susom / biocatalyst

Biocatalyst

Setup

Install Gradle

Download Gradle from their Releases page: https://gradle.org/releases/ Alternatively, if you use Homebrew you can run brew install gradle

Install Docker

Download it from a link such as: https://docs.docker.com/docker-for-mac/install/

Increase memory allocated to Docker

As we're running a number of containers, we must increase the default memory allocated to docker. Open the docker settings and set the memory to 4GB.

Make scripts executable (Mac)

If you're on a Mac, you'll need to give the scripts in this project executable permissions. Open terminal, and cd to the project repo. Then, run:

chmod +x scripts/*.sh
scripts/setup.sh

Follow the next steps and start the stack with docker compose:

cd docker
docker-compose up -d

Try it out

Open a web browser and navigate to http://localhost:4200 and you should be up and running!

Utility scripts

You can run scripts/clean_refresh.sh It's highly recommended to run this script after a failed integration to ensure a clean starting point.

Developer notes

You can run this either as a local docker stack (as above), which requires you to create a new local docker image with each code change. You can run gradle docker to build and tag with latest. Then, run clean_refresh.sh to pick up the newer container. This is using the docker set of configuration properties, e.g. docker.properties in the Spring apps' resources directory.

You can also run individual Spring applications with gradle bootRun using your IDE. This is much faster for local development, particularly if you're working on one or more service. This would use local.properties.

You can also mix and match and create your own custom configuration based on your needs.

In the event you make local changes and are running "in docker mode" - you can recreate all the docker containers with the latest tag locally by re-running setup.sh.

Deployment

As these are containers, the plan is to provide environment-specific properties files and add them to the application classpath.

biocatalyst's Issues

Integration configuration instructions object (important_tokens, delimiter_positions, etc) being overwritten as empty on refresh

Steps to reproduce:

1. Configure an integration with two data sources
2. Configure ID modal for both. Modal should change to ID Format Configured
3. Refresh the page. You'll note the Configure ID button has returned to Configure ID and the information is lost from elastic