HealthDoc

This is a research group headed up by Chrysanne DiMarco.

healthdoc.cs and inkpotinc.ca Server

ST's

• https://www.cs.uwaterloo.ca/cscf/internal/request/UpdateRequest?68127
• https://www.cs.uwaterloo.ca/cscf/internal/request/UpdateRequest?72516
• https://www.cs.uwaterloo.ca/cscf/internal/request/UpdateRequest?72414
• https://www.cs.uwaterloo.ca/cscf/internal/request/UpdateRequest?72415

Access

• ssh cscf-adm@healthdoc.cs

Install

• See: UbuntuImageCreation
• apt-get install ntpdate

Email

• See: https://www.cs.uwaterloo.ca/twiki/view/CF/UbuntuEmail
• apt-get install dovecot-imapd
• vi /etc/dovecot/dovecot.conf
  • Update Configuration if needed
• /etc/init.d/dovecot restart
• Install and configure EXIM4
  • apt-get install exim4
  • dpkg-reconfigure exim4-config
    • internet site; mail is sent and received directly using SMTP
    • System mail name: inkpotinc.ca
    • IP-addresses to listen on for incoming SMTP connections:
    • Other destinations for which mail is accepted: healthdoc.uwaterloo.ca;inkpotinc.ca
    • Domains to relay mail for:
    • Machines to relay mail for:
    • Keep number of DNS-queries minimal (Dial-on-Demand)? No
    • Delivery method for local mail: mbox format in /var/mail/
    • Split configuration into small files? No

Apache

• apt-get install apache2
• apt-get install libapache2-mod-gnutls
• vi /etc/apache2/local.conf
  • Append:

      # ===============================================================
      # Local MODS
      # MIKE GORE

      <IfModule mod_userdir.c>
         UserDir public_html
         #UserDir disabled root
      </IfModule>

Make Virtual Hosts

• cd /var/www
• mkdir inpotsoftware inkpot
• cd /etc/apache2/sites-available
• vi default

      # ================================================================
      # We have two virtual hosts here
      # HEALTHDOC.CS
      # INKPOTINC.CA   (disabled 29/10/09 7:16:24 PM)
      # ================================================================

      # ================================================================
      # HEALTHDOC.CS
      # ================================================================
      <VirtualHost *:80>
         ServerName healthdoc.cs.uwaterloo.ca
         ServerAdmin webmaster@localhost
         
         DocumentRoot /var/www/healthdoc
         <Directory />
            Options FollowSymLinks
            AllowOverride None
         </Directory>
         <Directory /var/www/healthdoc>
            Options Indexes FollowSymLinks MultiViews
            AllowOverride None
            Order allow,deny
            allow from all
         </Directory>

         ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
         <Directory "/usr/lib/cgi-bin">
            AllowOverride None
            Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
            Order allow,deny
            Allow from all
         </Directory>

         ErrorLog /var/log/apache2/error.log

         # Possible values include: debug, info, notice, warn, error, crit,
         # alert, emerg.
         LogLevel warn

         CustomLog /var/log/apache2/access.log combined

         <Location /trac>
            SetHandler mod_python
            PythonInterpreter main_interpreter
            PythonHandler trac.web.modpython_frontend 
            PythonOption TracEnv /var/trac
            #PythonOption TracUriRoot /trac
            AuthType Basic
            AuthName "Password Required"
            AuthUserFile /home/hdpr/web/users
            AuthGroupFile /home/hdpr/web/groups
            Require group tcde
         </Location>

         ScriptAlias /cgi/ /var/www/healthdoc/cgi/
         <Directory "/var/www/healthdoc/cgi">
            AllowOverride None
            Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
            Options +ExecCGI
            Order allow,deny
            Allow from all
         </Directory>
      Include /etc/mediawiki/apache.conf
      </VirtualHost>

      # ================================================================
      # INKPOTINC
      # ================================================================
      <VirtualHost *:80>
         ServerName inkpotinc.ca
         ServerAdmin hdpr@localhost
      #
      #        #UserDir disabled
      #        #UserDir disabled root
      #
      #   AccessFileName .htaccess
      #
      #   DocumentRoot /var/www/inkpotinc
      #
         <Directory /var/www/inkpotinc>
            AuthType Basic
            AuthName "Password Required"
            AuthUserFile /home/hdpr/web/users
            AuthGroupFile /home/hdpr/web/groups
            Require group Inkpot
            AllowOverride AuthConfig

            Options Indexes FollowSymLinks MultiViews
            Order allow,deny
            allow from all
         </Directory>

      #
      #   ScriptAlias /cgi/ /var/www/inkpotinc/cgi/
      #   <Directory /var/www/inkpotinc/cgi>
      #      AllowOverride None
      #      Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
      #      Options +ExecCGI
      #      Order allow,deny
      #      Allow from all
      #   </Directory>
      #
      #   ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
      #   <Directory "/usr/lib/cgi-bin">
      #      AllowOverride None
      #      Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
      #      Order allow,deny
      #      Allow from all
      #   </Directory>
      #
      #   ErrorLog /var/log/apache2/error.log
      #
      #   # Possible values include: debug, info, notice, warn, error, crit,
      #   # alert, emerg.
      #   LogLevel warn
      #
      #   CustomLog /var/log/apache2/access.log combined
      #
      Include /etc/mediawiki/apache.conf
      </VirtualHost>

MySQL

• apt-get install libdbd-mysql-perl libmysqlclient15off mysql-client mysql-client-5.0 mysql-common mysql-server mysql-server-5.0
• mysql -u root -p
• See ST#68127

PHP

• apt-get install libapache2-mod-php5 php5 php5-cli php5-common php5-gd php5-mcrypt php5-mysql phpmyadmin
• Edit Config if needed:
  • vi /etc/phpmyadmin/apache.conf
• *mysqladmin -u root password

Media Wiki Installation

• apt-get install mediawiki
• apt-get install imagemagick mediawiki-math php5-gd
• vi /etc/mediawiki/apache.conf
  • Change:

      # Uncomment this to add an alias.
      # This does not work properly with virtual hosts..
      # 14May2010 Mike Gore
      # I added another Include directive to this file from with the healthdoc.cs Virtual Host directive
      # So it should now work
      Alias /mediawiki /var/lib/mediawiki

• Insert Include /etc/mediawiki/apache.conf into each Apache virtual host directive
  • vi /etc/apache2/sites-enabled/00-default
• Restart Apache /etc/init.d/apache2 restart
• Continue with the Configuration Section below CF.Healthdoc#Configuration

Configuration

• Launch Web Browser =firefox http://localhost/mediawiki=
• Wiki name: rhetfig
• Contact e-mail: webmaster@localhost
• Admin username: WikiSysop
• Password: (password safe)
• Object caching: No caching
• Memcached servers:
• E-mail features: Enabled
• User-to-user e-mail: Enabled
• E-mail notification about changes: Enabled for changes to user discussion pages, and to pages on watchlists (not recommended for large wikis)
• E-Machines to relay mail for: address authentication: Enabled
• Database type: MySQL
• Database host: localhost
• Database name: wikidb
• DB username: wikiuser
• DB password: (see password safe)
• Superuser account: Use superuser account
• Superuser name: root
• Superuser password: (see password safe)
• Database table prefix: healthdoc_
• Storage Engine Select one: InnoDB
• Database character set Select one: MySQL 4.1/5.0 binary

Finish and Secure

• chmod a+rwx /var/lib/mediawiki/config
• mv /var/lib/mediawiki/config/LocalSettings.php /etc/mediawiki
• chmod 600 /etc/mediawiki/LocalSettings.php
• rm -Rf /var/lib/mediawiki/config
• vi LocalSettings.php
• Append these settings:

   # Mike Gore 19May2010
   # See: http://linuxclues.blogspot.com/2008/04/installing-configuring-mediawiki-ubuntu.html
   #Global permissions 
   # Anonymous
   $wgGroupPermissions['*' ]['createaccount'] = false;
   $wgGroupPermissions['*' ]['read'] = true;
   $wgGroupPermissions['*' ]['edit'] = false;
   $wgGroupPermissions['*' ]['delete'] = false;
   $wgGroupPermissions['*' ]['createpage'] = false;
   $wgGroupPermissions['*' ]['upload'] = false;
   $wgGroupPermissions['*' ]['move'] = false;
   #Logged users
   $wgGroupPermissions['user' ]['createaccount'] = true;
   $wgGroupPermissions['user' ]['read'] = true;
   $wgGroupPermissions['user' ]['edit'] = true;
   $wgGroupPermissions['user' ]['delete'] = false;
   $wgGroupPermissions['user' ]['createpage'] = true;
   $wgGroupPermissions['user' ]['upload'] = true;
   $wgGroupPermissions['user' ]['move'] = false;

• /etc/init.d/apache2 restart

Rhetorical Figures project

One of the projects that Chrysanne is working on is the RhetoricalFiguresProject. This is being done jointly with the English Department, specifically Randy Harris. We are currently developing an application that will run on healthdoc.cs to aid them in this project. For more details, see: RhetoricalFiguresProject