Installation v4.0

petercyli edited this page Mar 20, 2017 · 26 revisions

These instructions are for installing the most up-to-date version of popHealth. The instructions are based on installing from the current master branch of the popHealth repository, which should be considered a work in progress until it's tagged with a version number.

There is also a development environment installation instructions. The difference between the two installations is that these set of instructions use Phusion Passenger/Apache as the web application server. With this installation you gain significant performance via optimization provided by the Passenger / Apache application server. For those who wants to try out popHealth and see the performance of popHealth, you should use these set of instructions.

Currently there are some compatibility issues with Firefox. Please use Chrome or IE for the best user experience.

You will need an NLM VSAC account to download value set definitions and finalize the installation of the VM. You can sign up for an NLM VSAC account at https://uts.nlm.nih.gov/home.html (click the "Sign Up" link in the upper right corner of the page.)

The instructions assume that a system user named 'pophealth' wants to install the app in their home directory. This is not a requirement; any user with sudo privileges can install pophealth. Just be sure to adjust the directory paths in the commands below.

1. Installing Ubuntu

The ISO for ubuntu 14.04 LTS can be downloaded from the following URL: http://releases.ubuntu.com/trusty/

These instructions were developed against the "64-bit PC (AMD64) server install CD" (ubuntu-14.04.2-server-amd64.iso).

Installing Ubuntu is a fairly straight-forward process, but for more details on installing Ubuntu please visit the following URLs:

Graphical install using the desktop CD: https://help.ubuntu.com/community/GraphicalInstall

Installation using the Alternate CD (more configuration options): https://help.ubuntu.com/14.04/installation-guide/index.html

Once Ubuntu has been installed you need to update the Apt packages.  Apt is a software package management system used by Ubuntu. Note: the last command in the group below is only necessary if any packages were actually upgraded.

sudo apt-get update
sudo apt-get upgrade
sudo shutdown -r now

2. Configure Proxy Settings

This step is only required if the server you are installing popHealth onto needs to go through an HTTP proxy server to reach the internet. These steps will ensure that the appropriate proxy settings are in place for every user that logs into the system.

Use your favourite text editor to create a file in /etc/profile.d named http_proxy.sh with the following contents. In the sample below, replace your.proxy.host.com with the fully-qualified host name of your proxy server, and your.proxy.port with the port number that the proxy server uses.

# Set up system-wide HTTP proxy settings for all users
http_proxy='http://your.proxy.host.com:your.proxy.port/'
https_proxy='http://your.proxy.host.com:your.proxy.port/'
export http_proxy https_proxy

Set proper permissions on the new file, and load the settings into the current environment. NOTE: the proxy settings will automatically be loaded when a user logs in, but we are manually loading them here, to avoid having to log out and log back in again.

sudo chmod 0644 /etc/profile.d/http_proxy.sh
source /etc/profile.d/http_proxy.sh

Make sure that the sudo command will allow the new proxy settings to be passed to commands it launches. This is done by using your text editor to create a file in the /etc/sudoers.d directory named http_proxy (no extension) with the following contents:

# keep http_proxy environment variables.
Defaults env_keep += "http_proxy https_proxy"

Set proper permissions on the new file:

sudo chmod 0440 /etc/sudoers.d/http_proxy

3. Installing Git

Git is a source control system.  It will be used later to download the popHealth source code.

sudo apt-get install git-core

4. Installing RVM and Ruby 2.1.5

RVM is a system that allows managing different versions of Ruby.  It will allow the correct version of ruby to be easily installed on the system. Ruby is the development language used for the popHealth application.

First we will need to install some dependencies:

sudo apt-get install build-essential openssl libssl-dev libreadline6 libreadline6-dev curl zlib1g zlib1g-dev libyaml-dev libsqlite3-dev sqlite3 libxml2-dev libxslt-dev autoconf libc6-dev ncurses-dev automake libtool bison subversion pkg-config unzip

Next install RVM. This will install RVM for all users

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys D39DC0E3
curl -sSL get.rvm.io | sudo bash -l -s stable

Source the RVM environment so we can use it here:

bash
source /usr/local/rvm/scripts/rvm

Log out, and then log back in again so that the settings RVM installs will be loaded in your environment. Once you have logged back in, run the following commands. These will install some more dependencies.

We will install these dependencies using an admin console. The admin console can be opened with the following command:

sudo -i

Next we want to set the autolibs flag in rvm

rvm autolibs enable

Next we want to install Ruby 2.1.5 using RVM

rvm install 2.1.5

If you get a message about installing dependencies, press 'q'.  We have already installed everything we will need.

Set ruby version 2.1.5 to be the default version:

rvm --default 2.1.5

Finally install bundler.  Bundler is a Ruby Gem that allows downloading additional dependencies once we have the popHealth source code:

gem install bundler -v '1.7.2'

Close the admin console by running:

exit

setup rvm for the admin user:

source /etc/profile.d/rvm.sh
rvm use 2.1.5
rvm --default 2.1.5

5. Installing MongoDB

MongoDB is the database used by popHealth.  To install MongoDB run the commands:

sudo sh -c "echo 'deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen' >> /etc/apt/sources.list"
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10
sudo apt-get update
sudo apt-get install -y mongodb-org

To test connection (wait at least 15 seconds to let the db start up), run the command below. If the command exits with a error about not being able to connect, then reboot, and log back in as the admin user. Sometimes mongodb fails to create a network socket when it is started immediately after installation. It should automatically start when the system is rebooted.

mongo

This should output MongoDB shell version: 2.6.x

Note that the version must read 2.4.0 or later (at the time these instructions were written, the current release version of mongodb was 2.6.11).

Type 'exit' to exit the mongo shell

exit

6. Downloading PopHealth source code

Downloading the pophealth source code from github. The following commands assume that your current directory is located at /home/pophealth

git clone https://github.com/osehra/popHealth.git
cd popHealth
git checkout 2997442a1cbb45669dbaf30235bf71f0dc68af63

Install popHealth and all its dependencies:

bundle install

7. Import the measure bundle

popHealth releases measure bundles that contain the measure artifacts that are needed to begin the measure calculation process:

In addition to the measure bundle, the value sets need to be loaded into popHealth from the NLM VSAC Service. You will need an NLM account in order to complete this step and load value sets from the VSAC service._ Register for an account at: https://uts.nlm.nih.gov/home.html

Run the following commands to create a needed folder sudo mkdir bundles

Run the following command to download and install the measure bundle

bundle exec rake pophealth:download_update_install version=2.6.0 RAILS_ENV=production

8. Configure popHealth mode

popHealth has two modes - 'Multiple Practice mode', and 'Regular mode'.

The 'Regular mode' functions the same way popHealth has been functioning to date.

The 'Multiple Practice mode' is for users that want to report on multiple organizations at once, and have aggregate report capabilities. This mode allows multiple sites/groups/practices/clinics in the same instance of popHealth, while segregating the data through user accounts and role based access.

The popHealth instance is set to 'Regular Mode' by default. To switch to the 'Multiple Practice mode', please do the following:

In the file popHealth.yml which resides in the config folder in the application directory, (filepath - config/popHealth.yml), change the line

use_opml_structure: true

to

use_opml_structure: false

Save and close the file. More information about 'Multiple Practice mode' and role-based access can be found in the Pull request here - https://github.com/OSEHRA/popHealth/pull/10

***Switching from one mode to another is not supported and may cause issues with the application. If you want to switch from one mode to the other, you have to first empty the collections for providers, patients, users, practices, and the caches from MongoDB, and then proceed with #10.

10. Creating an administrator user account

To create the default admin user account, run the following command:

bundle exec rake admin:create_admin_account RAILS_ENV=production

Default Username: pophealth, Password: pophealth

You can change the account password once you log in and go to the 'Edit Account' page from the top right menu.

11. Configure Startup Processes

Please note that the following scripts from step 11 to 13 assumes that the pophealth code are located at /home/pophealth/popHealth. Please modify the script accordingly if the code are placed at a different location

Configure delayed job to start up on server startup. At this point, you should still have a shell open as the pophealth user:

cd ~
echo -e '#!/bin/bash\ncd /home/pophealth/popHealth\n. /usr/local/rvm/scripts/rvm\nbundle exec rake jobs:work RAILS_ENV=production\n' > start_delayed_job.sh
chmod +x start_delayed_job.sh

echo -e 'start on started mongod\nstop on stopping mongod\n\nscript\nexec sudo -u pophealth /home/pophealth/start_delayed_job.sh >> /tmp/delayed_worker.log 2>&1\nend script\n' > /tmp/delayed_worker.conf
sudo mv /tmp/delayed_worker.conf /etc/init/delayed_worker.conf
sudo start delayed_worker

12. Precompile Assets

To set up the asset pipeline and make sure all the images and fonts are included, run the following from the application directory

cd popHealth
rake assets:precompile RAILS_ENV=production RAILS_RELATIVE_URL_ROOT=/home/pophealth/popHealth

13. Configure Passenger / Apache

Install apache and passenger with the following commands:

sudo -i
apt-get install apache2=2.4.*
gem install passenger -v '4.0.50'

These should be the dependencies required for passenger:

apt-get install libcurl4-openssl-dev apache2-prefork-dev libapr1-dev libaprutil1-dev

Install the apache passenger module.  If you need other dependencies, the installer will tell you:

passenger-install-apache2-module

The end of the passenger apache module install will tell you to edit two files.

The following set of commands will do those edits for you.  Update the site configuration with (please note that the script below assume that the pophealth code is installed on /home/pophealth/popHealth):

cat << POPHEALTH_SITE_END > /etc/apache2/sites-available/pophealth
 <VirtualHost *:80>
   PassengerRuby /usr/local/rvm/wrappers/ruby-2.1.5/ruby
   DocumentRoot /home/pophealth/popHealth/public
   TimeOut 1200
   <Directory /home/pophealth/popHealth/public>
      AllowOverride all
      Options -MultiViews
      # comment out the next line if you're on Apache < 2.4
      Require all granted
   </Directory>
  </VirtualHost>
POPHEALTH_SITE_END

Make the default apache site be the pophealth provided content:

rm /etc/apache2/sites-enabled/000-default*
ln -s ../sites-available/pophealth /etc/apache2/sites-enabled/000-default.conf

Update the apache configuration with the following commands:

cat << POPHEALTH_MOD_END > /etc/apache2/conf-available/pophealth
SetEnv SECRET_KEY_BASE `cat /dev/urandom | env LC_CTYPE=c tr -dc 'a-e0-9' | fold -w 64 | head -n 1`
POPHEALTH_MOD_END

ln -s /etc/apache2/conf-available/pophealth /etc/apache2/conf-enabled/pophealth.conf

cat << PASSENGER_CONF_END > /etc/apache2/mods-available/pophealth.conf
LoadModule passenger_module /usr/local/rvm/gems/ruby-2.1.5/gems/passenger-4.0.50/buildout/apache2/mod_passenger.so
PassengerRoot /usr/local/rvm/gems/ruby-2.1.5/gems/passenger-4.0.50
PassengerDefaultRuby /usr/local/rvm/wrappers/ruby-2.1.5/ruby
PASSENGER_CONF_END

ln -f -s /etc/apache2/mods-available/pophealth.conf /etc/apache2/mods-enabled/pophealth.conf

Restart apache:

service apache2 restart

Exit the root shell:

exit

To open the popHealth web app you'll need the server IP address. Open a web browser and enter

http://<server_ip_address>/

14. Importing test patients

There are two methods for importing patient data into popHealth - manual upload of patient file via the popHealth UI or patient API upload via http post. For testing purpose, you can download a test QRDA CAT I patient zip file derived from the Cypress tool version 2.6.1 and manually import the zip file using the popHealth administrator user interface. The test patient zip file can be accessed from https://github.com/OSEHRA/cqmtest/raw/master/cypress2.6-OSEHRA-popHealth/patient_qrda_pophealth.zip.

To import, login into the popHealth application. The import function is located under the Administrator->Patients menu at the top right corner of the user interface. After the import, you should see a total of 56 patients loaded. To perform the CQM calculation, go to the Administrator->Providers menu, and select "Orphans" provider. This will take you to the CQM dashboard. Select reporting period from 1-1-2013 to 12-31-2013 and the CQM to perform the eCQM calculation. Note that the test patient data contain patient encounters dated in 2013 hence you will only see results if the reporting period is set to 2013.

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