App Store Code Structure

Terminology

Explanation of important files

Configuration Files

Django Apps

Other Directories

How to set up the App Store on your computer

The App Store requires the following software packages. If you're on a Mac, this can be installed with Homebrew. If you're on Linux, use your distribution's package manager.

Note that the versions specified here are not mandatory. They only indicate the version with which I've tested the App Store.

The following Python packages are also required. Each can be installed with pip install. If you don't have pip, type: easy_install pip.

Why not virtualenv?

virtualenv is a tool for Python projects that allows encapsulating a project's dependencies. These dependencies are available only for that project and don't pollute the Python library dependencies of another project. virtualenv works great if a project's dependencies are only available through pip. However, that's not the case with this codebase, since it needs non-Python libraries like xapian or libjpeg.

Making sure GeoIP is working

  1. Open settings.py and make sure the GEOIP_* variables are set correctly.

    • GEOIP_LIBRARY_PATH points to the specific location of the GeoIP library file. For example: GEOIP_LIBRARY_PATH = '/usr/local/Cellar/geoip/1.4.8/lib/libGeoIP.1.dylib'

    • GEOIP_PATH points to the directory of GeoIP data files.

  2. Type python manage.py shell. Enter: 

    • import django.contrib.gis.geoip
django.contrib.gis.geoip.HAS_GEOIP

  3. You should see True. If it's False, GeoIP is not configured correctly.

How requests are handled

         ||             |                               |                    |                    |            ||
Request=>|| ==Apache==> | == sites-enabled/appstore ==> | == django.wsgi ==> | == settings.py ==> | == urls.py ||
         ||             |                               |                    |                    |            ||
  1. An HTTP request is made to the Apache server.

  2. Apache looks in /etc/apache2/sites-enabled to see how to handle the request. The appstore configuration file is set to handle requests made to http://apps.cytoscape.org.

  3. appstore tells Apache to use mod_wsgi. mod_wsgi runs a Python interpreter within Apache. appstore tells mod_wsgi to start Python with /var/www/CyAppStore/django.wsgi.

  4. django.wsgi starts the Django library. It also tells Django the location of settings.py, which Django needs to start the site.

  5. settings.py contains the location of urls.py (defined in the ROOT_URLCONF variable), which is a list of URLs (in the form of regular expressions) and the Python functions that handle them.

  6. urls.py in the top directory of the App Store merely imports additional URLs from each Django app. It dispatches the request to the appropriate function that is designated to handle requests for a given URL. Functions are defined in the views.py file in each Django app.

  7. The handler function returns with a processed HTML page.

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 are correct: 

      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. If you're getting an HTTP 500 error, you can get the stack trace by turning on debug mode then reloading the page. Note that debug mode exposes sensitive information about the site to the public. Make sure to keep debug mode off as much as possible. Change to following line to True: 

        DEBUG = False

      2. You can poke at the code by running a Python shell. Enter this command at the shell prompt in the same directory as settings.py: 

        python manage.py shell
        You can check to see if the site's code is working correctly without having debug mode on. For example, to see if the list of all apps is working, enter this into the Python interpreter: 
        from apps.models import App
App.objects.all()

      3. The SQL database settings are specified by the DATABASES variable: 

        DATABASES = {
        'default': deploy_database
}

        Make sure that 'default' is pointing to te correct dictionary: 

        deploy_database = {
        'ENGINE':   'django.db.backends.mysql',
        'NAME':     ...
        'USER':     ...,
        'PASSWORD': ...
}

      4. 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 Django can connect to the SQL database.

      5. If you make changes to a Python file but you're not seeing the changes taking effect, you may have to delete all the .pyc files. To do so, type this: 

        make svnclean

Tips

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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