From 12c95e0da7d65780d987c9da1ec1ce08a420267c Mon Sep 17 00:00:00 2001
From: Mirco Nasuti <mirco.nasuti@chuv.ch>
Date: Fri, 1 Jul 2016 10:12:10 +0200
Subject: [PATCH] refactoring
---
.../hbp/mip/controllers/ExperimentApi.java | 232 ++++++++----------
src/main/java/org/hbp/mip/utils/JSONUtil.java | 5 +
2 files changed, 106 insertions(+), 131 deletions(-)
diff --git a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
index 48721d090..5adbdaa35 100644
--- a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
@@ -19,11 +19,11 @@ import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
-import java.io.*;
-import java.net.HttpURLConnection;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
import java.net.MalformedURLException;
-import java.net.ProtocolException;
-import java.net.URL;
import java.util.LinkedList;
import java.util.List;
import java.util.UUID;
@@ -260,110 +260,7 @@ public class ExperimentApi {
return new ResponseEntity<>(new Gson().toJson(catalog), HttpStatus.valueOf(code));
}
- private void sendExperiment(Experiment experiment) throws MalformedURLException {
- URL obj = new URL(experimentUrl);
-
- // this runs in the background. For future optimization: use a thread pool
- new Thread() {
- @Override
- public void run() {
- try {
- String query = experiment.computeQuery();
- HttpURLConnection con = createConnection(obj, query);
- writeQueryBody(con, query);
- String response = readResponse(con);
-
- // write to experiment
- experiment.setResult(response.replace("\0", ""));
- experiment.setHasError(con.getResponseCode() >= 400);
- experiment.setHasServerError(con.getResponseCode() >= 500);
-
- } catch (ProtocolException pe) {
- LOGGER.trace(pe);
- } catch (IOException ioe) {
- // write error to
- LOGGER.trace(ioe);
- LOGGER.warn("Experiment failed to run properly !");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(ioe.getMessage());
- }
- experiment.finish();
- }
- }.start();
- }
-
- private void sendExaremeExperiment(Experiment experiment) {
- new Thread() {
- @Override
- public void run() {
- try {
- String query = experiment.computeExaremeQuery();
- String url = miningExaremeQueryUrl + "/" + EXAREME_LR_ALGO;
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, query, results);
-
- experiment.setResult(results.toString().replace("\0", ""));
- experiment.setHasError(code >= 400);
- experiment.setHasServerError(code >= 500);
-
- if(!JSONUtil.isJSONValid(experiment.getResult()))
- {
- experiment.setResult("Unsupported variables !");
- }
- } catch (Exception e) {
- LOGGER.trace(e);
- LOGGER.warn("Failed to run Exareme algorithm !");
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
- experiment.finish();
- }
- }.start();
- }
-
- public ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
- Experiment experiment;
- UUID experimentUuid;
- User user = mipApplication.getUser();
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- LOGGER.trace(iae);
- LOGGER.warn("An invalid Experiment UUID was received !");
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Transaction transaction = null;
- try {
- transaction = session.beginTransaction();
-
- Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
- hibernateQuery.setParameter("uuid", experimentUuid);
- experiment = (Experiment) hibernateQuery.uniqueResult();
-
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
-
- experiment.setShared(shared);
- session.update(experiment);
-
- transaction.commit();
- } catch (Exception e) {
- // 404 here probably
- if(transaction != null)
- {
- transaction.rollback();
- }
- throw e;
- }
-
- return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
- }
-
- public ResponseEntity<String> doListExperiments(
+ private ResponseEntity<String> doListExperiments(
boolean mine,
int maxResultCount,
String modelSlug
@@ -419,34 +316,107 @@ public class ExperimentApi {
return new ResponseEntity<>(gson.toJson(experiments), HttpStatus.OK);
}
- private static String readResponse(HttpURLConnection con) throws IOException {
- InputStream stream = con.getResponseCode() < 400 ? con.getInputStream() : con.getErrorStream();
- BufferedReader in = new BufferedReader(new InputStreamReader(stream));
- String inputLine;
- StringBuilder response = new StringBuilder();
- while ((inputLine = in.readLine()) != null) {
- response.append(inputLine + '\n');
+ private ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
+ Experiment experiment;
+ UUID experimentUuid;
+ User user = mipApplication.getUser();
+ try {
+ experimentUuid = UUID.fromString(uuid);
+ } catch (IllegalArgumentException iae) {
+ LOGGER.trace(iae);
+ LOGGER.warn("An invalid Experiment UUID was received !");
+ return ResponseEntity.badRequest().body("Invalid Experiment UUID");
+ }
+
+ Session session = HibernateUtil.getSessionFactory().getCurrentSession();
+ Transaction transaction = null;
+ try {
+ transaction = session.beginTransaction();
+
+ Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
+ hibernateQuery.setParameter("uuid", experimentUuid);
+ experiment = (Experiment) hibernateQuery.uniqueResult();
+
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
+
+ experiment.setShared(shared);
+ session.update(experiment);
+
+ transaction.commit();
+ } catch (Exception e) {
+ // 404 here probably
+ if(transaction != null)
+ {
+ transaction.rollback();
+ }
+ throw e;
}
- in.close();
- return response.toString();
+
+ return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
+ }
+
+ private void sendExperiment(Experiment experiment) throws MalformedURLException {
+ // this runs in the background. For future optimization: use a thread pool
+ new Thread() {
+ @Override
+ public void run() {
+ String url = experimentUrl;
+ String query = experiment.computeQuery();
+
+ // Results are stored in the experiment object
+ try {
+ executeExperiment(url, query, experiment);
+ } catch (IOException e) {
+ LOGGER.trace(e);
+ LOGGER.warn("Experiment failed to run properly !");
+ setExperimentError(e, experiment);
+ }
+
+ experiment.finish();
+ }
+ }.start();
+ }
+
+ private void sendExaremeExperiment(Experiment experiment) {
+ // this runs in the background. For future optimization: use a thread pool
+ new Thread() {
+ @Override
+ public void run() {
+ String query = experiment.computeExaremeQuery();
+ String url = miningExaremeQueryUrl + "/" + EXAREME_LR_ALGO;
+
+ // Results are stored in the experiment object
+ try {
+ executeExperiment(url, query, experiment);
+ } catch (IOException e) {
+ LOGGER.trace(e);
+ LOGGER.warn("Exareme experiment failed to run properly !");
+ setExperimentError(e, experiment);
+ }
+
+ if(!JSONUtil.isJSONValid(experiment.getResult()))
+ {
+ experiment.setResult("Unsupported variables !");
+ }
+
+ experiment.finish();
+ }
+ }.start();
}
- private static void writeQueryBody(HttpURLConnection con, String query) throws IOException {
- DataOutputStream wr = new DataOutputStream(con.getOutputStream());
- wr.write(query.getBytes("UTF8"));
- wr.flush();
- wr.close();
+ private static void executeExperiment(String url, String query, Experiment experiment) throws IOException {
+ StringBuilder results = new StringBuilder();
+ int code = HTTPUtil.sendPost(url, query, results);
+ experiment.setResult(results.toString().replace("\0", ""));
+ experiment.setHasError(code >= 400);
+ experiment.setHasServerError(code >= 500);
}
- private static HttpURLConnection createConnection(URL url, String query) throws IOException {
- HttpURLConnection con = (HttpURLConnection) url.openConnection();
- con.setRequestMethod("POST");
- con.addRequestProperty("Content-Type", "application/json");
- con.setRequestProperty("Content-Length", Integer.toString(query.length()));
- con.setInstanceFollowRedirects(true);
- con.setReadTimeout(3600000); // 1 hour: 60*60*1000 ms
- con.setDoOutput(true);
- return con;
+ private static void setExperimentError(IOException e, Experiment experiment) {
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ experiment.setResult(e.getMessage());
}
private static boolean isExaremeAlgo(Experiment experiment) {
diff --git a/src/main/java/org/hbp/mip/utils/JSONUtil.java b/src/main/java/org/hbp/mip/utils/JSONUtil.java
index ee987f480..938cfbb70 100644
--- a/src/main/java/org/hbp/mip/utils/JSONUtil.java
+++ b/src/main/java/org/hbp/mip/utils/JSONUtil.java
@@ -11,6 +11,11 @@ public class JSONUtil {
private static final Logger LOGGER = Logger.getLogger(JSONUtil.class);
+ private JSONUtil() {
+ /* Hide implicit public constructor */
+ throw new IllegalAccessError("JSONUtil class");
+ }
+
public static boolean isJSONValid(String test) {
try {
new JsonParser().parse(test);
--
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