sample-tracker

sample-tracker: a light weight flask,react and MySQL based web app to store and track status of incoming samples and their associated information.

Update instructions

Once you pull a latest copy of Sample-Tracker , use the following commands to update the schema and JS bundle
```
    npm run build # to update JS bunble
    export FLASK_APP=sample_tracker.py
    flask db upgrade # to update database schema if necessary
```
Once you update JS bundle and db schema, restart flask server for changes to take effect.

Installation instructions for ubuntu

Please make sure that your account has sudo permissions before proceeding with these installation steps and commands.

 apt-get update
 apt-get install -y python3 python3-pip git mysql-server vim npm

Then, start mysql-server using

   service mysql start

Clone this git repo into your current working directory using

 cd sample-tracker
 git clone https://github.com/ccmbioinfo/sample-tracker

After cloning, cd into the clone'd repo folder and install python3 modules using

 pip3 install -r requirements.txt

After installing python3 modules, cd into static folder and install JS dependencies using

   cd static
   npm install -g

Then, create the minifi'ed JS bundle using the command

  npm run build

Now access the mysql command line using the command mysql -u root and create a new user in mysql. The following command creates a user 'test' and grants the user all priviliges to the database sample_tracker. Change the username from 'test' to whatever you see fit.

  mysql -uroot
  create user 'test'@'localhost' identified by 'test';
  create database sample_tracker;
  grant all privileges on sample_tracker.* to 'test'@'localhost';

Once this user is created, create a python class config.py in the sample-tracker root folder that will contain the following lines.

  cd .. # if you are in static folder. if not, make sure that you are in the sample-tracker folder (root folder).
  vim config.py # this could be any editor. I use vim.
  # add the following lines to config.py
  import os

  class Config(object):
    SECRET_KEY = 'YOUR_SECRET_KEY' # this should be a long random string
    SQLALCHEMY_DATABASE_URI = 'mysql+pymysql://test:test@localhost/sample_tracker' #replace test:test with the username and password you used to create a new user in mysql.
    SQLALCHEMY_TRACK_MODIFICATIONS=False

Now create a directory for downloading gene level reports:

  mkdir gene_reports
  mv ~/2019-12-12.sample_wise.csv ./gene_reports
  mv ~/2019-12-12.variant_wise.csv ./gene_reports

Sample wise and variant wise reports should contain counts of variants occuring across samples in the cohort. The reports have one requirement --- they must contain a column called "Gene". Python scripts to generate these reports from our typical WES reports are here: https://github.com/dennis-kao/cre/tree/master/gene.database

sample-tracker uses flask-talisman module to https'ise traffic by default, which will not work unless you deploy the website with gunicorn, nginx and with a proper https keys. Lets comment this module for our test instance to work.

Open the script app/__init__.py in your favorite editor and comment out the following lines - To comment lines in python, insert the character '#' at the front of the line as shown below.

from flask import Flask, render_template,redirect,url_for
#from flask_talisman import Talisman # COMMENT THIS LINE
from flask_sqlalchemy import SQLAlchemy
from flask_login import LoginManager
from flask_migrate import Migrate
from config import Config
from flask_wtf.csrf import CSRFProtect

csp = {
  'default-src': [
      '\'self\''
  ],
  'script-src': ['\'self\'','\'unsafe-inline\''],
  'style-src': ['\'self\'','\'unsafe-inline\''],
  'img-src': ['\'self\'','data:'],
}

app = Flask(__name__, static_folder='../static/dist', template_folder='../static')
app.config.from_object(Config)
#talisman = Talisman(app, content_security_policy=csp) #COMMENT THIS LINE
csrf = CSRFProtect(app)
login = LoginManager(app)
login.login_view = "login"
login.session_protection = "strong"
db=SQLAlchemy(app)
migrate=Migrate(app,db)

from app import routes

Now, initialize the database with sample-tracker's latest schema by using the following commands (from the root folder)

  export FLASK_APP=sample_tracker.py
  export LC_ALL=C.UTF-8
  export LANG=C.UTF-8
  flask db upgrade

Finally, start the development flask server using the following command

  flask run --host=0.0.0.0

Now, you should be able to access sample-tracker at http://localhost:5000

As discussed above, this setup of sample-tracker without https, gunicorn, nginx and flask-talisman should only be used for testing purposes. If you want to deploy sample-tracker, please serve flask using gunicorn, nginx and https'ise sample-tracker's traffic using flask-talisman (i.e. uncomment the flask-talisman lines from app/init.py and use a https key to secure the traffic).

Teja