This documentation is intended for developers. For more user focused documentation, see here
If you are on an ubuntu system, you can download them like so:
sudo apt update
sudo apt install nodejs npm
- navigate into whatever system from which you plan to serve
- git clone this repository
- CRITICAL: follow step 3 in the 'Contribution workflow' section below
npm install. Note: there is a problem with a create-react-app dependency and npm 7+, which you're likely using. See Step 4 in "Contribute workflow" at the sentence that starts To "fix"...npm run buildYou may move thebuild/directory, which results from this cmd, to anywhere on your system from which you want to serve the files. A common spot on ubuntu would be/var/www/
- fork the repository into your own github account
- clone the fork onto your local
- CRITICAL: add a file called called
/src/config.json. It must be in /src and it must be calledconfig.json. It must include at least the key value pairs included below, with correct values for your use case. Here is an example (repeat: the keys below are required for the site to function):
{
"ORGANISM": "KN99",
"PUBLIC_TABLES_URL": "http://3.21.241.229/metadata_tables/",
"DATABASE_API_ROOT": "http://3.21.241.229/api/v1/",
"SERVER_ROOT": "http://3.21.241.229/",
"MAX_NEW_SAMPLES": 100,
"FIRST_TABLE": "BioSample",
"CREDENTIALS_ERROR_MSG": "You have not signed in. Sign in using your issued credentials, or email [email protected] for new credentials",
"CODEBASE_DOCUMENTATION": "http://18.116.65.9/docs/frontend/0.1.0/"
}
-
npm install. However, NOTE: There is an open issue as of 20210505 with a create-react-app dependency that conflicts with new versions ofnpm. To "fix" it currently, runnpm update --legacy-peer-depsafternpm install. Keep an eye on the issue though -- this should be resolved at some point. See this issue report -
Look through the documentation, and the code. Choose an
@todoto work on. Register the issue on the brentlab github repo (not your fork). Please look through the@todofirst, but if your issue isn't already noted in the@todo, just register a new issue on n the brentlab github repo.
- Important: If you have not configured your local computer for git, then follow these instructions from git. In particular, use the commit.template.
- Create a branch (in your local repo), name it something descriptive related to the issue report, and knock out that
@todo/issue. Use the 'issue' number as the Ticket: number in your commit messages. Commit frequently. However, when your feature is done, squish down your commits so that the log isn't littered, rebase your branch, and merge with your master branch. See this for help or ask [email protected]. Make sure your master branch on github is up to date with your local (including these git log revisions/etc), and issue a pull request to the brentlab github repo.
-
if you run into any issues with
npm installaside from those noted here, you might try with the--forceflag. -
In addition to the dependency issue described in step 4 above, there are also three npm warnings which pop up when you do
npm install. I'm not concerned about those -- they have to do with some security vulnerabilities that don't apply to this project. Resolve them if you wish.
In the project directory, you can run:
Runs the app in the development mode.
Open http://localhost:3000 to view it in the browser.
The page will reload if you make edits.
You will also see any lint errors in the console.
Launches the test runner in the interactive watch mode.
See the section about running tests for more information.
Builds the app for production to the build folder.
It correctly bundles React in production mode and optimizes the build for the best performance.
The build is minified and the filenames include the hashes.
Your app is ready to be deployed!
I have used nginx to serve this site from AWS. Instructions can be found {@tutorial deployment}
The suggestion from react/node is to deploy following the instructions here for more information.
Note: this is a one-way operation. Once you eject, you can’t go back!
If you aren’t satisfied with the build tool and configuration choices, you can eject at any time. This command will remove the single build dependency from your project.
Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except eject will still work, but they will point to the copied scripts so you can tweak them. At this point you’re on your own.
You don’t have to ever use eject. The curated feature set is suitable for small and middle deployments, and you shouldn’t feel obligated to use this feature. However we understand that this tool wouldn’t be useful if you couldn’t customize it when you are ready for it.
Generate the documentation
You can learn more in the Create React App documentation.
To learn React, check out the React documentation.
This section has moved here: https://facebook.github.io/create-react-app/docs/code-splitting
This section has moved here: https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size
This section has moved here: https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app
This section has moved here: https://facebook.github.io/create-react-app/docs/advanced-configuration
This section has moved here: https://facebook.github.io/create-react-app/docs/deployment
This section has moved here: https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify
This project was bootstrapped with Create React App.