Fix deleteOrganismFeatures: use REQUIRES_NEW propagation in service methods

The controller class has @transactional(readOnly=true). Service methods with
default PROPAGATION_REQUIRED join the read-only transaction, making delete()
calls silently ignored. Using REQUIRES_NEW forces a writable transaction.

Also:
- Use preferenceService.getOrganismForTokenInDB for consistent organism lookup
- Add debug logging to trace deletion flow
- Fix response.status ordering (before render) in error handler

Co-Authored-By: Claude Opus 4.6 <[email protected]>

Author: cmdcolin

grails-app/controllers/org/bbop/apollo/OrganismController.groovy

@@ -167,9 +167,9 @@ class OrganismController {
     render responseObject as JSON
   }
 
-  @Transactional
   def deleteOrganismFeatures() {
     JSONObject organismJson = permissionService.handleInput(request, params)
+    log.info "deleteOrganismFeatures called with organism: ${organismJson.organism}"
     try {
       permissionService.hasPermissions(organismJson,PermissionEnum.READ)
       if ( !permissionService.hasGlobalPermissions(organismJson, PermissionEnum.ADMINISTRATE)
@@ -188,13 +188,15 @@ class OrganismController {
         throw new Exception("Can not find organism for ${organismJson.organism} to remove features of")
       }
 
+      log.info "Found organism: ${organism.commonName} (id=${organism.id})"
+
       if (organismJson.sequences) {
         List<String> sequenceNames = organismJson.sequences.toString().split(",")
         List<Sequence> sequences = Sequence.findAllByOrganismAndNameInList(organism, sequenceNames)
-        int deleted = organismService.deleteAllFeaturesForSequences(sequences)
+        def deleted = organismService.deleteAllFeaturesForSequences(sequences)
         log.info "Deleted ${deleted} features for sequences ${sequenceNames} of organism ${organism.commonName}"
       } else {
-        int deleted = organismService.deleteAllFeaturesForOrganism(organism)
+        def deleted = organismService.deleteAllFeaturesForOrganism(organism)
         log.info "Deleted ${deleted} features for organism ${organism.commonName}"
       }
 

grails-app/services/org/bbop/apollo/OrganismService.groovy

@@ -2,6 +2,7 @@ package org.bbop.apollo
 
 import grails.gorm.transactions.Transactional
 import groovy.io.FileType
+import org.springframework.transaction.annotation.Propagation
 import org.bbop.apollo.gwt.shared.FeatureStringEnum
 import org.bbop.apollo.sequence.SequenceTranslationHandler
 import org.bbop.apollo.sequence.TranslationTable
@@ -42,6 +43,7 @@ class OrganismService {
         return null
 
     }
+    @Transactional(propagation = Propagation.REQUIRES_NEW)
     def deleteAllFeaturesForSequences(List<Sequence> sequences) {
 
         int totalDeleted = 0
@@ -98,6 +100,7 @@ class OrganismService {
         return totalDeleted
 
     }
+    @Transactional(propagation = Propagation.REQUIRES_NEW)
     def deleteAllFeaturesForOrganism(Organism organism) {
 
         int totalDeleted = 0