Connect to FHIR Data in Google Apps Script

Google Apps Script gives you the ability to create custom functionality within your Google documents, including Google Sheets, Google Docs, and more. With the CData SQL Gateway, you can create a MySQL interface for any ODBC driver, including the 200+ drivers by CData for sources like FHIR. The MySQL protocol is natively supported through the JDBC service in Google Apps Script, so by utilizing the SQL Gateway, you gain access to live FHIR data within your Google documents.

This article discusses connecting to the ODBC Driver for FHIR from Google Apps Script, walking through the process of configuring the SQL Gateway and providing sample scripting for processing FHIR data in a Google Spreadsheet.

Real-Time Connectivity Through SQL Gateway

With SQL Gateway, your local ODBC data sources can look and behave like a standard MySQL database. Simply create a new MySQL remoting service in the SQL Gateway for the ODBC Driver for FHIR and ensure that the SQL Gateway is installed on a web-facing machine (or can connect to a hosted SSH server).

Connect to FHIR Data

If you have not already done so, provide values for the required connection properties in the data source name (DSN). You can use the built-in Microsoft ODBC Data Source Administrator to configure the DSN. This is also the last step of the driver installation. See the "Getting Started" chapter in the help documentation for a guide to using the Microsoft ODBC Data Source Administrator to create and configure a DSN.

Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.

Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.

Sample Service Base URLs

• Generic: http://my_fhir_server/r4b/
• Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
• AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
• Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/

Generic FHIR Instances

The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.

Create a MySQL Remoting Service for FHIR Data

See the SQL Gateway Overview to set up connectivity to FHIR data as a virtual MySQL database. You will configure a MySQL remoting service that listens for MySQL requests from clients. The service can be configured in the SQL Gateway UI.

Configure Remote Access

If your ODBC Driver and the remoting service are installed on-premise (and not accessible from Google Apps Script), you can use the reverse SSH tunneling feature to enable remote access. For detailed instructions, read our Knowledge Base article: SQL Gateway SSH Tunneling Capabilities.

Connecting to FHIR Data with Apps Script

At this point, you should have configured the SQL Gateway for FHIR data. All that is left now is to use Google Apps Script to access the MySQL remoting service and work with your FHIR data in Google Sheets.

In this section, you will create a script (with a menu option to call the script) to populate a spreadsheet with FHIR data. We have created a sample script and explained the different parts. You can view the raw script at the end of the article.

1. Create an Empty Script

To create a script for your Google Sheet, click Tools Script editor from the Google Sheets menu:

2. Declare Class Variables

Create a handful of class variables to be available for any functions created in the script.

//replace the variables in this block with real values as needed
var address = 'my.server.address:port';
var user = 'SQL_GATEWAY_USER';
var userPwd = 'SQL_GATEWAY_PASSWORD';
var db = 'CData FHIR Sys';

var dbUrl = 'jdbc:mysql://' + address + '/' + db;

3. Add a Menu Option

This function adds a menu option to your Google Sheet, allowing you to use the UI to call your function.

function onOpen() {
  var spreadsheet = SpreadsheetApp.getActive();
  var menuItems = [
    {name: 'Write data to a sheet', functionName: 'connectToFHIRData'}
  ];
  spreadsheet.addMenu('FHIR Data', menuItems);
} 

4. Write a Helper Function

This function is used to find the first empty row in a spreadsheet.

/*
 * Finds the first empty row in a spreadsheet by scanning an array of columns
 * @return The row number of the first empty row.
 */
function getFirstEmptyRowByColumnArray(spreadSheet, column) {
  var column = spreadSheet.getRange(column + ":" + column);
  var values = column.getValues(); // get all data in one call
  var ct = 0;
  while ( values[ct] && values[ct][0] != "" ) {
    ct++;
  }
  return (ct+1);
}

5. Write a Function to Write FHIR Data to a Spreadsheet

The function below writes the FHIR data, using the Google Apps Script JDBC functionality to connect to the MySQL remoting service, SELECT data, and populate a spreadsheet. When the script is run, two input boxes will appear:

The first one asking the user to input the name of a sheet to hold the data (if the spreadsheet does not exist, the function creates it)

and the second one asking the user to input the name of a FHIR table to read. If an invalid table is chosen, an error message appears and the function is exited.

It is worth noting that, while the function is designed to be used as a menu option, it could be extended for use as a formula in a spreadsheet.

/*
 * Reads data from a specified FHIR 'table' and writes it to the specified sheet.
 *    (If the specified sheet does not exist, it is created.)
 */
function connectToFHIRData() {
  var thisWorkbook = SpreadsheetApp.getActive();

  //select a sheet and create it if it does not exist
  var selectedSheet = Browser.inputBox('Which sheet would you like the data to post to?',Browser.Buttons.OK_CANCEL);
  if (selectedSheet == 'cancel')
    return;

  if (thisWorkbook.getSheetByName(selectedSheet) == null)
    thisWorkbook.insertSheet(selectedSheet);
  var resultSheet = thisWorkbook.getSheetByName(selectedSheet);
  var rowNum = 2;

  //select a FHIR 'table'
  var table = Browser.inputBox('Which table would you like to pull data from?',Browser.Buttons.OK_CANCEL);
  if (table == 'cancel')
    return;

  var conn = Jdbc.getConnection(dbUrl, user, userPwd);

  //confirm that var table is a valid table/view
  var dbMetaData = conn.getMetaData();
  var tableSet = dbMetaData.getTables(null, null, table, null);
  var validTable = false;
  while (tableSet.next()) {
    var tempTable = tableSet.getString(3);
    if (table.toUpperCase() == tempTable.toUpperCase()){
      table = tempTable;
      validTable = true;
      break;
    }
  } 
  tableSet.close();
  if (!validTable) {
    Browser.msgBox("Invalid table name: " + table, Browser.Buttons.OK);
    return;
  }

  var stmt = conn.createStatement();

  var results = stmt.executeQuery('SELECT * FROM ' + table);
  var rsmd = results.getMetaData();
  var numCols = rsmd.getColumnCount();

  //if the sheet is empty, populate the first row with the headers
  var firstEmptyRow = getFirstEmptyRowByColumnArray(resultSheet, "A");
  if (firstEmptyRow == 1) {
    //collect column names
    var headers = new Array(new Array(numCols));
    for (var col = 0; col < numCols; col++){
      headers[0][col] = rsmd.getColumnName(col+1);
    }
    resultSheet.getRange(1, 1, headers.length, headers[0].length).setValues(headers);
  } else {
    rowNum = firstEmptyRow;
  }

  //write rows of FHIR data to the sheet
  var values = new Array(new Array(numCols));
  while (results.next()) {
    for (var col = 0; col < numCols; col++) {
      values[0][col] = results.getString(col + 1);
    }
    resultSheet.getRange(rowNum, 1, 1, numCols).setValues(values);
    rowNum++;
  }

  results.close();
  stmt.close();
}
  

When the function is completed, you have a spreadsheet populated with your FHIR data and you can now leverage all of the calculating, graphing, and charting functionality of Google Sheets anywhere you have access to the Internet.

Complete Google Apps Script

//replace the variables in this block with real values as needed
var address = 'my.server.address:port';
var user = 'SQL_GATEWAY_USER';
var userPwd = 'SQL_GATEWAY_PASSWORD';
var db = 'CData FHIR Sys';

var dbUrl = 'jdbc:mysql://' + address + '/' + db;

function onOpen() {
  var spreadsheet = SpreadsheetApp.getActive();
  var menuItems = [
    {name: 'Write table data to a sheet', functionName: 'connectToFHIRData'}
  ];
  spreadsheet.addMenu('FHIR Data', menuItems);
}

/*
 * Finds the first empty row in a spreadsheet by scanning an array of columns
 * @return The row number of the first empty row.
 */
function getFirstEmptyRowByColumnArray(spreadSheet, column) {
  var column = spreadSheet.getRange(column + ":" + column);
  var values = column.getValues(); // get all data in one call
  var ct = 0;
  while ( values[ct] && values[ct][0] != "" ) {
    ct++;
  }
  return (ct+1);
}

/*
 * Reads data from a specified 'table' and writes it to the specified sheet.
 *    (If the specified sheet does not exist, it is created.)
 */
function connectToFHIRData() {
  var thisWorkbook = SpreadsheetApp.getActive();

  //select a sheet and create it if it does not exist
  var selectedSheet = Browser.inputBox('Which sheet would you like the data to post to?',Browser.Buttons.OK_CANCEL);
  if (selectedSheet == 'cancel')
    return;

  if (thisWorkbook.getSheetByName(selectedSheet) == null)
    thisWorkbook.insertSheet(selectedSheet);
  var resultSheet = thisWorkbook.getSheetByName(selectedSheet);
  var rowNum = 2;

  //select a FHIR 'table'
  var table = Browser.inputBox('Which table would you like to pull data from?',Browser.Buttons.OK_CANCEL);
  if (table == 'cancel')
    return;

  var conn = Jdbc.getConnection(dbUrl, user, userPwd);

  //confirm that var table is a valid table/view
  var dbMetaData = conn.getMetaData();
  var tableSet = dbMetaData.getTables(null, null, table, null);
  var validTable = false;
  while (tableSet.next()) {
    var tempTable = tableSet.getString(3);
    if (table.toUpperCase() == tempTable.toUpperCase()){
      table = tempTable;
      validTable = true;
      break;
    }
  } 
  tableSet.close();
  if (!validTable) {
    Browser.msgBox("Invalid table name: " + table, Browser.Buttons.OK);
    return;
  }

  var stmt = conn.createStatement();

  var results = stmt.executeQuery('SELECT * FROM ' + table);
  var rsmd = results.getMetaData();
  var numCols = rsmd.getColumnCount();

  //if the sheet is empty, populate the first row with the headers
  var firstEmptyRow = getFirstEmptyRowByColumnArray(resultSheet, "A");
  if (firstEmptyRow == 1) {
    //collect column names
    var headers = new Array(new Array(numCols));
    for (var col = 0; col < numCols; col++){
      headers[0][col] = rsmd.getColumnName(col+1);
    }
    resultSheet.getRange(1, 1, headers.length, headers[0].length).setValues(headers);
  } else {
    rowNum = firstEmptyRow;
  }

  //write rows of FHIR data to the sheet
  var values = new Array(new Array(numCols));
  while (results.next()) {
    for (var col = 0; col < numCols; col++) {
      values[0][col] = results.getString(col + 1);
    }
    resultSheet.getRange(rowNum, 1, 1, numCols).setValues(values);
    rowNum++;
  }

  results.close();
  stmt.close();
}