Nils Paulhe - Initial work - MetaboHUB, INRAE, PFEM.
• William Garrier, Paul-Emeric Saunier - Design and implement initial GUI and TS code - UCA.
• Olivier Filangi - Discovery - MetaboHUB, INRAE, P2M2.
• Franck Giacomoni - project management - MetaboHUB, INRAE, PFEM.

See also the list of contributors who participated in this project.

License

MetaboHUB - Forvm Library is distributed under the CeCILL-2.1 (compatible GNU-GPL) license.

Please refer to LICENSE.txt file for further details.

Acknowledgments

• MetaboHUB
• INRAE

Additional Resources

• FORVM WebApp
• API Documentation