TNRS

TNRSweb is a web interface for the Taxonomic Name Resolution Service (TNRS), an application for the correction and standardization of scientific names. The main TNRS application repository is at https://github.com/ojalaquellueva/TNRSbatch. Other TNRS interfaces include the TNRS API (https://github.com/ojalaquellueva/TNRSapi) and the RTNRS R package (https://github.com/EnquistLab/RTNRS).

How to contribute

This project is written in JavaScript and uses Node.js intepreter. The first step to contribute is to install node in your machine.

You can find help to install node here.

If you are on MacOSX, cosider downloading and installing npm from https://nodejs.org/en/ (mac homebrew package manager doesn't have npm).

Make sure you have npm installed before you continue:

❯ npm --version
6.14.8

After you install npm you can proceed and clone this repository.

You also need node:

❯ node --version
v15.14.0

The next steps are to run npm install inside this folder. This command will install all the packages listed in packages.json that are required by this project.

The command npm run dev will start an http server on http://localhost:3000 that should be accessible through your web browser.

After running npm run dev, wait a while until you see all of the following:

ready - started server on http://localhost:3000
event - compiled successfully
event - build page: /
wait  - compiling...
event - compiled successfully

Development Server

We are currently deploying the project at https://tnrs.xyz

How to deploy to Apache

1. Download the deploy.sh script from the repository:

wget https://raw.githubusercontent.com/EnquistLab/TNRSweb/main/deploy.sh

2. For safety purposes, it is recommended to create a backup of the current version that has been deployed in the Apache folder.

3. Run the script with sudo:

sudo sh deploy.sh <apache folder>

Project structure

1. We kept the API calls and logic inside the actions folder.
2. JSX components were kept inside components.
3. To add new routes, add a js file inside pages.

Adding code to the actions folder

If you're adding another API call, you can add it to the api-requests folder. Then add the corresponding export to index.js If the code does not contain a call, add it to the root and also add the export to index.js.

Adding code to components

If you need to add new components, add them to the components folder. We prefer to have a folder per container. For example, if you want to add a custom button, consider adding a folder called custom-button to components, and inside custom-button a file called custom-button.jsx. Then add the export inside the index.js file in the root of components.

The export would look like:

export * from "./custom-button/custom-button";

Adding new routes (pages)

If you add another file to pages it will be accessible trough the HTTP. For example, adding new-file.js to pages will make a new route http://project-addres/new-file.

There is one component called layout that renders the header and footer, and takes children components that will be rendered between the header and footer.

Development

The next.config.js controls which version of the API is being used. There are three instances of the API: development-public, development-private, and production.

To start the development instance, run:

npm run dev

You can edit the port and find more options inside the package.json file under scripts.