Merge branch 'release/1.0.0'

Author: pbchase

.gitignore

@@ -7,3 +7,5 @@ redcap/
 build
 *.pyc
 .idea
+settings/*.ini
+v

AUTHORS.md

@@ -0,0 +1,12 @@
+# Contributors
+
+The REDCap Deployment project would not be possible without generous contributions from our authors and funders.
+
+David R Nelson, Director of the University of Florida Clinical Translational Science Institute, provides funding support for the UF CTSI REDCap team via UF CTSA Award and matching funds from the UF Office of Research.
+
+Matthew McConnell provided excellent examples of Fabric API tools in his work on the [Quality Improvement Registry](https://github.com/ctsit/qipr_approver).
+
+Philip Chase ([email protected]) was the principle designer on the project.  The development team includes Philip Chase, Sreeja Kannagundla, Stewart Wehmeyer, Taryn Stoffs, and Erik C. Schmidt.
+
+Taryn Stoffs, Amber L. Allen, Christopher P. Barnes, Matthew McConnell, Patrick F. White, Kevin S. Hanson, and Taryn Stoffs provided valuable contributions to documentation and publications.
+

CHANGELOG.md

@@ -2,6 +2,19 @@
 All notable changes to the REDCap Deployment project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [1.0.0] - 2017-05-19
+### Changed
+- Replace Vagrant-based REDCap deployment with Fabric-based deployment (Philip Chase)
+- Clean up files on the root of the project (Philip Chase)
+- Add test_plugin task to fabfile to test a plugin under development in the host OS (Philip Chase)
+- Moved settings/*.ini files to *.example
+
+### Added
+- Add Authors file (Philip Chase)
+
+### Removed
+- Remove old hooks, plugins, and config files (Philip Chase)
+
 
 ## [0.9.1] - 2017-04-21
 ### Added

Makefile

@@ -2,7 +2,7 @@
 
 ## Overview
 
-This project provides tools for scripted deployments and upgrades of REDCap instances and the extensions installed within them. The toolset achieves this through scripted building of packages of the REDCap with extensions as well as the scripted deployment of those packages to hosts. The goal of the project is to provide a tool set that can build packages rapidly and consistently across REDCap version numbers and deploy those packages to new and existing REDCap instances. This will reduce the variability between development, testing, and production environments. This in turn will reduce the error rates, the cost of testing, and the costs of upgrading REDCap instances.
+This project provides tools for scripted deployments and upgrades of REDCap instances and the extensions installed within them. The toolset achieves this through scripted building of packages of the REDCap with extensions as well as the scripted deployment of those packages to hosts. The goal of the project is to provide a tool set that can build packages rapidly and consistently across REDCap version numbers and deploy those packages to new and existing REDCap instances. This reduces the variability between development, testing, and production environments. This in turn reduces the error rates, the cost of testing, and the costs of upgrading REDCap instances.
 
 Ancillary to this goal, this project provides a local REDCap instance that can be used as an educational REDCap tool and/or a software development test bed. You can use this project for any or all of these goals.
 
@@ -17,11 +17,11 @@ root folder of this project. It should not be renamed.
 
 ### Virtual Machine
 
-This project provides a virtual machine wherein it hosts the local REDCap instance. Creating the virtual machine (VM) the software packages Vagrant, VirtualBox, the vagrant-hostsupdater plugin and the vagrant-env plugin be installed on the host system.
+This project provides a virtual machine wherein it hosts the local REDCap instance. Creating the virtual machine (VM) required the software packages Vagrant, VirtualBox, the vagrant-hostsupdater plugin and the vagrant-env plugin be installed on the host system.
 
 ### Packaging and Deployment
 
-The packaging and deployment tools are designed to deploy REDCap to Debian Linux hosts. They may or may not work with non-Debian REDCap hosts and cannot deploy REDCap to Windows hosts. The packaging and deployment tools written using the [Fabric](http://www.fabfile.org/) system. Fabric is written in Python, so both Python 2.7 and Fabric must be installed to do packaging and deployment.
+The packaging and deployment tools are designed to deploy REDCap to Debian Linux hosts. They may or may not work with non-Debian REDCap hosts.  They cannot deploy REDCap to Windows hosts. The packaging and deployment tools are written using the [Fabric](http://www.fabfile.org/) system. Fabric is written in Python, so both Python 2.7 and Fabric must be installed to do packaging and deployment.
 
 
 ## Installing dependencies
@@ -41,8 +41,8 @@ On a Mac OSX machine:
 On Mac OSX users using [Homebrew](http://brew.sh/) can install these packages
 using the _brew_ command.  Run these commands at a shell:
 
-    brew install virtualbox
-    brew install vagrant
+    brew cask install virtualbox
+    brew cask install vagrant
 
 
 ### Install Vagrant plugins
@@ -52,7 +52,7 @@ Vagrant will need a few plugins for this VM. On any platform, run these commands
     vagrant plugin install vagrant-hostsupdater
     vagrant plugin install vagrant-env
 
-Mac OSX users might enjoy the functionality of the vagrant-triggers plugin.  CTS-IT used it to open the Chrome browser to the just -deployed REDCap instance. Run this command at a shell to install it.
+Mac OSX users might enjoy the functionality of the vagrant-triggers plugin.  CTS-IT uses it to open the Chrome browser to the root of the web site. Run this command at a shell to install it.
 
     vagrant plugin install vagrant-triggers
 
@@ -61,9 +61,7 @@ For more details about Vagrant software you can go to [why-vagrant](https://docs
 
 ### Get your REDCap zip file
 
-You must provide a copy of the REDCap software from https://projectredcap.org/. Save the .zip file with its default name to the root of this repository. This ensures the packaging and provisioning scripts can locate the REDCap code when needed.
-
-If you put multiple redcap\*.zip files in the root folder, the provisioning script will default to using the one with the highest version number.
+You must provide a copy of the REDCap software from <https://projectredcap.org/>. Save the .zip file with its default name to the root of this repository. This ensures the packaging and provisioning scripts can locate the REDCap code when needed.
 
 
 ## Configure the Virtual Machine
@@ -81,17 +79,48 @@ With the above requirements and configuration completed, start the VM with the c
 
     vagrant up
 
-After about two minutes, the VM should be accessible at the value you set for _URL\_OF\_DEPLOYED\_APP_ is set to in _.env_  By default this is [http://redcap.dev/redcap/](http://redcap.dev/redcap/)
+The vagrant-hostsupdater plugin will make modifications to your hosts file as the VM starts.  If it prompts you for a password, provide the password you use to login to your computer.
+
+After about two minutes, the VM should be accessible at the value of the variable _URL\_OF\_DEPLOYED\_APP_ set in _.env_  By default this is [http://redcap.dev/redcap/](http://redcap.dev/redcap/)
 
 
 ## (Re)deploying REDCap with Fabric Tools
 
-In addition to the REDCap deployed by the Vagrant provisioning scripts, this repository includes a suite of deployment and upgrade tools that can configure a host for deployment, package REDCap with numerous extensions, deploy a new REDCap instance and upgrade an existing one.  You can use these commands any host where you have sufficient privileges or against this vagrant-deployed VM.  If you had a REDCap zip file, say redcap7.2.2.zip, you could deploy it to the local Vagrant REDCap instance with these commands:
+In addition to the REDCap deployed by the Vagrant provisioning scripts, this repository includes a suite of deployment and upgrade tools that can configure a host for deployment, package REDCap with numerous extensions, deploy a new REDCap instance and upgrade an existing one.  You can use these commands any host where you have sufficient privileges or against this vagrant-deployed VM.
+
+### Fabric Prerequisites
+
+The Fabric tools require a few python libraries that might not be installed on your computer.  To install them run these commands:
+
+    pip install fabric
+    pip install configparser
+    pip install pycurl
+    pip install cryptography
+
+If you have problems install or using these libraries, you might be well-served to setup a Python _virtual environment_. For more information on that see [Virtual Environment Notes](docs/virtual_env_notes.md)
+
+
+### Configure Fabric for the Virtual Machine
 
-    fab vagrant setup_server
+The Fabric tools need to be configured for the Vagrant VM before they can be used.
+Copy the file settings/example.vagrant.ini to the name settings/vagrant.ini customize it to your needs.
+
+    cp settings/example.vagrant.ini settings/vagrant.ini
+
+Customization is not _required_ but it is useful to add patches and language modules.
+
+
+### REDCap Deployment
+
+If you have a REDCap zip file, say redcap7.2.2.zip, you can deploy it to the local Vagrant REDCap instance with these commands:
+
+    fab vagrant server_setup
     fab vagrant package:redcap7.2.2.zip
     fab vagrant delete_all_tables deploy:redcap-7.2.2.tgz
 
+
+### REDCap upgrade
+
 Any upgrade to 7.3.0 would be as simple as
 
     fab vagrant package:redcap7.3.0_upgrade.zip

README.md

@@ -26,12 +26,8 @@ echo "Import environment variables from /vagrant/.env"
 # Indicate where the vagrant folder is mounted in the guest file system
 SHARED_FOLDER=/vagrant
 
-# Use the latest redcap*.zip file in $SHARED_FOLDER
-REDCAP_ZIP=`ls $SHARED_FOLDER/redcap*.zip | grep "redcap[0-9]\{1,2\}\.[0-9]\{1,2\}\.[0-9]\{1,2\}\.zip" | sort -n | tail -n 1`
-
 # 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..."
@@ -61,39 +57,14 @@ if [ -L /var/www/redcap ]; then
     rm /var/www/redcap
 fi
 
-# 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/
+mkdir /var/www/redcap
+cp /vagrant/files/prompt_to_install.html /var/www/redcap/index.html
 
-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 the empty databases
 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 the mail server
 configure_exim4
-check_redcap_status
-
-# deploy extensions with developer settings
-
-export PATH_TO_APP_IN_GUEST_FILESYSTEM
-
-/vagrant/deploy_hooks.sh
-/vagrant/deploy_plugins.sh

aliases

@@ -25,14 +25,7 @@ function install_utils() {
     apt-get install -y git vim ack-grep unzip \
         tree colordiff libxml2-utils xmlstarlet nmap
 
-    cp /vagrant/dot_files/bash_aliases  /home/vagrant/.bash_aliases
-    cp /vagrant/dot_files/bashrc        /home/vagrant/.bashrc
-    cp /vagrant/dot_files/vimrc         /home/vagrant/.vimrc
     chown -R vagrant.vagrant /home/vagrant
-
-    cp /vagrant/dot_files/bash_aliases  /root/.bash_aliases
-    cp /vagrant/dot_files/bashrc        /root/.bashrc
-    cp /vagrant/dot_files/vimrc         /root/.vimrc
 }
 
 function install_prereqs() {
@@ -96,7 +89,7 @@ END
 
     log "Link config files for apache port 443"
     find /etc/apache2/sites-* | xargs -i ls -l {}
-    cp /vagrant/apache-ssl.conf /etc/apache2/sites-available/default-ssl.conf
+    cp /vagrant/files/apache-ssl.conf /etc/apache2/sites-available/default-ssl.conf
     ln -sfv /etc/apache2/sites-available/default-ssl.conf /etc/apache2/sites-enabled/apache-ssl.conf
 
     log "Link config files for apache port 80"
@@ -106,7 +99,7 @@ END
     OLD_APACHE_DEFAULT=/etc/apache2/sites-available/000-default.conf
     if [ -e $OLD_APACHE_DEFAULT ]; then rm $OLD_APACHE_DEFAULT; fi
 
-    cp /vagrant/apache-default.conf /etc/apache2/sites-available/000-default.conf
+    cp /vagrant/files/apache-default.conf /etc/apache2/sites-available/000-default.conf
     ln -sfv /etc/apache2/sites-available/000-default.conf  /etc/apache2/sites-enabled/000-default.conf
 
     log "Enable apache modules"

bootstrap.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+set -e
+
+export MYTARGETDIR=$1
+
+# determine the directory where this script resides
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# get source files
+TEMPDIR=`mktemp -d`
+git clone ssh://[email protected]/form_render_skip_logic.git $TEMPDIR
+
+# If you need to checkout code from another branch, uncomment and adjust this line
+# git --git-dir=$TEMPDIR/.git --work-tree=$TEMPDIR checkout develop
+
+# copy files to the correct target locations
+mkdir -p $MYTARGETDIR
+cp $TEMPDIR/frsl_data_collection_instruments.php $MYTARGETDIR
+cp $TEMPDIR/frsl_record_home_page.php $MYTARGETDIR
+cp $TEMPDIR/frsl_dashboard.php $MYTARGETDIR
+
+rm -rf $TEMPDIR