App Store Code Structure

Terminology

• Django app: Django organizes websites into separate modules called apps. Each app has its own directory at the top level typically containing files like __init__.py, model.py, and views.py.

• templates: HTML files with placeholders, which Django processes by filling in Python code.

• static files: general website files (images, Java Script, CSS) that are served as is without any processing from Django.

• media files: general website files referenced by the database backend.

Explanation of important files

• settings.py: Django settings file for configuring things like the database, location of templates, static files, and so on.

• urls.py: the general URL layout of the entire site. Each URL entry in this file delegates URL paths to each Django app.

• django.wsgi: the configuration file used when the App Store is deployed to an Apache server using mod_wsgi.

• apps: navigation of Cytoscape apps and app pages.

• users: user login/logout.

• search: free text searching.

• backend: programs can obtain details of apps from the backend; used by the Cytoscape App Manager

• help: about, contact us, getting started pages

• submit_app: Cytoscape 3.0 app submission pages and jar verification

• templates: Templates in this directory are used throughout the App Store.

• static: Each subdirectory has static files for a Django app. The common subdirectory has static files that belong to the entire site. When deploying the site to Apache, Apache should directly serve these files instead of through Django.

• util: small utility functions used throughout the site's code

Debugging

1. /etc/apache2/sites-enabled/appstore

   • This file tells Apache and mod_wsgi where to find the site. The most important line is this:

     WSGIScriptAlias / /var/www/CyAppStore/django.wsgi

     This tells Apache and mod_wsgi where to locate the site code. Make sure the path to django.wsgi is correct.

2. /var/www/CyAppStore/django.wsgi

   • This file invokes Django's WSGI handler. It needs to correctly reference settings.py to start the site. Make sure these two lines correctly reference the location of the site:

     SITE_PARENT_DIR = '/var/www'
     SITE_DIR = filejoin(SITE_PARENT_DIR, 'CyAppStore')

     To check if these variables are being defined correctly, you can launch a separate Python interpreter and enter these lines:

     from os.path import join as filejoin
     SITE_PARENT_DIR = '/var/www'
     SITE_DIR = filejoin(SITE_PARENT_DIR, 'CyAppStore')

     Then check if the variables SITE_PARENT_DIR and SITE_DIR are correct.

3. /var/www/CyAppStore/settings.py

   • This file is pretty complicated. But if you've checked everything at this point, here's some ways to pinpoint problems in settings.py.

     1. s

     2. If you're getting database errors, enter this command at the shell prompt in the same directory as settings.py:

        python manage.py dbshell

        If you're able to get a SQL prompt, that means the log in settings into the SQL database is correct.