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README.md

WormBase Website Repository

This repository contains the WormBase Web application.

The repository for WormBase Mobile can be found at WormBase/website-mobile

Technical Overview

The technical stack of WormBase website consits of:

Italic indicates services whose deployment are managed separately from what is in this repository.

For devOps, we use Docker, docker-compose, Jenkins, AWS Elastic Beanstalk.

Development

Development environment can be setup easily, using a shared development machine and docker-compose.

For Legacy instructions that set up without docker or docker-compose, please visit the Manual Setup Guide.

Prerequisite:

  • Obtain access and login to the shared development instance, where data and legacy software are stored.

  • Ensure environment variable CATALYST_PORT and WEBPACK_SERVER_PORT are set.

  • Ensure /usr/local/bin/ is on your $PATH, as dependencies such as docker-compose and yarn are installed there.

To start your development stack:

make dev and wait for website/Catalyst and webpack(DevServer) to start.

To shutdown your development stack cleanly:

make dev-down

Development Environment Troubleshooting

make dev appears stuck

The first time that make dev runs, it takes longer due to installation of dependencies. Subsequent startup should take a few seconds.

The stdout is jumbled

The stdout of docker-compose combines the stdouts of the containers. To make it easier to read, stdout of individual containers can be accessed via SERVICE=[name_of_service] make console, where the name of service could be website, webpack, etc as found in docker-compose.yml and docker-compose.dev.yml.

docker-compose cli commands not taking effect

The Makefile exports user-specific environment variable COMPOSE_PROJECT_NAME to allow multiple instances of the development stack to run on the same machine. If you use docker-compose cli directly, please set COMPOSE_PROJECT_NAME accordingly to interact with your particular development instance.

Unable to connect to ACeDB

ACeDB container isn't started as part the development stack to reduce memory footprint. Instead, we rely on a shared acedb container, which is expected to run on the docker networked wb-network. If the shared acedb container is down, instructions to start the shared acedb container is found here.

Prettier git pre-commit hook doesn't trigger

JavaScript dependencies (such as prettier and husky) need to be installed on the host for code formatting and other git pre-commit hooks to work.

Compilation failure: You must configure a default store type unless you use exactly one store plugin.

This problem seems to show up occasionally, when I modify the wormbase_local.conf while the server is running. Try make dev-down and then make dev, and repeat a few times until the problem resolves itself.

Staging Environment

WormBase staging site is hosted on the shared development instance. Its deployment is automated, triggered by committing to the staging branch on Github.

Continuous integration for staging environment is handled by Jenkins. Jenkins runs the jenkins-ci-deploy.sh script to for deployment and testing. For detailed setup, please visit the Jenkins web console.

Production Environment

WormBase production site is hosted with AWS Elastic Beanstalk. For details about customizing the production deployment, please visit the WormBase Beanstalk Guide for Website.

Prepare for a website release

  • Change the WS release number in wormbase.conf, in particular, wormbase_release, rest_server, and search_server properties

  • Update the volume snapshot for the WS release here

  • Create the release branch, such as release/273

  • At the release branch:

    make release  # to build the assets (ie containers) required for deployment
    make eb-create  # to create and deploy to the pre-production environment
  • Login to the AWS Management Console, and navigate to Elastic Beanstalk, and then to the website Application.

    • Wait for the deployment to complete, and verify the pre-production environment is working
      • If ACeDB TreeView isn't working, which seems to be caused by a race condition between setting up the file system and starting ACeDB container, the problem can be fixed by re-deploying to the same environment make production-deploy.

Go live with a release

  • Login to the AWS Management Console, and navigate to Elastic Beanstalk, and then to the website Application.
    • Swap the URL between the pre-production environment and the current production environment
    • After making sure the new production environment is working, wait until the DNS TTL passes on Nginx before shutting down the previous production environment

Hotfix production environment

  • Grant permission to the instance by attaching the wb-catalyst-beanstalk-ec2-role.

  • Prior to applying the hotfix, ensure you are at the appropriate git branch for production.

  • Then run the following commands,

     VERSION=[GIT_TAG_TO_BE_CREATED] make release  # the tag should look like WS273.1
     make production-deploy

Production Deployment without AWS Beanstalk

For instances not managed by Beanstalk, deployment can be performed with:

  • Checkout the latest of the release branch, such as release/273

  • Ensure port 5000 is available, and run:

make production-deploy-no-eb

Contributing

Our development workflow can be found here:

http://wiki.wormbase.org/index.php/Development_workflow_-_webdev

Todd Harris (todd@wormbase.org)

Acknowledgements

BrowserStack

Thanks to BrowserStack for allowing us to perform interactive cross browser and cross OS testing.

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