diff --git a/pom.xml b/pom.xml
index af7c98035d8d7f354bf6730240deef5b94d9d464..a9cb39f28e7cf809c411420afed6756ec9965b9e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,13 +11,6 @@
<name>backend-services</name>
<description>Medical Informatics Platform : backend restful services</description>
- <distributionManagement>
- <repository>
- <id>central</id>
- <name>8a59c6752bef-releases</name>
- <url>http://hbps1.chuv.ch/artifactory/libs-release-local</url>
- </repository>
- </distributionManagement>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
@@ -165,6 +158,33 @@
</dependency>
</dependencies>
+
+
+ <pluginRepositories>
+ <pluginRepository>
+ <id>jcenter-snapshots</id>
+ <name>jcenter</name>
+ <url>http://oss.jfrog.org/artifactory/oss-snapshot-local/</url>
+ </pluginRepository>
+ <pluginRepository>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>jcenter-releases</id>
+ <name>jcenter</name>
+ <url>http://jcenter.bintray.com</url>
+ </pluginRepository>
+ </pluginRepositories>
+
+ <properties>
+ <asciidoctor.maven.plugin.version>1.5.3</asciidoctor.maven.plugin.version>
+ <asciidoctorj.pdf.version>1.5.0-alpha.11</asciidoctorj.pdf.version>
+ <asciidoctorj.version>1.5.4</asciidoctorj.version>
+ <sonar.host.url>http://dockerhost:9000</sonar.host.url>
+ <sonar.projectName>MIP Backend</sonar.projectName>
+ <sonar.sources>src/main/java/</sonar.sources>
+ </properties>
+
<build>
<resources>
<resource>
@@ -172,8 +192,8 @@
<includes>
<include>**/*.xml</include>
<include>**/*.json</include>
+ <include>**/*.csv</include>
</includes>
- <excludes><exclude>**/*.csv</exclude></excludes>
<filtering>true</filtering>
</resource>
</resources>
@@ -182,7 +202,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
- <version>2.4</version>
+ <version>2.3</version>
<configuration>
<!-- specify UTF-8, ISO-8859-1 or any other file encoding -->
<encoding>UTF-8</encoding>
@@ -192,28 +212,19 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
- <plugin>
- <groupId>de.juplo</groupId>
- <artifactId>hibernate-maven-plugin</artifactId>
- <version>2.0.0</version>
- <executions>
- <execution>
- <phase>compile</phase>
- <goals>
- <goal>create</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <export>false</export>
- <show>true</show>
- <format>true</format>
- </configuration>
- </plugin>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
+ <groupId>de.juplo</groupId>
+ <artifactId>hibernate4-maven-plugin</artifactId>
+ <version>1.1.0</version>
+ <executions>
+ <execution>
+ <phase>compile</phase>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
<artifactId>maven-compiler-plugin</artifactId>
- <version>3.5.1</version>
+ <version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
@@ -224,6 +235,43 @@
<artifactId>flyway-maven-plugin</artifactId>
<version>4.0.1</version>
</plugin>
+ <plugin>
+ <groupId>io.github.swagger2markup</groupId>
+ <artifactId>swagger2markup-maven-plugin</artifactId>
+ <version>1.0.0</version>
+ <configuration>
+ <swaggerInput>http://localhost:8080/services/v2/api-docs</swaggerInput>
+ <outputFile>${project.build.directory}/asciidoc/api</outputFile>
+ <config>
+ <swagger2markup.markupLanguage>ASCIIDOC</swagger2markup.markupLanguage>
+ </config>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.asciidoctor</groupId>
+ <artifactId>asciidoctor-maven-plugin</artifactId>
+ <version>${asciidoctor.maven.plugin.version}</version>
+ <dependencies>
+ <dependency>
+ <groupId>org.asciidoctor</groupId>
+ <artifactId>asciidoctorj-pdf</artifactId>
+ <version>${asciidoctorj.pdf.version}</version>
+ </dependency>
+ </dependencies>
+ <configuration>
+ <sourceDirectory>${project.build.directory}/asciidoc</sourceDirectory>
+ <backend>pdf</backend>
+ <attributes>
+ <toc/>
+ <idseparator>-</idseparator>
+ </attributes>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.sonarsource.scanner.maven</groupId>
+ <artifactId>sonar-maven-plugin</artifactId>
+ <version>3.0.1</version>
+ </plugin>
</plugins>
</build>
diff --git a/src/main/java/org/hbp/mip/MIPApplication.java b/src/main/java/org/hbp/mip/MIPApplication.java
index 0c44fef61108fcd62b46653bdc996ceb42480967..f6d5aeb3d156eeac8afd31340c8bf1b190065e61 100644
--- a/src/main/java/org/hbp/mip/MIPApplication.java
+++ b/src/main/java/org/hbp/mip/MIPApplication.java
@@ -3,27 +3,13 @@
* 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;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiParam;
+import org.apache.log4j.Logger;
import org.hbp.mip.model.User;
import org.hbp.mip.utils.CORSFilter;
import org.hbp.mip.utils.HibernateUtil;
@@ -92,6 +78,8 @@ import java.security.Principal;
@Api(value = "/", description = "MIP API")
public class MIPApplication extends WebSecurityConfigurerAdapter {
+ private static final Logger LOGGER = Logger.getLogger(MIPApplication.class);
+
@Autowired
OAuth2ClientContext oauth2ClientContext;
@@ -178,12 +166,11 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
try {
String userJSON = mapper.writeValueAsString(getUser());
Cookie cookie = new Cookie("user", URLEncoder.encode(userJSON, "UTF-8"));
+ cookie.setSecure(true);
cookie.setPath("/");
response.addCookie(cookie);
- } catch (JsonProcessingException e) {
- e.printStackTrace();
- } catch (UnsupportedEncodingException e) {
- e.printStackTrace();
+ } catch (JsonProcessingException | UnsupportedEncodingException e) {
+ LOGGER.trace(e);
}
return principal;
}
@@ -222,7 +209,7 @@ public class MIPApplication extends WebSecurityConfigurerAdapter {
http.addFilterBefore(new CORSFilter(), ChannelProcessingFilter.class);
http.antMatcher("/**")
.authorizeRequests()
- .antMatchers("/", "/frontend/**", "/webjars/**").permitAll()
+ .antMatchers("/", "/frontend/**", "/webjars/**", "/v2/api-docs").permitAll()
.anyRequest().authenticated()
.and().exceptionHandling().authenticationEntryPoint(new CustomLoginUrlAuthenticationEntryPoint("/login/hbp"))
.and().logout().logoutSuccessUrl("/login/hbp").permitAll()
@@ -274,8 +261,7 @@ 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 aa0bd2357c08c99f8e121ccc85ecb71af9ef6f7c..b89ef31b4836ba1e52966ae8a002e341bdb13546 100644
--- a/src/main/java/org/hbp/mip/controllers/AppsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/AppsApi.java
@@ -5,6 +5,7 @@
package org.hbp.mip.controllers;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.App;
import org.hbp.mip.model.User;
@@ -32,6 +33,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/apps", description = "the apps API")
public class AppsApi {
+ private static final Logger LOGGER = Logger.getLogger(AppsApi.class);
+
@Autowired
MIPApplication mipApplication;
@@ -106,6 +109,7 @@ public class AppsApi {
}
catch (ConstraintViolationException cve)
{
+ LOGGER.trace(cve);
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
@@ -114,6 +118,7 @@ public class AppsApi {
}
catch (NonUniqueObjectException nuoe)
{
+ LOGGER.trace(nuoe);
if(session.getTransaction() != null)
{
session.getTransaction().rollback();
diff --git a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
index 8a0a15e52e478f36a86eb326239cfa3c7f0d7f88..99fe8334aef8fa27ba2fde647794b472b1cdb196 100644
--- a/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ArticlesApi.java
@@ -7,6 +7,7 @@ package org.hbp.mip.controllers;
import com.github.slugify.Slugify;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.Article;
import org.hbp.mip.model.User;
@@ -31,6 +32,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@Api(value = "/articles", description = "the articles API")
public class ArticlesApi {
+ private static final Logger LOGGER = Logger.getLogger(ArticlesApi.class);
+
@Autowired
MIPApplication mipApplication;
@@ -57,11 +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();
@@ -99,7 +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);
@@ -128,13 +126,7 @@ public class ArticlesApi {
}
} while(count > 0);
- Slugify slg = null;
- try {
- slg = new Slugify();
- } catch (IOException e) {
- e.printStackTrace();
- }
- String slug = slg.slugify(article.getTitle());
+ String slug = new Slugify().slugify(article.getTitle());
i = 0;
do {
@@ -156,8 +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();
@@ -191,7 +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 868b7ed860f08eb63d1bb88a572355d00f30c486..5adbdaa35ffd233717ea958b54e6a3cdfc7f78a2 100644
--- a/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ExperimentApi.java
@@ -2,23 +2,28 @@ package org.hbp.mip.controllers;
import com.google.gson.*;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
-import org.hbp.mip.model.*;
+import org.hbp.mip.model.Experiment;
+import org.hbp.mip.model.Model;
+import org.hbp.mip.model.User;
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.hibernate.exception.DataException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
-import java.io.*;
-import java.net.*;
-import java.util.Date;
+import java.io.BufferedReader;
+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;
@@ -34,6 +39,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@javax.annotation.Generated(value = "class io.swagger.codegen.languages.SpringMVCServerCodegen", date = "2016-01-07T07:38:20.227Z")
public class ExperimentApi {
+ private static final Logger LOGGER = Logger.getLogger(ExperimentApi.class);
+
private static final String EXAREME_ALGO_JSON_FILE="data/exareme_algorithms.json";
private static final Gson gson = new GsonBuilder()
@@ -42,6 +49,8 @@ public class ExperimentApi {
.excludeFieldsWithoutExposeAnnotation()
.create();
+ private static final String EXAREME_LR_ALGO = "WP_LINEAR_REGRESSION";
+
@Value("#{'${workflow.experimentUrl:http://dockerhost:8087/experiment}'}")
private String experimentUrl;
@@ -54,72 +63,6 @@ public class ExperimentApi {
@Autowired
MIPApplication mipApplication;
- private void sendPost(Experiment experiment) throws MalformedURLException {
- URL obj = new URL(experimentUrl);
-
- // this runs in the background. For future optimization: use a thread pool
- new Thread() {
- 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) {} // 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();
-
- // write to experiment
- experiment.setResult(response.toString().replace("\0", ""));
- experiment.setHasError(con.getResponseCode() >= 400);
- experiment.setHasServerError(con.getResponseCode() >= 500);
-
- } catch (IOException ioe) {
- // write error to
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(ioe.getMessage());
- }
-
- experiment.setFinished(new Date());
-
- // finally
- try {
- Session session = HibernateUtil.getSessionFactory().openSession();
- Transaction transaction = session.beginTransaction();
- session.update(experiment);
- transaction.commit();
- session.close();
- } catch (DataException e) {
- throw e;
- }
-
- }
- }.start();
- }
@ApiOperation(value = "Send a request to the workflow to run an experiment", response = Experiment.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@@ -149,8 +92,12 @@ public class ExperimentApi {
transaction.commit();
} catch (Exception e) {
- transaction.rollback();
- e.printStackTrace();
+ 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);
}
@@ -158,125 +105,28 @@ public class ExperimentApi {
try {
if(isExaremeAlgo(experiment))
{
- sendExaremePost(experiment);
+ sendExaremeExperiment(experiment);
}
else
{
- sendPost(experiment);
+ sendExperiment(experiment);
}
- } catch (MalformedURLException mue) {} // ignore
+ } catch (MalformedURLException mue) { LOGGER.trace(mue.getMessage()); } // ignore
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
- private void sendExaremePost(Experiment experiment) {
-
- Model model = experiment.getModel();
- String algoCode = "WP_LINEAR_REGRESSION";
-
- LinkedList<ExaremeQueryElement> queryElements = new LinkedList<>();
- for (Variable var : model.getQuery().getVariables())
- {
- ExaremeQueryElement el = new ExaremeQueryElement();
- el.setName("variable");
- el.setDesc("");
- el.setValue(var.getCode());
- queryElements.add(el);
- }
- for (Variable var : model.getQuery().getCovariables())
- {
- ExaremeQueryElement el = new ExaremeQueryElement();
- el.setName("covariables");
- el.setDesc("");
- el.setValue(var.getCode());
- queryElements.add(el);
- }
- for (Variable var : model.getQuery().getGrouping())
- {
- ExaremeQueryElement el = new ExaremeQueryElement();
- el.setName("groupings");
- el.setDesc("");
- el.setValue(var.getCode());
- queryElements.add(el);
- }
-
- ExaremeQueryElement tableEl = new ExaremeQueryElement();
- tableEl.setName("showtable");
- tableEl.setDesc("");
- tableEl.setValue("TotalResults");
- queryElements.add(tableEl);
-
- ExaremeQueryElement formatEl = new ExaremeQueryElement();
- formatEl.setName("format");
- formatEl.setDesc("");
- formatEl.setValue("True");
- queryElements.add(formatEl);
-
- String jsonQuery = new Gson().toJson(queryElements);
-
- new Thread() {
- public void run() {
- try {
- String url = miningExaremeQueryUrl + "/" + algoCode;
- StringBuilder results = new StringBuilder();
- int code = HTTPUtil.sendPost(url, jsonQuery, results);
-
- experiment.setResult(results.toString().replace("\0", ""));
- experiment.setHasError(code >= 400);
- experiment.setHasServerError(code >= 500);
-
- if(!isJSONValid(experiment.getResult()))
- {
- experiment.setResult("Unsupported variables !");
- }
- } catch (Exception e) {
- experiment.setHasError(true);
- experiment.setHasServerError(true);
- experiment.setResult(e.getMessage());
- }
-
- experiment.setFinished(new Date());
-
- try {
- Session session = HibernateUtil.getSessionFactory().openSession();
- Transaction transaction = session.beginTransaction();
- session.update(experiment);
- transaction.commit();
- session.close();
- } catch (DataException e) {
- throw e;
- }
-
- }
- }.start();
- }
-
- public boolean isJSONValid(String test) {
- try {
- new JsonParser().parse(test);
- } catch (JsonParseException jpe)
- {
- return false;
- }
- return true;
- }
-
- 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");
- }
-
@ApiOperation(value = "get an experiment", response = Experiment.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
public ResponseEntity<String> getExperiment(@ApiParam(value = "uuid", required = true) @PathVariable("uuid") String uuid) {
-
Experiment experiment;
UUID experimentUuid;
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
+ LOGGER.trace(iae);
+ LOGGER.warn("An invalid Experiment UUID was received !");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -291,7 +141,10 @@ public class ExperimentApi {
session.getTransaction().commit();
} catch (Exception e) {
// 404 here probably
- session.getTransaction().rollback();
+ if(session.getTransaction() != null)
+ {
+ session.getTransaction().rollback();
+ }
throw e;
}
@@ -312,6 +165,8 @@ public class ExperimentApi {
try {
experimentUuid = UUID.fromString(uuid);
} catch (IllegalArgumentException iae) {
+ LOGGER.trace(iae);
+ LOGGER.warn("An invalid Experiment UUID was received !");
return ResponseEntity.badRequest().body("Invalid Experiment UUID");
}
@@ -333,56 +188,16 @@ public class ExperimentApi {
transaction.commit();
} catch (Exception e) {
// 404 here probably
- transaction.rollback();
- throw e;
- }
-
- if (experiment == null) {
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
- return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
- }
-
- public ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
-
- Experiment experiment;
- UUID experimentUuid;
- User user = mipApplication.getUser();
- try {
- experimentUuid = UUID.fromString(uuid);
- } catch (IllegalArgumentException iae) {
- return ResponseEntity.badRequest().body("Invalid Experiment UUID");
- }
-
- Session session = HibernateUtil.getSessionFactory().getCurrentSession();
- Transaction transaction = null;
- try {
- transaction = session.beginTransaction();
-
- Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
- hibernateQuery.setParameter("uuid", experimentUuid);
- experiment = (Experiment) hibernateQuery.uniqueResult();
-
- if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
- return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
-
- experiment.setShared(shared);
- session.update(experiment);
-
- transaction.commit();
- } catch (Exception e) {
- // 404 here probably
- transaction.rollback();
+ if(transaction != null)
+ {
+ transaction.rollback();
+ }
throw e;
}
- if (experiment == null) {
- return new ResponseEntity<>("Not found", HttpStatus.NOT_FOUND);
- }
return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
-
@ApiOperation(value = "get an experiment", response = Experiment.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
@RequestMapping(value = "/{uuid}/markAsShared", method = RequestMethod.GET)
@@ -397,7 +212,55 @@ public class ExperimentApi {
return doMarkExperimentAsShared(uuid, false);
}
- public ResponseEntity<String> doListExperiments(
+ @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
+ @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
+ @RequestMapping(value = "/mine", method = RequestMethod.GET, params = {"maxResultCount"})
+ public ResponseEntity<String> listExperiments(
+ @ApiParam(value = "maxResultCount", required = false) @RequestParam int maxResultCount
+ ) {
+ return doListExperiments(true, maxResultCount, null);
+ }
+
+ @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
+ @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
+ @RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
+ public ResponseEntity<String> listExperiments(
+ @ApiParam(value = "slug", required = false) @RequestParam("slug") String modelSlug,
+ @ApiParam(value = "maxResultCount", required = false) @RequestParam("maxResultCount") int maxResultCount
+ ) {
+
+ 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);
+ }
+
+ return doListExperiments(false, maxResultCount, modelSlug);
+ }
+
+ @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 IOException {
+
+ StringBuilder response = new StringBuilder();
+
+ int code = HTTPUtil.sendGet(listMethodsUrl, response);
+ if (code < 200 || code > 299) {
+ return new ResponseEntity<>(response.toString(), HttpStatus.valueOf(code));
+ }
+
+ JsonObject catalog = new JsonParser().parse(response.toString()).getAsJsonObject();
+
+ InputStream is = ExperimentApi.class.getClassLoader().getResourceAsStream(EXAREME_ALGO_JSON_FILE);
+ InputStreamReader isr = new InputStreamReader(is);
+ BufferedReader br = new BufferedReader(isr);
+ JsonObject exaremeAlgo = new JsonParser().parse(br).getAsJsonObject();
+
+ catalog.get("algorithms").getAsJsonArray().add(exaremeAlgo);
+
+ return new ResponseEntity<>(new Gson().toJson(catalog), HttpStatus.valueOf(code));
+ }
+
+ private ResponseEntity<String> doListExperiments(
boolean mine,
int maxResultCount,
String modelSlug
@@ -415,10 +278,11 @@ 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");
+ baseQuery += " AND e.model.slug = :slug";
+ hibernateQuery = session.createQuery(baseQuery);
hibernateQuery.setParameter("slug", modelSlug);
}
hibernateQuery.setParameter("user", user);
@@ -440,59 +304,125 @@ public class ExperimentApi {
}
} catch (Exception e) {
// 404 here probably
+ LOGGER.trace(e);
throw e;
} finally {
- session.getTransaction().rollback();
+ if(session.getTransaction() != null)
+ {
+ session.getTransaction().rollback();
+ }
}
return new ResponseEntity<>(gson.toJson(experiments), HttpStatus.OK);
}
- @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
- @RequestMapping(value = "/mine", method = RequestMethod.GET, params = {"maxResultCount"})
- public ResponseEntity<String> listExperiments(
- @ApiParam(value = "maxResultCount", required = false) @RequestParam int maxResultCount
- ) {
- return doListExperiments(true, maxResultCount, null);
- }
+ private ResponseEntity<String> doMarkExperimentAsShared(String uuid, boolean shared) {
+ Experiment experiment;
+ UUID experimentUuid;
+ User user = mipApplication.getUser();
+ try {
+ experimentUuid = UUID.fromString(uuid);
+ } catch (IllegalArgumentException iae) {
+ LOGGER.trace(iae);
+ LOGGER.warn("An invalid Experiment UUID was received !");
+ return ResponseEntity.badRequest().body("Invalid Experiment UUID");
+ }
- @ApiOperation(value = "list experiments", response = Experiment.class, responseContainer = "List")
- @ApiResponses(value = { @ApiResponse(code = 200, message = "Success") })
- @RequestMapping(method = RequestMethod.GET, params = {"slug", "maxResultCount"})
- public ResponseEntity<String> listExperiments(
- @ApiParam(value = "slug", required = false) @RequestParam("slug") String modelSlug,
- @ApiParam(value = "maxResultCount", required = false) @RequestParam("maxResultCount") int maxResultCount
- ) {
+ Session session = HibernateUtil.getSessionFactory().getCurrentSession();
+ Transaction transaction = null;
+ try {
+ transaction = session.beginTransaction();
- if (maxResultCount <= 0 && (modelSlug == null || modelSlug.equals(""))) {
- return new ResponseEntity<>("You must provide at least a slug or a limit of result", HttpStatus.BAD_REQUEST);
+ Query hibernateQuery = session.createQuery("from Experiment as experiment where experiment.uuid = :uuid");
+ hibernateQuery.setParameter("uuid", experimentUuid);
+ experiment = (Experiment) hibernateQuery.uniqueResult();
+
+ if (!experiment.getCreatedBy().getUsername().equals(user.getUsername()))
+ return new ResponseEntity<>("You're not the owner of this experiment", HttpStatus.BAD_REQUEST);
+
+ experiment.setShared(shared);
+ session.update(experiment);
+
+ transaction.commit();
+ } catch (Exception e) {
+ // 404 here probably
+ if(transaction != null)
+ {
+ transaction.rollback();
+ }
+ throw e;
}
- return doListExperiments(false, maxResultCount, modelSlug);
+ return new ResponseEntity<>(gson.toJson(experiment), HttpStatus.OK);
}
- @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 {
+ private void sendExperiment(Experiment experiment) throws MalformedURLException {
+ // this runs in the background. For future optimization: use a thread pool
+ new Thread() {
+ @Override
+ public void run() {
+ String url = experimentUrl;
+ String query = experiment.computeQuery();
- StringBuilder response = new StringBuilder();
+ // Results are stored in the experiment object
+ try {
+ executeExperiment(url, query, experiment);
+ } catch (IOException e) {
+ LOGGER.trace(e);
+ LOGGER.warn("Experiment failed to run properly !");
+ setExperimentError(e, experiment);
+ }
- int code = HTTPUtil.sendGet(listMethodsUrl, response);
- if (code < 200 || code > 299) {
- return new ResponseEntity<>(response.toString(), HttpStatus.valueOf(code));
- }
+ experiment.finish();
+ }
+ }.start();
+ }
- JsonObject catalog = new JsonParser().parse(response.toString()).getAsJsonObject();
+ private void sendExaremeExperiment(Experiment experiment) {
+ // this runs in the background. For future optimization: use a thread pool
+ new Thread() {
+ @Override
+ public void run() {
+ String query = experiment.computeExaremeQuery();
+ String url = miningExaremeQueryUrl + "/" + EXAREME_LR_ALGO;
- InputStream is = ExperimentApi.class.getClassLoader().getResourceAsStream(EXAREME_ALGO_JSON_FILE);
- InputStreamReader isr = new InputStreamReader(is);
- BufferedReader br = new BufferedReader(isr);
- JsonObject exaremeAlgo = new JsonParser().parse(br).getAsJsonObject();
+ // Results are stored in the experiment object
+ try {
+ executeExperiment(url, query, experiment);
+ } catch (IOException e) {
+ LOGGER.trace(e);
+ LOGGER.warn("Exareme experiment failed to run properly !");
+ setExperimentError(e, experiment);
+ }
- catalog.get("algorithms").getAsJsonArray().add(exaremeAlgo);
+ if(!JSONUtil.isJSONValid(experiment.getResult()))
+ {
+ experiment.setResult("Unsupported variables !");
+ }
- return new ResponseEntity<>(new Gson().toJson(catalog), HttpStatus.valueOf(code));
+ experiment.finish();
+ }
+ }.start();
+ }
+
+ private static void executeExperiment(String url, String query, Experiment experiment) throws IOException {
+ StringBuilder results = new StringBuilder();
+ int code = HTTPUtil.sendPost(url, query, results);
+ experiment.setResult(results.toString().replace("\0", ""));
+ experiment.setHasError(code >= 400);
+ experiment.setHasServerError(code >= 500);
}
+
+ private static void setExperimentError(IOException e, Experiment experiment) {
+ experiment.setHasError(true);
+ experiment.setHasServerError(true);
+ experiment.setResult(e.getMessage());
+ }
+
+ private static boolean isExaremeAlgo(Experiment experiment) {
+ JsonArray algorithms = new JsonParser().parse(experiment.getAlgorithms()).getAsJsonArray();
+ String algoCode = algorithms.get(0).getAsJsonObject().get("code").getAsString();
+ return "glm_exareme".equals(algoCode);
+ }
+
}
diff --git a/src/main/java/org/hbp/mip/controllers/ModelsApi.java b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
index 7041bbe76420928f5a0785f4301fb5fb300f681f..21b102e1858a508f92bff344a4aded93006c10f2 100644
--- a/src/main/java/org/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/org/hbp/mip/controllers/ModelsApi.java
@@ -6,6 +6,7 @@ package org.hbp.mip.controllers;
import com.github.slugify.Slugify;
import io.swagger.annotations.*;
+import org.apache.log4j.Logger;
import org.hbp.mip.MIPApplication;
import org.hbp.mip.model.*;
import org.hbp.mip.utils.CSVUtil;
@@ -28,6 +29,8 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@javax.annotation.Generated(value = "class io.swagger.codegen.languages.SpringMVCServerCodegen", date = "2016-01-07T07:38:20.227Z")
public class ModelsApi {
+ private static final Logger LOGGER = Logger.getLogger(ModelsApi.class);
+
@Autowired
MIPApplication mipApplication;
@@ -57,11 +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";
@@ -92,7 +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;
@@ -100,7 +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)
@@ -160,13 +158,7 @@ public class ModelsApi {
}
} while(count > 0);
- Slugify slg = null;
- try {
- slg = new Slugify();
- } catch (IOException e) {
- e.printStackTrace();
- }
- String slug = slg.slugify(model.getTitle());
+ String slug = new Slugify().slugify(model.getTitle());
i = 0;
do {
@@ -192,6 +184,8 @@ public class ModelsApi {
session.save(model);
session.getTransaction().commit();
+ } catch (IOException e) {
+ LOGGER.trace(e);
} catch (Exception e)
{
if(session.getTransaction() != null)
@@ -215,7 +209,6 @@ public class ModelsApi {
Session session = HibernateUtil.getSessionFactory().getCurrentSession();
Model model = null;
- Query query;
try {
session.beginTransaction();
@@ -260,45 +253,48 @@ public class ModelsApi {
}
}
- List<Variable> vars = new LinkedList<>();
- for (Variable var : q.getVariables()) {
- Variable v = new Variable();
- v.setCode(var.getCode());
- vars.add(v);
- }
+ if(q != null) {
- List<Variable> covs = new LinkedList<>();
- for (Variable cov : q.getCovariables()) {
- Variable v = new Variable();
- v.setCode(cov.getCode());
- covs.add(v);
- }
+ List<Variable> vars = new LinkedList<>();
+ for (Variable var : q.getVariables()) {
+ Variable v = new Variable();
+ v.setCode(var.getCode());
+ vars.add(v);
+ }
- List<Variable> grps = new LinkedList<>();
- for (Variable grp : q.getGrouping()) {
- Variable v = new Variable();
- v.setCode(grp.getCode());
- grps.add(v);
- }
+ List<Variable> covs = new LinkedList<>();
+ for (Variable cov : q.getCovariables()) {
+ Variable v = new Variable();
+ v.setCode(cov.getCode());
+ covs.add(v);
+ }
- List<Filter> fltrs = new LinkedList<>();
- for (Filter fltr : q.getFilters()) {
- Filter f = new Filter();
- f.setId(fltr.getId());
- f.setOperator(fltr.getOperator());
- f.setValues(fltr.getValues());
- f.setVariable(fltr.getVariable());
- fltrs.add(f);
- }
+ List<Variable> grps = new LinkedList<>();
+ for (Variable grp : q.getGrouping()) {
+ Variable v = new Variable();
+ v.setCode(grp.getCode());
+ grps.add(v);
+ }
- org.hbp.mip.model.Query myQuery = new org.hbp.mip.model.Query();
- myQuery.setId(q.getId());
- myQuery.setVariables(vars);
- myQuery.setCovariables(covs);
- myQuery.setGrouping(grps);
- myQuery.setFilters(fltrs);
+ List<Filter> fltrs = new LinkedList<>();
+ for (Filter fltr : q.getFilters()) {
+ Filter f = new Filter();
+ f.setId(fltr.getId());
+ f.setOperator(fltr.getOperator());
+ f.setValues(fltr.getValues());
+ f.setVariable(fltr.getVariable());
+ fltrs.add(f);
+ }
- model.setQuery(myQuery);
+ org.hbp.mip.model.Query myQuery = new org.hbp.mip.model.Query();
+ myQuery.setId(q.getId());
+ myQuery.setVariables(vars);
+ myQuery.setCovariables(covs);
+ myQuery.setGrouping(grps);
+ myQuery.setFilters(fltrs);
+
+ model.setQuery(myQuery);
+ }
Dataset ds = CSVUtil.parseValues(DATA_FILE, model.getQuery());
model.setDataset(ds);
@@ -380,41 +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..b7821db0ca22566bb2aff06a847d566fff0a40e7 100644
--- a/src/main/java/org/hbp/mip/model/Article.java
+++ b/src/main/java/org/hbp/mip/model/Article.java
@@ -26,12 +26,12 @@ public class Article {
@NotNull
@Size(min = 1, max = 255)
- private String title = null;
+ private String title;
private String status = null;
- @Column(columnDefinition = "text")
- private String _abstract = null;
+ @Column(columnDefinition = "text", name = "abstract")
+ private String abstractText = null;
@Column(columnDefinition = "text")
private String content = null;
@@ -55,6 +55,10 @@ public class Article {
public Article() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
+ title = "";
}
@@ -87,11 +91,11 @@ public class Article {
@JsonProperty("abstract")
public String getAbstract() {
- return _abstract;
+ return abstractText;
}
- public void setAbstract(String _abstract) {
- this._abstract = _abstract;
+ public void setAbstract(String abstractText) {
+ this.abstractText = abstractText;
}
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..d87949be04dc8da5d7080d4e20ace726e22ff267 100644
--- a/src/main/java/org/hbp/mip/model/Experiment.java
+++ b/src/main/java/org/hbp/mip/model/Experiment.java
@@ -5,12 +5,19 @@ import com.google.gson.GsonBuilder;
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 javax.persistence.*;
import javax.persistence.Entity;
import javax.persistence.Table;
import java.util.Date;
+import java.util.LinkedList;
+import java.util.List;
import java.util.UUID;
/**
@@ -20,6 +27,8 @@ import java.util.UUID;
@Table(name = "`experiment`")
public class Experiment {
+ private static final Logger LOGGER = Logger.getLogger(Experiment.class);
+
private static final Gson gson = new GsonBuilder()
.serializeNulls()
.setDateFormat("yyyy-MM-dd'T'HH:mm:ssZ")
@@ -78,6 +87,9 @@ public class Experiment {
private boolean resultsViewed = false;
public Experiment() {
+ /*
+ * Empty constructor is needed by Hibernate
+ */
}
public String computeQuery() {
@@ -91,6 +103,63 @@ public class Experiment {
return outgoingQuery.toString();
}
+ public String computeExaremeQuery() {
+ List<ExaremeQueryElement> queryElements = new LinkedList<>();
+ for (Variable var : model.getQuery().getVariables())
+ {
+ ExaremeQueryElement el = new ExaremeQueryElement();
+ el.setName("variable");
+ el.setDesc("");
+ el.setValue(var.getCode());
+ queryElements.add(el);
+ }
+ for (Variable var : model.getQuery().getCovariables())
+ {
+ ExaremeQueryElement el = new ExaremeQueryElement();
+ el.setName("covariables");
+ el.setDesc("");
+ el.setValue(var.getCode());
+ queryElements.add(el);
+ }
+ for (Variable var : model.getQuery().getGrouping())
+ {
+ ExaremeQueryElement el = new ExaremeQueryElement();
+ el.setName("groupings");
+ el.setDesc("");
+ el.setValue(var.getCode());
+ queryElements.add(el);
+ }
+
+ ExaremeQueryElement tableEl = new ExaremeQueryElement();
+ tableEl.setName("showtable");
+ tableEl.setDesc("");
+ tableEl.setValue("TotalResults");
+ queryElements.add(tableEl);
+
+ ExaremeQueryElement formatEl = new ExaremeQueryElement();
+ formatEl.setName("format");
+ formatEl.setDesc("");
+ formatEl.setValue("True");
+ queryElements.add(formatEl);
+
+ return new Gson().toJson(queryElements);
+ }
+
+ 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;
+ }
+ }
+
public String getValidations() {
return validations;
}
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..9feb2895dd7af50acfcb61e0e35810e3a71d2ebe 100644
--- a/src/main/java/org/hbp/mip/utils/CORSFilter.java
+++ b/src/main/java/org/hbp/mip/utils/CORSFilter.java
@@ -9,6 +9,7 @@ import java.io.IOException;
*/
public class CORSFilter implements Filter {
+ @Override
public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
HttpServletResponse response = (HttpServletResponse) res;
response.setHeader("Access-Control-Allow-Origin", "*");
@@ -18,7 +19,13 @@ public class CORSFilter implements Filter {
chain.doFilter(req, res);
}
- public void init(FilterConfig filterConfig) {}
+ @Override
+ public void init(FilterConfig filterConfig) {
+ /* Nothing to do */
+ }
- public void destroy() {}
+ @Override
+ 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 4ac7fd269d736166e12daf3fdd5716ad115a398a..b3f6850be795983ec8728624da7dfcf733369dfe 100644
--- a/src/main/java/org/hbp/mip/utils/CSVUtil.java
+++ b/src/main/java/org/hbp/mip/utils/CSVUtil.java
@@ -1,5 +1,6 @@
package org.hbp.mip.utils;
+import org.apache.log4j.Logger;
import org.hbp.mip.model.Dataset;
import org.hbp.mip.model.Query;
import org.hbp.mip.model.Variable;
@@ -19,14 +20,22 @@ import java.util.stream.Collectors;
*/
public class CSVUtil {
+ 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);
Dataset result = new Dataset();
- String code = GenerateDSCode(query);
+ String code = generateDSCode(query);
Date date = new Date();
List<String> header = new LinkedList<>();
List<String> grouping = new LinkedList<>();
@@ -140,7 +149,7 @@ public class CSVUtil {
data.put(c, ll);
}
} catch (IOException e) {
- e.printStackTrace();
+ LOGGER.trace(e);
}
result.setCode(code);
result.setDate(date);
@@ -155,7 +164,7 @@ public class CSVUtil {
private static List<String[]> getRows(String filename) {
List<String[]> rows = new LinkedList<>();
try {
- InputStream is = Dataset.class.getClassLoader().getResourceAsStream(filename);
+ InputStream is = CSVUtil.class.getClassLoader().getResourceAsStream(filename);
InputStreamReader isr = new InputStreamReader(is);
BufferedReader br = new BufferedReader(isr);
String[] firstRow = br.readLine().split(SEPARATOR, -1); // 1st row -> headers
@@ -167,7 +176,8 @@ public class CSVUtil {
isr.close();
is.close();
} catch (IOException e) {
- e.printStackTrace();
+ LOGGER.trace(e);
+ LOGGER.warn("A problem occured while trying to read a CSV file !");
}
return rows;
@@ -181,7 +191,7 @@ public class CSVUtil {
return -1;
}
- private static String GenerateDSCode(Query query) {
+ private static String generateDSCode(Query query) {
String prefix = "DS";
String queryStr = Integer.toString(query.hashCode());
String memId;
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 3048e20b8f338a7ce22d047f9701ac89176d98b8..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();
@@ -21,8 +31,8 @@ public class HibernateUtil {
configuration.getProperties()).build();
sessionFactory = configuration.buildSessionFactory(serviceRegistry);
return sessionFactory;
- } catch (Throwable ex) {
- System.err.println("Initial SessionFactory creation failed." + ex);
+ } catch (RuntimeException ex) {
+ LOGGER.error("Initial SessionFactory creation failed." + ex);
throw new ExceptionInInitializerError(ex);
}
}
diff --git a/src/main/java/org/hbp/mip/utils/JSONUtil.java b/src/main/java/org/hbp/mip/utils/JSONUtil.java
new file mode 100644
index 0000000000000000000000000000000000000000..938cfbb70a26974495782707d151089fad9b4d01
--- /dev/null
+++ b/src/main/java/org/hbp/mip/utils/JSONUtil.java
@@ -0,0 +1,30 @@
+package org.hbp.mip.utils;
+
+import com.google.gson.JsonParseException;
+import com.google.gson.JsonParser;
+import org.apache.log4j.Logger;
+
+/**
+ * Created by mirco on 01.07.16.
+ */
+public class JSONUtil {
+
+ private static final Logger LOGGER = Logger.getLogger(JSONUtil.class);
+
+ private JSONUtil() {
+ /* Hide implicit public constructor */
+ throw new IllegalAccessError("JSONUtil class");
+ }
+
+ public static boolean isJSONValid(String test) {
+ try {
+ new JsonParser().parse(test);
+ } catch (JsonParseException jpe)
+ {
+ LOGGER.trace(jpe); // This is the normal behavior when the input string is not JSON-ified
+ return false;
+ }
+ return true;
+ }
+
+}