diff --git a/src/main/java/org/hbp/mip/MIPApplication.java b/src/main/java/org/hbp/mip/MIPApplication.java
index 7aceb7ed511311627a294faa0e4b2977743a9572..1b1b9fc648c1dd102927b80fc9779a733c2fb3e4 100644
--- a/src/main/java/org/hbp/mip/MIPApplication.java
+++ b/src/main/java/org/hbp/mip/MIPApplication.java
@@ -24,6 +24,7 @@ import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiParam;
+import org.apache.log4j.Logger;
import org.hbp.mip.model.User;
import org.hbp.mip.utils.CORSFilter;
import org.hbp.mip.utils.HibernateUtil;
@@ -92,6 +93,8 @@ import java.security.Principal;
@Api(value = "/", description = "MIP API")
public class MIPApplication extends WebSecurityConfigurerAdapter {
+ private Logger logger = Logger.getLogger(this.getClass());
+
@Autowired
OAuth2ClientContext oauth2ClientContext;
@@ -181,9 +184,9 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
cookie.setPath("/");
response.addCookie(cookie);
} catch (JsonProcessingException e) {
- e.printStackTrace();
+ logger.trace(e);
} catch (UnsupportedEncodingException e) {
- e.printStackTrace();
+ logger.trace(e);
}
return principal;
}
diff --git a/src/main/java/org/hbp/mip/controllers/AppsApi.java b/src/main/java/org/hbp/mip/controllers/AppsApi.java
index aa0bd2357c08c99f8e121ccc85ecb71af9ef6f7c..705fc0736e7d4ecdf2d6c73218d21d310508c558 100644
--- a/src/main/java/org/hbp/mip/controllers/AppsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/AppsApi.java
@@ -5,6 +5,7 @@
package org.hbp.mip.controllers;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.App;
import org.hbp.mip.model.User;
@@ -32,6 +33,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/apps", description = "the apps API")
public class AppsApi {
+ private Logger logger = Logger.getLogger(this.getClass());
+
@Autowired
MIPApplication mipApplication;
@@ -106,6 +109,7 @@ public class AppsApi {
}
catch (ConstraintViolationException cve)
{
+ logger.trace(cve);
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
@@ -114,6 +118,7 @@ public class AppsApi {
}
catch (NonUniqueObjectException nuoe)
{
+ logger.trace(nuoe);
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
diff --git a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
index c3de97577e77150b61e97828f2598652930dce5e..3fb3febd15833459e7fb9b54055aed423cf8f88b 100644
--- a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
@@ -7,6 +7,7 @@ package org.hbp.mip.controllers;
import com.github.slugify.Slugify;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.Article;
import org.hbp.mip.model.User;
@@ -31,6 +32,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/articles", description = "the articles API")
public class ArticlesApi {
+ private Logger logger = Logger.getLogger(this.getClass());
+
@Autowired
MIPApplication mipApplication;
@@ -132,7 +135,7 @@ public class ArticlesApi {
try {
slg = new Slugify();
} catch (IOException e) {
- e.printStackTrace();
+ logger.trace(e);
}
String slug = slg != null ? slg.slugify(article.getTitle()) : "";
diff --git a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
index 8cb6c074b1edf47bd83dc62de6817f602b899e94..cadf43ea34a878031348bf7b916c512887df902a 100644
--- a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
@@ -2,6 +2,7 @@ package org.hbp.mip.controllers;
import com.google.gson.*;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.*;
import org.hbp.mip.utils.HTTPUtil;
@@ -34,6 +35,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@javax.annotation.Generated(value = "class io.swagger.codegen.languages.SpringMVCServerCodegen", date = "2016-01-07T07:38:20.227Z")
public class ExperimentApi {
+ private Logger logger = Logger.getLogger(this.getClass());
+
private static final String EXAREME_ALGO_JSON_FILE="data/exareme_algorithms.json";
private static final Gson gson = new GsonBuilder()
@@ -69,7 +72,7 @@ public class ExperimentApi {
// create query
try {
con.setRequestMethod("POST");
- } catch (ProtocolException pe) {} // ignore; won't happen
+ } catch (ProtocolException pe) { logger.trace(pe); } // ignore; won't happen
con.addRequestProperty("Content-Type", "application/json");
con.setRequestProperty("Content-Length", Integer.toString(query.length()));
con.setFollowRedirects(true);
@@ -99,6 +102,8 @@ public class ExperimentApi {
} 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());
@@ -153,7 +158,8 @@ public class ExperimentApi {
{
transaction.rollback();
}
- e.printStackTrace();
+ logger.trace(e);
+ logger.warn("Cannot create experiment to run ! This is probably caused by a bad request !");
// 400 here probably
return new ResponseEntity<>(e.getMessage(), HttpStatus.BAD_REQUEST);
}
@@ -167,7 +173,7 @@ public class ExperimentApi {
{
sendPost(experiment);
}
- } catch (MalformedURLException mue) {} // ignore
+ } catch (MalformedURLException mue) { logger.trace(mue.getMessage()); } // ignore
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
@@ -233,6 +239,8 @@ public class ExperimentApi {
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());
@@ -259,6 +267,7 @@ public class ExperimentApi {
new JsonParser().parse(test);
} catch (JsonParseException jpe)
{
+ logger.trace(jpe); // This is the normal behavior when the input string is not JSON-ified
return false;
}
return true;
@@ -280,6 +289,8 @@ public class ExperimentApi {
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");
}
@@ -318,6 +329,8 @@ public class ExperimentApi {
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");
}
@@ -357,6 +370,8 @@ public class ExperimentApi {
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");
}
diff --git a/src/main/java/org/hbp/mip/controllers/ModelsApi.java b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
index 42c130cdce9ced7f6a15b18972246121d90fdd38..4679b0857750323e85bc34aecac6c1b8221db550 100644
--- a/src/main/java/org/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
@@ -6,6 +6,7 @@ package org.hbp.mip.controllers;
import com.github.slugify.Slugify;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.*;
import org.hbp.mip.utils.CSVUtil;
@@ -28,6 +29,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@javax.annotation.Generated(value = "class io.swagger.codegen.languages.SpringMVCServerCodegen", date = "2016-01-07T07:38:20.227Z")
public class ModelsApi {
+ private Logger logger = Logger.getLogger(this.getClass());
+
@Autowired
MIPApplication mipApplication;
@@ -166,7 +169,7 @@ public class ModelsApi {
slg = new Slugify();
slug = slg.slugify(model.getTitle());
} catch (IOException e) {
- e.printStackTrace();
+ logger.trace(e);
}
i = 0;
diff --git a/src/main/java/org/hbp/mip/utils/CSVUtil.java b/src/main/java/org/hbp/mip/utils/CSVUtil.java
index f2360b7be9dd248a0ec62994a8c7fe5171e16a35..c001e83b3bd467d814d122299df88bdb22d35a00 100644
--- a/src/main/java/org/hbp/mip/utils/CSVUtil.java
+++ b/src/main/java/org/hbp/mip/utils/CSVUtil.java
@@ -1,5 +1,6 @@
package org.hbp.mip.utils;
+import org.apache.log4j.Logger;
import org.hbp.mip.model.Dataset;
import org.hbp.mip.model.Query;
import org.hbp.mip.model.Variable;
@@ -19,6 +20,8 @@ import java.util.stream.Collectors;
*/
public class CSVUtil {
+ private static Logger logger = Logger.getLogger(CSVUtil.class);
+
private static final String SEPARATOR = ",";
public static Dataset parseValues(String filename, Query query)
@@ -26,7 +29,7 @@ public class CSVUtil {
List<String[]> rows = getRows(filename);
Dataset result = new Dataset();
- String code = GenerateDSCode(query);
+ String code = generateDSCode(query);
Date date = new Date();
List<String> header = new LinkedList<>();
List<String> grouping = new LinkedList<>();
@@ -140,7 +143,7 @@ public class CSVUtil {
data.put(c, ll);
}
} catch (IOException e) {
- e.printStackTrace();
+ logger.trace(e);
}
result.setCode(code);
result.setDate(date);
@@ -167,7 +170,8 @@ public class CSVUtil {
isr.close();
is.close();
} catch (IOException e) {
- e.printStackTrace();
+ logger.trace(e);
+ logger.warn("A problem occured while trying to read a CSV file !");
}
return rows;
@@ -181,7 +185,7 @@ public class CSVUtil {
return -1;
}
- private static String GenerateDSCode(Query query) {
+ private static String generateDSCode(Query query) {
String prefix = "DS";
String queryStr = Integer.toString(query.hashCode());
String memId;