diff --git a/src/main/java/org/hbp/mip/MIPApplication.java b/src/main/java/org/hbp/mip/MIPApplication.java
index 37c7473f430094dbe024dba5b2928d058df12a5e..2ba48af629a20704c80c688d091fa424c493d15e 100644
--- a/src/main/java/org/hbp/mip/MIPApplication.java
+++ b/src/main/java/org/hbp/mip/MIPApplication.java
@@ -11,9 +11,8 @@ 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.repositories.UserRepository;
import org.hbp.mip.utils.CORSFilter;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
@@ -84,6 +83,9 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
@Autowired
OAuth2ClientContext oauth2ClientContext;
+ @Autowired
+ UserRepository userRepository;
+
public static void main(String[] args) {
SpringApplication.run(MIPApplication.class, args);
@@ -107,26 +109,10 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
* @return
*/
public synchronized User getUser() {
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
User user = new User(getUserInfos());
- try {
- session.beginTransaction();
- Boolean agreeNDA = (Boolean) session
- .createQuery("SELECT agreeNDA FROM User WHERE username= :username")
- .setString("username", user.getUsername())
- .uniqueResult();
- user.setAgreeNDA(agreeNDA);
- session.merge(user);
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
+ User foundUser = userRepository.findOne(user.getUsername());
+ user.setAgreeNDA(foundUser.getAgreeNDA());
+ userRepository.save(user);
return user;
}
@@ -173,28 +159,11 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
@RequestMapping(path = "/user", method = RequestMethod.POST)
public ResponseEntity<Void> postUser(@ApiParam(value = "Has the user agreed on the NDA") @RequestParam(value = "agreeNDA", required = true) Boolean agreeNDA) {
String username = getUser().getUsername();
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try {
- session.beginTransaction();
- User user = (User) session
- .createQuery("from User where username= :username")
- .setString("username", username)
- .uniqueResult();
- if (user != null) {
- user.setAgreeNDA(agreeNDA);
- session.update(user);
- }
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
+ User user = userRepository.findOne(username);
+ if (user != null) {
+ user.setAgreeNDA(agreeNDA);
+ userRepository.save(user);
}
-
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
diff --git a/src/main/java/org/hbp/mip/controllers/AppsApi.java b/src/main/java/org/hbp/mip/controllers/AppsApi.java
index b89ef31b4836ba1e52966ae8a002e341bdb13546..a1f644a93243b362ece5568e3528193c37e68355 100644
--- a/src/main/java/org/hbp/mip/controllers/AppsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/AppsApi.java
@@ -8,12 +8,7 @@ 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;
-import org.hbp.mip.model.Vote;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.NonUniqueObjectException;
-import org.hibernate.Query;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.AppRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -22,10 +17,6 @@ import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
-import javax.validation.ConstraintViolationException;
-import java.util.LinkedList;
-import java.util.List;
-
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@@ -38,29 +29,15 @@ public class AppsApi {
@Autowired
MIPApplication mipApplication;
+ @Autowired
+ AppRepository appRepository;
+
@ApiOperation(value = "Get apps", response = App.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getApps(
+ public ResponseEntity<Iterable> getApps(
) {
- List apps = new LinkedList<>();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try {
- session.beginTransaction();
- Query query = session.createQuery("FROM App");
- apps = query.list();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(apps);
+ return ResponseEntity.ok(appRepository.findAll());
}
@ApiOperation(value = "Post a vote")
@@ -71,68 +48,38 @@ public class AppsApi {
@ApiParam(value = "value", required = true) @PathVariable("value") Integer value
) {
- User user = mipApplication.getUser();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try {
- session.beginTransaction();
-
- Vote vote = (Vote) session.createQuery("" +
- "SELECT v FROM Vote v, User u, App a " +
- "WHERE u=v.user " +
- "AND a=v.app " +
- "AND u.username= :username " +
- "AND a.id= :app_id")
- .setString("username", user.getUsername())
- .setLong("app_id", id)
- .uniqueResult();
- App app = (App) session.createQuery("FROM App where id= :id").setLong("id", id).uniqueResult();
-
- if (vote != null) {
- vote.setValue(value);
-
- session.update(vote);
- session.getTransaction().commit();
- return new ResponseEntity<>(HttpStatus.NO_CONTENT);
- }
- else
- {
- vote = new Vote();
- vote.setUser(user);
- vote.setValue(value);
- vote.setApp(app);
-
- session.save(vote);
- session.getTransaction().commit();
- return new ResponseEntity<>(HttpStatus.CREATED);
- }
- }
- catch (ConstraintViolationException cve)
- {
- LOGGER.trace(cve);
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- }
- return new ResponseEntity<>(HttpStatus.BAD_REQUEST);
- }
- catch (NonUniqueObjectException nuoe)
- {
- LOGGER.trace(nuoe);
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- }
- return new ResponseEntity<>(HttpStatus.CONFLICT);
+ /*User user = mipApplication.getUser();
+
+ Vote vote = (Vote) session.createQuery("" +
+ "SELECT v FROM Vote v, User u, App a " +
+ "WHERE u=v.user " +
+ "AND a=v.app " +
+ "AND u.username= :username " +
+ "AND a.id= :app_id")
+ .setString("username", user.getUsername())
+ .setLong("app_id", id)
+ .uniqueResult();
+ App app = (App) session.createQuery("FROM App where id= :id").setLong("id", id).uniqueResult();
+
+ if (vote != null) {
+ vote.setValue(value);
+
+ session.update(vote);
+ return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
- catch (Exception e)
+ else
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
- }
+ vote = new Vote();
+ vote.setUser(user);
+ vote.setValue(value);
+ vote.setApp(app);
+
+ session.save(vote);
+ session.getTransaction().commit();
+ return new ResponseEntity<>(HttpStatus.CREATED);
+ }*/
+
+ return new ResponseEntity<>(HttpStatus.CREATED);
+
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
index 99fe8334aef8fa27ba2fde647794b472b1cdb196..6d2f1d96efba6d8f60b59565082acb2defc1be3d 100644
--- a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
@@ -11,9 +11,7 @@ import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.Article;
import org.hbp.mip.model.User;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.ArticleRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -22,8 +20,6 @@ import org.springframework.web.bind.annotation.*;
import javax.validation.Valid;
import java.io.IOException;
import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -37,16 +33,19 @@ public class ArticlesApi {
@Autowired
MIPApplication mipApplication;
+ @Autowired
+ ArticleRepository articleRepository;
+
@ApiOperation(value = "Get articles", response = Article.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getArticles(
+ public ResponseEntity<Iterable> getArticles(
@ApiParam(value = "Only ask own articles") @RequestParam(value = "own", required = false) Boolean own,
@ApiParam(value = "Only ask results matching status", allowableValues = "{values=[draft, published, closed]}") @RequestParam(value = "status", required = false) String status,
@ApiParam(value = "Only ask articles from own team") @RequestParam(value = "team", required = false) Boolean team
) {
- User user = mipApplication.getUser();
+ /*User user = mipApplication.getUser();
String queryString = "SELECT a FROM Article a, User u WHERE a.createdBy=u.username";
if(status != null)
@@ -62,28 +61,18 @@ public class ArticlesApi {
queryString += " AND (status='published' or u.username= :username)";
}
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
List articles = new LinkedList<>();
- try {
- session.beginTransaction();
- Query query = session.createQuery(queryString);
- if (status != null) {
- query.setString("status", status);
- }
- query.setString("username", user.getUsername());
- articles = query.list();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
+ Query query = session.createQuery(queryString);
+ if (status != null) {
+ query.setString("status", status);
}
+ query.setString("username", user.getUsername());
+ articles = query.list();
+ session.getTransaction().commit();
+ return ResponseEntity.ok(articles);*/
- return ResponseEntity.ok(articles);
+ return ResponseEntity.ok(articleRepository.findAll());
}
@@ -103,61 +92,44 @@ public class ArticlesApi {
article.setCreatedBy(user);
Long count;
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try{
- session.beginTransaction();
+ int i = 0;
+ do{
+ i++;
+ count = articleRepository.countByTitle(article.getTitle());
- int i = 0;
- do{
- i++;
- count = (Long) session
- .createQuery("select count(*) from Article where title= :title")
- .setString("title", article.getTitle())
- .uniqueResult();
-
- if(count > 0)
- {
- String title = article.getTitle();
- if(i > 1)
- {
- title = title.substring(0, title.length()-4);
- }
- article.setTitle(title + " (" + i + ")");
- }
- } while(count > 0);
-
- String slug = new Slugify().slugify(article.getTitle());
-
- i = 0;
- do {
- i++;
- count = (Long) session
- .createQuery("select count(*) from Article where slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
- if(count > 0)
+ if(count > 0)
+ {
+ String title = article.getTitle();
+ if(i > 1)
{
- if(i > 1)
- {
- slug = slug.substring(0, slug.length()-2);
- }
- slug += "-"+i;
+ title = title.substring(0, title.length()-4);
}
- article.setSlug(slug);
- } while(count > 0);
+ article.setTitle(title + " (" + i + ")");
+ }
+ } while(count > 0);
- session.save(article);
- session.getTransaction().commit();
+ String slug = null;
+ try {
+ slug = new Slugify().slugify(article.getTitle());
} catch (IOException e) {
- LOGGER.trace(e);
- } catch (Exception e) {
- if(session.getTransaction() != null)
+ slug = "";
+ LOGGER.trace(e);
+ }
+
+ i = 0;
+ do {
+ i++;
+ if(articleRepository.exists(slug))
{
- session.getTransaction().rollback();
- throw e;
+ if(i > 1)
+ {
+ slug = slug.substring(0, slug.length()-2);
+ }
+ slug += "-"+i;
}
- return new ResponseEntity<>(HttpStatus.INTERNAL_SERVER_ERROR);
- }
+ article.setSlug(slug);
+ } while(count > 0);
+ articleRepository.save(article);
return new ResponseEntity<>(HttpStatus.CREATED);
}
@@ -171,32 +143,12 @@ public class ArticlesApi {
) {
User user = mipApplication.getUser();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Article article = null;
- try{
- session.beginTransaction();
-
- article = (Article) session
- .createQuery("FROM Article WHERE slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
-
- session.getTransaction().commit();
-
- if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername()))
- {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
- } catch (Exception e)
+ Article article;
+ article = articleRepository.findOne(slug);
+ if (!"published".equals(article.getStatus()) && !article.getCreatedBy().getUsername().equals(user.getUsername()))
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
+ return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
-
return ResponseEntity.ok(article);
}
@@ -209,12 +161,8 @@ public class ArticlesApi {
@RequestBody @ApiParam(value = "Article to update", required = true) @Valid Article article
) {
- User user = mipApplication.getUser();
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
+ /*User user = mipApplication.getUser();
try{
- session.beginTransaction();
-
String author = (String) session
.createQuery("select U.username from User U, Article A where A.createdBy = U.username and A.slug = :slug")
.setString("slug", slug)
@@ -261,7 +209,7 @@ public class ArticlesApi {
session.getTransaction().rollback();
throw e;
}
- }
+ }*/
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
diff --git a/src/main/java/org/hbp/mip/controllers/DatasetsApi.java b/src/main/java/org/hbp/mip/controllers/DatasetsApi.java
index 4f3b67bfb063cd6504f7df85cf99c8cc4089a1d7..05fc11d6a8b93a573e0c5ffe149de1e2d2a9a1fc 100644
--- a/src/main/java/org/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/DatasetsApi.java
@@ -7,8 +7,8 @@ package org.hbp.mip.controllers;
import io.swagger.annotations.*;
import org.hbp.mip.model.Dataset;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.DatasetRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -22,32 +22,16 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/datasets", description = "the datasets API")
public class DatasetsApi {
+ @Autowired
+ DatasetRepository datasetRepository;
+
@ApiOperation(value = "Get a dataset", response = Dataset.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(value = "/{code}", method = RequestMethod.GET)
public ResponseEntity<Dataset> getADataset(
@ApiParam(value = "code", required = true) @PathVariable("code") String code
) {
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Dataset dataset = null;
- try{
- session.beginTransaction();
- dataset = (Dataset) session
- .createQuery("from Dataset where code= :code")
- .setString("code", code)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(dataset);
+ return ResponseEntity.ok(datasetRepository.findOne(code));
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
index 5adbdaa35ffd233717ea958b54e6a3cdfc7f78a2..508839d0c809dd8e03e5fb614dec5537f0e4268d 100644
--- a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
@@ -5,14 +5,11 @@ import io.swagger.annotations.*;
import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.Experiment;
-import org.hbp.mip.model.Model;
import org.hbp.mip.model.User;
+import org.hbp.mip.repositories.ExperimentRepository;
+import org.hbp.mip.repositories.ModelRepository;
import org.hbp.mip.utils.HTTPUtil;
-import org.hbp.mip.utils.HibernateUtil;
import org.hbp.mip.utils.JSONUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
-import org.hibernate.Transaction;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
@@ -24,8 +21,6 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.MalformedURLException;
-import java.util.LinkedList;
-import java.util.List;
import java.util.UUID;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -63,6 +58,12 @@ public class ExperimentApi {
@Autowired
MIPApplication mipApplication;
+ @Autowired
+ ModelRepository modelRepository;
+
+ @Autowired
+ ExperimentRepository experimentRepository;
+
@ApiOperation(value = "Send a request to the workflow to run an experiment", response = Experiment.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@@ -74,33 +75,12 @@ public class ExperimentApi {
experiment.setUuid(UUID.randomUUID());
User user = mipApplication.getUser();
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Transaction transaction = session.beginTransaction();
-
- try {
-
- experiment.setAlgorithms(incomingQuery.get("algorithms").toString());
- experiment.setValidations(incomingQuery.get("validations").toString());
- experiment.setName(incomingQuery.get("name").getAsString());
- experiment.setCreatedBy(user);
-
- Query hibernateQuery = session.createQuery("from Model as model where model.slug = :slug");
- hibernateQuery.setParameter("slug", incomingQuery.get("model").getAsString());
- experiment.setModel((Model)hibernateQuery.uniqueResult());
-
- session.save(experiment);
- transaction.commit();
-
- } catch (Exception e) {
- if(transaction != null)
- {
- transaction.rollback();
- }
- 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);
- }
+ experiment.setAlgorithms(incomingQuery.get("algorithms").toString());
+ experiment.setValidations(incomingQuery.get("validations").toString());
+ experiment.setName(incomingQuery.get("name").getAsString());
+ experiment.setCreatedBy(user);
+ experiment.setModel(modelRepository.findOne(incomingQuery.get("model").getAsString()));
+ experimentRepository.save(experiment);
try {
if(isExaremeAlgo(experiment))
@@ -130,23 +110,7 @@ public class ExperimentApi {
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
-
- try {
- session.beginTransaction();
-
- Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
- hibernateQuery.setParameter("uuid", experimentUuid);
- experiment = (Experiment) hibernateQuery.uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e) {
- // 404 here probably
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- }
- throw e;
- }
+ experiment = experimentRepository.findOne(experimentUuid);
if (experiment == null) {
return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
@@ -170,31 +134,11 @@ public class ExperimentApi {
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.setResultsViewed(true);
- session.update(experiment);
-
- transaction.commit();
- } catch (Exception e) {
- // 404 here probably
- if(transaction != null)
- {
- transaction.rollback();
- }
- throw e;
- }
-
+ experiment = experimentRepository.findOne(experimentUuid);;
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
+ experiment.setResultsViewed(true);
+ experimentRepository.save(experiment);
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
@@ -265,14 +209,10 @@ public class ExperimentApi {
int maxResultCount,
String modelSlug
) {
- List<Experiment> experiments = new LinkedList<>();
+ /*List<Experiment> experiments = new LinkedList<>();
User user = mipApplication.getUser();
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
-
try {
- session.beginTransaction();
-
Query hibernateQuery;
String baseQuery = "from Experiment as e WHERE ";
@@ -313,7 +253,9 @@ public class ExperimentApi {
}
}
- return new ResponseEntity<>(gson.toJson(experiments), HttpStatus.OK);
+ return new ResponseEntity<>(gson.toJson(experiments), HttpStatus.OK);*/
+
+ return new ResponseEntity<>("", HttpStatus.OK);
}
private ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
@@ -328,30 +270,13 @@ public class ExperimentApi {
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 = experimentRepository.findOne(experimentUuid);
- experiment.setShared(shared);
- session.update(experiment);
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
- transaction.commit();
- } catch (Exception e) {
- // 404 here probably
- if(transaction != null)
- {
- transaction.rollback();
- }
- throw e;
- }
+ experiment.setShared(shared);
+ experimentRepository.save(experiment);
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
diff --git a/src/main/java/org/hbp/mip/controllers/GroupsApi.java b/src/main/java/org/hbp/mip/controllers/GroupsApi.java
index 9f23ad3b43b379ceb8c148900aaac129ac3ae0ad..48574e48cec79d8a23005db34c3125521d7f9c7a 100644
--- a/src/main/java/org/hbp/mip/controllers/GroupsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/GroupsApi.java
@@ -9,8 +9,8 @@ import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiResponse;
import io.swagger.annotations.ApiResponses;
import org.hbp.mip.model.Group;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.GroupRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
@@ -23,32 +23,16 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/groups", description = "the groups API")
public class GroupsApi {
+ private static final String ROOT_CODE = "root";
+
+ @Autowired
+ GroupRepository groupRepository;
+
@ApiOperation(value = "Get the root group (containing all subgroups)", response = Group.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<Group> getTheRootGroup() {
-
- String rootCode = "root";
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Group group = null;
- try{
- session.beginTransaction();
- group = (Group) session
- .createQuery("FROM Group WHERE code= :code")
- .setString("code", rootCode)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(group);
+ return ResponseEntity.ok(groupRepository.findOne(ROOT_CODE));
}
diff --git a/src/main/java/org/hbp/mip/controllers/ModelsApi.java b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
index 21b102e1858a508f92bff344a4aded93006c10f2..65da841f7adb89f24507d9b63042de0387ce3ef0 100644
--- a/src/main/java/org/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
@@ -9,10 +9,10 @@ import io.swagger.annotations.*;
import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.*;
+import org.hbp.mip.repositories.DatasetRepository;
+import org.hbp.mip.repositories.ModelRepository;
+import org.hbp.mip.repositories.QueryRepository;
import org.hbp.mip.utils.CSVUtil;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -34,19 +34,28 @@ public class ModelsApi {
@Autowired
MIPApplication mipApplication;
+ @Autowired
+ DatasetRepository datasetRepository;
+
+ @Autowired
+ ModelRepository modelRepository;
+
+ @Autowired
+ QueryRepository queryRepository;
+
private static final String DATA_FILE = "data/values.csv";
@ApiOperation(value = "Get models", response = Model.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List<Model>> getModels(
+ public ResponseEntity<Iterable> getModels(
@ApiParam(value = "Max number of results") @RequestParam(value = "limit", required = false) Integer limit,
@ApiParam(value = "Only ask own models") @RequestParam(value = "own", required = false) Boolean own,
@ApiParam(value = "Only ask models from own team") @RequestParam(value = "team", required = false) Boolean team,
@ApiParam(value = "Only ask published models") @RequestParam(value = "valid", required = false) Boolean valid
) {
- User user = mipApplication.getUser();
+ /*User user = mipApplication.getUser();
String queryString = "SELECT m FROM Model m, User u WHERE m.createdBy=u.username";
if(valid != null && valid)
@@ -64,56 +73,27 @@ public class ModelsApi {
queryString += " ORDER BY m.createdAt DESC";
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
List<Model> models = new LinkedList<>();
- try{
- session.beginTransaction();
- Query query = session.createQuery(queryString);
- if(valid != null)
- {
- query.setBoolean("valid", valid);
- }
- query.setString("username", user.getUsername());
- if(limit != null)
- {
- query.setMaxResults(limit); // Pagination : Use query.setFirstResult(...) to set begining index
- }
- models = query.list();
- session.getTransaction().commit();
- } catch (Exception e)
+ Query query = session.createQuery(queryString);
+ if(valid != null)
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
+ query.setBoolean("valid", valid);
+ }
+ query.setString("username", user.getUsername());
+ if(limit != null)
+ {
+ query.setMaxResults(limit); // Pagination : Use query.setFirstResult(...) to set begining index
}
+ models = query.list();
- for(Model model:models){
- String dsCode = model.getDataset().getCode();
-
- session = HibernateUtil.getSessionFactory().getCurrentSession();
- Dataset dataset = null;
- try{
- session.beginTransaction();
- dataset = (Dataset) session
- .createQuery("from Dataset where code= :code")
- .setString("code", dsCode)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
- model.setDataset(dataset);
+ for(Model model:models){
+ model.setDataset(datasetRepository.findOne(model.getDataset().getCode()));
}
- return new ResponseEntity<List<Model>>(HttpStatus.OK).ok(models);
+ return new ResponseEntity<List<Model>>(HttpStatus.OK).ok(models);*/
+
+ return new ResponseEntity<>(HttpStatus.OK).ok(modelRepository.findAll());
}
@@ -135,65 +115,51 @@ public class ModelsApi {
}
Long count;
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- try{
- session.beginTransaction();
+ int i = 0;
+ do{
+ i++;
+ count = modelRepository.countByTitle(model.getTitle());
- int i = 0;
- do{
- i++;
- count = (Long) session
- .createQuery("select count(*) from Model where title= :title")
- .setString("title", model.getTitle())
- .uniqueResult();
-
- if(count > 0)
- {
- String title = model.getTitle();
- if(i > 1)
- {
- title = title.substring(0, title.length()-4);
- }
- model.setTitle(title + " (" + i + ")");
- }
- } while(count > 0);
-
- String slug = new Slugify().slugify(model.getTitle());
-
- i = 0;
- do {
- i++;
- count = (Long) session
- .createQuery("select count(*) from Model where slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
- if(count > 0)
+ if(count > 0)
+ {
+ String title = model.getTitle();
+ if(i > 1)
{
- if(i > 1)
- {
- slug = slug.substring(0, slug.length()-2);
- }
- slug += "-"+i;
+ title = title.substring(0, title.length()-4);
}
- model.setSlug(slug);
- } while(count > 0);
-
- Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
- map.put("text", model.getTitle());
- model.getConfig().setTitle(map);
+ model.setTitle(title + " (" + i + ")");
+ }
+ } while(count > 0);
- session.save(model);
- session.getTransaction().commit();
+ String slug = null;
+ try {
+ slug = new Slugify().slugify(model.getTitle());
} catch (IOException e) {
+ slug = "";
LOGGER.trace(e);
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
+ }
+
+ i = 0;
+ boolean alreadyExists;
+ do {
+ i++;
+ alreadyExists = modelRepository.exists(slug);
+ if(count > 0)
{
- session.getTransaction().rollback();
- throw e;
+ if(i > 1)
+ {
+ slug = slug.substring(0, slug.length()-2);
+ }
+ slug += "-"+i;
}
- }
+ model.setSlug(slug);
+ } while(alreadyExists);
+
+ Map<String, String> map = new HashMap<>(model.getConfig().getTitle());
+ map.put("text", model.getTitle());
+ model.getConfig().setTitle(map);
+
+ modelRepository.save(model);
return new ResponseEntity<Model>(HttpStatus.CREATED).ok(model);
}
@@ -207,51 +173,18 @@ public class ModelsApi {
User user = mipApplication.getUser();
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
Model model = null;
- try {
- session.beginTransaction();
- model = (Model) session
- .createQuery("FROM Model WHERE slug= :slug")
- .setString("slug", slug)
- .uniqueResult();
- session.getTransaction().commit();
-
- if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername()))
- {
- return new ResponseEntity<>(HttpStatus.FORBIDDEN);
- }
-
- } catch (Exception e)
+ model = modelRepository.findOne(slug);
+ if (!model.getValid() && !model.getCreatedBy().getUsername().equals(user.getUsername()))
{
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
+ return new ResponseEntity<>(HttpStatus.FORBIDDEN);
}
-
if(model != null) {
- session = HibernateUtil.getSessionFactory().getCurrentSession();
org.hbp.mip.model.Query q = null;
- try {
- session.beginTransaction();
- q = (org.hbp.mip.model.Query) session
- .createQuery("FROM Query WHERE id= :id")
- .setLong("id", model.getQuery().getId())
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
+ q = queryRepository.findOne(model.getQuery().getId());
if(q != null) {
@@ -296,7 +229,7 @@ public class ModelsApi {
model.setQuery(myQuery);
}
- Dataset ds = CSVUtil.parseValues(DATA_FILE, model.getQuery());
+ Dataset ds = new CSVUtil().parseValues(DATA_FILE, model.getQuery());
model.setDataset(ds);
}
@@ -313,14 +246,11 @@ public class ModelsApi {
@RequestBody @ApiParam(value = "Model to update", required = true) Model model
) {
- User user = mipApplication.getUser();
+ /*User user = mipApplication.getUser();
model.setTitle(model.getConfig().getTitle().get("text"));
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
try{
- session.beginTransaction();
-
String author = (String) session
.createQuery("select U.username from User U, Model M where M.createdBy = U.username and M.slug = :slug")
.setString("slug", slug)
@@ -371,7 +301,7 @@ public class ModelsApi {
session.getTransaction().rollback();
throw e;
}
- }
+ }*/
return new ResponseEntity<>(HttpStatus.NO_CONTENT);
}
diff --git a/src/main/java/org/hbp/mip/controllers/RequestsApi.java b/src/main/java/org/hbp/mip/controllers/RequestsApi.java
index b60a53b558a33a205bb07ff404a25bba7e5af2d1..e41da4f755a0a1e471686e1dce1ed2973f6959a7 100644
--- a/src/main/java/org/hbp/mip/controllers/RequestsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/RequestsApi.java
@@ -29,10 +29,7 @@ public class RequestsApi {
public ResponseEntity<Dataset> postRequests(
@RequestBody @ApiParam(value = "Query to process", required = true) Query query
) {
-
- Dataset dataset = CSVUtil.parseValues(DATA_FILE, query);
-
- return ResponseEntity.ok(dataset);
+ return ResponseEntity.ok(new CSVUtil().parseValues(DATA_FILE, query));
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/StatsApi.java b/src/main/java/org/hbp/mip/controllers/StatsApi.java
index e40a3becf1ee8715ecca6dea068dcc09cb855823..3f6883f28f9d19e7887519105e9a07bd58d5679d 100644
--- a/src/main/java/org/hbp/mip/controllers/StatsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/StatsApi.java
@@ -9,9 +9,10 @@ import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiResponse;
import io.swagger.annotations.ApiResponses;
import org.hbp.mip.model.GeneralStats;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Query;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.ArticleRepository;
+import org.hbp.mip.repositories.UserRepository;
+import org.hbp.mip.repositories.VariableRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
@@ -24,44 +25,25 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/stats", description = "the stats API")
public class StatsApi {
+ @Autowired
+ UserRepository userRepository;
+
+ @Autowired
+ ArticleRepository articleRepository;
+
+ @Autowired
+ VariableRepository variableRepository;
+
@ApiOperation(value = "Get general statistics", response = GeneralStats.class)
@ApiResponses(value = {@ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
@RequestMapping(method = RequestMethod.GET)
public ResponseEntity<GeneralStats> getGeneralStatistics() {
GeneralStats stats = new GeneralStats();
- Long nbUsers = 0L;
- Long nbArticles = 0L;
- Long nbVariables = 0L;
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
-
- try{
-
- session.beginTransaction();
-
- Query countUsersQuery = session.createQuery("SELECT COUNT(*) FROM User");
- Query countArticlesQuery = session.createQuery("SELECT COUNT(*) FROM Article");
- Query countVariablesQuery = session.createQuery("SELECT COUNT(*) FROM Variable");
-
- nbUsers = (Long) countUsersQuery.uniqueResult();
- nbArticles = (Long) countArticlesQuery.uniqueResult();
- nbVariables = (Long) countVariablesQuery.uniqueResult();
-
- session.getTransaction().commit();
-
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
- stats.setUsers(nbUsers);
- stats.setArticles(nbArticles);
- stats.setVariables(nbVariables);
+ stats.setUsers(userRepository.count());
+ stats.setArticles(articleRepository.count());
+ stats.setVariables(variableRepository.count());
return ResponseEntity.ok(stats);
}
diff --git a/src/main/java/org/hbp/mip/controllers/UsersApi.java b/src/main/java/org/hbp/mip/controllers/UsersApi.java
index bdd2e6745173a7fb9362ae31392ca157007d8231..eabeffca1e196a3201a9068b46c1dc395946f2fb 100644
--- a/src/main/java/org/hbp/mip/controllers/UsersApi.java
+++ b/src/main/java/org/hbp/mip/controllers/UsersApi.java
@@ -6,8 +6,8 @@ package org.hbp.mip.controllers;
import io.swagger.annotations.*;
import org.hbp.mip.model.User;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.UserRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -21,6 +21,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/users", description = "the users API")
public class UsersApi {
+ @Autowired
+ UserRepository userRepository;
@ApiOperation(value = "Get a user", response = User.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Found"), @ApiResponse(code = 404, message = "Not found") })
@@ -28,25 +30,6 @@ public class UsersApi {
public ResponseEntity<User> getAUser(
@ApiParam(value = "username", required = true) @PathVariable("username") String username
) {
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- User user = null;
- try{
- session.beginTransaction();
- user = (User) session
- .createQuery("from User where username= :username")
- .setString("username", username)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(user);
+ return ResponseEntity.ok(userRepository.findOne(username));
}
}
diff --git a/src/main/java/org/hbp/mip/controllers/VariablesApi.java b/src/main/java/org/hbp/mip/controllers/VariablesApi.java
index f69f98dedd82c9eb8707b858e86e27a0fd55a2fb..b5f2d72f2f5ea151070fb2598007f22a49b475f6 100644
--- a/src/main/java/org/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/VariablesApi.java
@@ -8,12 +8,11 @@ package org.hbp.mip.controllers;
import io.swagger.annotations.*;
import org.hbp.mip.model.Value;
import org.hbp.mip.model.Variable;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.VariableRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
-import java.util.LinkedList;
import java.util.List;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -23,10 +22,13 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/variables", description = "the variables API")
public class VariablesApi {
+ @Autowired
+ VariableRepository variableRepository;
+
@ApiOperation(value = "Get variables", response = Variable.class, responseContainer = "List")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<List> getVariables(
+ public ResponseEntity<Iterable> getVariables(
@ApiParam(value = "List of groups formatted like : (\"val1\", \"val2\", ...)") @RequestParam(value = "group", required = false) String group,
@ApiParam(value = "List of subgroups formatted like : (\"val1\", \"val2\", ...)") @RequestParam(value = "subgroup", required = false) String subgroup,
@ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isVariable", required = false) String isVariable,
@@ -34,25 +36,7 @@ public class VariablesApi {
@ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isCovariable", required = false) String isCovariable,
@ApiParam(value = "Boolean value formatted like : (\"0\") or (\"1\") or (\"false\") or (\"true\")") @RequestParam(value = "isFilter", required = false) String isFilter
) {
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- List variables = new LinkedList<>();
- try{
- session.beginTransaction();
- variables = session
- .createQuery("from Variable")
- .list();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(variables);
+ return ResponseEntity.ok(variableRepository.findAll());
}
@ApiOperation(value = "Get a variable", response = Variable.class)
@@ -61,27 +45,7 @@ public class VariablesApi {
public ResponseEntity<Variable> getAVariable(
@ApiParam(value = "code of the variable ( multiple codes are allowed, separated by \",\" )", required = true) @PathVariable("code") String code
) {
-
- // Query DB
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Variable variable = null;
- try{
- session.beginTransaction();
- variable = (Variable) session
- .createQuery("from Variable where code= :code")
- .setString("code", code)
- .uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(variable);
+ return ResponseEntity.ok(variableRepository.findOne(code));
}
@@ -92,27 +56,7 @@ public class VariablesApi {
@ApiParam(value = "code", required = true) @PathVariable("code") String code,
@ApiParam(value = "Pattern to match") @RequestParam(value = "q", required = false) String q
) {
-
- // Query DB
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- List values = new LinkedList<>();
- try{
- session.beginTransaction();
- values = session
- .createQuery("select values from Variable where code= :code")
- .setString("code", code)
- .list();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
- return ResponseEntity.ok(values);
+ return ResponseEntity.ok(variableRepository.findOne(code).getValues());
}
diff --git a/src/main/java/org/hbp/mip/model/Experiment.java b/src/main/java/org/hbp/mip/model/Experiment.java
index d87949be04dc8da5d7080d4e20ace726e22ff267..53e4c13c818c14d396dee0118a85f3e5cbcbe9ce 100644
--- a/src/main/java/org/hbp/mip/model/Experiment.java
+++ b/src/main/java/org/hbp/mip/model/Experiment.java
@@ -6,15 +6,11 @@ import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.annotations.Expose;
import org.apache.log4j.Logger;
-import org.hbp.mip.utils.HibernateUtil;
-import org.hibernate.Session;
-import org.hibernate.Transaction;
-import org.hibernate.annotations.*;
-import org.hibernate.exception.DataException;
+import org.hbp.mip.repositories.ExperimentRepository;
+import org.hibernate.annotations.Cascade;
+import org.springframework.beans.factory.annotation.Autowired;
import javax.persistence.*;
-import javax.persistence.Entity;
-import javax.persistence.Table;
import java.util.Date;
import java.util.LinkedList;
import java.util.List;
@@ -35,6 +31,9 @@ public class Experiment {
.excludeFieldsWithoutExposeAnnotation()
.create();
+ @Autowired
+ ExperimentRepository experimentRepository;
+
@Id
@Column(columnDefinition = "uuid")
@org.hibernate.annotations.Type(type="pg-uuid")
@@ -147,17 +146,7 @@ public class Experiment {
public void finish() {
this.setFinished(new Date());
-
- try {
- Session session = HibernateUtil.getSessionFactory().openSession();
- Transaction transaction = session.beginTransaction();
- session.update(this);
- transaction.commit();
- session.close();
- } catch (DataException e) {
- LOGGER.trace(e);
- throw e;
- }
+ experimentRepository.save(this);
}
public String getValidations() {
diff --git a/src/main/java/org/hbp/mip/repositories/AppRepository.java b/src/main/java/org/hbp/mip/repositories/AppRepository.java
index d45a237160fbdb4dfca3be2d98634ad80cce54e3..450837ecbd6aa86b089ce7e7d3c5aef5a05bc673 100644
--- a/src/main/java/org/hbp/mip/repositories/AppRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/AppRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.App;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface AppRepository extends Repository<App, String> {
+public interface AppRepository extends CrudRepository<App, String> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/ArticleRepository.java b/src/main/java/org/hbp/mip/repositories/ArticleRepository.java
index d64979cc255db43218c00844ff35badef860005d..dfbbd1227898ed3721c6e63387786c392fcca04f 100644
--- a/src/main/java/org/hbp/mip/repositories/ArticleRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/ArticleRepository.java
@@ -1,10 +1,11 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Article;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface ArticleRepository extends Repository<Article, String> {
+public interface ArticleRepository extends CrudRepository<Article, String> {
+ Long countByTitle(String title);
}
diff --git a/src/main/java/org/hbp/mip/repositories/ConfigRepository.java b/src/main/java/org/hbp/mip/repositories/ConfigRepository.java
index e09f83fd58f1a96e0629f0b8286ec34af8dffd90..bb90c48e03637ab505cca3e4f74b14113ea6ebfd 100644
--- a/src/main/java/org/hbp/mip/repositories/ConfigRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/ConfigRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Config;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface ConfigRepository extends Repository<Config, Long> {
+public interface ConfigRepository extends CrudRepository<Config, Long> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/DatasetRepository.java b/src/main/java/org/hbp/mip/repositories/DatasetRepository.java
index 09d2933f796146ba4a9779239b1aa156b021ed7f..4d0a62bb76a2d7ff0a8e503b7e930d53b8c89d0b 100644
--- a/src/main/java/org/hbp/mip/repositories/DatasetRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/DatasetRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Dataset;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface DatasetRepository extends Repository<Dataset, String> {
+public interface DatasetRepository extends CrudRepository<Dataset, String> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/org/hbp/mip/repositories/ExperimentRepository.java
index 14aa1d23a89ea77ac2baff66c671bf8531e4490e..99513acdd08123645adfcd366f8eea8f3ae49dc7 100644
--- a/src/main/java/org/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/ExperimentRepository.java
@@ -1,12 +1,12 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Experiment;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
import java.util.UUID;
/**
* Created by mirco on 11.07.16.
*/
-public interface ExperimentRepository extends Repository<Experiment, UUID> {
+public interface ExperimentRepository extends CrudRepository<Experiment, UUID> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/FilterRepository.java b/src/main/java/org/hbp/mip/repositories/FilterRepository.java
index 2b5eb3caa261f7cf936684304828064554654919..0c1794243fda1fa6b72542f992d17770d808b9ad 100644
--- a/src/main/java/org/hbp/mip/repositories/FilterRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/FilterRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Filter;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface FilterRepository extends Repository<Filter, Long> {
+public interface FilterRepository extends CrudRepository<Filter, Long> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/GroupRepository.java b/src/main/java/org/hbp/mip/repositories/GroupRepository.java
index 3b2db555f5e386525197ad0da347ec3be91f8073..57f5eee9b84e8e9a03f2657b45928d71d00aec56 100644
--- a/src/main/java/org/hbp/mip/repositories/GroupRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/GroupRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Group;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface GroupRepository extends Repository<Group, String> {
+public interface GroupRepository extends CrudRepository<Group, String> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/ModelRepository.java b/src/main/java/org/hbp/mip/repositories/ModelRepository.java
index 7612e86d378b2d4a6def03a629b1c024011e1ad1..91aaa95dc860f96449c3cb2e04b05f3eba2a04e8 100644
--- a/src/main/java/org/hbp/mip/repositories/ModelRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/ModelRepository.java
@@ -1,10 +1,11 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Model;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface ModelRepository extends Repository<Model, String> {
+public interface ModelRepository extends CrudRepository<Model, String> {
+ Long countByTitle(String Title);
}
diff --git a/src/main/java/org/hbp/mip/repositories/QueryRepository.java b/src/main/java/org/hbp/mip/repositories/QueryRepository.java
index a690a4f4d676a30cd337cbdb5573fa878029cf77..6d07a73161f9809fbde758c589d67eca39474a2e 100644
--- a/src/main/java/org/hbp/mip/repositories/QueryRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/QueryRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Query;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface QueryRepository extends Repository<Query, Long> {
+public interface QueryRepository extends CrudRepository<Query, Long> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/TagRepository.java b/src/main/java/org/hbp/mip/repositories/TagRepository.java
index e122e500faa528300b93373e41753fabd9eadb36..9b613de352caf443ba6731c498c24e4b9c217213 100644
--- a/src/main/java/org/hbp/mip/repositories/TagRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/TagRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Tag;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface TagRepository extends Repository<Tag, String> {
+public interface TagRepository extends CrudRepository<Tag, String> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/UserRepository.java b/src/main/java/org/hbp/mip/repositories/UserRepository.java
index 750ceafa594744cbe321afb3aafb0d7638375a79..d5e1f126e50b6d53e86c00b388bd5bf055b00565 100644
--- a/src/main/java/org/hbp/mip/repositories/UserRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/UserRepository.java
@@ -1,10 +1,11 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.User;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface UserRepository extends Repository<User, String> {
+public interface UserRepository extends CrudRepository<User, String> {
+
}
diff --git a/src/main/java/org/hbp/mip/repositories/ValueRepository.java b/src/main/java/org/hbp/mip/repositories/ValueRepository.java
index 02e9df7876ddd4448cfcbc88091ac04623d54892..f17fe13490590c7b211928035dec2c78555ee8f2 100644
--- a/src/main/java/org/hbp/mip/repositories/ValueRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/ValueRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Value;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface ValueRepository extends Repository<Value, String> {
+public interface ValueRepository extends CrudRepository<Value, String> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/VariableRepository.java b/src/main/java/org/hbp/mip/repositories/VariableRepository.java
index 466280b91468314a3d9db6d666acf3148d95ecff..ff6eeb985c4483353b7b864b77049c8c6544c95e 100644
--- a/src/main/java/org/hbp/mip/repositories/VariableRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/VariableRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Variable;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface VariableRepository extends Repository<Variable, String> {
+public interface VariableRepository extends CrudRepository<Variable, String> {
}
diff --git a/src/main/java/org/hbp/mip/repositories/VoteRepository.java b/src/main/java/org/hbp/mip/repositories/VoteRepository.java
index d652f36a57887c47bbeb6f8762e96aef847522fc..bd858bd3ee961514669849c56be52269f5be6752 100644
--- a/src/main/java/org/hbp/mip/repositories/VoteRepository.java
+++ b/src/main/java/org/hbp/mip/repositories/VoteRepository.java
@@ -1,10 +1,10 @@
package org.hbp.mip.repositories;
import org.hbp.mip.model.Vote;
-import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface VoteRepository extends Repository<Vote, Long> {
+public interface VoteRepository extends CrudRepository<Vote, Long> {
}
diff --git a/src/main/java/org/hbp/mip/utils/CSVUtil.java b/src/main/java/org/hbp/mip/utils/CSVUtil.java
index b3f6850be795983ec8728624da7dfcf733369dfe..a91d390ce42533abaef1f65f00aab7ca9e57a394 100644
--- a/src/main/java/org/hbp/mip/utils/CSVUtil.java
+++ b/src/main/java/org/hbp/mip/utils/CSVUtil.java
@@ -4,7 +4,8 @@ import org.apache.log4j.Logger;
import org.hbp.mip.model.Dataset;
import org.hbp.mip.model.Query;
import org.hbp.mip.model.Variable;
-import org.hibernate.Session;
+import org.hbp.mip.repositories.VariableRepository;
+import org.springframework.beans.factory.annotation.Autowired;
import java.io.BufferedReader;
import java.io.IOException;
@@ -24,13 +25,10 @@ public class CSVUtil {
private static final String SEPARATOR = ",";
- private CSVUtil()
- {
- /* Hide implicit public constructor */
- throw new IllegalAccessError("CSVUtil class");
- }
+ @Autowired
+ VariableRepository variableRepository;
- public static Dataset parseValues(String filename, Query query)
+ public Dataset parseValues(String filename, Query query)
{
List<String[]> rows = getRows(filename);
@@ -161,7 +159,7 @@ public class CSVUtil {
return result;
}
- private static List<String[]> getRows(String filename) {
+ private List<String[]> getRows(String filename) {
List<String[]> rows = new LinkedList<>();
try {
InputStream is = CSVUtil.class.getClassLoader().getResourceAsStream(filename);
@@ -183,7 +181,7 @@ public class CSVUtil {
return rows;
}
- private static int find(String code, String[] firstRow) {
+ private int find(String code, String[] firstRow) {
for (int i = 0; i < firstRow.length; i++) {
if (firstRow[i].equals(code))
return i;
@@ -191,7 +189,7 @@ public class CSVUtil {
return -1;
}
- private static String generateDSCode(Query query) {
+ private String generateDSCode(Query query) {
String prefix = "DS";
String queryStr = Integer.toString(query.hashCode());
String memId;
@@ -206,24 +204,9 @@ public class CSVUtil {
return prefix + memId;
}
- private static String getTypeFromDB(Variable v)
+ private String getTypeFromDB(Variable v)
{
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- String type = null;
- try{
- session.beginTransaction();
- org.hibernate.Query q = session.createQuery("SELECT type FROM Variable where code= :code").setString("code", v.getCode());
- type = (String) q.uniqueResult();
- session.getTransaction().commit();
- } catch (Exception e)
- {
- if(session.getTransaction() != null)
- {
- session.getTransaction().rollback();
- throw e;
- }
- }
-
+ String type = variableRepository.findOne(v.getCode()).getType();
if(type == null)
{
type = "unknown";
diff --git a/src/main/java/org/hbp/mip/utils/HibernateUtil.java b/src/main/java/org/hbp/mip/utils/HibernateUtil.java
deleted file mode 100644
index 87cde9618993e4070518b70d2bf6e4d058d54760..0000000000000000000000000000000000000000
--- a/src/main/java/org/hbp/mip/utils/HibernateUtil.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/**
- * Created by mirco on 07.12.15.
- */
-
-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();
- configuration.configure();
- serviceRegistry = new StandardServiceRegistryBuilder().applySettings(
- configuration.getProperties()).build();
- sessionFactory = configuration.buildSessionFactory(serviceRegistry);
- return sessionFactory;
- } catch (RuntimeException ex) {
- LOGGER.error("Initial SessionFactory creation failed." + ex);
- throw new ExceptionInInitializerError(ex);
- }
- }
-
- public static SessionFactory getSessionFactory() {
- return sessionFactory;
- }
-}