ambition-edc 0.1.12

Ambition Trial EDC (https://doi.org/10.1186/ISRCTN72509687)

Ambition Edc

(P.I. Joe Jarvis)

http://www.isrctn.com/ISRCTN72509687

VENV Installation

See also [docker install](#docker-install)

There are three requirements files

• requirements_dev.txt # installs all in editable mode from your workspace

• requirements_production.txt # installs each by tag

• requirements.txt # installs each from develop branch (for ci / tests)

See ambition/ubuntu.txt for required ubuntu packages

Decide on the user account for the installation. E.g. ambition.

sudo su ambition

create folders

mkdir  ~/.venvs
mkdir -p ~/source/ambition/log/

create VENV

python3 -m venv ~/.venvs/ambition

activate VENV

source ~/.venvs/ambition/bin/activate

update pip

pip install -U pip ipython

clone main project

cd ~/source/ \
&& git clone https://github.com/ambition-trial/ambition.git

change to project folder

cd ~/source/ambition

copy your .env file into the project root

cp /some/path/to/.env ~/source/ambition/.env

install requirements, select the require file. See requirements options above.

   # pip install -r requirements.txt

   pip install -r requirements_production.txt

create database and populate timezone table

   mysql -u <user> -p -Bse 'create database ambition character set utf8;' \
   && mysql_tzinfo_to_sql /usr/share/zoneinfo | mysql -u root -p mysql

migrate database

python manage.py migrate

import required data

python manage.py import_randomization_list \
&& python manage.py import_holidays

check

python manage.py check

Environment variables

Settings variables are store in the environment. See django-environ and 12-factor-django.

Place your .env file in the root of the project.

Note

Available variables are listed in env_file.sample.

Logging

If logging through syslog is implemented, you need to configure rsyslog.

   nano /etc/rsyslog.d/30-ambition.conf

add this to the file

   # /etc/rsyslog.d/30-ambition.conf
   local7.*                                             /var/log/ambition.log
   & ~  # This stops local7.* from going anywhere else.

restart rsyslog

   sudo service rsyslog restart

view the log

tail -n 25 -f /var/log/ambition.log

Docker Install

Install Docker Compose.

create a droplet for the host

…

log into your host and create a user account for the app

useradd ambition
usermod -aG docker ambition
usermod -aG sudo ambition

log out and log back in as user ambition

ssh [e-mail]

The rest of the steps assume you are logged into your host as user ambition

checkout the main ambition repo into app

cd ~/
git checkout -b develop git https://github.com/ambition-trial/ambition.git app

make a folder on your host for the container volumes

sudo mkdir -p /srv/ambition/

copy or scp your .env file into the app root

cp /some/path/to/.env ~/app/.env

scp .production [e-mail]:~/app/.env

edit ~/app/.env file as required, for example

from app/ build images for ambition_production and mysql and bring them up

docker-compose -f compose/local.yml build \
&& docker-compose -f compose/local.yml up

Note

if you need to generate keys set DJANGO_AUTO_CREATE_KEYS=True in the .env, docker-compose up, change back to false and docker-compose up again. If needed, copy keys to container (e.g. you are using existing keys)

docker cp /some/path/to/crypto_keys/ ambition_production:$DJANGO_KEY_FOLDER

Copy the randomization_list.csv file to the container

docker cp /some/path/to/randomization_list.csv ambition_production:$DJANGO_ETC_FOLDER

In another shell, log into the container

docker exec -it ambition_production /bin/bash

run migrations and other management commands as required

python manage.py migrate
python manage.py import_holidays
python manage.py migrate import_randomization_list

While still in the container, run check

python manage.py check

Start runserver

python manage.py runserver 0.0.0.0:8000