Connect to FHIR Data in Google Apps Script

Google Apps Script empowers users to build custom functionality within their Google documents, including Google Sheets and Google Docs. Apps Script natively supports SQL Server connectivity via JDBC, providing a powerful extensibility tool for connecting Google cloud applications to external data. Paired with the SQL connectivity offered by CData Connect Cloud, users can easily access live FHIR data directly from within their Google documents.

This article shows how to connect to FHIR in Connect Cloud and provides sample scripting for processing FHIR data in a Google Spreadsheet.

Configure FHIR Connectivity for Google Apps Scripts

Connectivity to FHIR from Google Apps Scripts is made possible through CData Connect Cloud. To work with FHIR data from Google Apps Scripts, we start by creating and configuring a FHIR connection.

CData Connect Cloud uses a straightforward, point-and-click interface to connect to data sources.

1. Log into Connect Cloud, click Connections and click Add Connection
2. Select "FHIR" from the Add Connection panel
3. Enter the necessary authentication properties to connect to FHIR.

   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.

4. Click Create & Test
5. Navigate to the Permissions tab in the Add FHIR Connection page and update the User-based permissions.

Add a Personal Access Token

If you are connecting from a service, application, platform, or framework that does not support OAuth authentication, you can create a Personal Access Token (PAT) to use for authentication. Best practices would dictate that you create a separate PAT for each service, to maintain granularity of access.

1. Click on your username at the top right of the Connect Cloud app and click User Profile.
2. On the User Profile page, scroll down to the Personal Access Tokens section and click Create PAT.
3. Give your PAT a name and click Create.
4. The personal access token is only visible at creation, so be sure to copy it and store it securely for future use.

With the connection configured, you are ready to connect to FHIR data from Google Apps Script.

Connect to FHIR Data from Apps Script

At this point, you should have configured a connection FHIR in Connect Cloud. All that is left new is to use Google Apps Script to access Connect Cloud 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 and 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 = 'tds.cdata.com:14333';
var user = 'CONNECT_USER'; // [email protected]
var userPwd = 'CONNECT_USER_PAT';
var db = 'FHIR1';

var dbUrl = 'jdbc:sqlserver://' + address + ';databaseName=' + 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 Connect Cloud, SELECT data, and populate a spreadsheet. When the script is run, two input boxes will appear:

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

The second asks 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.

Note, while the function is designed for use as a menu option, you can extend it for use as a spreadsheet formula.

/*
 * 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 name = Jdbc.getConnection(dbUrl, {
    user: user, 
    password: userPwd
	}	
  );

  //confirm that var table is a valid table/view
  var dbMetaData = name.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 = name.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 = 'tds.cdata.com:14333';
var user = 'CONNECT_USER'; // [email protected]
var userPwd = 'CONNECT_USER_PAT';
var db = 'FHIR1';

var dbUrl = 'jdbc:sqlserver://' + address + ';databaseName=' + 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 name = Jdbc.getConnection(dbUrl, {
    user: user, 
    password: userPwd
	}
  );

  //confirm that var table is a valid table/view
  var dbMetaData = name.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 = name.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();
}