FEMR - Fast Electronic Medical Records

Description

fEMR is a fast EMR solution for remote clinics who depend on speed and ease of use rather than complex features. Check out Team fEMR's website for more information and a live demo.

Community

1. Slack
2. JIRA
3. Team FEMR

Dependencies

• Play Framework

Installation and Deployment

For more information on contributing, please see the CONTRIBUTING.md file. For details regarding installation and deployment, continue reading.

1. Edit application.conf accordingly.

2. Enter the console.

sbt clean compile test dist

3. This will generate a script used for executing FEMR.

CI

This repo uses Github Actions workflows for continuous integration, which can be found under the Actions tab in Github (https://github.com/CPSECapstone/zzs-femr/actions?query=workflow%3A%22Scala+CI%22). The Scala CI workflow runs 'sbt test' whenever code is pushed or a pull request is made to the main branch.

Installation and Deployment

For detailed instructions regarding installation and deployment, please follow the directions in the following link.

• Installation Instructions

Prerequisites: Have MySQL, MySQLWorkbench, and IntelliJ IDEA Ultimate installed on a local machine.

1. Download Scala and Play Framework plugins.

2. Make a new file in the conf folder named application.dev.conf containing database information (see link for more details).

3. Create a new schema "femr_db" in SQL Workbench.

4. Add a Play2 App Configuration on IntelliJ with 2 environment variables: user.dir and config.file.

5. Click the sbt refresh button.

6. Run the configuration on IntelliJ.

Setting up weekly backup reminder

• It is very important for the administrator to backup local data to the remote database.
• A cronjob can be set up before a kit is deployed to automatically display a message once a week.

1. In the command line, type crontab -e
2. A text editor should appear.
3. Add the following line to this file: 0 11 * * 5 /util/WeeklyReminder.sh
4. This will display a reminder pop up at 11:00AM every Friday.

Warnings

• fEMR is not HIPAA compliant (... yet).
• fEMR is not meant to diagnose, treat, cure or prevent disease.
• fEMR may attempt to establish a secure remote connection when internet access becomes available. This behavior is configurable and turned off by default.

Questions?

Email: kevin.zurek@teamfemr.org

Setting up the project with IntelliJ

Required downloads

1. MySQL 5.7
2. Scala Build Tool
3. Java JDK 1.8
4. IntelliJ IDEA Ultimate
5. Git

1. Configure Java JDK 1.8

Download JDK 1.8 using this link or use the following command:

sudo apt-get update
sudo apt-get install openjdk-8-jdk
java -version

You should see the following version:

openjdk version "1.8.0_265"
OpenJDK Runtime Environment (build 1.8.0_265-8u265-b01-0ubuntu2~20.04-b01)
OpenJDK 64-Bit Server VM (build 25.265-b01, mixed mode)

If the correct version of Java isn't shown, run one of the following two commands to switch to JDK 8:

sudo update-alternatives --config java
export JAVA_HOME=`/usr/libexec/java_home -v 1.8`

When prompted, select the JDK 8 alternative.

2. Setup and install SBT

Download Scala Build Tool using this link or with the following command:

echo "deb https://dl.bintray.com/sbt/debian /" | sudo tee -a /etc/apt/sources.list.d/sbt.list
curl -sL "https://keyserver.ubuntu.com/pks/lookup?op=get&search=0x2EE0EA64E40A89B84B2DF73499E82A75642AC823" | sudo apt-key add
sudo apt-get update
sudo apt-get install sbt

SBT runs within the JVM so whichever Java version is set to your JAVA_HOME path will be used.

3. MySQL database setup

Install and configure MySQL using this link or with the following command:

sudo apt update
sudo apt install mysql-server
sudo mysql_secure_installation

Start mysql with one of the two following commands:

sudo mysql
mysql -u USERNAME -p

Create a database with the name femr:

mysql> CREATE DATABASE femr;

Create a user for the database (you will use this later to login to the fEMR app):

mysql> CREATE USER 'user_name'@'localhost' IDENTIFIED BY 'user_password';

Grant access to the mysql database to that user:

mysql> GRANT ALL PRIVILEGES ON femr.* TO 'user_name'@'localhost';

4. Clone the fEMR project

Simply cd into the directory where you want the project to be then clone the fEMR repo:

git clone https://github.com/FEMR/femr.git

5. IntelliJ setup

Install the Scala plugin for IntelliJ.

With IntelliJ open on the welcome screen, press control+shift+a or cmd+shift+a to bring up the quick search bar. Type new project from existing sources and click: import project from existing sources

Select the folder where your fEMR project is located.s

In the project settings, select auto-import and choose your JDK. It should be Java version 1.8. Click finish.

Create a file named application.dev.conf inside /femr/conf and copy and paste the information from application.example.conf into it.

Change two lines in application.dev.conf to match up with your MySQL database user you created:

db.default.username="user_name"
db.default.password="user_password"

In application.conf change four lines to match up with your MySQL database user you created:

default.admin.username="user_name"
default.admin.password="user_password"

db.default.username="user_name"
db.default.password="user_password

If you have IntelliJ Ultimate, you're done! You can run the project. If not we need to do a bit more configuration.

Edit your project configuration. Add two new environment variables:

Name        |    Value
--------------------------
user.dir    |    .../femr
config.file |    .../femr/conf/application.dev.conf

Once those variables are setup, you should be able to run the project. To do so enter run in the sbt shell (the tab should be at the bottom left of the IntelliJ window).

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