207 flatten json v5

.gitignore

@@ -6,6 +6,7 @@ local-dev/
 !gradle/wrapper/gradle-wrapper.jar
 !**/src/main/**
 !**/src/test/**
+*.csv
 
 ### STS ###
 .apt_generated

build.gradle

@@ -51,6 +51,8 @@ dependencies {
 	implementation group: 'org.webjars', name: 'swagger-ui', version: '3.24.0'
 	implementation group: 'org.aspectj', name: 'aspectjweaver', version: '1.8.8'
 	implementation group: 'com.google.cloud', name: 'google-cloud-bigquery', version: '1.124.7'
+	implementation group: 'com.google.code.gson', name: 'gson', version: '2.8.5'
+	implementation group: 'com.jayway.jsonpath', name: 'json-path', version: '2.4.0'
 
 	// These dependencies are required to load the logback config file.
 	implementation group: 'org.codehaus.groovy', name: 'groovy', version: '3.0.7'

src/main/java/bio/terra/cda/app/aop/TimerAspect.java

@@ -1,6 +1,7 @@
 package bio.terra.cda.app.aop;
 
 import org.aspectj.lang.ProceedingJoinPoint;
+
 import org.aspectj.lang.Signature;
 import org.aspectj.lang.annotation.Around;
 import org.aspectj.lang.annotation.Aspect;
@@ -19,8 +20,10 @@ public Object executionTimer(ProceedingJoinPoint joinPoint) throws Throwable {
     long start = System.currentTimeMillis();
     Object proceed = joinPoint.proceed();
     long executionTime = System.currentTimeMillis() - start;
+
     Signature signature = joinPoint.getSignature();
     logger.info("--Execution Timer: {} executed in {}ms", signature, executionTime);
+
     return proceed;
   }
 }

src/main/java/bio/terra/cda/app/controller/QueryApiController.java

@@ -15,6 +15,15 @@
 import bio.terra.cda.generated.model.QueryCreatedData;
 import bio.terra.cda.generated.model.QueryResponseData;
 import com.google.cloud.bigquery.BigQueryException;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Collections;
+import java.util.Set;
+import javax.servlet.http.HttpServletRequest;
+import javax.validation.Valid;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -63,9 +72,11 @@ private String createNextUrl(String jobId, int offset, int limit) {
 
   @TrackExecutionTime
   @Override
-  public ResponseEntity<QueryResponseData> query(String id, Integer offset, Integer limit) {
-    var result = queryService.getQueryResults(id, offset, limit);
-    var response =
+  public ResponseEntity<QueryResponseData> query(
+      String id, Integer offset, Integer limit, String format, String includeHeaders) {
+    QueryService.QueryResult result =
+        queryService.getQueryResults(id, offset, limit, format, includeHeaders);
+    QueryResponseData response =
         new QueryResponseData()
             .result(Collections.unmodifiableList(result.items))
             .totalRowCount(result.totalRowCount)