diff --git a/src/main/java/eu/hbp/mip/MIPApplication.java b/src/main/java/eu/hbp/mip/MIPApplication.java index 9af69bdd9cdc04e555a24f8a0ca4e7b3882206ed..f4001f93c477307cf0d464f76e8b22b2905af198 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 50fbe43aeb71ed201651aaab2ac630bf21e1b7f9..7b9eab4563d9c71af0a0eac7d6bae42d798df93b 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 7910e809f48118daea416f71fb2b2596aa25430a..41888d3ea276138e425e790cde46867f8ce3e31b 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 909d2c1c81dc040c78bba7c29d4f43bcb1e925ca..181bc639c05ea4b3987459cf36a62664db6812cb 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 796f900a59d4f895c22f4f4bb44e66160992a63a..c4dc2a28bce39732a0ca57e16539ee46fa813bd8 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 d427203447ea3b362ead598310ace2ad54ff8a0b..454007298e1e663380b3e44e67c816af9cc923ac 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 d5fc161b11dab3b68bbc22932df82e229a54f8a0..79168b42aa9b842b9c98d0697d2070f276319285 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 0f3f3c2bb5f4216e92f4863a93c1999d02c0d469..2c9e08a7e50d841067f0e2b0fefea82bf113637e 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 c8b1193f812144aec66a31de8ca541c93ed2cd07..0c07b5f05e3c851870b1a5fc2ba19a7a9b093a41 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 612dce6ca5b557f23deafdf873978c0f442eb1d9..609163e8920ad3443e908c36aea6143ba69533c1 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 541c50765e25e7ce68504026ed437f906104e2ce..0000000000000000000000000000000000000000 --- 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 2ee8e0ba401191508fa72258d35f997f8fba9509..e96f74c44a96ad32717b873ac84552ab7eddbeb9 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 0e1e9a9ff49408a4cfa034a6262e48f6001e8ef7..a94e5da1c177648965a8f3f192356fa5c2da8a07 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 0a49c5ad672aa0b14e6830bf6d683f95a08af6b4..1a6d8b99d41b4129c85b2b3591cc6ea3f89c950f 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 64ade455bc623298c173edad1ddd60919517bc1c..797fe092552d26304dae5b0c7dbde29c4281cd10 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 6a4580e81bbf9e7e371cf4c8297723d3b946f9c0..2a8887b5f22a309ecf2befcc69e1191a7c00576c 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 77a171358b54561e3492dcb317acd835aeaa645f..2703e742541faf9f715ed19485076d397697059e 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 089a6a626ed1e0d38306c911b515edd3fa8fa5f0..ca7d98fe51e55cd60914893283f2c30b6fcf90be 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 edefd63266a8d1678bf82d057882e4eccab112cc..96d8aa8efa089599093fed13ac8e0d0a4be81f42 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 4b01b38198d52e25d0f9455f770a9a5918d77874..496ee2dfebf50324b1443774cc48edd4e32c2de0 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 5f6589ab5e61499aff08022ed0af52efb1e2edc0..0000000000000000000000000000000000000000 --- 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 5f2c8dc7643799b1a2f5a7a15773140376ff5756..4efb1613b5480167a2d5c14df93cf39faa29124d 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 4a3a7c69893f01a20f5cf860498bdfd1173a62bf..99ae0b1dcfc237e875e7ba458175ae8441ec8c8e 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 3d881537315d5635f815ad8894c1e46e460068db..e1a4a7350abf108f5f3605464b3c324f6a50e544 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 3f6bb87b00683c13ea8684c4464a135c337f7ff6..829b4bfa074480f3225af0636bd489c32c6ad9d7 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 076249e0becac36fbb64db83eae5e758c56d4161..8a79bf61e1aaae72806ba572b18c8e35c67601b3 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 cdbe41c9ef2bb110266d8d13d14cb809ed2a66fb..117bead85fa676c6cd0cb8d5180743535272fca4 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;