Telomere

Record audit information for the telomere length study

Requirements

sudo apt-get install libmysqlclient-dev python-dev
sudo easy_install flask
sudo easy_install flask-sqlalchemy
sudo easy_install mysql-python
sudo easy_install flask-login
sudo apt-get install libldap2-dev
sudo apt-get install libsasl2-dev
sudo pip install python-ldap
sudo pip install Flask-WTF
sudo pip WTForms-Components
sudo pip install openpyxl
sudo pip install numpy

Install

1. Copy or clone the source from the git repository.
2. Copy the defaultSettings.py file to settings.py
3. Edit the settings.py file and change the following settings:
   1. Change Debug to be false
   2. Change SECRET_KEY to a secret key.
   3. Change DATABASE to the database name
   4. Change SQLALCHEMY_DATABASE_URI to a valid MySQL connection string
   5. Change LDAP_URL to be include the server and port for the LDAP service
   6. Change LDAP_BASEDN to be a valid one of those things.
   7. Change SPREADSHEET_UPLOAD_DIRECTORY to be a valid directory for which the user wwwrun has read and write permission.

Create the database

The Telomere application creates the tables that it requires, but first you must create the database and give the user then necessary permissions.

1. CREATE DATABASE telomere;
2. GRANT ALL PRIVILEGES ON telomere.* to {username}@127.0.0.1 identified by '{password}';

Installation on University of Leicester LAMP servers

See Here.

Run the Application in Dev

1. Install the requirements by running the command:

pip install -r requirements.txt

2. Run the Application by running the command:

python run.py

3. Test the application by running the command:

pytest