fix: revert transactional

opal-core-ws/src/main/java/org/obiba/opal/web/BaseResource.java

@@ -13,16 +13,16 @@
 import jakarta.ws.rs.OPTIONS;
 import jakarta.ws.rs.core.Response;
 
-public abstract class BaseResource {
+public interface BaseResource {
 
   /**
-   * OPTIONS implementation, so that {@link org.obiba.opal.web.security.AuthorizationInterceptor} can
+   * Default OPTIONS implementation, so that {@link org.obiba.opal.web.security.AuthorizationInterceptor} can
    * set the Allow header with appropriate HTTP methods.
    *
    * @return
    */
   @OPTIONS
-  public Response getOptions() {
+  default Response getOptions() {
     return Response.ok().build();
   }
 }

opal-core-ws/src/main/java/org/obiba/opal/web/magma/AbstractValueTableResource.java

@@ -17,14 +17,13 @@
 import org.obiba.magma.Variable;
 import org.obiba.magma.VariableEntity;
 import org.obiba.magma.js.views.JavascriptClause;
-import org.obiba.opal.web.BaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 
 import jakarta.annotation.Nullable;
 import java.util.*;
 
-abstract class AbstractValueTableResource extends BaseResource {
+abstract class AbstractValueTableResource {
 
   private ValueTable valueTable;
 

opal-core-ws/src/main/java/org/obiba/opal/web/magma/ValueSetsResource.java

@@ -20,8 +20,9 @@
 
 import org.obiba.magma.ValueTable;
 import org.obiba.magma.VariableValueSource;
+import org.obiba.opal.web.BaseResource;
 
-public interface ValueSetsResource {
+public interface ValueSetsResource extends BaseResource {
 
   void setValueTable(ValueTable valueTable);
 

opal-core-ws/src/main/java/org/obiba/opal/web/project/ProjectResource.java

@@ -11,17 +11,32 @@
 
 import com.google.common.collect.Lists;
 import com.google.common.eventbus.EventBus;
+import jakarta.annotation.Nullable;
+import jakarta.ws.rs.DELETE;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.PUT;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.PathParam;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Request;
+import jakarta.ws.rs.core.Response;
 import org.apache.commons.vfs2.FileSystemException;
 import org.obiba.magma.Datasource;
 import org.obiba.magma.security.Authorizer;
 import org.obiba.magma.security.shiro.ShiroAuthorizer;
 import org.obiba.opal.core.domain.Project;
-import org.obiba.opal.core.service.ProjectsState;
 import org.obiba.opal.core.event.DatasourceDeletedEvent;
 import org.obiba.opal.core.runtime.NoSuchServiceException;
 import org.obiba.opal.core.runtime.OpalRuntime;
 import org.obiba.opal.core.security.OpalKeyStore;
-import org.obiba.opal.core.service.*;
+import org.obiba.opal.core.service.NoSuchProjectException;
+import org.obiba.opal.core.service.ProjectService;
+import org.obiba.opal.core.service.ProjectsState;
+import org.obiba.opal.core.service.SubjectProfileService;
+import org.obiba.opal.core.service.VCFSamplesMappingService;
 import org.obiba.opal.core.service.security.ProjectsKeyStoreService;
 import org.obiba.opal.spi.vcf.VCFStoreService;
 import org.obiba.opal.web.BaseResource;
@@ -35,18 +50,13 @@
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.annotation.Transactional;
 
-import jakarta.annotation.Nullable;
-import jakarta.ws.rs.*;
-import jakarta.ws.rs.core.Context;
-import jakarta.ws.rs.core.Request;
-import jakarta.ws.rs.core.Response;
 import java.util.List;
 import java.util.stream.Collectors;
 
 @Component
 @Scope("request")
 @Path("/project/{name}")
-public class ProjectResource extends BaseResource {
+public class ProjectResource implements BaseResource {
 
   private final static Authorizer authorizer = new ShiroAuthorizer();
 
@@ -84,15 +94,13 @@ public ProjectResource(
   }
 
   @GET
-  @Transactional(readOnly = true)
   public Projects.ProjectDto get(@Context Request request, @PathParam("name") String name) {
     Project project = getProject(name);
     return Dtos.asDto(project, projectService);
   }
 
   @GET
   @Path("/summary")
-  @Transactional(readOnly = true)
   public Projects.ProjectSummaryDto getSummary(@Context Request request, @PathParam("name") String name) {
     Project project = getProject(name);
     return Dtos.asSummaryDto(project, projectService);

opal-core-ws/src/main/java/org/obiba/opal/web/project/ProjectsResource.java

@@ -10,6 +10,14 @@
 package org.obiba.opal.web.project;
 
 import com.google.common.collect.Lists;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.Context;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.core.UriInfo;
 import org.obiba.magma.NoSuchDatasourceException;
 import org.obiba.magma.security.Authorizer;
 import org.obiba.magma.security.shiro.ShiroAuthorizer;
@@ -23,27 +31,21 @@
 import org.obiba.opal.web.ws.security.NoAuthorization;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
-import org.springframework.transaction.annotation.Transactional;
 
-import jakarta.ws.rs.*;
-import jakarta.ws.rs.core.Context;
-import jakarta.ws.rs.core.Response;
-import jakarta.ws.rs.core.UriInfo;
 import java.net.URI;
 import java.util.List;
 import java.util.regex.Pattern;
 
 @Component
 @Path("/projects")
-public class ProjectsResource extends BaseResource {
+public class ProjectsResource implements BaseResource {
 
   private final static Authorizer authorizer = new ShiroAuthorizer();
 
   @Autowired
   private ProjectService projectService;
 
   @GET
-  @Transactional(readOnly = true)
   @NoAuthorization
   public List<Projects.ProjectDto> getProjects(@QueryParam("digest") @DefaultValue("false") boolean digest) {
     List<Projects.ProjectDto> projects = Lists.newArrayList();

opal-core-ws/src/main/java/org/obiba/opal/web/project/resource/ProjectResourceReferenceResource.java

@@ -29,7 +29,7 @@
 
 @Component
 @Path("/project/{project}/resource/{name}")
-public class ProjectResourceReferenceResource extends BaseResource {
+public class ProjectResourceReferenceResource implements BaseResource {
 
   private final static Authorizer authorizer = new ShiroAuthorizer();
 

opal-core-ws/src/main/java/org/obiba/opal/web/project/resource/ProjectResourceReferencesResource.java

@@ -33,7 +33,7 @@
 
 @Component
 @Path("/project/{name}/resources")
-public class ProjectResourceReferencesResource extends BaseResource {
+public class ProjectResourceReferencesResource implements BaseResource {
 
   private final static Authorizer authorizer = new ShiroAuthorizer();
 

opal-core-ws/src/main/java/org/obiba/opal/web/security/AbstractPermissionsResource.java

@@ -19,7 +19,7 @@
 
 import static org.obiba.opal.core.domain.security.SubjectAcl.SubjectType;
 
-public abstract class AbstractPermissionsResource extends BaseResource {
+public abstract class AbstractPermissionsResource implements BaseResource {
 
   public static final String DOMAIN = "opal";
 

opal-shell/src/main/java/org/obiba/opal/web/shell/AbstractCommandsResource.java

@@ -18,7 +18,7 @@
 import org.obiba.opal.web.BaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
 
-public abstract class AbstractCommandsResource extends BaseResource {
+public abstract class AbstractCommandsResource implements BaseResource {
 
   protected CommandJobService commandJobService;
 

opal-shell/src/main/java/org/obiba/opal/web/shell/ProjectCommandsResource.java

@@ -30,7 +30,7 @@
 @Scope("request")
 @Path("/project/{name}/commands")
 @SuppressWarnings("OverlyCoupledClass")
-public class ProjectCommandsResource extends BaseResource {
+public class ProjectCommandsResource implements BaseResource {
 
   private static final Logger log = LoggerFactory.getLogger(ProjectCommandsResource.class);
 

opal-shell/src/main/java/org/obiba/opal/web/shell/RClusterCommandsResource.java

@@ -29,7 +29,7 @@
 @Component
 @Scope("request")
 @Path("/service/r/cluster/{cname}/commands")
-public class RClusterCommandsResource extends BaseResource {
+public class RClusterCommandsResource implements BaseResource {
 
   private static final Logger log = LoggerFactory.getLogger(RClusterCommandsResource.class);