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README.md

ISB-CGC Web Application

The ISB-CGC Web Application provides a GUI for browsing, curating, and analyzing TCGA, TARGET, and CCLE data. It is built in Django 1.11 (Python 2.7) with MySQL 5.7, and is deployed on Google AppEngine Flex.

Installation Instructions For Local Development

The system uses Vagrant to setup a consistent, platform independent development environment. To setup your development environment to run locally, you will need to install the following:

From there simply perform these steps.

  1. Once you've installed PyCharm and cloned the repositories, create a directory within the PycharmProjects directory (the parent directory of your repositories) called secure_files/.
  2. Copy the sample.env file to a file named .env in secure_files/
  3. Fill out the .env file with the proper values
  • For most development environments, MYSQL_ROOT_PASSWORD and DATABASE_PASSWORD can be the same, and DATABASE_USER can be root
  • GCLOUD_PROJECT_ID is available after creating a project in the Google Cloud Dashboard
  • GOOGLE_CLIENT_ID and GOOGLE_CLIENT_SECRET can also be obtained in the Google Cloud Dashboard by going to API & Auth > Credentials > Add New > OAuth 2.0 Client > Web Application
  • Be sure when developing locally that you have 127.0.0.1 in the list of allowed domains for the OAuth 2.0 key

Configuring PyCharm

PyCharm Pro can be used to run your server through Vagrant and the Google App Engine.

Setup

  1. Go to your PyCharm Settings (On Mac, Go to Preferences; CMD+,)
  2. Select Project: ISB-CGC-Webapp > Project Interpreter
  3. Click the icon next to the Project Interpreter drop down at the top of the main area
  4. Click Add Remote
  5. Select Vagrant (if it asks to start the machine, say yes)
  6. Set the Python interpreter path to /home/vagrant/www/shell/python-su.sh and click Ok
  7. Select Languages & Frameworks > Google App Engine
  8. Change the SDK directory to /home/vagrant/google_appengine/
  9. Click Ok to save
  10. Go to Run > Edit Configurations
  11. If there is not a Django Configuration, add one
  12. Set the host to 0.0.0.0
  13. Set the Python Interpreter to the Vagrant Machine (if it is not set to that already)
  14. Set the working directory to /home/vagrant/www
  15. Click ... next to the Environment variables:, box and add the following values: SECURE_LOCAL_PATH = ../parentDir/secure_files/ PYTHONPATH = /home/vagrant/www:/home/vagrant/www/lib:/home/vagrant/google_appengine DJANGO_SETTINGS_MODULE = GenespotRE.settings PYTHONUNBUFFERED = 1
  16. Click ok to save

You will also need to set the shell/python-su.sh file to be executable. You can do this in the vagrant machines command line with the command chmod +x /home/vagrant/www/shell/python-su.sh

Running

To run your server in PyCharm:

  1. Make sure your Vagrant machine is running by going to Tools > Vagrant > Up
  2. Click on the Run or Debug icons in the toolbar (upper-right corner of the PyCharm GUI)

Your server will start and the PyCharm console should show all the logs and output from the system. If you are running in debug, you can also use breakpoints to stop the execution and examine variables and code as it runs.

Adding Python Dependencies

To add Python Libraries or Dependencies, you should add them to the requirements.txt file and they will automatically be pulled down when a new developer starts the system.

To update your existing python dependencies because of a change or to pull down additional libraries you need, SSH into the virtual machine and run pip install. Through PyCharm, you can take the following steps.

  1. Click Tools > Start SSH session...
  2. Select the Vagrant VM Connection you set up
  3. Type cd www; sudo pip install -r requirements.txt --upgrade -t lib/

Or from the command line, you can do this by doing the following

  1. Open a terminal in the project directory
  2. Type vagrant ssh to login to the virtual machine
  3. Change directory to the www directory (/home/vagrant/www/ is the full path)
  4. Run pip install -r requirements.txt --upgrade -t lib/
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