diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 13fc6577970ede925089895265e8a3f6b0a409ae..4e723b8a3b27ed8f420e8b7f6293277ad17194f0 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -2,7 +2,7 @@
# See http://docs.spring.io/spring-boot/docs/current/reference/html/common-application-properties.html
spring:
- portalDatasource:
+ portal-datasource:
url: {{ default .Env.PORTAL_DB_URL "jdbc:postgresql://172.22.0.1:5432/portal" }}
schema: {{ default .Env.PORTAL_DB_SCHEMA "public" }}
username: {{ default .Env.PORTAL_DB_USER "postgres" }}
@@ -16,6 +16,8 @@ spring:
jpa:
hibernate:
dialect: org.hibernate.dialect.PostgreSQL9Dialect
+ ddl-auto: validate
+
# SPRING RESOURCES HANDLING
resources:
chain:
diff --git a/pom.xml b/pom.xml
index 2caa3f34994694784cfff87419af578ebb9786e0..02129ae2b41f261b610ddea13d43a978d895141c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -14,9 +14,7 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
- <version>1.3.8.RELEASE</version>
- <relativePath/>
-
+ <version>2.3.5.RELEASE</version>
</parent>
<properties>
@@ -25,16 +23,18 @@
<sonar.projectName>MIP portal-backend</sonar.projectName>
<sonar.sources>src/main/java/</sonar.sources>
<java.version>1.8</java.version>
+ <springfox-swagger.version>2.5.0</springfox-swagger.version>
+ <spring-context.version>5.2.10.RELEASE</spring-context.version>
+ <springfox-boot-starter.version>3.0.0</springfox-boot-starter.version>
<asciidoctor.maven.plugin.version>1.5.5</asciidoctor.maven.plugin.version>
<asciidoctorj.pdf.version>1.5.0-alpha.15</asciidoctorj.pdf.version>
<asciidoctorj.version>1.5.5</asciidoctorj.version>
- <spring-data-commons.version>1.12.3.RELEASE</spring-data-commons.version>
<angularjs.version>1.5.7</angularjs.version>
<jquery.version>3.0.0</jquery.version>
<bootstrap.version>3.3.7</bootstrap.version>
+ <webjars-locator.version>0.36</webjars-locator.version>
<h2.version>1.4.192</h2.version>
<postgresql.version>42.2.1</postgresql.version>
- <springfox-swagger.version>2.5.0</springfox-swagger.version>
<gson.version>2.7</gson.version>
<slugify.version>2.1.5</slugify.version>
<maven-resources-plugin.version>3.0.1</maven-resources-plugin.version>
@@ -42,15 +42,12 @@
<swagger2markup-maven-plugin.version>1.0.0</swagger2markup-maven-plugin.version>
<maven-compiler-plugin.version>3.5.1</maven-compiler-plugin.version>
<hibernate4-maven-plugin.version>1.1.1</hibernate4-maven-plugin.version>
+ <commons-dbcp.version>2.7.0</commons-dbcp.version>
<flyway-core.version>4.2.0</flyway-core.version>
<hibernate-jpa-2.1-api.version>1.0.0.Final</hibernate-jpa-2.1-api.version>
- <hibernate.version>4.3.11.Final</hibernate.version>
- <spring-data-jpa.version>1.10.11.RELEASE</spring-data-jpa.version>
- <spring-boot-starter-actuator.version>1.4.7.RELEASE</spring-boot-starter-actuator.version>
+ <hibernate.version>5.4.10.Final</hibernate.version>
<aspectjweaver.version>1.8.9</aspectjweaver.version>
<javax-inject.version>1</javax-inject.version>
- <akka.version>2.5.22</akka.version>
- <spring-context.version>4.3.4.RELEASE</spring-context.version>
<protobuf-java.version>3.1.0</protobuf-java.version>
</properties>
@@ -66,32 +63,39 @@
</repositories>
<dependencies>
-
+ <dependency>
+ <groupId>net.logstash.logback</groupId>
+ <artifactId>logstash-logback-encoder</artifactId>
+ <version>6.4</version>
+ </dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.springframework.security.oauth.boot</groupId>
+ <artifactId>spring-security-oauth2-autoconfigure</artifactId>
+ <version>2.0.1.RELEASE</version>
+ </dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
- <version>${spring-boot-starter-actuator.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
- <version>${spring-data-commons.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
- <groupId>org.springframework.boot</groupId>
- <artifactId>spring-boot-starter-web</artifactId>
+ <groupId>org.springframework.security</groupId>
+ <artifactId>spring-security-oauth2-resource-server</artifactId>
</dependency>
<dependency>
- <groupId>org.springframework.security.oauth</groupId>
- <artifactId>spring-security-oauth2</artifactId>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
@@ -115,6 +119,7 @@
<dependency>
<groupId>org.webjars</groupId>
<artifactId>webjars-locator</artifactId>
+ <version>${webjars-locator.version}</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
@@ -148,13 +153,8 @@
</dependency>
<dependency>
<groupId>io.springfox</groupId>
- <artifactId>springfox-swagger2</artifactId>
- <version>${springfox-swagger.version}</version>
- </dependency>
- <dependency>
- <groupId>io.springfox</groupId>
- <artifactId>springfox-swagger-ui</artifactId>
- <version>${springfox-swagger.version}</version>
+ <artifactId>springfox-boot-starter</artifactId>
+ <version>${springfox-boot-starter.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
@@ -169,11 +169,11 @@
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
- <version>${spring-data-jpa.version}</version>
</dependency>
<dependency>
- <groupId>commons-dbcp</groupId>
- <artifactId>commons-dbcp</artifactId>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-dbcp2</artifactId>
+ <version>${commons-dbcp.version}</version>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
@@ -192,9 +192,9 @@
<version>${javax-inject.version}</version>
</dependency>
<dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-context</artifactId>
- <version>${spring.version}</version>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-context</artifactId>
+ <version>${spring-context.version}</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
@@ -243,6 +243,11 @@
<artifactId>java-jwt</artifactId>
<version>3.11.0</version>
</dependency>
+ <dependency>
+ <groupId>org.springframework.security.oauth</groupId>
+ <artifactId>spring-security-oauth2</artifactId>
+ <version>2.5.0.RELEASE</version>
+ </dependency>
</dependencies>
<build>
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index c8024e1bffa90604da6d13712bc07cbac815b3d7..bca25598a6e59827a6a938e30fc9db1b9b5d5614 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -1,10 +1,12 @@
package eu.hbp.mip.configuration;
import org.flywaydb.core.Flyway;
-import org.springframework.boot.autoconfigure.jdbc.DataSourceBuilder;
import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.boot.orm.jpa.EntityScan;
-import org.springframework.context.annotation.*;
+import org.springframework.boot.jdbc.DataSourceBuilder;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.DependsOn;
+import org.springframework.context.annotation.Primary;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.orm.jpa.JpaVendorAdapter;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -18,12 +20,11 @@ import javax.sql.DataSource;
@Configuration
@EnableJpaRepositories("eu.hbp.mip.repositories")
-@EntityScan(basePackages = "eu.hbp.mip.model")
public class PersistenceConfiguration {
@Primary
- @Bean(name = "portalDatasource")
- @ConfigurationProperties(prefix = "spring.portalDatasource")
+ @Bean(name = "portal-datasource")
+ @ConfigurationProperties(prefix = "spring.portal-datasource")
public DataSource portalDataSource() {
return DataSourceBuilder.create().build();
}
@@ -32,11 +33,12 @@ public class PersistenceConfiguration {
@Bean(name = "entityManagerFactory")
@DependsOn("flyway")
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
- LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
- em.setDataSource(portalDataSource());
+ LocalContainerEntityManagerFactoryBean emfb = new LocalContainerEntityManagerFactoryBean();
+ emfb.setDataSource(portalDataSource());
JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
- em.setJpaVendorAdapter(vendorAdapter);
- return em;
+ emfb.setJpaVendorAdapter(vendorAdapter);
+ emfb.setPackagesToScan("eu.hbp.mip.model.DAOs");
+ return emfb;
}
@Bean(name = "flyway", initMethod = "migrate")
diff --git a/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java b/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java
deleted file mode 100644
index 352b1d156558ef42b9862b644ed5668070899708..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/configuration/PortalErrorAttributes.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package eu.hbp.mip.configuration;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.boot.autoconfigure.web.DefaultErrorAttributes;
-import org.springframework.stereotype.Component;
-import org.springframework.web.context.request.RequestAttributes;
-
-import java.util.HashMap;
-import java.util.Map;
-
-@Component
-public class PortalErrorAttributes extends DefaultErrorAttributes {
-
- private static final Logger LOGGER = LoggerFactory.getLogger(PortalErrorAttributes.class);
-
- @Override
- public Map<String, Object> getErrorAttributes(RequestAttributes requestAttributes, boolean includeStackTrace) {
- Map<String, Object> errorAttributes = super.getErrorAttributes(requestAttributes, includeStackTrace);
-
- Throwable throwable = getError(requestAttributes);
- StringBuilder sb = new StringBuilder("[");
- for (String attr : requestAttributes.getAttributeNames(RequestAttributes.SCOPE_REQUEST)) {
- Object v = requestAttributes.getAttribute(attr, RequestAttributes.SCOPE_REQUEST);
- sb.append(attr).append(" = ").append(v).append('\n');
- }
- sb.append("]");
- LOGGER.error("Reporting server error on request with attributes " + sb.toString(), throwable);
-
- if (throwable != null) {
-
- Throwable cause = throwable.getCause();
- if (cause != null) {
- Map<String, Object> causeErrorAttributes = new HashMap<>();
- causeErrorAttributes.put("exception", cause.getClass().getName());
- causeErrorAttributes.put("message", cause.getMessage());
- errorAttributes.put("cause", causeErrorAttributes);
- }
- }
-
- return errorAttributes;
- }
-}
diff --git a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
index 4ea52570fd3bde8c8b21253fe202aa3fc61363d4..afd3e56ed97164627dd5694e945eed97f18f9aaa 100644
--- a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
@@ -9,7 +9,7 @@ import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.security.oauth2.resource.AuthoritiesExtractor;
import org.springframework.boot.autoconfigure.security.oauth2.resource.ResourceServerProperties;
import org.springframework.boot.autoconfigure.security.oauth2.resource.UserInfoTokenServices;
-import org.springframework.boot.context.embedded.FilterRegistrationBean;
+import org.springframework.boot.web.servlet.FilterRegistrationBean;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
diff --git a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java b/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
index a5b514dfb815c9df88c0475b7c3ce24df1f06803..17e38a5eea2931d756375af4420b77953d737f51 100644
--- a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
@@ -2,7 +2,6 @@ package eu.hbp.mip.configuration;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.DependsOn;
import org.springframework.data.web.config.EnableSpringDataWebSupport;
import springfox.documentation.builders.ApiInfoBuilder;
import springfox.documentation.builders.RequestHandlerSelectors;
@@ -10,7 +9,6 @@ import springfox.documentation.service.ApiInfo;
import springfox.documentation.service.Contact;
import springfox.documentation.spi.DocumentationType;
import springfox.documentation.spring.web.plugins.Docket;
-import springfox.documentation.swagger.web.UiConfiguration;
import springfox.documentation.swagger2.annotations.EnableSwagger2;
/**
@@ -22,10 +20,10 @@ import springfox.documentation.swagger2.annotations.EnableSwagger2;
@EnableSpringDataWebSupport
public class WebConfiguration {
- @Bean
- public UiConfiguration swaggerUiConfig() {
- return UiConfiguration.DEFAULT;
- }
+// @Bean
+// public String[] swaggerUiConfig() {
+// return UiConfiguration.Constants.DEFAULT_SUBMIT_METHODS;
+// }
@Bean
public Docket swaggerDocumentation() {
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index d28d8aac35cf08c7be49f96e64b1bfb5410e2662..c3b93cbe14120208c6fbc40ceab186305028f348 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,6 +1,5 @@
package eu.hbp.mip.controllers;
-import com.google.gson.Gson;
import eu.hbp.mip.model.DTOs.ExperimentDTO;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.services.ExperimentService;
@@ -8,13 +7,10 @@ import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
import org.springframework.web.bind.annotation.*;
-import java.util.List;
-
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
/*
@@ -35,8 +31,13 @@ public class ExperimentApi {
@ApiOperation(value = "Get experiments", response = ExperimentDTO.class, responseContainer = "List")
@RequestMapping(method = RequestMethod.GET)
- public ResponseEntity<String> getExperiments() {
- return experimentService.getExperiments("(GET) /experiments");
+ public ResponseEntity<String> getExperiments(
+ @RequestParam(name = "name", required = false) String name,
+ @RequestParam(name = "algorithm", required = false) String algorithm,
+ @RequestParam(name = "shared", required = false) Boolean shared,
+ @RequestParam(name = "viewed", required = false) Boolean viewed
+ ) {
+ return experimentService.getExperiments(name, algorithm, shared, viewed, "(GET) /experiments");
}
@ApiOperation(value = "Get an experiment", response = ExperimentDTO.class)
diff --git a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
index 4e412aea08da5612f47d60baafd4bac791f2fc6e..ff8d70a80405ad2e7579198c5ef4f8a9a42d38d5 100644
--- a/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/SecurityApi.java
@@ -5,7 +5,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
import eu.hbp.mip.configuration.SecurityConfiguration;
-import eu.hbp.mip.model.User;
+import eu.hbp.mip.model.DAOs.UserDAO;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.repositories.UserRepository;
import eu.hbp.mip.utils.Logging;
@@ -70,7 +70,7 @@ public class SecurityApi {
@RequestMapping(path = "/user", method = RequestMethod.POST)
public ResponseEntity<Void> postUser(
@ApiParam(value = "Has the user agreed on the NDA") @RequestParam(value = "agreeNDA") Boolean agreeNDA) {
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
if (user != null) {
user.setAgreeNDA(agreeNDA);
userRepository.save(user);
diff --git a/src/main/java/eu/hbp/mip/controllers/UsersApi.java b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
index b791a7858e216d8ce0f8cd36610763c5c123e66a..886ad1ac90776e3c8b66025a6f7a22c223eadb6a 100644
--- a/src/main/java/eu/hbp/mip/controllers/UsersApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
@@ -4,7 +4,7 @@
package eu.hbp.mip.controllers;
-import eu.hbp.mip.model.User;
+import eu.hbp.mip.model.DAOs.UserDAO;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.repositories.UserRepository;
import eu.hbp.mip.utils.Logging;
@@ -31,13 +31,13 @@ public class UsersApi {
@Autowired
private UserInfo userInfo;
- @ApiOperation(value = "Get a user", response = User.class)
+ @ApiOperation(value = "Get a user", response = UserDAO.class)
@RequestMapping(value = "/{username}", method = RequestMethod.GET)
- public ResponseEntity<User> getAUser(
+ public ResponseEntity<UserDAO> getAUser(
@ApiParam(value = "username", required = true) @PathVariable("username") String username
) {
Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /users/{username}", "Loaded a user with username : " + userInfo.getUser().getUsername());
- return ResponseEntity.ok(userRepository.findOne(username));
+ return ResponseEntity.ok(userRepository.findByUsername(username));
}
}
diff --git a/src/main/java/eu/hbp/mip/model/Article.java b/src/main/java/eu/hbp/mip/model/DAOs/ArticleDAO.java
similarity index 87%
rename from src/main/java/eu/hbp/mip/model/Article.java
rename to src/main/java/eu/hbp/mip/model/DAOs/ArticleDAO.java
index b79f2a33a8275484a0e9a680a93619dbea2ea5c2..541c50765e25e7ce68504026ed437f906104e2ce 100644
--- a/src/main/java/eu/hbp/mip/model/Article.java
+++ b/src/main/java/eu/hbp/mip/model/DAOs/ArticleDAO.java
@@ -2,7 +2,7 @@
* Created by mirco on 04.12.15.
*/
-package eu.hbp.mip.model;
+package eu.hbp.mip.model.DAOs;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
@@ -13,15 +13,13 @@ import javax.persistence.*;
import javax.validation.constraints.NotNull;
import javax.validation.constraints.Size;
import java.util.Date;
-import java.util.LinkedList;
-import java.util.List;
@Entity
@Table(name = "`article`")
@ApiModel
@JsonInclude(JsonInclude.Include.NON_NULL)
@Validated
-public class Article {
+public class ArticleDAO {
@Id
private String slug = null;
@@ -46,13 +44,13 @@ public class Article {
@ManyToOne
@JoinColumn(name = "createdby_username")
- private User createdBy = null;
+ private UserDAO createdBy = null;
@ManyToOne
@JoinColumn(name = "updatedby_username")
- private User updatedBy = null;
+ private UserDAO updatedBy = null;
- public Article() {
+ public ArticleDAO() {
/*
* Empty constructor is needed by Hibernate
*/
@@ -133,20 +131,20 @@ public class Article {
}
- public User getCreatedBy() {
+ public UserDAO getCreatedBy() {
return createdBy;
}
- public void setCreatedBy(User createdBy) {
+ public void setCreatedBy(UserDAO createdBy) {
this.createdBy = createdBy;
}
- public User getUpdatedBy() {
+ public UserDAO getUpdatedBy() {
return updatedBy;
}
- public void setUpdatedBy(User updatedBy) {
+ public void setUpdatedBy(UserDAO updatedBy) {
this.updatedBy = updatedBy;
}
diff --git a/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java b/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
index 682f121cea95c13bf88c83c71ddcd5815ffe7884..30d6c87da9603b828fd9efe3d4d457800fc576de 100644
--- a/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
+++ b/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
@@ -1,11 +1,12 @@
package eu.hbp.mip.model.DAOs;
+import com.fasterxml.jackson.annotation.JsonInclude;
import com.google.gson.Gson;
import com.google.gson.annotations.Expose;
import eu.hbp.mip.model.DTOs.AlgorithmDTO;
import eu.hbp.mip.model.DTOs.ExperimentDTO;
-import eu.hbp.mip.model.User;
import eu.hbp.mip.utils.JsonConverters;
+import io.swagger.annotations.ApiModel;
import javax.persistence.*;
import java.util.Date;
@@ -16,51 +17,62 @@ import java.util.UUID;
*/
@Entity
@Table(name = "`experiment`")
+@ApiModel
+@JsonInclude(JsonInclude.Include.NON_NULL)
public class ExperimentDAO {
private static final Gson gson = new Gson();
+ @Expose
@Id
@Column(columnDefinition = "uuid", updatable = false)
@org.hibernate.annotations.Type(type = "pg-uuid")
- @Expose
private UUID uuid;
- @Column(columnDefinition = "TEXT")
@Expose
+ @Column(columnDefinition = "TEXT")
private String name;
@Expose
@ManyToOne
- @JoinColumn(name = "created_by_username")
- private User createdBy;
+ @JoinColumn(name = "created_by_username",columnDefinition = "CHARACTER VARYING")
+ private UserDAO createdBy;
- @Column(name="workflow_history_id", columnDefinition = "TEXT")
@Expose
+ @Column(name="workflow_history_id", columnDefinition = "TEXT")
private String workflowHistoryId;
- @Column(columnDefinition = "TEXT")
@Expose
+ @Column(columnDefinition = "TEXT")
private Status status;
- @Column(columnDefinition = "TEXT")
@Expose
+ @Column(columnDefinition = "TEXT")
private String result;
@Expose
+ @Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
private Date finished;
@Expose
+ @Column(columnDefinition = "TEXT")
+ private String algorithmDetails;
+
+ @Expose
+ @Column(columnDefinition = "TEXT")
private String algorithm;
@Expose
+ @Column(columnDefinition = "TIMESTAMP WITHOUT TIME ZONE")
private Date created = new Date();
@Expose
+ @Column(columnDefinition = "BOOLEAN")
private boolean shared = false;
// whether or not the experiment's result have been viewed by its owner
@Expose
+ @Column(columnDefinition = "BOOLEAN")
private boolean viewed = false;
public enum Status {
@@ -102,7 +114,7 @@ public class ExperimentDAO {
public ExperimentDTO convertToDTO()
{
ExperimentDTO experimentDTO = new ExperimentDTO();
- experimentDTO.setAlgorithm(JsonConverters.convertJsonStringToObject(this.algorithm, AlgorithmDTO.class));
+ experimentDTO.setAlgorithmDetails(JsonConverters.convertJsonStringToObject(this.algorithmDetails, AlgorithmDTO.class));
experimentDTO.setCreated(this.created);
experimentDTO.setCreatedBy(this.createdBy.getUsername());
experimentDTO.setName(this.name);
@@ -113,6 +125,14 @@ public class ExperimentDAO {
return experimentDTO;
}
+ public String getAlgorithmDetails() {
+ return algorithmDetails;
+ }
+
+ public void setAlgorithmDetails(String algorithmDetails) {
+ this.algorithmDetails = algorithmDetails;
+ }
+
public String getAlgorithm() {
return algorithm;
}
@@ -177,11 +197,11 @@ public class ExperimentDAO {
this.name = name;
}
- public User getCreatedBy() {
+ public UserDAO getCreatedBy() {
return createdBy;
}
- public void setCreatedBy(User createdBy) {
+ public void setCreatedBy(UserDAO createdBy) {
this.createdBy = createdBy;
}
diff --git a/src/main/java/eu/hbp/mip/model/User.java b/src/main/java/eu/hbp/mip/model/DAOs/UserDAO.java
similarity index 94%
rename from src/main/java/eu/hbp/mip/model/User.java
rename to src/main/java/eu/hbp/mip/model/DAOs/UserDAO.java
index f1ee34059054493bfc3c37ad7d762ffacb486c6f..1e35ac8315e000e21c6962472967b53fbdcaecf9 100644
--- a/src/main/java/eu/hbp/mip/model/User.java
+++ b/src/main/java/eu/hbp/mip/model/DAOs/UserDAO.java
@@ -2,7 +2,7 @@
* Created by mirco on 04.12.15.
*/
-package eu.hbp.mip.model;
+package eu.hbp.mip.model.DAOs;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;
@@ -20,7 +20,7 @@ import java.util.regex.Pattern;
@ApiModel
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonIgnoreProperties(value = {"appsVotes"})
-public class User {
+public class UserDAO {
@Id
@Expose
@@ -35,7 +35,7 @@ public class User {
private Boolean agreeNDA = null;
- public User() {
+ public UserDAO() {
/*
* Empty constructor is needed by Hibernate
*/
@@ -47,7 +47,7 @@ public class User {
*
* @param userInfo info from OpenID UserInfo endpoint
*/
- public User(String userInfo) {
+ public UserDAO(String userInfo) {
Pattern p;
Matcher m;
diff --git a/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java b/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
index b4214dd0a4de6aa50fa13f7aeb91652ce2c32137..e4b9d34a5f35baf8927bd6d5e26310671aca6ae6 100644
--- a/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
@@ -16,16 +16,29 @@ public class ExperimentDTO {
private ExperimentDTO.ResultDTO result;
private ExperimentDAO.Status status;
- private AlgorithmDTO algorithm;
+ private String algorithm;
+ private AlgorithmDTO algorithmDetails;
- public AlgorithmDTO getAlgorithm() {
+ public ExperimentDTO() {
+ }
+
+ public String getAlgorithm() {
return algorithm;
}
- public void setAlgorithm(AlgorithmDTO algorithm) {
+ public void setAlgorithm(String algorithm) {
this.algorithm = algorithm;
}
+ public AlgorithmDTO getAlgorithmDetails() {
+ return algorithmDetails;
+ }
+
+ public void setAlgorithmDetails(AlgorithmDTO algorithmDetails) {
+ this.algorithmDetails = algorithmDetails;
+ this.algorithm = algorithmDetails.getName();
+ }
+
public String getUuid() {
return uuid;
}
diff --git a/src/main/java/eu/hbp/mip/model/UserInfo.java b/src/main/java/eu/hbp/mip/model/UserInfo.java
index 7bd9a97f3a8f16847410f73afc924fd05ff905cd..cb61cfcea60c58275aaa0fac65c63a699efd58c7 100644
--- a/src/main/java/eu/hbp/mip/model/UserInfo.java
+++ b/src/main/java/eu/hbp/mip/model/UserInfo.java
@@ -1,5 +1,6 @@
package eu.hbp.mip.model;
+import eu.hbp.mip.model.DAOs.UserDAO;
import eu.hbp.mip.repositories.UserRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
@@ -26,7 +27,7 @@ public class UserInfo {
@Value("#{'${hbp.authentication.enabled:1}'}")
private boolean authentication;
- private User user;
+ private UserDAO user;
/**
* Set to true if using no-auth mode and user has clicked on the login button
@@ -45,18 +46,18 @@ public class UserInfo {
*
* @return the user for the current session
*/
- public User getUser() {
+ public UserDAO getUser() {
if (user == null) {
if (!authentication) {
- user = new User();
+ user = new UserDAO();
user.setUsername("anonymous");
user.setFullname("anonymous");
user.setEmail("anonymous@anonymous.com");
} else {
- user = new User(getUserInfos());
+ user = new UserDAO(getUserInfos());
}
- User foundUser = userRepository.findOne(user.getUsername());
+ UserDAO foundUser = userRepository.findByUsername(user.getUsername());
if (foundUser != null) {
user.setAgreeNDA(foundUser.getAgreeNDA());
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java b/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
index 1a93186ff064bf5833246d82b2cb0d35bf838312..5f6589ab5e61499aff08022ed0af52efb1e2edc0 100644
--- a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
@@ -1,17 +1,17 @@
package eu.hbp.mip.repositories;
-import eu.hbp.mip.model.Article;
-import eu.hbp.mip.model.User;
+import eu.hbp.mip.model.DAOs.ArticleDAO;
+import eu.hbp.mip.model.DAOs.UserDAO;
import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface ArticleRepository extends CrudRepository<Article, String> {
+public interface ArticleRepository extends CrudRepository<ArticleDAO, String> {
Long countByTitle(String title);
- Iterable<Article> findByCreatedBy(User user);
+ Iterable<ArticleDAO> findByCreatedBy(UserDAO user);
- Iterable<Article> findByStatusOrCreatedBy(String status, User user);
+ Iterable<ArticleDAO> findByStatusOrCreatedBy(String status, UserDAO user);
}
diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
index eb1d254156e38529de29335a7f3cdfdd49cd7686..a9fb10f2785cb680a19e090b6eb2e54fd6510bb5 100644
--- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
@@ -1,7 +1,7 @@
package eu.hbp.mip.repositories;
import eu.hbp.mip.model.DAOs.ExperimentDAO;
-import eu.hbp.mip.model.User;
+import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
import org.springframework.data.repository.CrudRepository;
import java.util.UUID;
@@ -10,8 +10,7 @@ import java.util.UUID;
* Created by mirco on 11.07.16.
*/
-public interface ExperimentRepository extends CrudRepository<ExperimentDAO, UUID> {
- Iterable<ExperimentDAO> findByCreatedBy(User user);
-
- Iterable<ExperimentDAO> findByShared(Boolean shared);
+public interface ExperimentRepository extends CrudRepository<ExperimentDAO, UUID>, JpaSpecificationExecutor<ExperimentDAO>
+{
+ ExperimentDAO findByUuid(UUID experimentUuid);
}
diff --git a/src/main/java/eu/hbp/mip/repositories/UserRepository.java b/src/main/java/eu/hbp/mip/repositories/UserRepository.java
index 3a0db7ee31cf9c56cdd68397d641f4a71e8c37a2..4a3a7c69893f01a20f5cf860498bdfd1173a62bf 100644
--- a/src/main/java/eu/hbp/mip/repositories/UserRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/UserRepository.java
@@ -1,12 +1,13 @@
package eu.hbp.mip.repositories;
-import eu.hbp.mip.model.User;
+import eu.hbp.mip.model.DAOs.UserDAO;
import org.springframework.data.repository.CrudRepository;
/**
* Created by mirco on 11.07.16.
*/
-public interface UserRepository extends CrudRepository<User, String> {
+public interface UserRepository extends CrudRepository<UserDAO, String> {
+ UserDAO findByUsername(String username);
}
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index bd0bed3596c6de60154cacd291e6d34e9a4a74c1..d8545b9be65c3ea612d6ec81cbeae6b5e70aa8e4 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -6,14 +6,13 @@ import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
-import com.google.common.collect.Lists;
import com.google.gson.*;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
import eu.hbp.mip.model.DAOs.ExperimentDAO;
+import eu.hbp.mip.model.DAOs.UserDAO;
import eu.hbp.mip.model.DTOs.AlgorithmDTO;
import eu.hbp.mip.model.DTOs.ExperimentDTO;
-import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
import eu.hbp.mip.model.galaxy.ErrorResponse;
import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
@@ -27,6 +26,7 @@ import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
+import org.springframework.data.jpa.domain.Specification;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.Authentication;
@@ -51,12 +51,6 @@ public class ExperimentService {
@Value("#{'${services.exareme.queryExaremeUrl}'}")
private String queryExaremeUrl;
- @Value("#{'${services.workflows.workflowUrl}'}")
- private String workflowUrl;
-
- @Value("#{'${services.workflows.jwtSecret}'}")
- private String jwtSecret;
-
@Value("#{'${services.galaxy.galaxyUrl}'}")
private String galaxyUrl;
@@ -75,7 +69,7 @@ public class ExperimentService {
public ResponseEntity<String> getExperiment(String uuid, String endpoint) {
ExperimentDAO experimentDAO;
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Loading Experiment with uuid : " + uuid);
@@ -97,7 +91,7 @@ public class ExperimentService {
}
public ResponseEntity<String> createExperiment(Authentication authentication, ExperimentDTO experimentDTO, String endpoint) {
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
//Checking if check (POST) /experiments has proper input.
if (checkPostExperimentProperInput(experimentDTO)){
@@ -106,11 +100,11 @@ public class ExperimentService {
return ResponseEntity.badRequest().body("Please provide proper input.");
}
// Get the type and name of algorithm
- String algorithmType = experimentDTO.getAlgorithm().getType();
- String algorithmName = experimentDTO.getAlgorithm().getName();
+ String algorithmType = experimentDTO.getAlgorithmDetails().getType();
+ String algorithmName = experimentDTO.getAlgorithmDetails().getName();
StringBuilder parametersLogMessage = new StringBuilder(", Parameters:\n");
- for (AlgorithmDTO.AlgorithmParamDTO params : experimentDTO.getAlgorithm().getParameters()) {
+ for (AlgorithmDTO.AlgorithmParamDTO params : experimentDTO.getAlgorithmDetails().getParameters()) {
parametersLogMessage
.append(" ")
.append(params.getLabel())
@@ -123,7 +117,7 @@ public class ExperimentService {
if (authenticationIsEnabled) {
// Getting the dataset from the experiment parameters
String experimentDatasets = null;
- for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithm().getParameters()) {
+ for (AlgorithmDTO.AlgorithmParamDTO parameter : experimentDTO.getAlgorithmDetails().getParameters()) {
if (parameter.getLabel().equals("dataset")) {
experimentDatasets = parameter.getValue();
break;
@@ -152,19 +146,18 @@ public class ExperimentService {
}
}
- public ResponseEntity<String> getExperiments( String endpoint) {
- User user = userInfo.getUser();
+ public ResponseEntity<String> getExperiments(String name,String algorithm, Boolean shared,Boolean viewed, String endpoint) {
+ UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Listing my experiments.");
+ Specification<ExperimentDAO> spec = Specification.where(new ExperimentSpecifications.ExperimentWithName(name))
+ .and(new ExperimentSpecifications.ExperimentWithAlgorithm(algorithm))
+ .and(new ExperimentSpecifications.ExperimentWithShared(shared))
+ .and(new ExperimentSpecifications.ExperimentWithViewed(viewed));
- Iterable<ExperimentDAO> myExperiments = experimentRepository.findByCreatedBy(user);
- List<ExperimentDAO> expList = Lists.newLinkedList(myExperiments);
- Iterable<ExperimentDAO> sharedExperiments = experimentRepository.findByShared(true);
- List<ExperimentDAO> sharedExpList = Lists.newLinkedList(sharedExperiments);
- expList.addAll(sharedExpList);
- Logging.LogUserAction(user.getUsername(), endpoint, "Successfully listed my experiments.");
- List<ExperimentDTO> experimentDTOs = new LinkedList<>();
+ List<ExperimentDAO> experimentDAOs = experimentRepository.findAll(spec);
- for (ExperimentDAO experimentDAO: expList){
+ List<ExperimentDTO> experimentDTOs= new ArrayList<>();
+ for (ExperimentDAO experimentDAO: experimentDAOs){
ExperimentDTO experimentDTO = experimentDAO.convertToDTO();
experimentDTOs.add(experimentDTO);
}
@@ -174,7 +167,7 @@ public class ExperimentService {
public ResponseEntity<String> updateExperiment(String uuid, ExperimentDTO experimentDTO, String endpoint)
{
ExperimentDAO experimentDAO;
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Updating experiment with uuid : " + experimentDTO.getUuid() + ".");
//Checking if check (PUT) /experiments has proper input.
if (checkPutExperimentProperInput(experimentDTO)){
@@ -186,7 +179,7 @@ public class ExperimentService {
if((experimentDTO.getName() == null || experimentDTO.getName().length() == 0)
&& experimentDTO.getShared() == null
&& experimentDTO.getViewed() == null
- && experimentDTO.getAlgorithm() == null)
+ && experimentDTO.getAlgorithmDetails() == null)
{
return ResponseEntity.badRequest().body("Input is required.");
}
@@ -222,7 +215,7 @@ public class ExperimentService {
public ResponseEntity<String> deleteExperiment(String uuid, String endpoint)
{
ExperimentDAO experimentDAO;
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Deleting experiment with uuid : " + uuid + ".");
experimentDAO = loadExperiment(uuid);
@@ -266,30 +259,31 @@ public class ExperimentService {
return null;
}
- return experimentRepository.findOne(experimentUuid);
+ return experimentRepository.findByUuid(experimentUuid);
}
private ExperimentDAO createExperiment(ExperimentDTO experimentDTO, String endpoint) {
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
ExperimentDAO experimentDAO = new ExperimentDAO();
experimentDAO.setUuid(UUID.randomUUID());
experimentDAO.setCreatedBy(user);
- experimentDAO.setAlgorithm(JsonConverters.convertObjectToJsonString(experimentDTO.getAlgorithm()));
+ experimentDAO.setAlgorithmDetails(JsonConverters.convertObjectToJsonString(experimentDTO.getAlgorithmDetails()));
+ experimentDAO.setAlgorithm(experimentDTO.getAlgorithm());
experimentDAO.setName(experimentDTO.getName());
experimentRepository.save(experimentDAO);
Logging.LogUserAction(user.getUsername(), endpoint, " id : " + experimentDAO.getUuid());
- Logging.LogUserAction(user.getUsername(), endpoint, " algorithms : " + experimentDAO.getAlgorithm());
+ Logging.LogUserAction(user.getUsername(), endpoint, " algorithms : " + experimentDAO.getAlgorithmDetails());
Logging.LogUserAction(user.getUsername(), endpoint, " name : " + experimentDAO.getName());
return experimentDAO;
}
private void saveExperiment(ExperimentDAO experimentDAO, String endpoint) {
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, " id : " + experimentDAO.getUuid());
- Logging.LogUserAction(user.getUsername(), endpoint, " algorithms : " + experimentDAO.getAlgorithm());
+ Logging.LogUserAction(user.getUsername(), endpoint, " algorithms : " + experimentDAO.getAlgorithmDetails());
Logging.LogUserAction(user.getUsername(), endpoint, " name : " + experimentDAO.getName());
Logging.LogUserAction(user.getUsername(), endpoint, " historyId : " + experimentDAO.getWorkflowHistoryId());
Logging.LogUserAction(user.getUsername(), endpoint, " status : " + experimentDAO.getStatus());
@@ -313,18 +307,18 @@ public class ExperimentService {
* @return the response to be returned
*/
public ResponseEntity<String> runExaremeAlgorithm(ExperimentDTO experimentDTO, String endpoint) {
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Running the algorithm...");
ExperimentDAO experimentDAO = createExperiment(experimentDTO, endpoint);
Logging.LogUserAction(user.getUsername(), endpoint, "Created experiment with uuid :" + experimentDAO.getUuid());
// Run the 1st algorithm from the list
- String algorithmName = experimentDTO.getAlgorithm().getName();
+ String algorithmName = experimentDTO.getAlgorithmDetails().getName();
// Get the parameters
List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
- = experimentDTO.getAlgorithm().getParameters();
+ = experimentDTO.getAlgorithmDetails().getParameters();
String body = gson.toJson(algorithmParameters);
String url = queryExaremeUrl + "/" + algorithmName;
@@ -375,7 +369,7 @@ public class ExperimentService {
* @return the response to be returned
*/
public ResponseEntity<String> runGalaxyWorkflow(ExperimentDTO experimentDTO, String endpoint) {
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
Logging.LogUserAction(user.getUsername(), endpoint, "Running a workflow...");
ExperimentDAO experimentDAO = createExperiment(experimentDTO, endpoint);
@@ -383,11 +377,11 @@ public class ExperimentService {
// Run the 1st algorithm from the list
- String workflowId = experimentDTO.getAlgorithm().getName();
+ String workflowId = experimentDTO.getAlgorithmDetails().getName();
// Get the parameters
List<AlgorithmDTO.AlgorithmParamDTO> algorithmParameters
- = experimentDTO.getAlgorithm().getParameters();
+ = experimentDTO.getAlgorithmDetails().getParameters();
// Convert the parameters to workflow parameters
HashMap<String, String> algorithmParamsIncludingEmpty = new HashMap<>();
@@ -481,7 +475,7 @@ public class ExperimentService {
* @return nothing, just updates the experiment
*/
public void updateWorkflowExperiment(ExperimentDAO experimentDAO, String endpoint) {
- User user = userInfo.getUser();
+ UserDAO user = userInfo.getUser();
if (experimentDAO == null) {
Logging.LogUserAction(user.getUsername(), endpoint, "The experiment does not exist.");
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java b/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
new file mode 100644
index 0000000000000000000000000000000000000000..6596a319ad510ed6bda468088e348ff70f618c1a
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
@@ -0,0 +1,82 @@
+package eu.hbp.mip.services;
+
+import eu.hbp.mip.model.DAOs.ExperimentDAO;
+import org.springframework.data.jpa.domain.Specification;
+
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Predicate;
+import javax.persistence.criteria.Root;
+
+public class ExperimentSpecifications {
+ public static class ExperimentWithName implements Specification<ExperimentDAO> {
+
+ private String name;
+ private String regExp;
+
+ public ExperimentWithName(String name){
+ this.name = name;
+ this.regExp = "%"+name+"%";
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb)
+ {
+ if (name == null) {
+ return cb.isTrue(cb.literal(true));
+ }
+
+ return cb.like( root.get( "name" ), regExp );
+ }
+ }
+ public static class ExperimentWithAlgorithm implements Specification<ExperimentDAO> {
+
+ private String algorithm;
+
+ public ExperimentWithAlgorithm(String algorithm){
+ this.algorithm = algorithm;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb)
+ {
+ if (algorithm == null) {
+ return cb.isTrue(cb.literal(true));
+ }
+
+ return cb.equal(root.get("algorithm"), this.algorithm);
+ }
+ }
+
+ public static class ExperimentWithViewed implements Specification<ExperimentDAO> {
+
+ private Boolean viewed;
+
+ public ExperimentWithViewed(Boolean viewed){
+ this.viewed = viewed;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> query, CriteriaBuilder cb) {
+ if (viewed == null) {
+ return cb.isTrue(cb.literal(true)); // always true = no filtering
+ }
+ return cb.equal(root.get("viewed"), this.viewed);
+ }
+ }
+
+ public static class ExperimentWithShared implements org.springframework.data.jpa.domain.Specification<ExperimentDAO> {
+
+ private Boolean shared;
+
+ public ExperimentWithShared(Boolean shared){
+ this.shared = shared;
+ }
+
+ public Predicate toPredicate(Root<ExperimentDAO> root, CriteriaQuery<?> criteriaQuery, CriteriaBuilder cb) {
+ if (shared == null) {
+ return cb.isTrue(cb.literal(true));
+ }
+ return cb.equal(root.get("shared"), this.shared);
+ }
+
+ }
+}
+
diff --git a/src/main/resources/db/migration/V7_0__NewExperimentStructure.sql b/src/main/resources/db/migration/V7_0__NewExperimentStructure.sql
index b69ae2b702742e36025e99ba04ebde23610c10f4..73a15addd8f1a7cd34594b9708595f7a4447bfb8 100644
--- a/src/main/resources/db/migration/V7_0__NewExperimentStructure.sql
+++ b/src/main/resources/db/migration/V7_0__NewExperimentStructure.sql
@@ -5,7 +5,7 @@ DROP COLUMN validations,
DROP COLUMN model_slug;
ALTER TABLE experiment
-RENAME algorithms TO algorithm;
+RENAME algorithms TO algorithmDetails;
ALTER TABLE experiment
RENAME createdby_username TO created_by_username;
ALTER TABLE experiment
@@ -15,6 +15,9 @@ RENAME resultsviewed TO viewed;
ALTER TABLE experiment
RENAME workflowstatus TO status;
+ALTER TABLE experiment
+ADD COLUMN algorithm text;
+
ALTER TABLE "user"
DROP COLUMN birthday,
DROP COLUMN city,