ALS-7778: Fix bottleneck in wildfly

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTFilter.java

@@ -296,7 +296,7 @@ private HashMap<String, Object> prepareRequestMap(ContainerRequestContext reques
                             Response formatResponse = resourceWebClient.queryFormat(resource.getResourceRSPath(), queryRequest);
                             if (formatResponse.getStatus() == 200) {
                                 // add the formatted query if available
-                                String formattedQuery = IOUtils.toString((InputStream) formatResponse.getEntity(), "UTF-8");
+                                String formattedQuery = (String) formatResponse.getEntity();
                                 logger.debug("Formatted response: " + formattedQuery);
                                 requestMap.put("formattedQuery", formattedQuery);
                             }

pic-sure-api-wildfly/src/test/java/edu/harvard/dbmi/avillach/AggregateResourceIT.java

@@ -145,7 +145,7 @@ public void testQuery() throws IOException {
         //Should throw an error if credentials missing or wrong
         System.out.println("401 URL: " + endpointUrl+"/query" + "|headers: " + headers + "|body: " + body);
         HttpResponse response = retrievePostResponse(endpointUrl+"/query", headers, body);
-//        System.out.println("Test Response: " + IOUtils.toString(response.getEntity().getContent(), "UTF-8"));
+//        System.out.println("Test Response: " + EntityUtils.toString(response.getEntity().getContent(), "UTF-8"));
         assertEquals("Missing credentials should return a 401", 401, response.getStatusLine().getStatusCode());
         JsonNode responseMessage = objectMapper.readTree(response.getEntity().getContent());
         assertNotNull("Response message should not be null", responseMessage);

pic-sure-api-wildfly/src/test/java/edu/harvard/dbmi/avillach/IRCTResourceIT.java

@@ -408,7 +408,7 @@ public void testQueryResult() throws UnsupportedOperationException, IOException
 		body = objectMapper.writeValueAsString(queryRequest);
 		response = retrievePostResponse(irctEndpointUrl+"pic-sure/v1.4/query/"+testQueryResultId+"/result", headers, body);
 		assertEquals("Correct request should return a 200",200, response.getStatusLine().getStatusCode());
-		String responseBody = IOUtils.toString(response.getEntity().getContent(), "UTF-8");
+		String responseBody = EntityUtils.toString(response.getEntity().getContent(), "UTF-8");
 		assertFalse("Response content should not be empty", responseBody.isEmpty());
 	}
 

pic-sure-api-wildfly/src/test/java/edu/harvard/dbmi/avillach/PicsureQueryServiceIT.java

@@ -150,7 +150,7 @@ public void testResult() throws Exception {
         //This should return some kind of result
         response = retrievePostResponse(uri, headers, objectMapper.writeValueAsString(resultRequest));
         assertEquals("Correct request should return a 200", 200, response.getStatusLine().getStatusCode());
-        String result = IOUtils.toString(response.getEntity().getContent(), "UTF-8");
+        String result = EntityUtils.toString(response.getEntity().getContent(), "UTF-8");
         assertNotNull("Result should not be null, result");
 
         //Nonexistent resultId

pic-sure-api-wildfly/src/test/java/edu/harvard/dbmi/avillach/SystemServiceIT.java

@@ -22,7 +22,7 @@ public void testStatusIsAccessibleToSystemUser() throws Exception {
 			get.setHeader(HttpHeaders.AUTHORIZATION, "Bearer "+ jwt);
 			HttpResponse response = client.execute(get);
 			assertEquals("Response status code should be 200", 200, response.getStatusLine().getStatusCode());
-			assertEquals("System status should be RUNNING'", "RUNNING", IOUtils.toString(response.getEntity().getContent(), "UTF-8"));
+			assertEquals("System status should be RUNNING'", "RUNNING", EntityUtils.toString(response.getEntity().getContent(), "UTF-8"));
 
 		}catch(Exception e) {
 			fail("Exception: " + e.getMessage());

pic-sure-initializer/src/main/java/edu/harvard/hms/dbmi/avillach/PicSureInitializer.java

@@ -75,8 +75,8 @@ private static void parseCommandLine(String[] args) throws ParseException, FileN
 			printHelpAndExit();
 		}
 		url = cmd.getOptionValue("p");
-		users = IOUtils.toString(new FileInputStream(cmd.getOptionValue("u")), "UTF-8");
-		resources = IOUtils.toString(new FileInputStream(cmd.getOptionValue("r")), "UTF-8");
+		users = EntityUtils.toString(new FileInputStream(cmd.getOptionValue("u")), "UTF-8");
+		resources = EntityUtils.toString(new FileInputStream(cmd.getOptionValue("r")), "UTF-8");
 		token = cmd.getOptionValue("t");
 	}
 

pic-sure-resources/pic-sure-ga4gh-dos/src/main/java/edu/harvard/hms/dbmi/avillach/GA4GHResourceRS.java

@@ -22,6 +22,7 @@
 
 import edu.harvard.dbmi.avillach.service.IResourceRS;
 import org.apache.http.message.BasicHeader;
+import org.apache.http.util.EntityUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -278,7 +279,7 @@ public QueryStatus query(QueryRequest queryJson) {
 		// If the HTTP Response is a success, then returns an object like so: {"resultId":230464}
 		//TODO later Add things like duration and expiration
 		try {
-			String responseBody = IOUtils.toString(response.getEntity().getContent(), "UTF-8");
+			String responseBody = EntityUtils.toString(response.getEntity(), "UTF-8");
 			JsonNode responseNode = json.readTree(responseBody);
 
             long endtime = new Date().getTime();

pic-sure-resources/pic-sure-ga4gh-dos/src/main/java/edu/harvard/hms/dbmi/avillach/HttpClientUtil.java

@@ -19,6 +19,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import edu.harvard.dbmi.avillach.util.exception.ResourceCommunicationException;
+import org.apache.http.util.EntityUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -56,7 +57,7 @@ public static HttpResponse retrievePostResponse(String uri, String token) {
 
 	public static <T> List<T> readListFromResponse(HttpResponse response, Class<T> expectedElementType) {
 		try {
-			String responseBody = IOUtils.toString(response.getEntity().getContent(), "UTF-8");
+			String responseBody = EntityUtils.toString(response.getEntity(), "UTF-8");
 			return json.readValue(responseBody, new TypeReference<List<T>>() {});
 		} catch (IOException e) {
 			e.printStackTrace();
@@ -66,7 +67,7 @@ public static <T> List<T> readListFromResponse(HttpResponse response, Class<T> e
 
 	public static <T> List<T> readDataObjectsFromResponse(HttpResponse response, Class<T> expectedElementType) {
 		try {
-			String responseBody = IOUtils.toString(response.getEntity().getContent(), "UTF-8");
+			String responseBody = EntityUtils.toString(response.getEntity(), "UTF-8");
 			// Get only the data_objects field from the returned structure. Ugly, but has to de- and then re-serialize
             JsonNode jn = json.readTree(responseBody);
             if (null == jn.get("data_objects")) {