Merge branch 'release/0.5.0'

Author: pbchase

.gitignore

@@ -1,3 +1,5 @@
+.env
 .vagrant
 ~$*
 redcap*.zip
+redcap/

CHANGELOG.md

@@ -3,6 +3,15 @@ All notable changes to the REDCap Deployment project will be documented in this
 This project adheres to [Semantic Versioning](http://semver.org/).
 
 
+## [0.5.0] - 2016-06-14
+### Changed
+- Refactor dev VM and its related deployment scripts to use the vagrant-env plugin, Debian Jessie, and MySQL Community Server (Philip Chase)
+- Fix formatting errors in 'Creating the Test VM With Vagrant' and embellish content (Philip Chase)
+- Use our apache ssl configuration (Philip Chase)
+- Check for box file updates at 'vagrant up' (Philip Chase)
+- Reconfigure how the autonotify plugin deployment integrates with apache (Philip Chase)
+
+
 ## [0.4.1] - 2016-04-25
 ### Changed
 - Correct documentation and make it more suitable for public consumption (Philip Chase)

README.md

@@ -12,22 +12,30 @@ production and staging instances of REDCap at the CTSI.
 
 ## Requirements
 
-A user of these tools will need to download and provide their own REDCap bits,
+A user of these tools will need to download and provide their own REDCap zip file,
 downloaded from Vanderbilt. This REDCap .zip should be placed in the root folder.
 It should not be renamed.
 
-This VM requires that Vagrant, VirtualBox and the vagrant-hostsupdater plugin be installed on the host system.
+This VM requires that Vagrant, VirtualBox, the vagrant-hostsupdater plugin and the vagrant-env plugin be installed on the host system.
 
-See [Creating the Test VM With Vagrant](docs/creating_the_test_vm_with_vagrant.rst) for details on how to mee those requirements.
+See [Creating the Test VM With Vagrant](docs/creating_the_test_vm_with_vagrant.rst) for details on how to meet those requirements.
 
 
-## Using the Development environment
+## Configure the Development Environment
 
-To with the above requirements met, start the VM with the command
+The development environment needs to be configured before it can be started.
+Copy the file _example.env.txt_ to the name _.env_ and customize it for your
+use. Minimally, you will need to set _smtp\_smarthost_ the dns name of a mail
+server your development host can use to deliver mail.  This will allow you to
+better test features that send email.
+
+## Using the Development Environment
+
+With the above requirements and configuration completed, start the VM with the command
 
     vagrant up
 
-After about two minutes, the VM should be accessible at [http://redcap.dev/redcap/](http://redcap.dev/redcap/) and at [https://redcap.dev/redcap/](https://redcap.dev/redcap/)
+After about two minutes, the VM should be accessible at [http://redcap.dev/redcap/](http://redcap.dev/redcap/) and at [https://redcap.dev/redcap/](https://redcap.dev/redcap/) (or whatever URL _URL\_OF\_DEPLOYED\_APP_ is set to in _.env_)
 
 
 ## Hook and Plugin deployment
@@ -49,7 +57,7 @@ ToDo: Convert steps of wiki article to shell script.
 
 ## REDCap installation
 
-We do not currently have a bare-metal installation procedure. That said, the
+CTS-IT does not currently have a bare-metal installation procedure. That said, the
 vagrant files presented in this repo contain many of the required steps in
 such a deployment process. Other steps can be found in the above upgrade
 instructions.

Vagrantfile

@@ -1,17 +1,52 @@
 # -*- mode: ruby -*-
 # vi: set ft=ruby :
 
-# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
-VAGRANTFILE_API_VERSION = "2"
+Vagrant.configure(2) do |config|
 
-Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
-  config.vm.box = "puppetlabs/debian-7.8-64-nocm"
-  config.vm.hostname = "redcap-deployment"
+  # Enable the vagrant env plugin
+  config.env.enable
+
+  config.vm.hostname = ENV["HOSTNAME_IN_GUEST"]
+  config.vm.box = ENV["CONFIG_VM_BOX"]
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  config.vm.box_check_update = true
+
+  config.vm.network "forwarded_port", guest: 80,  host: ENV["FORWARDED_PORT_80"]
+  config.vm.network "forwarded_port", guest: 443, host: ENV["FORWARDED_PORT_443"]
+
+  # Create a private network, which allows host-only access to the machine using a specific IP.
+  config.vm.network "private_network", ip: ENV["VM_IP"]
+
+  # Set the hostname using the vagrant hostupdater plugin
   config.hostsupdater.remove_on_suspend = false
-  config.hostsupdater.aliases = ["redcap.dev"]
-  config.vm.network "private_network", ip: "192.168.33.113"
+  config.hostsupdater.aliases = [ENV["HOSTNAME_IN_HOST"]]
+
+  config.vm.synced_folder "redcap", ENV["PATH_TO_APP_IN_GUEST_FILESYSTEM"],
+    owner: "www-data",
+    group: "vagrant"
+
+  config.vm.provider "virtualbox" do |vb|
+    # vb.memory = "1024"
+    # Get virtual box name vagrant env plugin
+    vb.name = ENV["HOSTNAME_IN_GUEST"]
+  end
+
+  # Run our customizations
   config.vm.provision "shell" do |s|
     s.path = "bootstrap.sh"
   end
-end
 
+  # Restart apache when all done (if using apache)
+  config.vm.provision "shell", run: "always", inline: "service apache2 restart"
+
+  # Help the developer to find the app :)
+  if Vagrant.has_plugin?('vagrant-triggers')
+    config.trigger.after [:up] do
+      system("open -a 'Google Chrome.app' #{ENV['URL_OF_DEPLOYED_APP']}")
+    end
+  end
+
+end

apache-default.conf

@@ -0,0 +1,25 @@
+<VirtualHost *:80>
+    ServerAdmin webmaster@localhost
+
+    DocumentRoot /var/www
+
+    <Directory "/var/www" >
+        AllowOverride all
+    </Directory>
+
+    # Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
+    # error, crit, alert, emerg.
+    # It is also possible to configure the loglevel for particular
+    # modules, e.g.
+    #LogLevel info ssl:warn
+    LogLevel info
+
+    ErrorLog ${APACHE_LOG_DIR}/error.log
+    CustomLog ${APACHE_LOG_DIR}/access.log combined
+
+    # Allow code to detect the testing environment and redirect emails
+    # using EMAIL_DEV_STAG_* php constants such as [email protected]
+    # defined in app/Config/constants.php for cake applications
+    SetEnv IS_MODE_STAGING
+
+</VirtualHost>

apache-ssl.conf

@@ -0,0 +1,41 @@
+<IfModule mod_ssl.c>
+	<VirtualHost _default_:443>
+		ServerAdmin webmaster@localhost
+
+		DocumentRoot /var/www
+
+		<Directory "/var/www" >
+			AllowOverride all
+		</Directory>
+
+		# Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
+		# error, crit, alert, emerg.
+		# It is also possible to configure the loglevel for particular
+		# modules, e.g.
+		#LogLevel info ssl:warn
+		LogLevel info
+
+		ErrorLog ${APACHE_LOG_DIR}/error.log
+		CustomLog ${APACHE_LOG_DIR}/access.log combined
+
+		#   SSL Engine Switch:
+		#   Enable/Disable SSL for this virtual host.
+		SSLEngine on
+
+		#   A self-signed (snakeoil) certificate can be created by installing
+		#   the ssl-cert package. See
+		#   /usr/share/doc/apache2/README.Debian.gz for more info.
+		#   If both key and certificate are stored in the same file, only the
+		#   SSLCertificateFile directive is needed.
+		SSLCertificateFile	/etc/ssl/certs/ssl-cert-snakeoil.pem
+		SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key
+
+		# Allow code to detect the testing environment and redirect emails
+		# using EMAIL_DEV_STAG_* php constants such as [email protected]
+		# defined in app/Config/constants.php for cake applications
+		SetEnv IS_MODE_STAGING
+
+	</VirtualHost>
+</IfModule>
+
+# vim: syntax=apache ts=4 sw=4 sts=4 sr noet

bootstrap.sh

@@ -20,6 +20,9 @@ export DEBIAN_FRONTEND=noninteractive
 # Exit on first error
 set -e
 
+echo "Import environment variables from /vagrant/.env"
+. /vagrant/.env
+
 # Indicate where the vagrant folder is mounted in the guest file system
 SHARED_FOLDER=/vagrant
 
@@ -28,15 +31,62 @@ REDCAP_ZIP=`ls $SHARED_FOLDER/redcap*.zip | grep "redcap[0-9]\{1,2\}\.[0-9]\{1,2
 
 # import helper functions
 . $SHARED_FOLDER/bootstrap_functions.sh
+. $SHARED_FOLDER/redcap_deployment_functions.sh
+
+# Pick a fast mirror...or at least one that works
+log "Picking a fast mirror in the US..."
+apt-get install -y netselect-apt
+cd /etc/apt/
+netselect-apt -c US > ~/netselect-apt.log 2>&1
 
-install_prereqs
-install_redcap
+# Update our repos
+log "Updating apt package indicies..."
+apt-get update
+
+# Install developer tools
+log "Execute: install_utils..."
 install_utils
+
+log "Execute: install_prereqs..."
+install_prereqs $MYSQL_REPO $DB_ROOT_PASS
+apt-get install -y php-pear php5-curl
+
+# prep the /var/www directory
+log "Prep the /var/www file system"
+rm -rf /var/www/redcap/*
+
+# extract a standard REDCap zip file as downloaded from Vanderbilt.
+unzip -o -q $REDCAP_ZIP -d /var/www/
+
+# adjust ownership so apache can write to the temp folders
+chown -R www-data.root $PATH_TO_APP_IN_GUEST_FILESYSTEM/edocs/
+chown -R www-data.root $PATH_TO_APP_IN_GUEST_FILESYSTEM/temp/
+
+REDCAP_VERSION_DETECTED=`ls $PATH_TO_APP_IN_GUEST_FILESYSTEM | grep redcap_v | cut -d 'v' -f2 | sort -n | tail -n 1`
+log "$REDCAP_ZIP content indicates REDCap version: $REDCAP_VERSION_DETECTED"
+
+# create the empty databases and update the cake configuration
+create_database $DB $DB_APP_USER $DB_APP_PASSWORD $DB_HOST $DB_ROOT_PASS
+
+# Configure REDCap to use this database
+update_redcap_connection_settings $PATH_TO_APP_IN_GUEST_FILESYSTEM $DB $DB_APP_USER $DB_APP_PASSWORD $DB_HOST $SALT
+
+# make a config file for the mysql clients
+write_dot_mysql_dot_cnf $DB $DB_APP_USER $DB_APP_PASSWORD $DB_ROOT_PASS
+
+create_redcap_tables $DB $DB_APP_USER $DB_APP_PASSWORD $PATH_TO_APP_IN_GUEST_FILESYSTEM $REDCAP_VERSION_DETECTED
+
+configure_redcap
+configure_php_for_redcap
+configure_redcap_cron
+move_edocs_folder
+set_hook_functions_file
+make_twilio_features_visible
 configure_exim4
 check_redcap_status
 
 # deploy extensions with developer settings
-export REDCAP_ROOT=/var/www/redcap
-export HOOKS_CONFIGURATION=redcap.dev
-export SHIB=0
+
+export PATH_TO_APP_IN_GUEST_FILESYSTEM
+
 /vagrant/deploy_extensions.sh