diff --git a/src/main/java/org/hbp/mip/MIPApplication.java b/src/main/java/org/hbp/mip/MIPApplication.java
index 1b1b9fc648c1dd102927b80fc9779a733c2fb3e4..e721ed77483285090be89a972ddf98d54881db3c 100644
--- a/src/main/java/org/hbp/mip/MIPApplication.java
+++ b/src/main/java/org/hbp/mip/MIPApplication.java
@@ -3,21 +3,6 @@
* Based on gregturn code at : 'https://github.com/spring-guides/tut-spring-boot-oauth2'.
*/
-/*
- * Copyright 2012-2015 the original author or authors.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
package org.hbp.mip;
import com.fasterxml.jackson.core.JsonProcessingException;
@@ -93,7 +78,7 @@ import java.security.Principal;
@Api(value = "/", description = "MIP API")
public class MIPApplication extends WebSecurityConfigurerAdapter {
- private Logger logger = Logger.getLogger(this.getClass());
+ private static final Logger LOGGER = Logger.getLogger(MIPApplication.class);
@Autowired
OAuth2ClientContext oauth2ClientContext;
@@ -184,9 +169,9 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
cookie.setPath("/");
response.addCookie(cookie);
} catch (JsonProcessingException e) {
- logger.trace(e);
+ LOGGER.trace(e);
} catch (UnsupportedEncodingException e) {
- logger.trace(e);
+ LOGGER.trace(e);
}
return principal;
}
@@ -277,8 +262,7 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
}
private CsrfTokenRepository csrfTokenRepository() {
- HttpSessionCsrfTokenRepository repository = httpSessionCsrfTokenRepository;
- return repository;
+ return httpSessionCsrfTokenRepository;
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/AppsApi.java b/src/main/java/org/hbp/mip/controllers/AppsApi.java
index 705fc0736e7d4ecdf2d6c73218d21d310508c558..b89ef31b4836ba1e52966ae8a002e341bdb13546 100644
--- a/src/main/java/org/hbp/mip/controllers/AppsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/AppsApi.java
@@ -33,7 +33,7 @@ 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());
+ private static final Logger LOGGER = Logger.getLogger(AppsApi.class);
@Autowired
MIPApplication mipApplication;
@@ -109,7 +109,7 @@ public class AppsApi {
}
catch (ConstraintViolationException cve)
{
- logger.trace(cve);
+ LOGGER.trace(cve);
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
@@ -118,7 +118,7 @@ public class AppsApi {
}
catch (NonUniqueObjectException nuoe)
{
- logger.trace(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 3fb3febd15833459e7fb9b54055aed423cf8f88b..99fe8334aef8fa27ba2fde647794b472b1cdb196 100644
--- a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
@@ -32,7 +32,7 @@ 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());
+ private static final Logger LOGGER = Logger.getLogger(ArticlesApi.class);
@Autowired
MIPApplication mipApplication;
@@ -60,11 +60,6 @@ public class ArticlesApi {
else
{
queryString += " AND (status='published' or u.username= :username)";
- if(team != null && team)
- {
- // TODO: decide if this is needed
- //queryString += " AND u.team= :team";
- }
}
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
@@ -102,7 +97,7 @@ public class ArticlesApi {
User user = mipApplication.getUser();
article.setCreatedAt(new Date());
- if (article.getStatus().equals("published")) {
+ if ("published".equals(article.getStatus())) {
article.setPublishedAt(new Date());
}
article.setCreatedBy(user);
@@ -131,13 +126,7 @@ public class ArticlesApi {
}
} while(count > 0);
- Slugify slg = null;
- try {
- slg = new Slugify();
- } catch (IOException e) {
- logger.trace(e);
- }
- String slug = slg != null ? slg.slugify(article.getTitle()) : "";
+ String slug = new Slugify().slugify(article.getTitle());
i = 0;
do {
@@ -159,8 +148,9 @@ public class ArticlesApi {
session.save(article);
session.getTransaction().commit();
- } catch (Exception e)
- {
+ } catch (IOException e) {
+ LOGGER.trace(e);
+ } catch (Exception e) {
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
@@ -194,7 +184,7 @@ public class ArticlesApi {
session.getTransaction().commit();
- if (!article.getStatus().equals("published") && !article.getCreatedBy().getUsername().equals(user.getUsername()))
+ if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername()))
{
return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
diff --git a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
index cadf43ea34a878031348bf7b916c512887df902a..0281039e3bb3bce2d514418cfc76fc25b4e0c2ca 100644
--- a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
@@ -35,7 +35,7 @@ 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 Logger LOGGER = Logger.getLogger(ExperimentApi.class);
private static final String EXAREME_ALGO_JSON_FILE="data/exareme_algorithms.json";
@@ -62,48 +62,25 @@ public class ExperimentApi {
// this runs in the background. For future optimization: use a thread pool
new Thread() {
+ @Override
public void run() {
try {
- HttpURLConnection con = (HttpURLConnection) obj.openConnection();
-
String query = experiment.computeQuery();
- System.out.println("Running experiment: " + query);
-
- // create query
- try {
- con.setRequestMethod("POST");
- } 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);
- con.setReadTimeout(3600000); // 1 hour: 60*60*1000 ms
-
- // write body of query
- con.setDoOutput(true);
- DataOutputStream wr = new DataOutputStream(con.getOutputStream());
- wr.write(query.getBytes("UTF8"));
- wr.flush();
- wr.close();
-
- // get response
- 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');
- }
- in.close();
+ HttpURLConnection con = createConnection(obj, query);
+ writeQueryBody(con, query);
+ String response = readResponse(con);
// write to experiment
- experiment.setResult(response.toString().replace("\0", ""));
+ 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 !");
+ LOGGER.trace(ioe);
+ LOGGER.warn("Experiment failed to run properly !");
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(ioe.getMessage());
@@ -126,6 +103,36 @@ public class ExperimentApi {
}.start();
}
+ 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');
+ }
+ in.close();
+ return response.toString();
+ }
+
+ 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 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;
+ }
+
@ApiOperation(value = "Send a request to the workflow to run an experiment", response = Experiment.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.POST)
@@ -158,8 +165,8 @@ public class ExperimentApi {
{
transaction.rollback();
}
- logger.trace(e);
- logger.warn("Cannot create experiment to run ! This is probably caused by a bad request !");
+ 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);
}
@@ -173,7 +180,7 @@ public class ExperimentApi {
{
sendPost(experiment);
}
- } catch (MalformedURLException mue) { logger.trace(mue.getMessage()); } // ignore
+ } catch (MalformedURLException mue) { LOGGER.trace(mue.getMessage()); } // ignore
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
@@ -183,7 +190,7 @@ public class ExperimentApi {
Model model = experiment.getModel();
String algoCode = "WP_LINEAR_REGRESSION";
- LinkedList<ExaremeQueryElement> queryElements = new LinkedList<>();
+ List<ExaremeQueryElement> queryElements = new LinkedList<>();
for (Variable var : model.getQuery().getVariables())
{
ExaremeQueryElement el = new ExaremeQueryElement();
@@ -224,6 +231,7 @@ public class ExperimentApi {
String jsonQuery = new Gson().toJson(queryElements);
new Thread() {
+ @Override
public void run() {
try {
String url = miningExaremeQueryUrl + "/" + algoCode;
@@ -239,8 +247,8 @@ public class ExperimentApi {
experiment.setResult("Unsupported variables !");
}
} catch (Exception e) {
- logger.trace(e);
- logger.warn("Failed to run Exareme algorithm !");
+ LOGGER.trace(e);
+ LOGGER.warn("Failed to run Exareme algorithm !");
experiment.setHasError(true);
experiment.setHasServerError(true);
experiment.setResult(e.getMessage());
@@ -267,7 +275,7 @@ 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
+ LOGGER.trace(jpe); // This is the normal behavior when the input string is not JSON-ified
return false;
}
return true;
@@ -276,7 +284,7 @@ public class ExperimentApi {
private boolean isExaremeAlgo(Experiment experiment) {
JsonArray algorithms = new JsonParser().parse(experiment.getAlgorithms()).getAsJsonArray();
String algoCode = algorithms.get(0).getAsJsonObject().get("code").getAsString();
- return algoCode.equals("glm_exareme");
+ return "glm_exareme".equals(algoCode);
}
@ApiOperation(value = "get an experiment", response = Experiment.class)
@@ -289,8 +297,8 @@ public class ExperimentApi {
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- logger.trace(iae);
- logger.warn("An invalid Experiment UUID was received !");
+ LOGGER.trace(iae);
+ LOGGER.warn("An invalid Experiment UUID was received !");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -329,8 +337,8 @@ public class ExperimentApi {
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- logger.trace(iae);
- logger.warn("An invalid Experiment UUID was received !");
+ LOGGER.trace(iae);
+ LOGGER.warn("An invalid Experiment UUID was received !");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -370,8 +378,8 @@ public class ExperimentApi {
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
- logger.trace(iae);
- logger.warn("An invalid Experiment UUID was received !");
+ LOGGER.trace(iae);
+ LOGGER.warn("An invalid Experiment UUID was received !");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -436,7 +444,7 @@ public class ExperimentApi {
baseQuery += mine ? "e.createdBy = :user" : "(e.createdBy = :user OR e.shared is true)";
- if (modelSlug == null || modelSlug.equals("")) {
+ if (modelSlug == null || "".equals(modelSlug)) {
hibernateQuery = session.createQuery(baseQuery);
} else {
hibernateQuery = session.createQuery(baseQuery + " AND e.model.slug = :slug");
@@ -489,7 +497,7 @@ public class ExperimentApi {
@ApiParam(value = "maxResultCount", required = false) @RequestParam("maxResultCount") int maxResultCount
) {
- if (maxResultCount <= 0 && (modelSlug == null || modelSlug.equals(""))) {
+ if (maxResultCount <= 0 && (modelSlug == null || "".equals(modelSlug))) {
return new ResponseEntity<>("You must provide at least a slug or a limit of result", HttpStatus.BAD_REQUEST);
}
@@ -499,7 +507,7 @@ public class ExperimentApi {
@ApiOperation(value = "List available methods and validations", response = String.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(path = "/methods", method = RequestMethod.GET)
- public ResponseEntity<String> listAvailableMethodsAndValidations() throws Exception {
+ public ResponseEntity<String> listAvailableMethodsAndValidations() throws IOException {
StringBuilder response = new StringBuilder();
diff --git a/src/main/java/org/hbp/mip/controllers/ModelsApi.java b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
index 4679b0857750323e85bc34aecac6c1b8221db550..21b102e1858a508f92bff344a4aded93006c10f2 100644
--- a/src/main/java/org/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
@@ -29,7 +29,7 @@ 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());
+ private static final Logger LOGGER = Logger.getLogger(ModelsApi.class);
@Autowired
MIPApplication mipApplication;
@@ -60,11 +60,6 @@ public class ModelsApi {
else
{
queryString += " AND (m.valid=true or u.username= :username)";
- if(team != null && team)
- {
- // TODO: decide if this is needed
- //queryString += " AND u.team= :team";
- }
}
queryString += " ORDER BY m.createdAt DESC";
@@ -95,7 +90,7 @@ public class ModelsApi {
}
for(Model model:models){
- String ds_code = model.getDataset().getCode();
+ String dsCode = model.getDataset().getCode();
session = HibernateUtil.getSessionFactory().getCurrentSession();
Dataset dataset = null;
@@ -103,7 +98,7 @@ public class ModelsApi {
session.beginTransaction();
dataset = (Dataset) session
.createQuery("from Dataset where code= :code")
- .setString("code", ds_code)
+ .setString("code", dsCode)
.uniqueResult();
session.getTransaction().commit();
} catch (Exception e)
@@ -163,14 +158,7 @@ public class ModelsApi {
}
} while(count > 0);
- Slugify slg = null;
- String slug = "";
- try {
- slg = new Slugify();
- slug = slg.slugify(model.getTitle());
- } catch (IOException e) {
- logger.trace(e);
- }
+ String slug = new Slugify().slugify(model.getTitle());
i = 0;
do {
@@ -196,6 +184,8 @@ public class ModelsApi {
session.save(model);
session.getTransaction().commit();
+ } catch (IOException e) {
+ LOGGER.trace(e);
} catch (Exception e)
{
if(session.getTransaction() != null)
@@ -219,7 +209,6 @@ public class ModelsApi {
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
Model model = null;
- Query query;
try {
session.beginTransaction();
@@ -387,41 +376,7 @@ public class ModelsApi {
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
- @ApiOperation(value = "Copy a model", response = Model.class)
- @ApiResponses(value = { @ApiResponse(code = 201, message = "Model copied"), @ApiResponse(code = 404, message = "Not found") })
- @RequestMapping(value = "/{slug}/copies", method = RequestMethod.POST)
- public ResponseEntity<Model> copyAModel(
- @ApiParam(value = "slug", required = true) @PathVariable("slug") String slug,
- @RequestBody @ApiParam(value = "Model to update", required = true) Model model
- ) {
-
- User user = mipApplication.getUser();
-
- String originalSlug = model.getSlug();
- String copySlug;
- do {
- copySlug = originalSlug+" copy_"+randomStr(20);
- } while (getAModel(copySlug) == null);
- model.setSlug(copySlug);
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try{
- session.beginTransaction();
- session.save(model);
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return new ResponseEntity<>(HttpStatus.CREATED).ok(model);
- }
-
- private String randomStr(int length) {
+ private static String randomStr(int length) {
char[] chars = "abcdefghijklmnopqrstuvwxyz0123456789".toCharArray();
StringBuilder sb = new StringBuilder();
Random random = new Random();
diff --git a/src/main/java/org/hbp/mip/model/App.java b/src/main/java/org/hbp/mip/model/App.java
index 38450ade304847675a0f02966eb79d0fef9e54b7..c328c36ca8330b538d66028cd085407959a4b5ca 100644
--- a/src/main/java/org/hbp/mip/model/App.java
+++ b/src/main/java/org/hbp/mip/model/App.java
@@ -44,6 +44,9 @@ public class App {
public App() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Article.java b/src/main/java/org/hbp/mip/model/Article.java
index 49e0fc8171d7d4ea26401312d708cc77c5689b34..26e36e60fc49e1d6e3b3adad37555e8e4671f26b 100644
--- a/src/main/java/org/hbp/mip/model/Article.java
+++ b/src/main/java/org/hbp/mip/model/Article.java
@@ -55,6 +55,9 @@ public class Article {
public Article() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Config.java b/src/main/java/org/hbp/mip/model/Config.java
index 555d7cece4fc591d29792f9ffdcbb5e30a67c1a7..08bed89798cda8f97015ae62717a7a2300b7126d 100644
--- a/src/main/java/org/hbp/mip/model/Config.java
+++ b/src/main/java/org/hbp/mip/model/Config.java
@@ -41,6 +41,9 @@ public class Config {
public Config() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Dataset.java b/src/main/java/org/hbp/mip/model/Dataset.java
index 61b5a5316cebdd78d10b4bb63045bffeb4541c35..023cecf06d6738dc31f7cfde5edb2dccf2dbd09f 100644
--- a/src/main/java/org/hbp/mip/model/Dataset.java
+++ b/src/main/java/org/hbp/mip/model/Dataset.java
@@ -39,6 +39,9 @@ public class Dataset {
public Dataset() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Experiment.java b/src/main/java/org/hbp/mip/model/Experiment.java
index a569c9719231a54e50f66f4d1b71a7421b1fdd32..dec5eee686865874502e036a07484350ac678cc0 100644
--- a/src/main/java/org/hbp/mip/model/Experiment.java
+++ b/src/main/java/org/hbp/mip/model/Experiment.java
@@ -78,6 +78,9 @@ public class Experiment {
private boolean resultsViewed = false;
public Experiment() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
public String computeQuery() {
diff --git a/src/main/java/org/hbp/mip/model/Filter.java b/src/main/java/org/hbp/mip/model/Filter.java
index c85bc140a47ab0bcef46c795ad9160a60edac1c1..27af1d69c9b26fd1475d1395f1e3a6432c86bf81 100644
--- a/src/main/java/org/hbp/mip/model/Filter.java
+++ b/src/main/java/org/hbp/mip/model/Filter.java
@@ -34,6 +34,9 @@ public class Filter {
public Filter() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/GeneralStats.java b/src/main/java/org/hbp/mip/model/GeneralStats.java
index 94b3b62b28b5dea3b2d727c66042272401827858..b9366c013e3e2913a220e598cfe6c3264d231b6a 100644
--- a/src/main/java/org/hbp/mip/model/GeneralStats.java
+++ b/src/main/java/org/hbp/mip/model/GeneralStats.java
@@ -17,6 +17,9 @@ public class GeneralStats {
public GeneralStats() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Group.java b/src/main/java/org/hbp/mip/model/Group.java
index 066f3f94905128fdb961b1d473b0d878948814ad..32cf44f662107d113c214901ee77113d6e434d85 100644
--- a/src/main/java/org/hbp/mip/model/Group.java
+++ b/src/main/java/org/hbp/mip/model/Group.java
@@ -32,6 +32,9 @@ public class Group {
public Group() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
@@ -70,15 +73,4 @@ public class Group {
this.groups = groups;
}
-
- public Group clone()
- {
- Group g = new Group();
- g.setCode(this.getCode());
- g.setLabel(this.getLabel());
- g.setParent(this.getParent());
- g.setGroups(this.getGroups());
- return g;
- }
-
}
diff --git a/src/main/java/org/hbp/mip/model/Model.java b/src/main/java/org/hbp/mip/model/Model.java
index 774b8e0cf75833d659a06a75a637c3d7e84b19cb..fb871152fe562a4fab41a0b7def52123cd26394b 100644
--- a/src/main/java/org/hbp/mip/model/Model.java
+++ b/src/main/java/org/hbp/mip/model/Model.java
@@ -59,6 +59,9 @@ public class Model {
public Model() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Query.java b/src/main/java/org/hbp/mip/model/Query.java
index ebcce263bb75713c521f0e34b25f1264038b3724..fddb0c7a7c68ffb5a79c733032d9a36c4564008b 100644
--- a/src/main/java/org/hbp/mip/model/Query.java
+++ b/src/main/java/org/hbp/mip/model/Query.java
@@ -52,6 +52,9 @@ public class Query {
public Query() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Tag.java b/src/main/java/org/hbp/mip/model/Tag.java
index e4c34e30bb9ca12ee306455e755018033ab928f7..6619bd75f57a66dfe66446e4f710b4d515663199 100644
--- a/src/main/java/org/hbp/mip/model/Tag.java
+++ b/src/main/java/org/hbp/mip/model/Tag.java
@@ -22,6 +22,9 @@ public class Tag {
public Tag() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/User.java b/src/main/java/org/hbp/mip/model/User.java
index f013859e96b02d12adeada9cbadf250b4429d9e9..7d12a47f5265f9f4aebd58463b7dcde0c93140b1 100644
--- a/src/main/java/org/hbp/mip/model/User.java
+++ b/src/main/java/org/hbp/mip/model/User.java
@@ -88,6 +88,9 @@ public class User {
public User() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
@@ -133,7 +136,7 @@ public class User {
p = Pattern.compile("title=([\\w ]+)");
m = p.matcher(userInfo);
if (m.find()) {
- if (m.group(1).equals("Mr")) {
+ if ("Mr".equals(m.group(1))) {
this.gender = "Male";
} else {
this.gender = "Female";
diff --git a/src/main/java/org/hbp/mip/model/Variable.java b/src/main/java/org/hbp/mip/model/Variable.java
index e651105c6f525d13345daf6a6b7f04b56d4f4fbf..2bc6a37c8637930c0ea1466633250bfb467ac9b2 100644
--- a/src/main/java/org/hbp/mip/model/Variable.java
+++ b/src/main/java/org/hbp/mip/model/Variable.java
@@ -59,6 +59,9 @@ public class Variable {
public Variable() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/model/Vote.java b/src/main/java/org/hbp/mip/model/Vote.java
index 91ce0b055d21cfd9dd65a9066d34dea1f9aa93db..b9981a8e92a96092b8c0fa8e4e833f70846dedfd 100644
--- a/src/main/java/org/hbp/mip/model/Vote.java
+++ b/src/main/java/org/hbp/mip/model/Vote.java
@@ -33,6 +33,9 @@ public class Vote {
public Vote() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
diff --git a/src/main/java/org/hbp/mip/utils/CORSFilter.java b/src/main/java/org/hbp/mip/utils/CORSFilter.java
index 30bea8de4bc436b3a9aa685424e89d7f6f7c92ab..02349cffae160c1f7fcc221676074ef7de84a452 100644
--- a/src/main/java/org/hbp/mip/utils/CORSFilter.java
+++ b/src/main/java/org/hbp/mip/utils/CORSFilter.java
@@ -18,7 +18,11 @@ public class CORSFilter implements Filter {
chain.doFilter(req, res);
}
- public void init(FilterConfig filterConfig) {}
+ public void init(FilterConfig filterConfig) {
+ /* Nothing to do */
+ }
- public void destroy() {}
+ public void destroy() {
+ /* Nothing to do */
+ }
}
diff --git a/src/main/java/org/hbp/mip/utils/CSVUtil.java b/src/main/java/org/hbp/mip/utils/CSVUtil.java
index c001e83b3bd467d814d122299df88bdb22d35a00..b3f6850be795983ec8728624da7dfcf733369dfe 100644
--- a/src/main/java/org/hbp/mip/utils/CSVUtil.java
+++ b/src/main/java/org/hbp/mip/utils/CSVUtil.java
@@ -20,10 +20,16 @@ import java.util.stream.Collectors;
*/
public class CSVUtil {
- private static Logger logger = Logger.getLogger(CSVUtil.class);
+ private static final Logger LOGGER = Logger.getLogger(CSVUtil.class);
private static final String SEPARATOR = ",";
+ private CSVUtil()
+ {
+ /* Hide implicit public constructor */
+ throw new IllegalAccessError("CSVUtil class");
+ }
+
public static Dataset parseValues(String filename, Query query)
{
List<String[]> rows = getRows(filename);
@@ -143,7 +149,7 @@ public class CSVUtil {
data.put(c, ll);
}
} catch (IOException e) {
- logger.trace(e);
+ LOGGER.trace(e);
}
result.setCode(code);
result.setDate(date);
@@ -170,8 +176,8 @@ public class CSVUtil {
isr.close();
is.close();
} catch (IOException e) {
- logger.trace(e);
- logger.warn("A problem occured while trying to read a CSV file !");
+ LOGGER.trace(e);
+ LOGGER.warn("A problem occured while trying to read a CSV file !");
}
return rows;
diff --git a/src/main/java/org/hbp/mip/utils/HTTPUtil.java b/src/main/java/org/hbp/mip/utils/HTTPUtil.java
index 92beffaf45e7f48e8c71d51e36414fb78ce827ae..0a524bb99d7fa8403af05fb94fdfec0c1e9d9a25 100644
--- a/src/main/java/org/hbp/mip/utils/HTTPUtil.java
+++ b/src/main/java/org/hbp/mip/utils/HTTPUtil.java
@@ -2,6 +2,7 @@ package org.hbp.mip.utils;
import java.io.BufferedReader;
import java.io.DataOutputStream;
+import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
@@ -11,20 +12,26 @@ import java.net.URL;
*/
public class HTTPUtil {
- public static int sendGet(String url, StringBuilder resp) throws Exception {
+ private HTTPUtil()
+ {
+ /* Hide implicit public constructor */
+ throw new IllegalAccessError("HTTPUtil class");
+ }
+
+ public static int sendGet(String url, StringBuilder resp) throws IOException {
return sendHTTP(url, "", resp, "GET");
}
- public static int sendPost(String url, String query, StringBuilder resp) throws Exception {
+ public static int sendPost(String url, String query, StringBuilder resp) throws IOException {
return sendHTTP(url, query, resp, "POST");
}
- public static int sendHTTP(String url, String query, StringBuilder resp, String httpVerb) throws Exception {
+ public static int sendHTTP(String url, String query, StringBuilder resp, String httpVerb) throws IOException {
URL obj = new URL(url);
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
- if(!httpVerb.equals("GET")) {
+ if(!"GET".equals(httpVerb)) {
con.setRequestMethod(httpVerb);
if(query != null && query.length() > 0)
{
diff --git a/src/main/java/org/hbp/mip/utils/HibernateUtil.java b/src/main/java/org/hbp/mip/utils/HibernateUtil.java
index bbb0296db496156b39b7c5cd140ba62c90fa07d3..87cde9618993e4070518b70d2bf6e4d058d54760 100644
--- a/src/main/java/org/hbp/mip/utils/HibernateUtil.java
+++ b/src/main/java/org/hbp/mip/utils/HibernateUtil.java
@@ -4,15 +4,25 @@
package org.hbp.mip.utils;
+import org.apache.log4j.Logger;
import org.hibernate.SessionFactory;
import org.hibernate.boot.registry.StandardServiceRegistryBuilder;
import org.hibernate.cfg.Configuration;
import org.hibernate.service.ServiceRegistry;
public class HibernateUtil {
+
+ private static final Logger LOGGER = Logger.getLogger(CSVUtil.class);
+
private static ServiceRegistry serviceRegistry;
+
private static SessionFactory sessionFactory = buildSessionFactory();
+ private HibernateUtil() {
+ /* Hide implicit public constructor */
+ throw new IllegalAccessError("HibernateUtil class");
+ }
+
private static SessionFactory buildSessionFactory() {
try {
Configuration configuration = new Configuration();
@@ -22,7 +32,7 @@ public class HibernateUtil {
sessionFactory = configuration.buildSessionFactory(serviceRegistry);
return sessionFactory;
} catch (RuntimeException ex) {
- System.err.println("Initial SessionFactory creation failed." + ex);
+ LOGGER.error("Initial SessionFactory creation failed." + ex);
throw new ExceptionInInitializerError(ex);
}
}