Moved REST controllers to package .api.v0

src/main/java/org/genesys2/server/servlet/controller/rest/RestController.java

@@ -21,10 +21,12 @@ import java.io.IOException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.genesys2.server.exception.NotFoundElement;
 import org.genesys2.server.service.impl.RESTApiException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.HttpStatus;
 import org.springframework.security.access.AccessDeniedException;
 import org.springframework.security.core.Authentication;
 import org.springframework.security.core.context.SecurityContextHolder;
@@ -32,6 +34,7 @@ import org.springframework.security.core.userdetails.UserDetails;
 import org.springframework.web.HttpRequestMethodNotSupportedException;
 import org.springframework.web.bind.annotation.ExceptionHandler;
 import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.ResponseStatus;
 
 public abstract class RestController {
 	protected final Logger LOG = LoggerFactory.getLogger(getClass());
@@ -93,4 +96,13 @@ public abstract class RestController {
 		return new ExceptionJson(ex);
 	}
 
+    @ResponseStatus(code = HttpStatus.NOT_FOUND)
+    @ExceptionHandler(NotFoundElement.class)
+    @ResponseBody
+    public ExceptionJson handleNotFound(final Exception e, final HttpServletRequest request) {
+        final Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
+        LOG.warn("{} {} for {}", request.getRequestURI(), e.getMessage(), (authentication != null ? ((UserDetails) authentication.getPrincipal()).getUsername() : "null"));
+        return new ExceptionJson(e);
+    }
+
 }

src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/AccessionController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -46,6 +46,8 @@ import org.genesys2.server.service.worker.AccessionOpResponse;
 import org.genesys2.server.service.worker.AccessionOpResponse.UpsertResult;
 import org.genesys2.server.service.worker.AccessionUploader;
 import org.genesys2.server.service.worker.InvalidApiUsageException;
+import org.genesys2.server.servlet.controller.rest.PleaseRetryException;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;

src/main/java/org/genesys2/server/servlet/controller/rest/CacheController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/CacheController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -22,6 +22,7 @@ import java.util.List;
 import java.util.Set;
 
 import org.genesys2.server.service.MappingService;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.Cache;
 import org.springframework.cache.CacheManager;

src/main/java/org/genesys2/server/servlet/controller/rest/CropsController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/CropsController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.List;
 
@@ -31,6 +31,9 @@ import org.genesys2.server.model.impl.CropTaxonomy;
 import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.TraitService;
+import org.genesys2.server.servlet.controller.rest.ModelValidationException;
+import org.genesys2.server.servlet.controller.rest.OAuth2Cleanup;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.i18n.LocaleContextHolder;

src/main/java/org/genesys2/server/servlet/controller/rest/DatasetController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/DatasetController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.io.IOException;
 import java.text.MessageFormat;
@@ -47,6 +47,9 @@ import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TraitService;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
+import org.genesys2.server.servlet.controller.rest.ModelValidationException;
+import org.genesys2.server.servlet.controller.rest.OAuth2Cleanup;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;

src/main/java/org/genesys2/server/servlet/controller/rest/GeoController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/GeoController.java

-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -6,6 +6,7 @@ import java.util.List;
 import org.genesys2.server.model.impl.GeoRegion;
 import org.genesys2.server.persistence.domain.CountryRepository;
 import org.genesys2.server.service.GeoRegionService;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.server.servlet.controller.rest.model.GeoJsData;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.MessageSource;

src/main/java/org/genesys2/server/servlet/controller/rest/InstituteGalleriesController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/InstituteGalleriesController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.io.IOException;
 import java.util.List;
@@ -35,6 +35,7 @@ import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.InstituteFilesService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

src/main/java/org/genesys2/server/servlet/controller/rest/KPIController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/KPIController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.Collection;
 import java.util.HashMap;
@@ -34,6 +34,8 @@ import org.genesys2.server.model.kpi.ExecutionDimension;
 import org.genesys2.server.model.kpi.KPIParameter;
 import org.genesys2.server.model.kpi.Observation;
 import org.genesys2.server.service.KPIService;
+import org.genesys2.server.servlet.controller.rest.ModelValidationException;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.server.servlet.controller.rest.model.ExecutionDimensionJson;
 import org.genesys2.server.servlet.controller.rest.model.ExecutionJson;
 import org.springframework.beans.factory.annotation.Autowired;

src/main/java/org/genesys2/server/servlet/controller/rest/LookupController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/LookupController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.List;
 import java.util.Locale;
@@ -27,6 +27,7 @@ import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TaxonomyService;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;

src/main/java/org/genesys2/server/servlet/controller/rest/OrganizationController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/OrganizationController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.io.IOException;
 import java.util.HashSet;
@@ -32,6 +32,8 @@ import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Organization;
 import org.genesys2.server.service.CRMException;
 import org.genesys2.server.service.OrganizationService;
+import org.genesys2.server.servlet.controller.rest.ModelValidationException;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;

src/main/java/org/genesys2/server/servlet/controller/rest/PermissionController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/PermissionController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -26,6 +26,7 @@ import org.genesys.blocks.security.model.AclSid;
 import org.genesys.blocks.security.service.CustomAclService;
 import org.genesys2.server.model.impl.User;
 import org.genesys2.server.service.UserService;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.server.servlet.model.PermissionJson;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;

src/main/java/org/genesys2/server/servlet/controller/rest/RequestsController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/RequestsController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import org.genesys2.server.model.genesys.MaterialRequest;
 import org.genesys2.server.model.genesys.MaterialSubRequest;
@@ -23,6 +23,7 @@ import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.RequestService;
 import org.genesys2.server.service.RequestService.NoPidException;
 import org.genesys2.server.service.impl.EasySMTAException;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;

src/main/java/org/genesys2/server/servlet/controller/rest/TraitsController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/TraitsController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.List;
 
@@ -35,6 +35,9 @@ import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.TraitService;
+import org.genesys2.server.servlet.controller.rest.ModelValidationException;
+import org.genesys2.server.servlet.controller.rest.OAuth2Cleanup;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;

src/main/java/org/genesys2/server/servlet/controller/rest/UserController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/UserController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.List;
 
@@ -31,6 +31,9 @@ import org.genesys2.server.model.impl.User;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TeamService;
 import org.genesys2.server.service.UserService;
+import org.genesys2.server.servlet.controller.rest.ModelValidationException;
+import org.genesys2.server.servlet.controller.rest.OAuth2Cleanup;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Sort;
 import org.springframework.http.MediaType;

src/main/java/org/genesys2/server/servlet/controller/rest/UsersController.java → src/main/java/org/genesys2/server/servlet/controller/rest/api/v0/UsersController.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller.rest;
+package org.genesys2.server.servlet.controller.rest.api.v0;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -27,6 +27,7 @@ import org.genesys2.server.model.impl.User;
 import org.genesys2.server.service.EMailVerificationService;
 import org.genesys2.server.service.TeamService;
 import org.genesys2.server.service.UserService;
+import org.genesys2.server.servlet.controller.rest.RestController;
 import org.genesys2.server.servlet.controller.rest.model.UserChangedDataJson;
 import org.genesys2.server.servlet.model.UserList;
 import org.genesys2.spring.ResourceNotFoundException;

src/test/java/org/genesys2/server/service/impl/AccessionHistoryTest.java

@@ -33,6 +33,8 @@ import org.junit.Before;
 import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
+import com.google.common.collect.Sets;
+
 /**
  * Ensure that deleted accessions end up as {@link AccessionHistoric} entities.
  */
@@ -87,8 +89,7 @@ public class AccessionHistoryTest extends GenesysServicesTest {
 		accession.setInstitute(faoInstitute);
 		accession.setTaxonomy(taxonomy2);
 		accession.setCountryOfOrigin(country);
-		accession.getAccessionId().getStorage().add(10);
-		accession.getAccessionId().getStorage().add(20);
+		accession.getAccessionId().setStorage(Sets.newHashSet(10, 20));
 
 		genesysService.saveAccessions(faoInstitute, Collections.singletonList(accession));
 

src/test/java/org/genesys2/tests/resttests/AbstractRestTest.java

@@ -75,74 +75,25 @@ import org.genesys2.server.persistence.domain.UserRepository;
 import org.genesys2.server.persistence.domain.kpi.KPIParameterRepository;
 import org.genesys2.server.persistence.domain.kpi.ObservationRepository;
 import org.genesys2.server.persistence.domain.mock.TraitServiceMock;
-import org.genesys2.server.service.ContentService;
-import org.genesys2.server.service.CropService;
-import org.genesys2.server.service.DatasetService;
-import org.genesys2.server.service.EMailService;
-import org.genesys2.server.service.EMailVerificationService;
-import org.genesys2.server.service.EasySMTA;
-import org.genesys2.server.service.ElasticSearchManagementService;
-import org.genesys2.server.service.ElasticService;
-import org.genesys2.server.service.GenesysFilterService;
-import org.genesys2.server.service.GenesysRESTService;
-import org.genesys2.server.service.GenesysService;
-import org.genesys2.server.service.GeoRegionService;
-import org.genesys2.server.service.GeoService;
-import org.genesys2.server.service.HtmlSanitizer;
-import org.genesys2.server.service.InstituteFilesService;
-import org.genesys2.server.service.InstituteService;
-import org.genesys2.server.service.KPIService;
-import org.genesys2.server.service.MappingService;
-import org.genesys2.server.service.OrganizationService;
-import org.genesys2.server.service.RequestService;
-import org.genesys2.server.service.TaxonomyService;
-import org.genesys2.server.service.TeamService;
-import org.genesys2.server.service.TokenVerificationService;
-import org.genesys2.server.service.TraitService;
-import org.genesys2.server.service.UserService;
-import org.genesys2.server.service.impl.ContentServiceImpl;
-import org.genesys2.server.service.impl.CropServiceImpl;
-import org.genesys2.server.service.impl.EMailServiceImpl;
-import org.genesys2.server.service.impl.EMailVerificationServiceImpl;
-import org.genesys2.server.service.impl.EasySMTAMockConnector;
-import org.genesys2.server.service.impl.ElasticSearchManagementServiceImpl;
-import org.genesys2.server.service.impl.ElasticsearchSearchServiceImpl;
-import org.genesys2.server.service.impl.FilterHandler;
-import org.genesys2.server.service.impl.GenesysFilterServiceImpl;
-import org.genesys2.server.service.impl.GenesysRESTServiceImpl;
-import org.genesys2.server.service.impl.GenesysServiceImpl;
-import org.genesys2.server.service.impl.GeoRegionServiceImpl;
-import org.genesys2.server.service.impl.GeoServiceImpl;
-import org.genesys2.server.service.impl.InstituteFilesServiceImpl;
-import org.genesys2.server.service.impl.InstituteServiceImpl;
-import org.genesys2.server.service.impl.KPIServiceImpl;
-import org.genesys2.server.service.impl.MappingServiceImpl;
-import org.genesys2.server.service.impl.OWASPSanitizer;
-import org.genesys2.server.service.impl.OrganizationServiceImpl;
-import org.genesys2.server.service.impl.RequestServiceImpl;
-import org.genesys2.server.service.impl.TaxonomyManager;
-import org.genesys2.server.service.impl.TaxonomyServiceImpl;
-import org.genesys2.server.service.impl.TeamServiceImpl;
-import org.genesys2.server.service.impl.TokenVerificationServiceImpl;
-import org.genesys2.server.service.impl.UserServiceImpl;
-import org.genesys2.server.service.worker.AccessionCounter;
-import org.genesys2.server.service.worker.AccessionUploader;
+import org.genesys2.server.service.*;
+import org.genesys2.server.service.impl.*;
 import org.genesys2.server.service.worker.ElasticUpdater;
 import org.genesys2.server.service.worker.GeoRegionDataCLDR;
 import org.genesys2.server.servlet.controller.admin.OAuthManagementController;
-import org.genesys2.server.servlet.controller.rest.AccessionController;
-import org.genesys2.server.servlet.controller.rest.CacheController;
-import org.genesys2.server.servlet.controller.rest.CropsController;
-import org.genesys2.server.servlet.controller.rest.DatasetController;
-import org.genesys2.server.servlet.controller.rest.InstituteGalleriesController;
-import org.genesys2.server.servlet.controller.rest.KPIController;
-import org.genesys2.server.servlet.controller.rest.LookupController;
-import org.genesys2.server.servlet.controller.rest.OrganizationController;
-import org.genesys2.server.servlet.controller.rest.PermissionController;
-import org.genesys2.server.servlet.controller.rest.RequestsController;
-import org.genesys2.server.servlet.controller.rest.TraitsController;
-import org.genesys2.server.servlet.controller.rest.UserController;
-import org.genesys2.server.servlet.controller.rest.UsersController;
+import org.genesys2.server.servlet.controller.rest.api.v0.AccessionController;
+import org.genesys2.server.servlet.controller.rest.api.v0.CacheController;
+import org.genesys2.server.servlet.controller.rest.api.v0.CropsController;
+import org.genesys2.server.servlet.controller.rest.api.v0.DatasetController;
+import org.genesys2.server.servlet.controller.rest.api.v0.InstituteGalleriesController;
+import org.genesys2.server.servlet.controller.rest.api.v0.KPIController;
+import org.genesys2.server.servlet.controller.rest.api.v0.LookupController;
+import org.genesys2.server.servlet.controller.rest.api.v0.OrganizationController;
+import org.genesys2.server.servlet.controller.rest.api.v0.PermissionController;
+import org.genesys2.server.servlet.controller.rest.api.v0.RequestsController;
+import org.genesys2.server.servlet.controller.rest.api.v1.SubsetRestController;
+import org.genesys2.server.servlet.controller.rest.api.v0.TraitsController;
+import org.genesys2.server.servlet.controller.rest.api.v0.UserController;
+import org.genesys2.server.servlet.controller.rest.api.v0.UsersController;
 import org.genesys2.server.test.PropertyPlacholderInitializer;
 import org.genesys2.tests.BaseSpringTest;
 import org.junit.runner.RunWith;
@@ -190,6 +141,11 @@ public abstract class AbstractRestTest extends BaseSpringTest {
 	@DirtiesContext(hierarchyMode = HierarchyMode.CURRENT_LEVEL, classMode = DirtiesContext.ClassMode.AFTER_CLASS)
 	public static class Config {
 
+	    @Bean
+        public SubsetService subsetService() {
+	        return new SubsetServiceImpl();
+        }
+
 		@Bean
 		public GenesysImageGalleryAspects imageGalleryAspects() {
 			// This thing makes galleries auto-fill with images
@@ -228,6 +184,11 @@ public abstract class AbstractRestTest extends BaseSpringTest {
 			return fsss;
 		}
 
+		@Bean
+        public SubsetRestController subsetRestController() {
+	        return new SubsetRestController();
+        }
+
 		@Bean
 		public RequestsController requestsController() {
 			return new RequestsController();

src/test/java/org/genesys2/tests/resttests/OrganizationControllerTest.java

@@ -13,7 +13,7 @@ import org.genesys2.server.model.impl.Article;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Organization;
 import org.genesys2.server.service.CRMException;
-import org.genesys2.server.servlet.controller.rest.OrganizationController;
+import org.genesys2.server.servlet.controller.rest.api.v0.OrganizationController;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;

src/test/java/org/genesys2/tests/resttests/TraitsControllerTest.java

@@ -18,7 +18,7 @@ import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.User;
 import org.genesys2.server.servlet.controller.rest.OAuth2Cleanup;
-import org.genesys2.server.servlet.controller.rest.TraitsController;
+import org.genesys2.server.servlet.controller.rest.api.v0.TraitsController;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Ignore;

src/test/java/org/genesys2/tests/resttests/UserControllerTest.java

@@ -16,7 +16,7 @@ import org.genesys.blocks.security.service.PasswordPolicy.PasswordPolicyExceptio
 import org.genesys2.server.model.UserRole;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.User;
-import org.genesys2.server.servlet.controller.rest.UserController;
+import org.genesys2.server.servlet.controller.rest.api.v0.UserController;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Ignore;