yusra-haider / embl_python_software_engineer_test

Test for Python Software Engineer at EMBL-EBI

EMBL Python Software Engineer Test

This app was developed using FastAPI as the web framework and SQLAlchemy as the means of connection with the given database.

This app is deployed to Heroku as a docker container. This is the main link for the app, and the documentation is available here

The endpoint is GET gene_search?name=<name>&species=<species>&limit=<result limit>, and a sample usage is here

There are three bash scripts in the repository for ease of testing, building and deploying the docker container

1. build_docker_image.sh: This script builds the docker image, runs the docker container and runs tests inside docker (if the argument yes is given). Use this script for locally testing and running the docker container. Sample usage (testing enabled): ./build_docker_image yes Run the script without arguments for building and running without tests. If the script is run with testing enabled and the tests failed, the docker container is stopped and the container removed. After this script is run, the app can be accessed via localhost:80

2. deploy_docker_to_heroku.sh: This script is for deploying to Heroku with docker. It takes the name of the deployment target heroku app as an argument. Sample usage: ./deploy_docker_to_heroku.sh <heroku_app_name> The script will fail if the heroku app name is not given.

3. build_test_deploy_docker_to_heroku.sh: This script combines both the above scripts. It executes build_docker_image.sh followed by deploy_docker_to_heroku.sh. It takes testing enabled / disabled as first argument and the heroku app name as the second one. Sample usages: build_test_deploy_docker_to_heroku.sh yes <heroku_app_name> (testing enabled) and build_test_deploy_docker_to_heroku.sh no <heroku_app_name> (without testing)

The repository is currently connected to Travis CI, and has the CI / CD pipeline in place. Tests are executed and if successful, the app is deployed to Heroku as a docker container. Currently, builds get executed on every pushed change and on every pull request.

Experimenting a CI/CD set up with GitHub actions is in progress on this branch

Instructions for running the app inside vagrant, using this vagrant file:

$ git clone https://github.com/yusra-haider/embl_python_software_engineer_test.git
$ cd embl_python_software_engineer_test.git
$ ./build_docker_image yes

This should get the docker container up and running inside vagrant. Access the app via localhost:8080, and the documentation via localhost:8080/docs A sample usage of the endpoint would look like http://localhost:8080/gene_search/?name=abc&species=amphilophus_citrinellus