Gene-Calc

Gene Calc - Website

The Gene-Calc is a constantly developed tool dedicated for calculations related to biological sciences, especially focused in field of genetics. Application offers couple of tools such as:

• Hardy–Weinberg equilibrium calculator
• Chi-square tests:
  • Independence (Associations) chi-square
• Chi-square goodness of fit test:
  • Estimator of genetic distance
  • Polymorphic information content and heterozygosity calculator
• Polymorphic information content & Heterozygosity
• Estimation of genetic distance
• Sequences Analysis Tools
  • Dot plot
  • Tool to obtain consensus sequence
  • Additional tools
• Machine Learning Tools
  • APMC - Automatic Predictive Model Constructor

Stack

• Python 3.7
• Flask
• MySQL 5.7
• Docker & Docker Compose

Prerequisites

Make sure you have installed all of the following prerequisites on your development machine:

• GIT
• Make
• Python 3.7
• Docker version >= 19.03.1
• docker-compose version >= 1.24.1

If you don't want to use Docker you have to install:

• MySQL 5.7

Local development [virtualenv]

Create a virtual environment

$ python3 -m venv venv

Run a virtualenv environment

$ source venv/bin/activate

Install required packages with dev dependencies

$ pip install -r requirements/dev.txt

If you have problems with installation mysqlclient package with the above command. Try to install it by hand with pip install mysqlclient

Create config.env file by copying config.env.tmp and fill these with required environment variables

Export local environment variables

On Mac OS

$ set -o allexport; source config.env; set +o allexport;

In your local MySQL database

$ mysql -u root
$ CREATE DATABASE gene_calc;
$ exit

Apply application migrations:

$ flask db migrate

Next import data into your local database:

$ mysql -u root gene_calc < fixtures/data.sql

To start application locally type:

$ flask run

Application should be available under URL:

http://127.0.0.1:5000

To login into userpanel

Login: test123
Password: test123test123

Important info

If you want to run tests without docker you have to physically install a few tools:

• wkhtmltopdf
• muscle

without this tools it is impossible to correctly run the tests

Local development [docker]

To start local development using docker:

Create config.env file by copying config.env.tmp and fill these with required environment variables

Export local environment variables

On Mac OS

$ set -o allexport; source config.env; set +o allexport;

Start local containers:

$ docker-compose -f docker-compose.local.yml up

Load data into docker container

$ docker exec -i database mysql -u$MYSQL_USER -p$MYSQL_PASSWORD $MYSQL_DATABASE < fixtures/data.sql

Docker hints:

Rebuild containers:
$ docker-compose -f docker-compose.local.yml up --build

Stop containers:
$ docker-compose -f docker-compose.local.yml down

Stop containers with volume delete:
$ docker-compose -f docker-compose.local.yml down -v

Application should be available under URL:

http://127.0.0.1:5000

To login into userpanel

Login: test123
Password: test123test123

Env variables

All required env variables are in config.env.tmp file

If you want to start local development by docker you have to remember to correctly set up env variables in config.env

DOCKER=1

In case local development by virtualenv

DOCKER=0

Tests

To run tests via docker-compose type (remember that containers should be running):

docker-compose -f docker-compose.local.yml exec backend pytest -v

If you want to run the tests without docker you have to install dependencies which I have mentioned before in section Local development [virtualenv] then in root app directory type:

pytest -v

Pre-commit config

We use a pre-commit hook which checking a quality of code. To install a hook on your local repository, you have to run a command given below, after install required packages:

$ pre-commit install

Makefile

We use Makefile to automate some common stuff

If you want to update dependencies type:

$ make update-deps

If you want to format code type:

$ make format

If you want to setup the whole docker environment type:

$ make start-docker

If you want to stop all project docker containers type:

$ make stop-docker

Git flow

Create your feature branch from master.

Branch naming:

• pattern: trello-task-id-short-description
• eg: trello-20-remove-flask-admin

Commit names conventions:

• pattern. [trello-task-id]: commit description
• eg. [trello-20]: Removed flask-admin package

After finishing implementation of your feature - create pull request to master branch.

CI/CD

We are using CircleCI for continuous integration and continuous deployment.

On each time when Github PR is created the tests are run on CircleCI. When all tests passed and there is minimum one approve from a code review, then merge is possible. After merge to master branch CircleCI run deployment. So after this, if everything goes correctly changes should be visible on production.

Monitoring:

We are using Sentry for monitoring app errors.

Troubleshooting

1. I have problem with mysql-client installation in virtualenv

Comment out mysql-client form requirements/dev.txt to complete installation all dev dependencies. Like black, pre-commit etc. And use docker instead of virtualenv.

Theoretical information available from:

https://gene-calc.pl/about

Authors

Szymon Miks & Jan Bińkowski

License

This project is licensed under the GNU GPL License

Moreover

If you have any questions or ideas how to develop this app, please let us know via e-mail: contact@gene-calc.pl