Setup Guide

Software Dependencies

The App Store requires the following software packages:

• Python 3.7
• Django 2.2.28
• Whoosh 2.7.4
• python-geoip (not sure if these is needed anymore)
• django-social-auth 0.7.28
• social-auth-app-django 3.1.0
• django-haystack 2.8.1
• sphinx
• urllib3
• Pillow
• gevent
• Database Server and appropriate client (AppStore uses Mysql)

NOTE: For exact requirements see requirements.txt file in this repo. Once python 3.7 is setup pip install -r requirements.txt will install all required packages

Migration

If you want to move the App Store to another machine running Ubuntu, here is what to do:

NOTE: These steps are derived from the bootstrap.sh script, available in this repo, used to spin up Vagrant Virtual Machine with AppStore installed.

1. Install the following packages:

   apt-get -y install apache2 apache2-dev apache2-utils ssl-cert wget
   apt-get -y install libapache2-mod-wsgi-py3 gcc g++ git
   apt-get -y install mysql-server
   apt-get -y install geoip-database # this may not be needed anymore

2. Install Miniconda (Anaconda could also be used with adjustments to paths below) to /opt/miniconda3 and set PATH so that python calls use that Python.

   # as root
   pushd /tmp
   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
   chmod a+x Miniconda3-latest-Linux-x86_64.sh
   /bin/rm Miniconda3-latest-Linux-x86_64.sh
   popd
   
   # Set paths 
   export PATH=/opt/miniconda3/bin:$PATH
   echo "export PATH=/opt/miniconda3/bin:$PATH" >> /root/.bash_profile
   echo "export PATH=/opt/miniconda3/bin:$PATH" >> /root/.bashrc

3. Install mysqlclient which is most easily done with conda:

   conda install -y mysqlclient

4. Install mod_wsgi:

   pip install mod_wsgi

5. Configure mod_wsgi. These commands are derived from instructions found here:

   # as root
   # update wsgi.conf configuration
   WSGI_CONF="/etc/apache2/mods-available/wsgi.conf"
   SITE_PKG=`find /opt/miniconda3 -regex "/opt/miniconda3/lib/python.*/site-packages$" -type d 2> /dev/null`
   echo "<IfModule mod_wsgi.c>" > $WSGI_CONF
   echo "   WSGIPythonHome /opt/miniconda3" >> $WSGI_CONF
   echo "   WSGIPythonPath $SITE_PKG" >> $WSGI_CONF
   echo "</IfModule>" >> $WSGI_CONF
   
   # update wsgi.load file
   mod_wsgi-express install-module | egrep "^LoadModule" > /etc/apache2/mods-available/wsgi.load 
   
   # enable wsgi
   a2enmod wsgi
   
   # updates shared library cache (might not be needed anymore)
   ldconfig

6. Create database

   # as root
   mysqladmin create AppStore

7. Create database user

   # log into mysql with superuser account
   # as root
   mysql -u root
   
   # run these commands replacing @@PASSWORD@@ with a password that needs to be set in settings file later
   CREATE USER 'appstoreuser'@'localhost' IDENTIFIED BY '@@PASSWORD@@';
   CREATE USER 'appstoreuser'@'127.0.0.1' IDENTIFIED BY '@@PASSWORD@@';
   GRANT ALL PRIVILEGES ON AppStore.* to 'appstoreuser'@'localhost';
   GRANT ALL PRIVILEGES ON AppStore.* to 'appstoreuser'@'127.0.0.1';
   GRANT ALL PRIVILEGES ON test_AppStore.* to 'appstoreuser'@'localhost';
   GRANT ALL PRIVILEGES ON test_AppStore.* to 'appstoreuser'@'127.0.0.1';
   FLUSH PRIVILEGES;

8. Check out the App Store GitHub repository to the new machine under /var/www directory: http://github.com/cytoscape/appstore

   # as root
   pushd /var/www
   git clone http://github.com/cytoscape/appstore
   cd appstore
   # make some needed directories
   mkdir logs
   mkdir /var/www/html/media
   mkdir /var/www/html/misc
   cp favicon.ico /var/www/html/misc/.
   cp google_oauth2_logo.png /var/www/html/misc/.

9. Install needed Python modules:

   # as root and in /var/www/appstore directory with /opt/miniconda/bin in PATH
   pip install -r requirements.txt

10. Create settings/production.py from settings/vagrant.py and update the following:

    • Update values in ADMINS
    • Update EMAIL_HOST, EMAIL_HOST_USER, EMAIL_ADDR, and EMAIL_HOST_PASSWORD
    • Check FULL_URL is correct
    • Update SOCIAL_AUTH_GOOGLE_OAUTH2_KEY, SOCIAL_AUTH_GOOGLE_OAUTH2_SECRET, & GOOGLE_API_KEY
    • Comment out EMAIL_BACKEND line since we want to use regular SMTP
    • Set EMAIL CONFIGURATION
    • Generate new SECRET_KEY and keep it secret. Click here for more information
    • Update database @@PASSWORD@@ to match value set above

11. Create the following daily cron jobs on the new machine:

    • Database backups described above in the subsection Backup System.

    • As root run:

      cd /var/www/appstore
      /opt/miniconda/bin/python manage.py rebuild_index`
      chown -R www-data.www-data /var/www/appstore/whoosh_index

12. Populate /var/www/html/static data

    cd /var/www/appstore
    /opt/miniconda3/bin/python manage.py collectstatic

13. Take a snapshot of the database using mysqldump then load it to the new machine's database:

    Run this on the old machine:

    mysqldump -u USER_NAME DB_NAME > CyAppStoreDbDump.sql
    

    Transfer CyAppStoreDbDump.sql from the old to new machine:

    Run this on the new machine:

    mysql -u USER_NAME DB_NAME < CyAppStoreDbDump.sql
    

14. Setup Lets Encrypt

15. Using bootstrap.sh as a guide copy over appstore.http.conf and appstore.include.conf

16. Restart Apache and run the test protocol that's described below.

    systemctl restart apache2