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FHIR Bulk Data
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Java - API Examples
Simple Java classes to query the 1upHealth FHIR Analytics server
FHIR Bulk Data Analytics APIs are currently available in the 1up development environment. View the examples below to test in dev.
JDBC Requirement
You need the JDBC driver for Athena connectivity to run the examples
Instructions
https://docs.aws.amazon.com/athena/latest/ug/connect-with-jdbc.htmlThe latest driver (requires JDK 8.0 or later)
https://s3.amazonaws.com/athena-downloads/drivers/JDBC/SimbaAthenaJDBC2.0.7/AthenaJDBC422.0.7.jar
Code
List FHIR Resources
public class ListFHIRresources {
// JDBC configuration and output area
private static final String ATHENA_JDBC_CLASS = "com.simba.athena.jdbc.Driver";
private static final String ATHENA_JDBC_DRIVER = "jdbc:awsathena://AwsRegion=us-east-1";
private static final String ATHENA_OUTPUT_BUCKET = "s3://1uphealth-bulkdata-analytics-dev-output/";
// 1uphealth-bulkdata user credentials
private static final String AWS_ACCESS_KEY_ID = "**CONTACT-1UPHEALTH-FOR-ACCESS**";
private static final String AWS_SECRET_ACCESS_KEY = "**CONTACT-1UPHEALTH-FOR-ACCESS**";
public static void main(String args[]) {
// Measure response time
long start = System.currentTimeMillis();
System.out.println("Starting query...");
disableWarnings();
// JDBC query variables
Connection conn;
Statement stmt;
ResultSet res;
// Result counter
int rowCount = 0;
// JDBC connection properties
Properties properties = new Properties();
properties.put("User", AWS_ACCESS_KEY_ID);
properties.put("Password", AWS_SECRET_ACCESS_KEY);
properties.put("S3OutputLocation", ATHENA_OUTPUT_BUCKET);
try {
// Set up the connection
Class.forName(ATHENA_JDBC_CLASS);
conn = DriverManager.getConnection(ATHENA_JDBC_DRIVER, properties);
// Prepare the sql statement
String sql = "SHOW TABLES FROM 1uphealthbulkdataanalytics";
System.out.println("Query = " + sql);
// Run the query
stmt = conn.createStatement();
res = stmt.executeQuery(sql);
// Output FHIR resources
System.out.println("FHIR Resource List");
while (res.next()) {
System.out.println(++rowCount + " - " + res.getObject(1).toString());
}
// Clean up
conn.close();
stmt.close();
res.close();
} catch (Exception e) {
e.printStackTrace();
}
// Output metrics
System.out.println("End query...");
System.out.println("Execution time: " + (System.currentTimeMillis() - start)*0.001);
System.out.println("Number of resources = " + rowCount);
}
Immunization Report
Query = 13 year old children in Boston who have been immunized for chickenpox (vaccine Code: 21)
Same connection code - Different SQL statement (& output processing)
public class ImmunizationReport {
// JDBC definitions and AWS output area
private static final String ATHENA_JDBC_CLASS = "com.simba.athena.jdbc.Driver";
private static final String ATHENA_JDBC_DRIVER = "jdbc:awsathena://AwsRegion=us-east-1";
private static final String ATHENA_OUTPUT_BUCKET = "s3://1uphealth-bulkdata-analytics-dev-output/";
// 1uphealth-bulkdata user credentials
private static final String AWS_ACCESS_KEY_ID = "**CONTACT-1UPHEALTH-FOR-ACCESS**";
private static final String AWS_SECRET_ACCESS_KEY = "**CONTACT-1UPHEALTH-FOR-ACCESS**";
public static void main(String args[]) {
// Measure response time
long start = System.currentTimeMillis();
System.out.println("Starting query...");
disableWarnings();
// JDBC query variables
Connection conn;
Statement stmt;
ResultSet res;
// Result counter
int rowCount = 0;
// JDBC connection properties
Properties properties = new Properties();
properties.put("User", AWS_ACCESS_KEY_ID);
properties.put("Password", AWS_SECRET_ACCESS_KEY);
properties.put("S3OutputLocation", ATHENA_OUTPUT_BUCKET);
try {
// Set up the connection
Class.forName(ATHENA_JDBC_CLASS);
conn = DriverManager.getConnection(ATHENA_JDBC_DRIVER, properties);
// Prepare the sql statement
String sql = "SELECT p.id AS PID, " +
"p.name[1].family[1] AS LastName, " +
"p.name[1].given[1] AS FirstName, " +
"p.birthdate AS DOB, " +
"i.vaccineCode.coding[1].code AS iCode, " +
"i.vaccineCode.coding[1].display AS iType, " +
"split_part(i.date,'T',1) AS iDate " +
"FROM 1uphealthbulkdataanalytics.patient p, 1uphealthbulkdataanalytics.immunization i " +
"WHERE p.id = (split_part(i.patient.reference, ':', 3)) " +
" AND i.vaccineCode.coding[1].code = '21' " +
" AND p.birthdate > '2015-01-01' " +
" AND p.birthdate < '2015-12-31' " +
" AND p.address[1].city = 'Boston' " +
"ORDER BY LastName, FirstName";
System.out.println("Query = " + sql);
// run the query
stmt = conn.createStatement();
res = stmt.executeQuery(sql);
// Go through query results
while (res.next()) {
rowCount++;
System.out.print("PID - ");
System.out.println(res.getObject(1)); // patient id
System.out.print(res.getObject(2) + ", "); // last name
System.out.print(res.getObject(3) + " "); // first name
System.out.print(res.getObject(4) + " "); // date of birth
System.out.print(res.getObject(5) + " "); // vaccine code
System.out.print(res.getObject(6) + " "); // vaccine text
System.out.println(res.getObject(7)); // vaccine date
}
// Clean-up
conn.close();
stmt.close();
res.close();
} catch (Exception e) {
e.printStackTrace();
}
// Output metrics
System.out.println("End query...");
System.out.println("Execution time: " + (System.currentTimeMillis() - start)*0.001);
System.out.println("Number of records = " + rowCount);
}
