Merge branch 'sonar_suggestions' into 'stable'

Sonar suggestions

Many changes following the code quality recommendations from Sonar.

See merge request !8

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;
     }
 
 }

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();

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);
             }

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();
 

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();

src/main/java/org/hbp/mip/model/App.java

@@ -44,6 +44,9 @@ public class App {
 
 
     public App() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

src/main/java/org/hbp/mip/model/Article.java

@@ -55,6 +55,9 @@ public class Article {
 
 
     public Article() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

src/main/java/org/hbp/mip/model/Config.java

@@ -41,6 +41,9 @@ public class Config {
 
 
     public Config() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

src/main/java/org/hbp/mip/model/Dataset.java

@@ -39,6 +39,9 @@ public class Dataset {
 
 
     public Dataset() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

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() {

src/main/java/org/hbp/mip/model/Filter.java

@@ -34,6 +34,9 @@ public class Filter {
 
 
     public Filter() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

src/main/java/org/hbp/mip/model/GeneralStats.java

@@ -17,6 +17,9 @@ public class GeneralStats {
 
 
     public GeneralStats() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

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;
-    }
-
 }

src/main/java/org/hbp/mip/model/Model.java

@@ -59,6 +59,9 @@ public class Model {
 
 
     public Model() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

src/main/java/org/hbp/mip/model/Query.java

@@ -52,6 +52,9 @@ public class Query {
 
 
     public Query() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

src/main/java/org/hbp/mip/model/Tag.java

@@ -22,6 +22,9 @@ public class Tag {
 
 
     public Tag() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

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";

src/main/java/org/hbp/mip/model/Variable.java

@@ -59,6 +59,9 @@ public class Variable {
 
 
     public Variable() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

src/main/java/org/hbp/mip/model/Vote.java

@@ -33,6 +33,9 @@ public class Vote {
 
 
     public Vote() {
+        /*
+        *  Empty constructor is needed by Hibernate
+        */
     }
 
 

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 */
+    }
 }