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CONTRIBUTING.md

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CONTRIBUTING

For additional info please check the myapp repository.

Clone flaski and the base myapp repo:

cd ~
git clone [email protected]:mpg-age-bioinformatics/myapp.git
git clone [email protected]:mpg-age-bioinformatics/flaski.git

Export secret variables:

cd ~/flaski
cat << EOF > .env
MYSQL_PASSWORD=$(openssl rand -base64 20 | tr -d '/')
MYSQL_ROOT_PASSWORD=$(openssl rand -base64 20 | tr -d '/')
REDIS_PASSWORD=$(openssl rand -base64 20 | tr -d '/')
SECRET_KEY=$(openssl rand -base64 20 | tr -d '/')
EOF

Create local folders:

mkdir -p ~/flaski23/backup/stats ~/flaski23/backup/users_data2 ~/flaski23/backup/users_data3 ~/flaski23/backup/mariadb ~/flaski23/private ~/flaski23/mpcdf ~/flaski23/submissions

To deploy flaski edit the docker-compose.yml accordingly and then pull pyflaski and build:

cd ~/flaski
git submodule update --init --recursive
docker-compose up -d --build

If running myapp on development mode you will have to start flask from inside the server container:

docker-compose exec server3 /bin/bash
flask run --host 0.0.0.0 --port 8000

Add the following line to your /etc/hosts

127.0.0.1       flaski.localhost

You can now access flaski over https://flaski.localhost/v3.

Adding administrator user:

docker-compose run --entrypoint="python3 /myapp/myapp.py admin --add [email protected]" init

Email logging

To use the SMTP debugging server from Python comment all email related env in docker-compose.yml. You can not using python's fake email server that accepts emails, but instead of sending them, it prints them to the console. To run this server, open a second terminal session and run the following command on it:

docker-compose exec server3 python3 -m smtpd -n -c DebuggingServer localhost:8025

pyflaski

pyflaski was added as a submodule of flaski:

cd ~/flaski
git submodule add [email protected]:mpg-age-bioinformatics/pyflaski.git pyflaski
git submodule init pyflaski

If making a fresh clone you will need to:

cd ~/flaski
git submodule update --init --recursive

To update from the remote:

git submodule update --recursive --remote

Commiting changes:

cd ~/flaski/pyflaski
git add -A . 
git commit -m "<describe your changes here>"
git push origin HEAD:master

then tell the main project to start tracking the updated version:

cd ~/flaski
git add pyflaski
git commit -m pyflaski
git push