diff --git a/pom.xml b/pom.xml index d5a08e25c3b4037cad62906e587b3d50ec173864..c9d5b258e91394e8ae72e7966d64d9b85b4cc7e5 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ <name>portal-backend</name> <description>Medical Informatics Platform - portal-backend</description> - <groupId>eu.hbp.mip</groupId> + <groupId>hbp.mip</groupId> <artifactId>portal-backend</artifactId> <version>1.0.0</version> <packaging>jar</packaging> diff --git a/src/main/java/eu/hbp/mip/MIPApplication.java b/src/main/java/hbp/mip/MIPApplication.java similarity index 94% rename from src/main/java/eu/hbp/mip/MIPApplication.java rename to src/main/java/hbp/mip/MIPApplication.java index f4001f93c477307cf0d464f76e8b22b2905af198..920f5e287647af4b038fbbed4bebf04a99065e9c 100644 --- a/src/main/java/eu/hbp/mip/MIPApplication.java +++ b/src/main/java/hbp/mip/MIPApplication.java @@ -2,7 +2,7 @@ * Created by mirco on 04.12.15. */ -package eu.hbp.mip; +package hbp.mip; import org.springframework.boot.SpringApplication; diff --git a/src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java b/src/main/java/hbp/mip/configurations/PersistenceConfiguration.java similarity index 92% rename from src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java rename to src/main/java/hbp/mip/configurations/PersistenceConfiguration.java index 23df36815b2305ed368cd9fa3e1aa0339528af9f..e74501504c7661556e831bc0cbaa36357fd5e1e0 100644 --- a/src/main/java/eu/hbp/mip/configurations/PersistenceConfiguration.java +++ b/src/main/java/hbp/mip/configurations/PersistenceConfiguration.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.configurations; +package hbp.mip.configurations; import org.flywaydb.core.Flyway; import org.springframework.boot.context.properties.ConfigurationProperties; @@ -16,7 +16,7 @@ import javax.sql.DataSource; @Configuration -@EnableJpaRepositories("eu.hbp.mip.repositories") +@EnableJpaRepositories("hbp.mip.repositories") public class PersistenceConfiguration { @Primary @@ -33,7 +33,7 @@ public class PersistenceConfiguration { emfb.setDataSource(portalDataSource()); JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter(); emfb.setJpaVendorAdapter(vendorAdapter); - emfb.setPackagesToScan("eu.hbp.mip.models.DAOs"); + emfb.setPackagesToScan("hbp.mip.models.DAOs"); return emfb; } diff --git a/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java b/src/main/java/hbp/mip/configurations/SecurityConfiguration.java similarity index 99% rename from src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java rename to src/main/java/hbp/mip/configurations/SecurityConfiguration.java index e57bc1432126556c0c931b56ce94c9947052f631..33b3279eaceb1e9ded52400e76d8e18c0cf5cf2e 100644 --- a/src/main/java/eu/hbp/mip/configurations/SecurityConfiguration.java +++ b/src/main/java/hbp/mip/configurations/SecurityConfiguration.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.configurations; +package hbp.mip.configurations; import lombok.RequiredArgsConstructor; import org.springframework.beans.factory.annotation.Value; diff --git a/src/main/java/eu/hbp/mip/controllers/ActiveUserAPI.java b/src/main/java/hbp/mip/controllers/ActiveUserAPI.java similarity index 89% rename from src/main/java/eu/hbp/mip/controllers/ActiveUserAPI.java rename to src/main/java/hbp/mip/controllers/ActiveUserAPI.java index 5aaeaa77ea48fd959bbee2205f246abb4ae6bbff..3ba191fdc21b3d343958a81fb91111d1262aeb22 100644 --- a/src/main/java/eu/hbp/mip/controllers/ActiveUserAPI.java +++ b/src/main/java/hbp/mip/controllers/ActiveUserAPI.java @@ -1,8 +1,8 @@ -package eu.hbp.mip.controllers; +package hbp.mip.controllers; -import eu.hbp.mip.models.DAOs.UserDAO; -import eu.hbp.mip.services.ActiveUserService; -import eu.hbp.mip.utils.Logger; +import hbp.mip.models.DAOs.UserDAO; +import hbp.mip.services.ActiveUserService; +import hbp.mip.utils.Logger; import org.springframework.http.ResponseEntity; import org.springframework.security.core.Authentication; import org.springframework.web.bind.annotation.*; diff --git a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java b/src/main/java/hbp/mip/controllers/AlgorithmsAPI.java similarity index 83% rename from src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java rename to src/main/java/hbp/mip/controllers/AlgorithmsAPI.java index 181c5eb22bda24b15971bbd9a47b565e4766ad24..fd477e768562885bb73e0dc3f70de1a21aacb431 100644 --- a/src/main/java/eu/hbp/mip/controllers/AlgorithmsAPI.java +++ b/src/main/java/hbp/mip/controllers/AlgorithmsAPI.java @@ -1,14 +1,13 @@ -package eu.hbp.mip.controllers; +package hbp.mip.controllers; -import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO; -import eu.hbp.mip.services.ActiveUserService; -import eu.hbp.mip.services.AlgorithmService; -import eu.hbp.mip.utils.Logger; +import hbp.mip.models.DTOs.ExaremeAlgorithmDTO; +import hbp.mip.services.ActiveUserService; +import hbp.mip.services.AlgorithmService; +import hbp.mip.utils.Logger; import org.springframework.http.ResponseEntity; import org.springframework.security.core.Authentication; import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.RequestMapping; -import org.springframework.web.bind.annotation.RequestMethod; import org.springframework.web.bind.annotation.RestController; import java.util.List; diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java b/src/main/java/hbp/mip/controllers/ExperimentAPI.java similarity index 96% rename from src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java rename to src/main/java/hbp/mip/controllers/ExperimentAPI.java index bdb82d8a20f528b23a71d6d19106a14d58e89981..6b379581821734289b6fc71d350e0e2762da3f8d 100644 --- a/src/main/java/eu/hbp/mip/controllers/ExperimentAPI.java +++ b/src/main/java/hbp/mip/controllers/ExperimentAPI.java @@ -1,10 +1,10 @@ -package eu.hbp.mip.controllers; +package hbp.mip.controllers; -import eu.hbp.mip.models.DTOs.ExperimentDTO; -import eu.hbp.mip.services.ActiveUserService; -import eu.hbp.mip.services.ExperimentService; -import eu.hbp.mip.utils.Logger; +import hbp.mip.models.DTOs.ExperimentDTO; +import hbp.mip.services.ActiveUserService; +import hbp.mip.services.ExperimentService; +import hbp.mip.utils.Logger; import org.springframework.http.HttpStatus; import org.springframework.http.ResponseEntity; import org.springframework.security.core.Authentication; diff --git a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java b/src/main/java/hbp/mip/controllers/PathologiesAPI.java similarity index 93% rename from src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java rename to src/main/java/hbp/mip/controllers/PathologiesAPI.java index 73c12fbea00972faac57caca22024a846362b718..d1a93e0212ab32cb57542b6f5dbbf62cad015c6d 100644 --- a/src/main/java/eu/hbp/mip/controllers/PathologiesAPI.java +++ b/src/main/java/hbp/mip/controllers/PathologiesAPI.java @@ -1,19 +1,20 @@ -package eu.hbp.mip.controllers; +package hbp.mip.controllers; import com.google.gson.Gson; import com.google.gson.reflect.TypeToken; -import eu.hbp.mip.models.DTOs.Exareme2AttributesDTO; -import eu.hbp.mip.models.DTOs.Exareme2CommonDataElement; -import eu.hbp.mip.models.DTOs.PathologyDTO; -import eu.hbp.mip.services.ActiveUserService; -import eu.hbp.mip.utils.*; -import eu.hbp.mip.utils.Exceptions.InternalServerError; +import hbp.mip.models.DTOs.Exareme2AttributesDTO; +import hbp.mip.models.DTOs.Exareme2CommonDataElement; +import hbp.mip.models.DTOs.PathologyDTO; +import hbp.mip.services.ActiveUserService; +import hbp.mip.utils.ClaimUtils; +import hbp.mip.utils.Exceptions.InternalServerError; +import hbp.mip.utils.HTTPUtil; +import hbp.mip.utils.Logger; import org.springframework.beans.factory.annotation.Value; import org.springframework.http.ResponseEntity; import org.springframework.security.core.Authentication; import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.RequestMapping; -import org.springframework.web.bind.annotation.RequestMethod; import org.springframework.web.bind.annotation.RestController; import java.util.*; diff --git a/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java b/src/main/java/hbp/mip/models/DAOs/ExperimentDAO.java similarity index 98% rename from src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java rename to src/main/java/hbp/mip/models/DAOs/ExperimentDAO.java index 244b55d6f1f3d64514952335cead321525b2001b..f2ac7ea97205f958d7458ada2928238fb71521d6 100644 --- a/src/main/java/eu/hbp/mip/models/DAOs/ExperimentDAO.java +++ b/src/main/java/hbp/mip/models/DAOs/ExperimentDAO.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.models.DAOs; +package hbp.mip.models.DAOs; import com.fasterxml.jackson.annotation.JsonInclude; import com.google.gson.Gson; diff --git a/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java b/src/main/java/hbp/mip/models/DAOs/UserDAO.java similarity index 96% rename from src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java rename to src/main/java/hbp/mip/models/DAOs/UserDAO.java index d1ab17988297d2d938d1c5818e7313a78a442bed..58968ceb43d5315f74792c44efb26ddb42942bea 100644 --- a/src/main/java/eu/hbp/mip/models/DAOs/UserDAO.java +++ b/src/main/java/hbp/mip/models/DAOs/UserDAO.java @@ -2,7 +2,7 @@ * Created by mirco on 04.12.15. */ -package eu.hbp.mip.models.DAOs; +package 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/models/DTOs/Exareme2AlgorithmDTO.java b/src/main/java/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java similarity index 99% rename from src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java rename to src/main/java/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java index db5095359df8827a5839b4b0c2ee46c1b1f01a3a..9c46445e222f47ce5e7bcf82237e30b01231b4bc 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/Exareme2AlgorithmDTO.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; import lombok.AllArgsConstructor; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java b/src/main/java/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java similarity index 98% rename from src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java rename to src/main/java/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java index 5562df1398aaa199617e82d5d0a9e761d67f8b34..1e6e21dc506386789cc6029df510eb015aab93e6 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/Exareme2AlgorithmRequestDTO.java @@ -1,7 +1,7 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; -import eu.hbp.mip.utils.JsonConverters; +import hbp.mip.utils.JsonConverters; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java b/src/main/java/hbp/mip/models/DTOs/Exareme2AttributesDTO.java similarity index 92% rename from src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java rename to src/main/java/hbp/mip/models/DTOs/Exareme2AttributesDTO.java index aaaa627db9582dee2c970ad2a7a4271dcf33d37e..3755dcdc23fbbc0b1509a46ed20b131b95da907f 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/Exareme2AttributesDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/Exareme2AttributesDTO.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; import lombok.AllArgsConstructor; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java b/src/main/java/hbp/mip/models/DTOs/Exareme2CommonDataElement.java similarity index 96% rename from src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java rename to src/main/java/hbp/mip/models/DTOs/Exareme2CommonDataElement.java index 786bf76308803119ffc3c22299fc91922127602a..5e23144a168128e1cd12bc15fc5937c8f3db287f 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/Exareme2CommonDataElement.java +++ b/src/main/java/hbp/mip/models/DTOs/Exareme2CommonDataElement.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java b/src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java similarity index 96% rename from src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java rename to src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java index be3e1f56c3454496822295399d5bc30c8682be06..20f4e5fcd09a8ff31fe978e06fdd1624d675dc32 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmDTO.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; import lombok.AllArgsConstructor; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java b/src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java similarity index 97% rename from src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java rename to src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java index ab80e2852bb8ef777ef68c4400c33304ad71a27e..2e0954b58927ec320ae75c5fb345ea88203d4b50 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmRequestParamDTO.java @@ -1,7 +1,7 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; -import eu.hbp.mip.utils.Exceptions.InternalServerError; +import hbp.mip.utils.Exceptions.InternalServerError; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java b/src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java similarity index 86% rename from src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java rename to src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java index 88b5fb627da14791c2e772fca65d06cef3a4f5e2..4d1f975850f9a8f0c8b85a797b590b424ffeb47e 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/ExaremeAlgorithmResultDTO.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java b/src/main/java/hbp/mip/models/DTOs/ExperimentDTO.java similarity index 93% rename from src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java rename to src/main/java/hbp/mip/models/DTOs/ExperimentDTO.java index 461df982261e01043d59d632db5b0f55c9ffb304..a94d87ef8136e629e3345e10f1be14218d6a10a1 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/ExperimentDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/ExperimentDTO.java @@ -1,8 +1,8 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.fasterxml.jackson.annotation.JsonInclude; -import eu.hbp.mip.models.DAOs.ExperimentDAO; -import eu.hbp.mip.utils.JsonConverters; +import hbp.mip.models.DAOs.ExperimentDAO; +import hbp.mip.utils.JsonConverters; import lombok.AllArgsConstructor; import lombok.Data; import lombok.NoArgsConstructor; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java b/src/main/java/hbp/mip/models/DTOs/MetadataHierarchyDTO.java similarity index 98% rename from src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java rename to src/main/java/hbp/mip/models/DTOs/MetadataHierarchyDTO.java index ff73005c49d910496980263f724344228e20fadf..0c91008097e8d611fa2aa887cfc4b69c20a6f132 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/MetadataHierarchyDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/MetadataHierarchyDTO.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; import lombok.AllArgsConstructor; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java b/src/main/java/hbp/mip/models/DTOs/PathologyDTO.java similarity index 91% rename from src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java rename to src/main/java/hbp/mip/models/DTOs/PathologyDTO.java index 127f1eb2d38a1bdd42c761d52d4ec343d95a334f..794a5ee7a25abb1105c5c342ce080e2d7aaa1657 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/PathologyDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/PathologyDTO.java @@ -1,7 +1,7 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.google.gson.annotations.SerializedName; -import eu.hbp.mip.utils.Exceptions.InternalServerError; +import hbp.mip.utils.Exceptions.InternalServerError; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/main/java/eu/hbp/mip/models/DTOs/UserDTO.java b/src/main/java/hbp/mip/models/DTOs/UserDTO.java similarity index 77% rename from src/main/java/eu/hbp/mip/models/DTOs/UserDTO.java rename to src/main/java/hbp/mip/models/DTOs/UserDTO.java index 448b50f1a506adce7bb7fae1bd68d1b7b0fed3b9..eb9d4736694877acb80135fcee76ed131b8975be 100644 --- a/src/main/java/eu/hbp/mip/models/DTOs/UserDTO.java +++ b/src/main/java/hbp/mip/models/DTOs/UserDTO.java @@ -1,10 +1,8 @@ -package eu.hbp.mip.models.DTOs; +package hbp.mip.models.DTOs; import com.fasterxml.jackson.annotation.JsonInclude; import com.google.gson.annotations.SerializedName; -import eu.hbp.mip.models.DAOs.ExperimentDAO; -import eu.hbp.mip.models.DAOs.UserDAO; -import eu.hbp.mip.utils.JsonConverters; +import hbp.mip.models.DAOs.UserDAO; import lombok.AllArgsConstructor; import lombok.Data; diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java b/src/main/java/hbp/mip/repositories/ExperimentRepository.java similarity index 88% rename from src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java rename to src/main/java/hbp/mip/repositories/ExperimentRepository.java index 733737cee94ec5aaa56fe92af5405abe8c41b37c..7b296584e159fec71e2b770c30842fc7d002a645 100644 --- a/src/main/java/eu/hbp/mip/repositories/ExperimentRepository.java +++ b/src/main/java/hbp/mip/repositories/ExperimentRepository.java @@ -1,13 +1,13 @@ -package eu.hbp.mip.repositories; +package hbp.mip.repositories; -import eu.hbp.mip.models.DAOs.ExperimentDAO; -import eu.hbp.mip.models.DAOs.UserDAO; -import eu.hbp.mip.models.DTOs.ExperimentDTO; -import eu.hbp.mip.utils.Exceptions.BadRequestException; -import eu.hbp.mip.utils.Exceptions.ExperimentNotFoundException; -import eu.hbp.mip.utils.Exceptions.InternalServerError; -import eu.hbp.mip.utils.JsonConverters; -import eu.hbp.mip.utils.Logger; +import hbp.mip.models.DAOs.ExperimentDAO; +import hbp.mip.models.DAOs.UserDAO; +import hbp.mip.models.DTOs.ExperimentDTO; +import hbp.mip.utils.Exceptions.BadRequestException; +import hbp.mip.utils.Exceptions.ExperimentNotFoundException; +import hbp.mip.utils.Exceptions.InternalServerError; +import hbp.mip.utils.JsonConverters; +import hbp.mip.utils.Logger; import org.springframework.data.jpa.repository.JpaSpecificationExecutor; import org.springframework.data.repository.CrudRepository; diff --git a/src/main/java/eu/hbp/mip/repositories/ExperimentSpecifications.java b/src/main/java/hbp/mip/repositories/ExperimentSpecifications.java similarity index 97% rename from src/main/java/eu/hbp/mip/repositories/ExperimentSpecifications.java rename to src/main/java/hbp/mip/repositories/ExperimentSpecifications.java index ba1f7babccedb3a49906fff66fd1cd5fe732a77c..5c5d86f1938ef123bf790c9fabd02afe4c91a936 100644 --- a/src/main/java/eu/hbp/mip/repositories/ExperimentSpecifications.java +++ b/src/main/java/hbp/mip/repositories/ExperimentSpecifications.java @@ -1,7 +1,7 @@ -package eu.hbp.mip.repositories; +package hbp.mip.repositories; -import eu.hbp.mip.models.DAOs.ExperimentDAO; -import eu.hbp.mip.utils.Exceptions.BadRequestException; +import hbp.mip.models.DAOs.ExperimentDAO; +import hbp.mip.utils.Exceptions.BadRequestException; import jakarta.persistence.criteria.*; import lombok.NonNull; import org.springframework.data.jpa.domain.Specification; diff --git a/src/main/java/eu/hbp/mip/repositories/UserRepository.java b/src/main/java/hbp/mip/repositories/UserRepository.java similarity index 71% rename from src/main/java/eu/hbp/mip/repositories/UserRepository.java rename to src/main/java/hbp/mip/repositories/UserRepository.java index cbfdc5b5bfd5bc392775470a961c2b1eabf5fd9d..11f5d3f6ca98b10301d7f58ec0e289fa573bbf63 100644 --- a/src/main/java/eu/hbp/mip/repositories/UserRepository.java +++ b/src/main/java/hbp/mip/repositories/UserRepository.java @@ -1,6 +1,6 @@ -package eu.hbp.mip.repositories; +package hbp.mip.repositories; -import eu.hbp.mip.models.DAOs.UserDAO; +import hbp.mip.models.DAOs.UserDAO; import org.springframework.data.repository.CrudRepository; public interface UserRepository extends CrudRepository<UserDAO, String> { diff --git a/src/main/java/eu/hbp/mip/services/ActiveUserService.java b/src/main/java/hbp/mip/services/ActiveUserService.java similarity index 96% rename from src/main/java/eu/hbp/mip/services/ActiveUserService.java rename to src/main/java/hbp/mip/services/ActiveUserService.java index 816a9a15b7d2585098b2074eb60b1098a507b60d..30ab4d0a2e1b09af7217c88740ee91658c5e587a 100644 --- a/src/main/java/eu/hbp/mip/services/ActiveUserService.java +++ b/src/main/java/hbp/mip/services/ActiveUserService.java @@ -1,7 +1,7 @@ -package eu.hbp.mip.services; +package hbp.mip.services; -import eu.hbp.mip.models.DAOs.UserDAO; -import eu.hbp.mip.repositories.UserRepository; +import hbp.mip.models.DAOs.UserDAO; +import hbp.mip.repositories.UserRepository; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Scope; import org.springframework.context.annotation.ScopedProxyMode; diff --git a/src/main/java/eu/hbp/mip/services/AlgorithmService.java b/src/main/java/hbp/mip/services/AlgorithmService.java similarity index 95% rename from src/main/java/eu/hbp/mip/services/AlgorithmService.java rename to src/main/java/hbp/mip/services/AlgorithmService.java index 87aeca1cf33c12e245bc98b28e9dad3803117352..c0085ea13a9cffbb2ddeb73f62523382ea9d217e 100644 --- a/src/main/java/eu/hbp/mip/services/AlgorithmService.java +++ b/src/main/java/hbp/mip/services/AlgorithmService.java @@ -1,13 +1,13 @@ -package eu.hbp.mip.services; +package hbp.mip.services; import com.google.gson.Gson; import com.google.gson.reflect.TypeToken; -import eu.hbp.mip.models.DTOs.Exareme2AlgorithmDTO; -import eu.hbp.mip.models.DTOs.ExaremeAlgorithmDTO; -import eu.hbp.mip.utils.CustomResourceLoader; -import eu.hbp.mip.utils.Exceptions.BadRequestException; -import eu.hbp.mip.utils.HTTPUtil; -import eu.hbp.mip.utils.Logger; +import hbp.mip.models.DTOs.Exareme2AlgorithmDTO; +import hbp.mip.models.DTOs.ExaremeAlgorithmDTO; +import hbp.mip.utils.CustomResourceLoader; +import hbp.mip.utils.Exceptions.BadRequestException; +import hbp.mip.utils.HTTPUtil; +import hbp.mip.utils.Logger; import org.springframework.beans.factory.annotation.Value; import org.springframework.core.io.Resource; import org.springframework.scheduling.annotation.Async; @@ -22,7 +22,7 @@ import java.util.List; import java.util.Objects; import java.util.Optional; -import static eu.hbp.mip.utils.InputStreamConverter.convertInputStreamToString; +import static hbp.mip.utils.InputStreamConverter.convertInputStreamToString; @EnableScheduling @Service diff --git a/src/main/java/eu/hbp/mip/services/ExperimentService.java b/src/main/java/hbp/mip/services/ExperimentService.java similarity index 97% rename from src/main/java/eu/hbp/mip/services/ExperimentService.java rename to src/main/java/hbp/mip/services/ExperimentService.java index 7715def2481483126980c3069ab828ebc75f1c6b..b23402e5dc0bbebd1cf56527a04cb06cef71b999 100644 --- a/src/main/java/eu/hbp/mip/services/ExperimentService.java +++ b/src/main/java/hbp/mip/services/ExperimentService.java @@ -1,22 +1,22 @@ -package eu.hbp.mip.services; +package hbp.mip.services; import com.google.gson.Gson; -import eu.hbp.mip.models.DAOs.ExperimentDAO; -import eu.hbp.mip.models.DAOs.UserDAO; -import eu.hbp.mip.models.DTOs.Exareme2AlgorithmRequestDTO; -import eu.hbp.mip.models.DTOs.ExaremeAlgorithmRequestParamDTO; -import eu.hbp.mip.models.DTOs.ExaremeAlgorithmResultDTO; -import eu.hbp.mip.models.DTOs.ExperimentDTO; -import eu.hbp.mip.repositories.ExperimentRepository; -import eu.hbp.mip.repositories.ExperimentSpecifications; -import eu.hbp.mip.utils.ClaimUtils; -import eu.hbp.mip.utils.Exceptions.BadRequestException; -import eu.hbp.mip.utils.Exceptions.InternalServerError; -import eu.hbp.mip.utils.Exceptions.NoContent; -import eu.hbp.mip.utils.Exceptions.UnauthorizedException; -import eu.hbp.mip.utils.HTTPUtil; -import eu.hbp.mip.utils.JsonConverters; -import eu.hbp.mip.utils.Logger; +import hbp.mip.models.DAOs.ExperimentDAO; +import hbp.mip.models.DAOs.UserDAO; +import hbp.mip.models.DTOs.Exareme2AlgorithmRequestDTO; +import hbp.mip.models.DTOs.ExaremeAlgorithmRequestParamDTO; +import hbp.mip.models.DTOs.ExaremeAlgorithmResultDTO; +import hbp.mip.models.DTOs.ExperimentDTO; +import hbp.mip.repositories.ExperimentRepository; +import hbp.mip.repositories.ExperimentSpecifications; +import hbp.mip.utils.ClaimUtils; +import hbp.mip.utils.Exceptions.BadRequestException; +import hbp.mip.utils.Exceptions.InternalServerError; +import hbp.mip.utils.Exceptions.NoContent; +import hbp.mip.utils.Exceptions.UnauthorizedException; +import hbp.mip.utils.HTTPUtil; +import hbp.mip.utils.JsonConverters; +import hbp.mip.utils.Logger; import org.springframework.beans.factory.annotation.Value; import org.springframework.data.domain.Page; import org.springframework.data.domain.PageRequest; diff --git a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java b/src/main/java/hbp/mip/utils/ClaimUtils.java similarity index 94% rename from src/main/java/eu/hbp/mip/utils/ClaimUtils.java rename to src/main/java/hbp/mip/utils/ClaimUtils.java index 27b79af9fc5f291d5112b7fc1c22dcb0ced8893e..51537a9fbb6a87d22a5f4d0e0c68ce9f16dec4df 100644 --- a/src/main/java/eu/hbp/mip/utils/ClaimUtils.java +++ b/src/main/java/hbp/mip/utils/ClaimUtils.java @@ -1,7 +1,7 @@ -package eu.hbp.mip.utils; +package hbp.mip.utils; -import eu.hbp.mip.models.DTOs.PathologyDTO; -import eu.hbp.mip.utils.Exceptions.UnauthorizedException; +import hbp.mip.models.DTOs.PathologyDTO; +import hbp.mip.utils.Exceptions.UnauthorizedException; import org.springframework.beans.factory.annotation.Value; import org.springframework.security.core.Authentication; import org.springframework.stereotype.Component; @@ -66,7 +66,7 @@ public class ClaimUtils { } public List<PathologyDTO> getAuthorizedPathologies(Logger logger, Authentication authentication, - List<PathologyDTO> allPathologies) { + List<PathologyDTO> allPathologies) { ArrayList<String> authorities = getAuthorityRoles(authentication); diff --git a/src/main/java/eu/hbp/mip/utils/ControllerExceptionHandler.java b/src/main/java/hbp/mip/utils/ControllerExceptionHandler.java similarity index 97% rename from src/main/java/eu/hbp/mip/utils/ControllerExceptionHandler.java rename to src/main/java/hbp/mip/utils/ControllerExceptionHandler.java index bd4fd42aefada816b535e173f9dd3b772e1dbea2..0cd1efa81bf8d9217e6fc7a1dc88efe305aed9d1 100644 --- a/src/main/java/eu/hbp/mip/utils/ControllerExceptionHandler.java +++ b/src/main/java/hbp/mip/utils/ControllerExceptionHandler.java @@ -1,6 +1,6 @@ -package eu.hbp.mip.utils; +package hbp.mip.utils; -import eu.hbp.mip.utils.Exceptions.*; +import hbp.mip.utils.Exceptions.*; import org.springframework.http.HttpStatus; import org.springframework.http.ResponseEntity; import org.springframework.web.bind.annotation.ControllerAdvice; diff --git a/src/main/java/eu/hbp/mip/utils/CustomResourceLoader.java b/src/main/java/hbp/mip/utils/CustomResourceLoader.java similarity index 92% rename from src/main/java/eu/hbp/mip/utils/CustomResourceLoader.java rename to src/main/java/hbp/mip/utils/CustomResourceLoader.java index d4d5d407f9be349ecd2a46abdf45b1bc4ae02598..89552146c0bb41e0691b1ac109b8f534e0da5897 100644 --- a/src/main/java/eu/hbp/mip/utils/CustomResourceLoader.java +++ b/src/main/java/hbp/mip/utils/CustomResourceLoader.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils; +package hbp.mip.utils; import lombok.NonNull; import org.springframework.context.ResourceLoaderAware; diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/BadRequestException.java b/src/main/java/hbp/mip/utils/Exceptions/BadRequestException.java similarity index 78% rename from src/main/java/eu/hbp/mip/utils/Exceptions/BadRequestException.java rename to src/main/java/hbp/mip/utils/Exceptions/BadRequestException.java index 6684cae281a0487aa5d39e78693b6c9f5bd04098..a83830665e1f44bd47e7818dc33c26a3def252ef 100644 --- a/src/main/java/eu/hbp/mip/utils/Exceptions/BadRequestException.java +++ b/src/main/java/hbp/mip/utils/Exceptions/BadRequestException.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils.Exceptions; +package hbp.mip.utils.Exceptions; public class BadRequestException extends RuntimeException { diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java b/src/main/java/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java similarity index 80% rename from src/main/java/eu/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java rename to src/main/java/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java index b8e05d7e667769537de9d540f436902dca6edc4e..30373550959da95aee81bbfc19ad1265d3da2e6e 100644 --- a/src/main/java/eu/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java +++ b/src/main/java/hbp/mip/utils/Exceptions/ExperimentNotFoundException.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils.Exceptions; +package hbp.mip.utils.Exceptions; public class ExperimentNotFoundException extends RuntimeException { diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/InternalServerError.java b/src/main/java/hbp/mip/utils/Exceptions/InternalServerError.java similarity index 78% rename from src/main/java/eu/hbp/mip/utils/Exceptions/InternalServerError.java rename to src/main/java/hbp/mip/utils/Exceptions/InternalServerError.java index 19bc88eed27b6e0e4ab36a05136f043be65725ec..31357164f5debe8110032c72fc8906e26ff2cc91 100644 --- a/src/main/java/eu/hbp/mip/utils/Exceptions/InternalServerError.java +++ b/src/main/java/hbp/mip/utils/Exceptions/InternalServerError.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils.Exceptions; +package hbp.mip.utils.Exceptions; public class InternalServerError extends RuntimeException { diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/NoContent.java b/src/main/java/hbp/mip/utils/Exceptions/NoContent.java similarity index 75% rename from src/main/java/eu/hbp/mip/utils/Exceptions/NoContent.java rename to src/main/java/hbp/mip/utils/Exceptions/NoContent.java index 9bb67d8114e71545b8a00a8eb0bcdb0f7285b714..6ac31b89957da53a258adb65be3e498993032682 100644 --- a/src/main/java/eu/hbp/mip/utils/Exceptions/NoContent.java +++ b/src/main/java/hbp/mip/utils/Exceptions/NoContent.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils.Exceptions; +package hbp.mip.utils.Exceptions; public class NoContent extends RuntimeException { diff --git a/src/main/java/eu/hbp/mip/utils/Exceptions/UnauthorizedException.java b/src/main/java/hbp/mip/utils/Exceptions/UnauthorizedException.java similarity index 78% rename from src/main/java/eu/hbp/mip/utils/Exceptions/UnauthorizedException.java rename to src/main/java/hbp/mip/utils/Exceptions/UnauthorizedException.java index 379911daeabe7227497f3d5bb622e54f6ccffb87..1cbe3cf20914032d1a88444bf5c68a00a41e21a1 100644 --- a/src/main/java/eu/hbp/mip/utils/Exceptions/UnauthorizedException.java +++ b/src/main/java/hbp/mip/utils/Exceptions/UnauthorizedException.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils.Exceptions; +package hbp.mip.utils.Exceptions; public class UnauthorizedException extends RuntimeException { diff --git a/src/main/java/eu/hbp/mip/utils/HTTPUtil.java b/src/main/java/hbp/mip/utils/HTTPUtil.java similarity index 98% rename from src/main/java/eu/hbp/mip/utils/HTTPUtil.java rename to src/main/java/hbp/mip/utils/HTTPUtil.java index 2ef8e58809e88d0c50eecb4659e0186f1bff3dbc..c5e6b08ec4642ee43b042f2a1a235686177c68a2 100644 --- a/src/main/java/eu/hbp/mip/utils/HTTPUtil.java +++ b/src/main/java/hbp/mip/utils/HTTPUtil.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils; +package hbp.mip.utils; import java.io.BufferedReader; import java.io.DataOutputStream; diff --git a/src/main/java/eu/hbp/mip/utils/InputStreamConverter.java b/src/main/java/hbp/mip/utils/InputStreamConverter.java similarity index 93% rename from src/main/java/eu/hbp/mip/utils/InputStreamConverter.java rename to src/main/java/hbp/mip/utils/InputStreamConverter.java index 050ba74604f9dc9b658ee439e4ed8a94ac518414..0926d6fa69be0a48fb5a1cb473354ee5e7edc8bf 100644 --- a/src/main/java/eu/hbp/mip/utils/InputStreamConverter.java +++ b/src/main/java/hbp/mip/utils/InputStreamConverter.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils; +package hbp.mip.utils; import java.io.ByteArrayOutputStream; import java.io.IOException; diff --git a/src/main/java/eu/hbp/mip/utils/JsonConverters.java b/src/main/java/hbp/mip/utils/JsonConverters.java similarity index 96% rename from src/main/java/eu/hbp/mip/utils/JsonConverters.java rename to src/main/java/hbp/mip/utils/JsonConverters.java index 74d01b851f44877fffe0e146d8f678ee3fb95dfb..fb8eaf5ff9b5dc0862095dd86218e30fde2b90ca 100644 --- a/src/main/java/eu/hbp/mip/utils/JsonConverters.java +++ b/src/main/java/hbp/mip/utils/JsonConverters.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils; +package hbp.mip.utils; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/src/main/java/eu/hbp/mip/utils/Logger.java b/src/main/java/hbp/mip/utils/Logger.java similarity index 92% rename from src/main/java/eu/hbp/mip/utils/Logger.java rename to src/main/java/hbp/mip/utils/Logger.java index 60e67c7aa8815ccb10b91909871024da4bb48a4a..faeed30eca1d6a54fa536e399a93891ee34a611c 100644 --- a/src/main/java/eu/hbp/mip/utils/Logger.java +++ b/src/main/java/hbp/mip/utils/Logger.java @@ -1,4 +1,4 @@ -package eu.hbp.mip.utils; +package hbp.mip.utils; import org.slf4j.LoggerFactory;