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iCare is a compability layer that stand between PHR (NLM PHR) and EHR (OpenMRS) data conversion

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iCare

iCare is a compability layer that stand between PHR (NLM PHR) and EHR (OpenMRS) data conversion

Project Member

No Profile Picture Member Name Github Userid Student Id Number Role
1. Alvin Callysta @alvincallysta11 0000012551 Product Owner
2. Cika Desela @cikadesela 0000011818 Sprinter
3. Feronia Meilinda @feroniameimei 00000012566 Sprinter
4. Octa Wahana Widiwijaya @octawijayaa 0000019399 Sprinter
5. Sudono Tanjung @sudtanj 00000012273 Scrum Master

Getting Started

Quick Start

  1. Register using the register tab
  2. Enter the personal information including email and password
  3. Click submit
  4. Open email and click the confirmation link
  5. Sign in with the newly created account
  6. Select one of the menu to do import

Main Scenario of Use

The main scenario in the use of this application is the scenario where the patient as the user wants to transfer data for the PHR application he has with the hospital owned EHR. This application will act as a compability layer between the two applications.

System Requirement

  1. Minimum System Requirement 1. Windows or Linux-based Operating System 2. 512 MB ram 3. PHP 5.5.9 4. MYSQL 5.5.57 5. Apache 2 6. Composer

Dependency

  1. phpmailer/phpmailer 6.0
  2. noetix/simple-orm dev-master
  3. bocharsky-bw/arrayzy 0.6.1

Login System

PHP files are colored with yellow color. Mailed PHP files are in blue color. All green color indicates display messages, grey color are the most important action in PHP. Meanwhile, form action file which is being called other than the file itself is in red.

There are three actions where a user can take on index.php page, there are:

  • login.php page : this action will lead user to do login to access their profile or account
  • register.php page : this action will lead user to do registration by fill their first name and last name in required field, signing up their email address and set a password.
  • forgot.php page :

In error.php file, the only thing that prints out the message from the $_SESSION[‘message’] variable, which will be set on the previous page. So, we need to start the session by calling “session_start()” function so we have access to $_SESSION global variable. We need to make sure that the variable is set with “isset()” and not empty “!empty()” functions before attempting to print it out. If the variable is not set, we redirect the user back to the “index.php” page with header() function. Below are the code for error.php

Inside the index.php file, we check if the form is being submitted with method=”post” by making sure the request_method of $_SERVER variable is equal to POST. we then check if the $_POST[‘login’] is set which is a variable of the login form, in that case we proceed to login.php by including the code with “require” keyword. Else if $_POST[‘register’] variable is set, which is a variable of the register form

<?php 
/* Main page with two forms: sign up and log in */
require 'db.php';
session_start();
?>
<!DOCTYPE html>
<html>
<head>
 <title>Sign-Up/Login Form</title>
 <?php include 'css/css.html'; ?>
</head>
<?php 
if ($_SERVER['REQUEST_METHOD'] == 'POST') 
{
   if (isset($_POST['login'])) { //user logging in
      require 'login.php';
   }
   elseif (isset($_POST['register'])) { //user registering
         require 'register.php';
   }
}
?>

Since we’re including login.php and register.php form at the same page, the inclusion of db.php and session_start() will also apply to any page which is being included from index.php, in this case login.php and register.php, so we won’t have to repeat database inclusion and session start function on either pages.

register.php

$_SESSION['email'] = $_POST['email'];
$_SESSION['first_name'] = $_POST['firstname'];
$_SESSION['last_name'] = $_POST['lastname'];


$first_name = $mysqli->escape_string($_POST['firstname']);
$last_name = $mysqli->escape_string($_POST['lastname']);
$email = $mysqli->escape_string($_POST['email']);
$password = $mysqli->escape_string( password_hash($_POST['password'], PASSWORD_BCRYPT) );


$hash = $mysqli->escape_string( md5( rand(0,1000) ) );


// Check if user with that email already exists
$result = $mysqli->query("SELECT * FROM users WHERE email='$email'") or die($mysqli->error);


// We know user email exists if the rows returned are more than 0
if ( $result->num_rows > 0 ) {
   $_SESSION['message'] = 'User with this email already exists!';
   header("location: error.php");
}
else { // Email doesn't already exist in a database, proceed...


   // active is 0 by DEFAULT (no need to include it here)
   $sql = "INSERT INTO users (first_name, last_name, email, password, hash) " 
         . "VALUES ('$first_name','$last_name','$email','$password', '$hash')";


   // Add user to the database
   if ( $mysqli->query($sql) ){
      $_SESSION['active'] = 0; //0 until user activates their account with verify.php
      $_SESSION['logged_in'] = true; // So we know the user has logged in
      $_SESSION['message'] =
            "Confirmation link has been sent to $email, please verify


            your account by clicking on the link in the message!";
      // Send registration confirmation link (verify.php)
      $to      = $email;
      $subject = 'Account Verification ( clevertechie.com )';
      $message_body = '
      Hello '.$first_name.',
      Thank you for signing up!
      Please click this link to activate your account:
      http://localhost/login-system/verify.php?email='.$email.'&hash='.$hash;  
      mail( $to, $subject, $message_body );
      header("location: profile.php"); 
   }

   else {
      $_SESSION['message'] = 'Registration failed!';
      header("location: error.php");
   }
}

We set some session variables which will be used to welcome the user on the profile.php which is where register.php will redirect on a successful register.

SQL

SQL code is used to create the database and user accounts which included in a folder “sql”. Add following code to create the database

CREATE DATABASE accounts;
CREATE TABLE `accounts`.`users` 
(
   `id` INT NOT NULL AUTO_INCREMENT,
   `first_name` VARCHAR(50) NOT NULL,
   `last_name` VARCHAR(50) NOT NULL,
   `email` VARCHAR(100) NOT NULL,
   `password` VARCHAR(100) NOT NULL,
   `hash` VARCHAR(32) NOT NULL,
   `active` BOOL NOT NULL DEFAULT 0,
PRIMARY KEY (`id`) 
);

File sql_import.php is included, which is a PHP script to execute the above SQL code. Make sure to set your own $user and $password variables to connect to MySQL Database

//connection variables
$host = 'localhost';
$user = '';
$password = '';
//create mysql connection


$mysqli = new mysqli($host,$user,$password);
if ($mysqli->connect_errno) {
   printf("Connection failed: %s\n", $mysqli->connect_error);
   die();
}
//create the database
if ( !$mysqli->query('CREATE DATABASE accounts') ) {
   printf("Errormessage: %s\n", $mysqli->error);
}
//create users table with all the fields
$mysqli->query('
CREATE TABLE `accounts`.`users` 
(
   `id` INT NOT NULL AUTO_INCREMENT,
   `first_name` VARCHAR(50) NOT NULL,
   `last_name` VARCHAR(50) NOT NULL,
   `email` VARCHAR(100) NOT NULL,
   `password` VARCHAR(100) NOT NULL,
   `hash` VARCHAR(32) NOT NULL,
   `active` BOOL NOT NULL DEFAULT 0,
PRIMARY KEY (`id`) 
);') or die($mysqli->error);

The db.php file, using PHP “require” construct on most pages, it will simply connects to the ‘accounts’ MySQL database.

The file error.php and success.php are simply for displaying success and error messages respectively.

<?php
/* Displays all error messages */
session_start();
?>
<!DOCTYPE html>
<html>
<head>
 <title>Error</title>
 <?php include 'css/css.html'; ?>
</head>
<body>
<div class="form">
   <h1>Error</h1>
   <p>
  <?php 
   if( isset($_SESSION['message']) AND !empty($_SESSION['message']) ): 
      echo $_SESSION['message'];    
   else:
      header( "location: index.php" );
   endif;
   ?>
   </p>     
   <a href="index.php"><button class="button button-block"/>Home</button></a>
</div>
</body>
</html>

In error.php, it prints out the message from the $_SESSION[‘message’] variable, which will be set on the previous page. First, we need to start the session by calling “session_start()” function so we have access to $_SESSION global variable. Then, we need to make sure that the variable is set with “isset()” and not empty “!empty()” functions before attempting to print it out. If the variable is not set, we redirect the user back to the “index.php” page.

The success.php contains exactly the same code with exception of different title and header.

<?php 
if ($_SERVER['REQUEST_METHOD'] == 'POST') 
{
   if (isset($_POST['login'])) { //user logging in
      require 'login.php';      
   }   
   elseif (isset($_POST['register'])) { //user registering     
      require 'register.php';
   }
}
?>

From a piece of code in index.php above, we check if the form is being submitted with method=”post” by making sure the request_method of $_SERVER variable is equal to POST. then check if the $_POST[‘login’] is set which is a variable of the login form, in that case we proceed to login.php by including the code with “require” keyword. Else if $_POST[‘register’] variable is set, which is a variable of the register form, we proceed to register.php by including it’s code.

Since we including the login.php and register.php in index.php, the inclusion of db.php and session_start will also apply to any page which is being included from index.php. Login.php and register.php won’t have to repeat database inclusion and session start function on either pages.

<?php
/* Registration process, inserts user info into the database 
   and sends account confirmation email message
 */
//Import PHPMailer classes into the global namespace
use PHPMailer\PHPMailer\PHPMailer;
use PHPMailer\PHPMailer\Exception;
require_once 'vendor/autoload.php';
// Set session variables to be used on profile.php page
$_SESSION['email'] = $_POST['email'];
$_SESSION['first_name'] = $_POST['firstname'];
$_SESSION['last_name'] = $_POST['lastname'];
// Escape all $_POST variables to protect against SQL injections
$first_name = $mysqli->escape_string($_POST['firstname']);
$last_name = $mysqli->escape_string($_POST['lastname']);
$email = $mysqli->escape_string($_POST['email']);
$password = $mysqli->escape_string(password_hash($_POST['password'], PASSWORD_BCRYPT));
$hash = $mysqli->escape_string( md5( rand(0,1000) ) );     
// Check if user with that email already exists
$result = $mysqli->query("SELECT * FROM users WHERE email='$email'") or die($mysqli->error());
// We know user email exists if the rows returned are more than 0
if ( $result->num_rows > 0 ) {    
    $_SESSION['message'] = 'User with this email already exists!';
    header("location: error.php");    
}
else { // Email doesn't already exist in a database, proceed...
    // active is 0 by DEFAULT (no need to include it here)
    $sql = "INSERT INTO users (first_name, last_name, email, password, hash) " 
            . "VALUES ('$first_name','$last_name','$email','$password', '$hash')";
    // Add user to the database
    if ( $mysqli->query($sql) ){
        $_SESSION['active'] = 0; //0 until user activates their account with verify.php
        $_SESSION['logged_in'] = true; // So we know the user has logged in
        $_SESSION['message'] =                
                 "Confirmation link has been sent to $email, please verify
                 your account by clicking on the link in the message!";
        // Send registration confirmation link (verify.php)
        $mail = new PHPMailer(true);
        $mail->isSMTP();
        $mail->Host = 'smtp.googlemail.com';  //gmail SMTP server
        $mail->SMTPAuth = true;
        $mail->Username = 'tifuphmedic2015@gmail.com';   //username
        $mail->Password = 'informatics2015';   //password
        $mail->SMTPSecure = 'ssl';
        $mail->Port = 465;                    //SMTP port
        $mail->setFrom('tifuphmedic2015@gmail.com', 'donotreply-ihealth');
        $mail->addAddress($email, $first_name);
       // $to      = $email;
        $mail->Subject = 'Account Verification ( iCare )'; // ( clevertechie.com)
        $mail->Body = '
        Hello '.$first_name.',
        Thank you for signing up!
        Please click this link to activate your account:
        http://'.$_SERVER['HTTP_HOST'].'/verify.php?email='.$email.'&hash='.$hash;  
        //mail( $to, $subject, $message_body );
        $mail->send();    
        header("location: profile.php"); 
    }
    else {
        $_SESSION['message'] = 'Registration failed!';
        header("location: error.php");
    }
}

In register.php, we set some session variables which will be used to welcome the user on the profile.php will redirect on a successful register. Then prepare all the $_POST variables by applying $mysqli->escape_string() function to protect again SQL injections.

$password = $mysqli->escape_string( password_hash($_POST['password'], PASSWORD_BCRYPT) );
$hash = $mysqli->escape_string( md5( rand(0,1000) ) );

The code above create secure password hash and generate a unique hash string. For the $password, it has used the built-in PHP function password_hash() which takes in two parameters, the first is the raw password provided by the user and the second is the encryption algorithm constant -- in this case, PASSWORD_BCRYPT.

To generate unique hash string,we simply use the rand() function which will generate a random number from 0 to 100, and then we use md5() function to generate a unique hash from the random number.

We then check, if the user with the entered email already exist in the database before proceeding, if they do, we redirect to error.php page. If you recall, whenever we run "SELECT" statement in a PHP SQL query, we get the result object returned, so it makes sense to call the variable $result. Here is what the object would look like if we used var_dump() function on it:

var_dump( $result );
//output: object(mysqli_result)#2 (5) { ["current_field"]=> int(0) ["field_count"]=> int(7) ["lengths"]=> NULL ["num_rows"]=> int(0) ["type"]=> int(0) }

there is "num_rows" property, which would be equal to 1 if the user with the email already existed in the database, that's how we find out if the user exists by running the following if statement:

// We know user email exists if the rows returned are more than 0
if ( $result->num_rows > 0 ) {
   $_SESSION['message'] = 'User with this email already exists!';
   header("location: error.php");
}

Else...if the user doesn't exist, we proceed by first preparing the SQL insert statement with all our previously set variables:

// active is 0 by DEFAULT (no need to include it here)
   $sql = "INSERT INTO users (first_name, last_name, email, password, hash) " 
         . "VALUES ('$first_name','$last_name','$email','$password', '$hash')";

We then check if the mysql->query() is successful, if it is, we know the user has been added to the database. Next we set some session variables to be used on the profile.php page

     $_SESSION['active'] = 0; //0 until user activates their account with verify.php
      $_SESSION['logged_in'] = true; // So we know the user has logged in
      $_SESSION['message'] =     
            "Confirmation link has been sent to $email, please verify
            your account by clicking on the link in the message!";

We know the account won't be activated when a user first registers, so we can safely set $_SESSION['active'] to zero. We set the session logged_in to true, so we know the user has logged in and finally the message to display that the account activation link has been sent. The final step, is to send the user an email with the account activation link:

   // Send registration confirmation link (verify.php)
      $to       $email;
      $subject = 'Account Verification ( clevertechie.com )';
      $message_body = '
      Hello '.$first_name.',
      Thank you for signing up!
      Please click this link to activate your account:
      http://localhost/login-system/verify.php?email='.$email.'&hash='.$hash;  
      mail( $to, $subject, $message_body );
      //redirect to profile.php page
      header("location: profile.php");

The PHP mail() function takes in three parameters - $to (user email where to send the message), $subject (email subject) and $message_body (the main body of the email message). The most important part of the verification message if the following URL which sends a user to verify.php with email and hash variables: http://localhost/login-system/verify.php?email='.$email.'&hash='.$hash; By passing email=$email&hash=$hash variables in this way, we'll be able to access them from verify.php from the $_GET global PHP varible and match the user email with their unique hash, so we can verify their account.

Convert OpenMRS

Input

  1. OpenMRS Converter required the OpenMRS user id to begin importing the health data log

Process

  1. OpenMRS Converter call the api from the link http://demo.openmrs.org/openmrs/ws/rest/v1/visit to access the data available via json format.
  2. OpenMRS Converter will fetch all the health data and get all the log information with the specified id
  3. OpenMRS Converter will insert all the data found in the api result to the iCare database and linked it with the user id that logged in at iCare.

MySQL Query

    INSERT INTO healthdata (emailkey,log) VALUES ($email,$visitlog[$i]);

Output

  1. OpenMRS Converter will output a success message whether it got any data or not.
  2. OpenMRS Converter will redirect user out from the module to the main page
  3. iCare will display the new result it got from the updated database.

Convert NLM PHR

Interface of NLM Data Importer

Diagram

Input

  1. Export the health data from NLM PHR export button
  2. Save the file result to the client local hard drive
  3. Upload the data to the NLM Data Import by clicking the choose file
  4. Click parse to continue

Process

  1. iCare app will unpack the uploaded data
  2. It will parse the data and search for the health log
  3. It will import all the health log info to the iCare central database

Output

  1. iCare will output a success importing message
  2. iCare will redirect back user to the main page which show the user profile and health log collection

About

iCare is a compability layer that stand between PHR (NLM PHR) and EHR (OpenMRS) data conversion

Topics

mysql html php healthcare compatibility ehr phr healthcare-application icare

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