From 12cbb8c2ca3b5af4af62665d8487b58de95912e7 Mon Sep 17 00:00:00 2001
From: ThanKarab <tkarabatsis@hotmail.com>
Date: Tue, 17 Nov 2020 10:37:56 -0800
Subject: [PATCH] Cleanup and beautification.
---
src/main/java/eu/hbp/mip/MIPApplication.java | 5 -
.../APIMetadataConfiguration.java} | 14 +-
.../GalaxyAuthentication.java | 6 +-
.../PersistenceConfiguration.java | 4 +-
.../SecurityConfiguration.java | 6 +-
.../eu/hbp/mip/controllers/AlgorithmsApi.java | 5 +-
.../eu/hbp/mip/controllers/ExperimentApi.java | 2 +-
.../hbp/mip/controllers/PathologiesApi.java | 2 +-
.../java/eu/hbp/mip/controllers/UsersApi.java | 4 +-
.../retrofit/RetroFitGalaxyClients.java | 6 +-
.../eu/hbp/mip/model/DAOs/ArticleDAO.java | 151 ------------------
.../{model => models}/DAOs/ExperimentDAO.java | 6 +-
.../mip/{model => models}/DAOs/UserDAO.java | 2 +-
.../{model => models}/DTOs/AlgorithmDTO.java | 2 +-
.../{model => models}/DTOs/ExperimentDTO.java | 4 +-
.../{model => models}/DTOs/PathologyDTO.java | 2 +-
.../galaxy/ErrorResponse.java | 2 +-
.../galaxy/GalaxyWorkflowResult.java | 2 +-
.../PostWorkflowToGalaxyDtoResponse.java | 2 +-
.../{model => models}/galaxy/WorkflowDTO.java | 4 +-
.../mip/repositories/ArticleRepository.java | 17 --
.../repositories/ExperimentRepository.java | 2 +-
.../hbp/mip/repositories/UserRepository.java | 2 +-
.../hbp/mip/services/ActiveUserService.java | 2 +-
.../hbp/mip/services/ExperimentService.java | 12 +-
.../services/ExperimentSpecifications.java | 2 +-
.../java/eu/hbp/mip/utils/ClaimUtils.java | 2 +-
27 files changed, 41 insertions(+), 229 deletions(-)
rename src/main/java/eu/hbp/mip/{configuration/WebConfiguration.java => configurations/APIMetadataConfiguration.java} (76%)
rename src/main/java/eu/hbp/mip/{configuration => configurations}/GalaxyAuthentication.java (89%)
rename src/main/java/eu/hbp/mip/{configuration => configurations}/PersistenceConfiguration.java (94%)
rename src/main/java/eu/hbp/mip/{configuration => configurations}/SecurityConfiguration.java (96%)
delete mode 100644 src/main/java/eu/hbp/mip/model/DAOs/ArticleDAO.java
rename src/main/java/eu/hbp/mip/{model => models}/DAOs/ExperimentDAO.java (97%)
rename src/main/java/eu/hbp/mip/{model => models}/DAOs/UserDAO.java (97%)
rename src/main/java/eu/hbp/mip/{model => models}/DTOs/AlgorithmDTO.java (95%)
rename src/main/java/eu/hbp/mip/{model => models}/DTOs/ExperimentDTO.java (97%)
rename src/main/java/eu/hbp/mip/{model => models}/DTOs/PathologyDTO.java (93%)
rename src/main/java/eu/hbp/mip/{model => models}/galaxy/ErrorResponse.java (96%)
rename src/main/java/eu/hbp/mip/{model => models}/galaxy/GalaxyWorkflowResult.java (99%)
rename src/main/java/eu/hbp/mip/{model => models}/galaxy/PostWorkflowToGalaxyDtoResponse.java (98%)
rename src/main/java/eu/hbp/mip/{model => models}/galaxy/WorkflowDTO.java (95%)
delete mode 100644 src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
diff --git a/src/main/java/eu/hbp/mip/MIPApplication.java b/src/main/java/eu/hbp/mip/MIPApplication.java
index 9af69bdd9..f4001f93c 100644
--- a/src/main/java/eu/hbp/mip/MIPApplication.java
+++ b/src/main/java/eu/hbp/mip/MIPApplication.java
@@ -7,17 +7,12 @@ package eu.hbp.mip;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
@SpringBootApplication
public class MIPApplication {
- private static final Logger LOGGER = LoggerFactory.getLogger(MIPApplication.class);
-
public static void main(String[] args) {
SpringApplication.run(MIPApplication.class, args);
}
-
}
diff --git a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java b/src/main/java/eu/hbp/mip/configurations/APIMetadataConfiguration.java
similarity index 76%
rename from src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
rename to src/main/java/eu/hbp/mip/configurations/APIMetadataConfiguration.java
index 50fbe43ae..7b9eab456 100644
--- a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configurations/APIMetadataConfiguration.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.configuration;
+package eu.hbp.mip.configurations;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@@ -10,13 +10,9 @@ import springfox.documentation.spi.DocumentationType;
import springfox.documentation.spring.web.plugins.Docket;
import springfox.documentation.swagger2.annotations.EnableSwagger2;
-/**
- * Created by mirco on 11.07.16.
- */
-
@Configuration
@EnableSwagger2
-public class WebConfiguration {
+public class APIMetadataConfiguration {
@Bean
public Docket swaggerDocumentation() {
@@ -31,10 +27,8 @@ public class WebConfiguration {
private ApiInfo metadata() {
return new ApiInfoBuilder()
.title("Medical Informatics Platform API")
- .description("Serve the MIP Frontend")
- .version("1.0")
- .contact(new Contact("Mirco Nasuti", "https://www.unil.ch/lren/en/home.html", "mirco.nasuti@chuv.ch"))
+ .description("Serving the MIP Frontend")
+ .contact(new Contact("Kostas Filippopolitis", "https://github.com/KFilippopolitis", "kostasfilippop@gmail.com"))
.build();
}
-
}
diff --git a/src/main/java/eu/hbp/mip/configuration/GalaxyAuthentication.java b/src/main/java/eu/hbp/mip/configurations/GalaxyAuthentication.java
similarity index 89%
rename from src/main/java/eu/hbp/mip/configuration/GalaxyAuthentication.java
rename to src/main/java/eu/hbp/mip/configurations/GalaxyAuthentication.java
index 7910e809f..41888d3ea 100644
--- a/src/main/java/eu/hbp/mip/configuration/GalaxyAuthentication.java
+++ b/src/main/java/eu/hbp/mip/configurations/GalaxyAuthentication.java
@@ -1,13 +1,11 @@
-package eu.hbp.mip.configuration;
+package eu.hbp.mip.configurations;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
-import eu.hbp.mip.configuration.SecurityConfiguration;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.Logging;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
@@ -16,8 +14,6 @@ import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.ResponseStatus;
import org.springframework.web.bind.annotation.RestController;
-import javax.servlet.http.HttpServletResponse;
-import java.io.IOException;
import java.util.Base64;
@RestController
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java
similarity index 94%
rename from src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
rename to src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java
index 909d2c1c8..181bc639c 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.configuration;
+package eu.hbp.mip.configurations;
import org.flywaydb.core.Flyway;
import org.springframework.boot.context.properties.ConfigurationProperties;
@@ -36,7 +36,7 @@ public class PersistenceConfiguration {
emfb.setDataSource(portalDataSource());
JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
emfb.setJpaVendorAdapter(vendorAdapter);
- emfb.setPackagesToScan("eu.hbp.mip.model.DAOs");
+ emfb.setPackagesToScan("eu.hbp.mip.models.DAOs");
return emfb;
}
diff --git a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java b/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
similarity index 96%
rename from src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
rename to src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
index 796f900a5..c4dc2a28b 100644
--- a/src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.configuration;
+package eu.hbp.mip.configurations;
import org.keycloak.adapters.KeycloakConfigResolver;
import org.keycloak.adapters.springboot.KeycloakSpringBootConfigResolver;
@@ -21,8 +21,6 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
-// Keycloak security with keycloak-spring-boot-starter
-
@Controller
@KeycloakConfiguration
public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter {
@@ -59,7 +57,7 @@ public class SecurityConfiguration extends KeycloakWebSecurityConfigurerAdapter
@GetMapping(value = "/logout")
public String logout() throws ServletException {
request.logout();
- return "redirect:" + logoutRedirectURL;
+ return String.format("redirect:%s", logoutRedirectURL);
}
@Bean
diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
index d42720344..454007298 100644
--- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java
@@ -8,16 +8,15 @@ import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.hbp.mip.controllers.galaxy.retrofit.RetroFitGalaxyClients;
import eu.hbp.mip.controllers.galaxy.retrofit.RetrofitClientInstance;
-import eu.hbp.mip.model.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.AlgorithmDTO;
import eu.hbp.mip.services.ActiveUserService;
-import eu.hbp.mip.model.galaxy.WorkflowDTO;
+import eu.hbp.mip.models.galaxy.WorkflowDTO;
import eu.hbp.mip.utils.CustomResourceLoader;
import eu.hbp.mip.utils.HTTPUtil;
import eu.hbp.mip.utils.Logging;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.http.ResponseEntity;
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index d5fc161b1..79168b42a 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,6 +1,6 @@
package eu.hbp.mip.controllers;
-import eu.hbp.mip.model.DTOs.ExperimentDTO;
+import eu.hbp.mip.models.DTOs.ExperimentDTO;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.services.ExperimentService;
import eu.hbp.mip.utils.JsonConverters;
diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
index 0f3f3c2bb..2c9e08a7e 100644
--- a/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/PathologiesApi.java
@@ -2,7 +2,7 @@ package eu.hbp.mip.controllers;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
-import eu.hbp.mip.model.DTOs.PathologyDTO;
+import eu.hbp.mip.models.DTOs.PathologyDTO;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.CustomResourceLoader;
diff --git a/src/main/java/eu/hbp/mip/controllers/UsersApi.java b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
index c8b1193f8..0c07b5f05 100644
--- a/src/main/java/eu/hbp/mip/controllers/UsersApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/UsersApi.java
@@ -2,13 +2,11 @@ package eu.hbp.mip.controllers;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.hbp.mip.model.DAOs.UserDAO;
-import eu.hbp.mip.repositories.UserRepository;
+import eu.hbp.mip.models.DAOs.UserDAO;
import eu.hbp.mip.services.ActiveUserService;
import eu.hbp.mip.utils.Logging;
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.ResponseEntity;
import org.springframework.web.bind.annotation.*;
diff --git a/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
index 612dce6ca..609163e89 100644
--- a/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
+++ b/src/main/java/eu/hbp/mip/controllers/galaxy/retrofit/RetroFitGalaxyClients.java
@@ -1,9 +1,9 @@
package eu.hbp.mip.controllers.galaxy.retrofit;
import com.google.gson.JsonObject;
-import eu.hbp.mip.model.galaxy.GalaxyWorkflowResult;
-import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
-import eu.hbp.mip.model.galaxy.WorkflowDTO;
+import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.models.galaxy.WorkflowDTO;
import retrofit2.Call;
import retrofit2.http.*;
diff --git a/src/main/java/eu/hbp/mip/model/DAOs/ArticleDAO.java b/src/main/java/eu/hbp/mip/model/DAOs/ArticleDAO.java
deleted file mode 100644
index 541c50765..000000000
--- a/src/main/java/eu/hbp/mip/model/DAOs/ArticleDAO.java
+++ /dev/null
@@ -1,151 +0,0 @@
-/*
- * Created by mirco on 04.12.15.
- */
-
-package eu.hbp.mip.model.DAOs;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import io.swagger.annotations.ApiModel;
-import org.springframework.validation.annotation.Validated;
-
-import javax.persistence.*;
-import javax.validation.constraints.NotNull;
-import javax.validation.constraints.Size;
-import java.util.Date;
-
-@Entity
-@Table(name = "`article`")
-@ApiModel
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@Validated
-public class ArticleDAO {
-
- @Id
- private String slug = null;
-
- @NotNull
- @Size(min = 1, max = 255)
- private String title;
-
- private String status = null;
-
- @Column(columnDefinition = "text", name = "abstract")
- private String abstractText = null;
-
- @Column(columnDefinition = "text")
- private String content = null;
-
- private Date publishedAt = null;
-
- private Date createdAt = null;
-
- private Date updatedAt = null;
-
- @ManyToOne
- @JoinColumn(name = "createdby_username")
- private UserDAO createdBy = null;
-
- @ManyToOne
- @JoinColumn(name = "updatedby_username")
- private UserDAO updatedBy = null;
-
- public ArticleDAO() {
- /*
- * Empty constructor is needed by Hibernate
- */
- title = "";
- }
-
-
- public String getStatus() {
- return status;
- }
-
- public void setStatus(String status) {
- this.status = status;
- }
-
-
- public String getTitle() {
- return title;
- }
-
- public void setTitle(String title) {
- this.title = title;
- }
-
-
- public String getSlug() {
- return slug;
- }
-
- public void setSlug(String slug) {
- this.slug = slug;
- }
-
-
- @JsonProperty("abstract")
- public String getAbstract() {
- return abstractText;
- }
-
- public void setAbstract(String abstractText) {
- this.abstractText = abstractText;
- }
-
-
- public String getContent() {
- return content;
- }
-
- public void setContent(String content) {
- this.content = content;
- }
-
-
- public Date getPublishedAt() {
- return publishedAt;
- }
-
- public void setPublishedAt(Date publishedAt) {
- this.publishedAt = publishedAt;
- }
-
-
- public Date getCreatedAt() {
- return createdAt;
- }
-
- public void setCreatedAt(Date createdAt) {
- this.createdAt = createdAt;
- }
-
-
- public Date getUpdatedAt() {
- return updatedAt;
- }
-
- public void setUpdatedAt(Date updatedAt) {
- this.updatedAt = updatedAt;
- }
-
-
- public UserDAO getCreatedBy() {
- return createdBy;
- }
-
- public void setCreatedBy(UserDAO createdBy) {
- this.createdBy = createdBy;
- }
-
-
- public UserDAO getUpdatedBy() {
- return 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/models/DAOs/ExperimentDAO.java
similarity index 97%
rename from src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
rename to src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
index 2ee8e0ba4..e96f74c44 100644
--- a/src/main/java/eu/hbp/mip/model/DAOs/ExperimentDAO.java
+++ b/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java
@@ -1,10 +1,10 @@
-package eu.hbp.mip.model.DAOs;
+package eu.hbp.mip.models.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.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExperimentDTO;
import eu.hbp.mip.utils.JsonConverters;
import io.swagger.annotations.ApiModel;
diff --git a/src/main/java/eu/hbp/mip/model/DAOs/UserDAO.java b/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
similarity index 97%
rename from src/main/java/eu/hbp/mip/model/DAOs/UserDAO.java
rename to src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
index 0e1e9a9ff..a94e5da1c 100644
--- a/src/main/java/eu/hbp/mip/model/DAOs/UserDAO.java
+++ b/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java
@@ -2,7 +2,7 @@
* Created by mirco on 04.12.15.
*/
-package eu.hbp.mip.model.DAOs;
+package eu.hbp.mip.models.DAOs;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.google.gson.annotations.Expose;
diff --git a/src/main/java/eu/hbp/mip/model/DTOs/AlgorithmDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
similarity index 95%
rename from src/main/java/eu/hbp/mip/model/DTOs/AlgorithmDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
index 0a49c5ad6..1a6d8b99d 100644
--- a/src/main/java/eu/hbp/mip/model/DTOs/AlgorithmDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/AlgorithmDTO.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.model.DTOs;
+package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
similarity index 97%
rename from src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
index 64ade455b..797fe0925 100644
--- a/src/main/java/eu/hbp/mip/model/DTOs/ExperimentDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java
@@ -1,6 +1,6 @@
-package eu.hbp.mip.model.DTOs;
+package eu.hbp.mip.models.DTOs;
-import eu.hbp.mip.model.DAOs.ExperimentDAO;
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
import java.util.Date;
import java.util.List;
diff --git a/src/main/java/eu/hbp/mip/model/DTOs/PathologyDTO.java b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
similarity index 93%
rename from src/main/java/eu/hbp/mip/model/DTOs/PathologyDTO.java
rename to src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
index 6a4580e81..2a8887b5f 100644
--- a/src/main/java/eu/hbp/mip/model/DTOs/PathologyDTO.java
+++ b/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java
@@ -1,4 +1,4 @@
-package eu.hbp.mip.model.DTOs;
+package eu.hbp.mip.models.DTOs;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java b/src/main/java/eu/hbp/mip/models/galaxy/ErrorResponse.java
similarity index 96%
rename from src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
rename to src/main/java/eu/hbp/mip/models/galaxy/ErrorResponse.java
index 77a171358..2703e7425 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/ErrorResponse.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/ErrorResponse.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java b/src/main/java/eu/hbp/mip/models/galaxy/GalaxyWorkflowResult.java
similarity index 99%
rename from src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
rename to src/main/java/eu/hbp/mip/models/galaxy/GalaxyWorkflowResult.java
index 089a6a626..ca7d98fe5 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/GalaxyWorkflowResult.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/GalaxyWorkflowResult.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java b/src/main/java/eu/hbp/mip/models/galaxy/PostWorkflowToGalaxyDtoResponse.java
similarity index 98%
rename from src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
rename to src/main/java/eu/hbp/mip/models/galaxy/PostWorkflowToGalaxyDtoResponse.java
index edefd6326..96d8aa8ef 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/PostWorkflowToGalaxyDtoResponse.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/PostWorkflowToGalaxyDtoResponse.java
@@ -3,7 +3,7 @@
* Copyright (c) 2019. MIT License
*/
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.annotations.SerializedName;
diff --git a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java b/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
similarity index 95%
rename from src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
rename to src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
index 4b01b3819..496ee2dfe 100644
--- a/src/main/java/eu/hbp/mip/model/galaxy/WorkflowDTO.java
+++ b/src/main/java/eu/hbp/mip/models/galaxy/WorkflowDTO.java
@@ -1,8 +1,8 @@
-package eu.hbp.mip.model.galaxy;
+package eu.hbp.mip.models.galaxy;
import com.google.gson.Gson;
import com.google.gson.annotations.SerializedName;
-import eu.hbp.mip.model.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.AlgorithmDTO;
import java.util.*;
diff --git a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java b/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
deleted file mode 100644
index 5f6589ab5..000000000
--- a/src/main/java/eu/hbp/mip/repositories/ArticleRepository.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package eu.hbp.mip.repositories;
-
-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<ArticleDAO, String> {
- Long countByTitle(String title);
-
- Iterable<ArticleDAO> findByCreatedBy(UserDAO 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 5f2c8dc76..4efb1613b 100644
--- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java
@@ -1,6 +1,6 @@
package eu.hbp.mip.repositories;
-import eu.hbp.mip.model.DAOs.ExperimentDAO;
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
import org.springframework.data.repository.CrudRepository;
diff --git a/src/main/java/eu/hbp/mip/repositories/UserRepository.java b/src/main/java/eu/hbp/mip/repositories/UserRepository.java
index 4a3a7c698..99ae0b1dc 100644
--- a/src/main/java/eu/hbp/mip/repositories/UserRepository.java
+++ b/src/main/java/eu/hbp/mip/repositories/UserRepository.java
@@ -1,6 +1,6 @@
package eu.hbp.mip.repositories;
-import eu.hbp.mip.model.DAOs.UserDAO;
+import eu.hbp.mip.models.DAOs.UserDAO;
import org.springframework.data.repository.CrudRepository;
/**
diff --git a/src/main/java/eu/hbp/mip/services/ActiveUserService.java b/src/main/java/eu/hbp/mip/services/ActiveUserService.java
index 3d8815373..e1a4a7350 100644
--- a/src/main/java/eu/hbp/mip/services/ActiveUserService.java
+++ b/src/main/java/eu/hbp/mip/services/ActiveUserService.java
@@ -1,6 +1,6 @@
package eu.hbp.mip.services;
-import eu.hbp.mip.model.DAOs.UserDAO;
+import eu.hbp.mip.models.DAOs.UserDAO;
import eu.hbp.mip.repositories.UserRepository;
import org.keycloak.KeycloakPrincipal;
import org.keycloak.representations.IDToken;
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/eu/hbp/mip/services/ExperimentService.java
index 3f6bb87b0..829b4bfa0 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentService.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentService.java
@@ -12,12 +12,12 @@ import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
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.galaxy.GalaxyWorkflowResult;
-import eu.hbp.mip.model.galaxy.PostWorkflowToGalaxyDtoResponse;
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
+import eu.hbp.mip.models.DAOs.UserDAO;
+import eu.hbp.mip.models.DTOs.AlgorithmDTO;
+import eu.hbp.mip.models.DTOs.ExperimentDTO;
+import eu.hbp.mip.models.galaxy.GalaxyWorkflowResult;
+import eu.hbp.mip.models.galaxy.PostWorkflowToGalaxyDtoResponse;
import eu.hbp.mip.repositories.ExperimentRepository;
import eu.hbp.mip.utils.ClaimUtils;
import eu.hbp.mip.utils.Exceptions.*;
diff --git a/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java b/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
index 076249e0b..8a79bf61e 100644
--- a/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
+++ b/src/main/java/eu/hbp/mip/services/ExperimentSpecifications.java
@@ -1,6 +1,6 @@
package eu.hbp.mip.services;
-import eu.hbp.mip.model.DAOs.ExperimentDAO;
+import eu.hbp.mip.models.DAOs.ExperimentDAO;
import org.springframework.data.jpa.domain.Specification;
import javax.persistence.criteria.CriteriaBuilder;
diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
index cdbe41c9e..117bead85 100644
--- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
+++ b/src/main/java/eu/hbp/mip/utils/ClaimUtils.java
@@ -1,7 +1,7 @@
package eu.hbp.mip.utils;
import com.google.gson.Gson;
-import eu.hbp.mip.model.DTOs.PathologyDTO;
+import eu.hbp.mip.models.DTOs.PathologyDTO;
import org.springframework.security.core.GrantedAuthority;
import java.util.ArrayList;
--
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