MetaboHUB - Forum Library

Metadata

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

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.

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.

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-client-library';
import '@metabohub/forum-client-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 emmited
      this.dataSearchResults.searchQuery = data;
    },
  },
};
</script>
<!-- Style -->
<style lang="scss">
form {
  fieldset {
    padding: 5px;

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

Developments

Prerequisites

Note: this section is for developers who want to get involved into this project.

• Node 16.15.0 (mandatory) - we recommand you to use Node Version Manager
• Vue 3 (mandatory) - install with npm install -g vue@next
• git (recommended) - used during build to extract current commit hash/tag into showcase webapp footer.
• curl (very optional) - only used for CI/CD

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 under MASTER_TOKEN CI/CD variable)

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

# 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 -- //forgemia.inra.fr/api/v4/projects/11325/packages/npm/:_authToken=__YOUR_GITLAB_TOKEN_HERE__
npm config set @metabohub:registry https://forgemia.inra.fr/api/v4/projects/11325/packages/npm/
# to install the library in your current Node.js project:
npm i --save \
  --registry=https://forgemia.inra.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.developement 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.

Versioning

We use GitLab for versioning. For the versions available, see the tags on this repository.

Consult the Changelog file for further informations about versions and changes.

Authors

• Nils Paulhe - Initial work - MetaboHUB, INRAE, PFEM.
• Olivier Filangi - Discovery - MetaboHUB, INRAE, P2M2.

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

License

This project is licensed under the CeCILL-C License - see the LICENSE.txt file for details

Acknowledgments

• MetaboHUB
• INRAE
• FORUM