fix: declare synchronized entity classes on native writes DHIS2-21963

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/analytics/hibernate/HibernateCategoryDimensionStore.java

@@ -79,8 +79,7 @@ public int updateCatDimensionCategoryRefs(
         set categoryid = :targetCategoryId
         where cd.categoryid in :sourceCategoryIds
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
         .setParameter("targetCategoryId", targetCategoryId)
         .setParameter("sourceCategoryIds", sourceCategoryIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/category/hibernate/HibernateCategoryComboStore.java

@@ -37,6 +37,7 @@
 import java.util.List;
 import java.util.Set;
 import org.hibernate.LockOptions;
+import org.hisp.dhis.category.Category;
 import org.hisp.dhis.category.CategoryCombo;
 import org.hisp.dhis.category.CategoryComboStore;
 import org.hisp.dhis.common.DataDimensionType;
@@ -96,8 +97,11 @@ public int updateCatComboCategoryRefs(Set<Long> sourceCategoryIds, long targetCa
         set categoryid = :targetCategoryId
         where cc_c.categoryid in :sourceCategoryIds
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
+        // categorycombos_categories backs both the cached CategoryCombo.categories and
+        // Category.categoryCombos collections. Collection regions are keyed by the collection's
+        // element entity, so naming both entities is what reaches both regions.
+        .addSynchronizedEntityClass(Category.class)
         .setParameter("targetCategoryId", targetCategoryId)
         .setParameter("sourceCategoryIds", sourceCategoryIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/category/hibernate/HibernateCategoryStore.java

@@ -39,6 +39,7 @@
 import javax.annotation.Nonnull;
 import org.hibernate.LockOptions;
 import org.hisp.dhis.category.Category;
+import org.hisp.dhis.category.CategoryOption;
 import org.hisp.dhis.category.CategoryStore;
 import org.hisp.dhis.common.DataDimensionType;
 import org.hisp.dhis.common.hibernate.HibernateIdentifiableObjectStore;
@@ -118,8 +119,11 @@ public int removeCatOptionCategoryRefs(Set<Long> sourceCategoryIds) {
               delete from categories_categoryoptions c_co
               where c_co.categoryid in :sourceCategoryIds
               """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
+        // categories_categoryoptions is the Category.categoryOptions collection table. Collection
+        // regions are keyed by the collection's element entity, so CategoryOption is what reaches
+        // that region, not the owning Category.
+        .addSynchronizedEntityClass(CategoryOption.class)
         .setParameter("sourceCategoryIds", sourceCategoryIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))
         .executeUpdate();

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/dataapproval/hibernate/HibernateDataApprovalWorkflowStore.java

@@ -66,8 +66,7 @@ public int updateCategoryComboRefs(Set<Long> sourceCategoryComboIds, long target
         set categorycomboid = :targetCategoryComboId
         where categorycomboid in :sourceCategoryComboIds
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
         .setParameter("targetCategoryComboId", targetCategoryComboId)
         .setParameter("sourceCategoryComboIds", sourceCategoryComboIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/dataset/hibernate/HibernateCompleteDataSetRegistrationStore.java

@@ -135,8 +135,7 @@ public void deleteCompleteDataSetRegistration(
           AND c.sourceid = (SELECT organisationunitid FROM organisationunit ou WHERE ou.uid = :ou)
           AND c.attributeoptioncomboid = (SELECT categoryoptioncomboid FROM categoryoptioncombo aoc WHERE aoc.uid = :aoc)
         """;
-    entityManager
-        .createNativeQuery(sql)
+    nativeSynchronizedQuery(sql)
         .setParameter("ds", dataSet.getValue())
         .setParameter("pe", period.getIsoDate())
         .setParameter("ou", orgUnit.getValue())

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/dataset/hibernate/HibernateDataSetStore.java

@@ -171,8 +171,11 @@ public int updateDataSetElementCategoryComboRefs(
         set categorycomboid = :targetCategoryComboId
         where categorycomboid in :sourceCategoryComboIds
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
+        // datasetelement is DataSetElement's own table. It is also the DataSet.dataSetElements
+        // collection table, and since collection regions are keyed by the collection's element
+        // entity, naming DataSetElement reaches that cached collection too.
+        .addSynchronizedEntityClass(DataSetElement.class)
         .setParameter("targetCategoryComboId", targetCategoryComboId)
         .setParameter("sourceCategoryComboIds", sourceCategoryComboIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/datavalue/hibernate/HibernateDataValueChangelogStore.java

@@ -73,7 +73,7 @@ public void deleteByOrgUnit(@Nonnull UID orgUnit) {
       DELETE FROM datavalueaudit dva
       WHERE dva.organisationunitid = (SELECT ou.organisationunitid FROM organisationunit ou WHERE ou.uid = :ou)""";
 
-    entityManager.createNativeQuery(sql).setParameter("ou", orgUnit.getValue()).executeUpdate();
+    nativeSynchronizedQuery(sql).setParameter("ou", orgUnit.getValue()).executeUpdate();
   }
 
   @Override
@@ -83,7 +83,7 @@ public void deleteByDataElement(@Nonnull UID dataElement) {
       DELETE FROM datavalueaudit dva
       WHERE dva.dataelementid = (SELECT de.dataelementid FROM dataelement de WHERE de.uid = :de)""";
 
-    entityManager.createNativeQuery(sql).setParameter("de", dataElement.getValue()).executeUpdate();
+    nativeSynchronizedQuery(sql).setParameter("de", dataElement.getValue()).executeUpdate();
   }
 
   @Override
@@ -93,8 +93,7 @@ public void deleteByOptionCombo(@Nonnull UID categoryOptionCombo) {
         DELETE FROM datavalueaudit dva
         WHERE dva.categoryoptioncomboid = (SELECT categoryoptioncomboid FROM categoryoptioncombo WHERE uid = :coc)
            OR dva.attributeoptioncomboid = (SELECT categoryoptioncomboid FROM categoryoptioncombo WHERE uid = :coc);""";
-    entityManager
-        .createNativeQuery(sql)
+    nativeSynchronizedQuery(sql)
         .setParameter("coc", categoryOptionCombo.getValue())
         .executeUpdate();
   }
@@ -258,14 +257,16 @@ IF NOT EXISTS (
           END IF;
       END;
       $$""";
-    getSession().createNativeQuery(sql).executeUpdate();
+    // DDL, not entity persistence, so it skips Hibernate and its cache invalidation
+    jdbcTemplate.execute(sql);
   }
 
   @Override
   public void disableAudit() {
     String sql =
         """
       DROP TRIGGER IF EXISTS trg_datavalue_audit ON datavalue""";
-    getSession().createNativeQuery(sql).executeUpdate();
+    // DDL, not entity persistence, so it skips Hibernate and its cache invalidation
+    jdbcTemplate.execute(sql);
   }
 }

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/datavalue/hibernate/HibernateDataValueTrimStore.java

@@ -87,8 +87,7 @@ public int updateDeletedIfNotZeroIsSignificant() {
           AND de.zeroissignificant = false
           AND dv.dataelementid = de.dataelementid
           AND (dv.value IS NULL OR dv.value = '')""";
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(1000))
         .executeUpdate();
   }

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/period/hibernate/HibernatePeriodStore.java

@@ -124,8 +124,7 @@ INSERT INTO period (periodid, periodtypeid, startdate, enddate, iso)
               if (pk != null) {
                 return pk;
               }
-              session
-                  .createNativeQuery(sql2)
+              nativeSynchronizedQuery(session, sql2)
                   .setParameter("type", period.getPeriodType().getName())
                   .setParameter("start", period.getStartDate())
                   .setParameter("end", period.getEndDate())
@@ -144,8 +143,7 @@ INSERT INTO period (periodid, periodtypeid, startdate, enddate, iso)
   public void delete(@Nonnull Period period) {
     String isoDate = period.getIsoDate();
     int deleted =
-        getSession()
-            .createNativeQuery("DELETE FROM period where iso = :iso")
+        nativeSynchronizedQuery("DELETE FROM period where iso = :iso")
             .setParameter("iso", isoDate)
             .executeUpdate();
     if (deleted > 0) {
@@ -261,7 +259,12 @@ INSERT INTO periodtype (periodtypeid, name)
               if (pk != null) {
                 return pk;
               }
-              session.createNativeQuery(sql2).setParameter("name", name).executeUpdate();
+              session
+                  .createNativeQuery(sql2)
+                  // PeriodType, not the store's own Period
+                  .addSynchronizedEntityClass(PeriodType.class)
+                  .setParameter("name", name)
+                  .executeUpdate();
               return session.createNativeQuery("SELECT lastval()").uniqueResult();
             });
     if (id instanceof Number n) {
@@ -286,6 +289,7 @@ public void updatePeriodType(PeriodType periodType) {
         session ->
             session
                 .createNativeQuery(sql)
+                .addSynchronizedEntityClass(PeriodType.class)
                 .setParameter("name", name)
                 .setParameter("label", label)
                 .executeUpdate());

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/program/hibernate/HibernateProgramIndicatorStore.java

@@ -118,8 +118,7 @@ WHEN attributecomboid IN (:sourceCategoryComboIds)
             categorycomboid IN (:sourceCategoryComboIds)
             OR attributecomboid IN (:sourceCategoryComboIds);
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
         .setParameter("targetCategoryComboId", targetCategoryComboId)
         .setParameter("sourceCategoryComboIds", sourceCategoryComboIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/scheduling/HibernateJobConfigurationStore.java

@@ -50,6 +50,7 @@
 import org.hibernate.query.NativeQuery;
 import org.hisp.dhis.common.UID;
 import org.hisp.dhis.common.hibernate.HibernateIdentifiableObjectStore;
+import org.hisp.dhis.fileresource.FileResource;
 import org.hisp.dhis.hibernate.jsonb.type.JsonJobParametersType;
 import org.hisp.dhis.security.acl.AclService;
 import org.springframework.context.ApplicationEventPublisher;
@@ -385,7 +386,10 @@ public boolean tryExecuteNow(@Nonnull UID jobId) {
         and (schedulingtype != 'ONCE_ASAP' or lastfinished is null)
         """;
     return runWriteInStatelessSession(
-            q -> q.createNativeQuery(sql).setParameter("id", jobId.getValue()).executeUpdate())
+            q ->
+                nativeSynchronizedQuery(q, sql)
+                    .setParameter("id", jobId.getValue())
+                    .executeUpdate())
         > 0;
   }
 
@@ -413,7 +417,10 @@ and not exists (
         )
         """;
     return runWriteInStatelessSession(
-            q -> q.createNativeQuery(sql).setParameter("id", jobId.getValue()).executeUpdate())
+            q ->
+                nativeSynchronizedQuery(q, sql)
+                    .setParameter("id", jobId.getValue())
+                    .executeUpdate())
         > 0;
   }
 
@@ -444,7 +451,10 @@ public boolean tryCancel(@Nonnull UID jobId) {
           )
         """;
     return runWriteInStatelessSession(
-            q -> q.createNativeQuery(sql).setParameter("id", jobId.getValue()).executeUpdate())
+            q ->
+                nativeSynchronizedQuery(q, sql)
+                    .setParameter("id", jobId.getValue())
+                    .executeUpdate())
         > 0;
   }
 
@@ -475,7 +485,7 @@ public boolean tryFinish(@Nonnull UID jobId, JobStatus status) {
         """;
     return runWriteInStatelessSession(
             q ->
-                q.createNativeQuery(sql)
+                nativeSynchronizedQuery(q, sql)
                     .setParameter("id", jobId.getValue())
                     .setParameter("status", status.name())
                     .executeUpdate())
@@ -503,7 +513,7 @@ public boolean trySkip(@Nonnull String queue) {
           or lastexecuted < (select lastexecuted from jobconfiguration where queuename = :queue and queueposition = 0 limit 1))
         """;
     return runWriteInStatelessSession(
-            q -> q.createNativeQuery(sql).setParameter("queue", queue).executeUpdate())
+            q -> nativeSynchronizedQuery(q, sql).setParameter("queue", queue).executeUpdate())
         > 0;
   }
 
@@ -521,7 +531,7 @@ public void updateProgress(
         """;
     runWriteInStatelessSession(
         q ->
-            q.createNativeQuery(sql)
+            nativeSynchronizedQuery(q, sql)
                 .setParameter("id", jobId.getValue())
                 .setParameter("json", progressJson)
                 .setParameter("errors", errorCodes)
@@ -539,7 +549,7 @@ public int updateDisabledJobs() {
         where jobstatus = 'SCHEDULED'
         and enabled = false
         """;
-    return runWriteInStatelessSession(q -> q.createNativeQuery(sql).executeUpdate());
+    return runWriteInStatelessSession(q -> nativeSynchronizedQuery(q, sql).executeUpdate());
   }
 
   @Override
@@ -557,7 +567,7 @@ and now() > lastfinished + :ttl * interval '1 minute'
     int deletedCount =
         runWriteInStatelessSession(
             q ->
-                q.createNativeQuery(sql)
+                nativeSynchronizedQuery(q, sql)
                     .setLockOptions(new LockOptions(LockMode.PESSIMISTIC_WRITE).setTimeOut(2000))
                     .setParameter("ttl", max(1, ttlMinutes))
                     .executeUpdate());
@@ -575,6 +585,7 @@ and uid not in (select uid from jobconfiguration where schedulingtype = 'ONCE_AS
     runWriteInStatelessSession(
         q ->
             q.createNativeQuery(sql2)
+                .addSynchronizedEntityClass(FileResource.class)
                 .setLockOptions(new LockOptions(LockMode.PESSIMISTIC_WRITE).setTimeOut(2000))
                 .executeUpdate());
     return deletedCount;
@@ -606,7 +617,7 @@ and now() > lastalive + :timeout * interval '1 minute'
         """;
     return runWriteInStatelessSession(
         q ->
-            q.createNativeQuery(sql)
+            nativeSynchronizedQuery(q, sql)
                 .setParameter("timeout", max(1, timeoutMinutes))
                 .executeUpdate());
   }
@@ -637,7 +648,10 @@ public boolean tryRevertNow(@Nonnull UID jobId) {
         and now() > jobconfiguration.lastalive + interval '1 minute'
       """;
     return runWriteInStatelessSession(
-            q -> q.createNativeQuery(sql).setParameter("id", jobId.getValue()).executeUpdate())
+            q ->
+                nativeSynchronizedQuery(q, sql)
+                    .setParameter("id", jobId.getValue())
+                    .executeUpdate())
         > 0;
   }
 

dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/user/hibernate/HibernateUserStore.java

@@ -63,6 +63,7 @@
 import org.hibernate.query.NativeQuery;
 import org.hibernate.query.Query;
 import org.hisp.dhis.cache.QueryCacheManager;
+import org.hisp.dhis.category.Category;
 import org.hisp.dhis.common.IdentifiableObjectUtils;
 import org.hisp.dhis.common.Locale;
 import org.hisp.dhis.common.UID;
@@ -742,8 +743,11 @@ WHERE dataelementcategoryid IN (:sourceCategoryIds)
             ORDER BY userid, dataelementcategoryid
         )
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
+        // users_catdimensionconstraints is the User.catDimensionConstraints collection table.
+        // Collection regions are keyed by the collection's element entity, so Category is what
+        // reaches that region, not the owning User.
+        .addSynchronizedEntityClass(Category.class)
         .setParameter("targetCategoryId", targetCategoryId)
         .setParameter("sourceCategoryIds", sourceCategoryIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))
@@ -759,8 +763,9 @@ public int deleteRemainingCatDimensionConstraints(Set<Long> sourceCategoryIds) {
         DELETE FROM users_catdimensionconstraints
         WHERE dataelementcategoryid IN (:sourceCategoryIds)
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
+        // see updateCatDimensionConstraintsCategoryRefs
+        .addSynchronizedEntityClass(Category.class)
         .setParameter("sourceCategoryIds", sourceCategoryIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))
         .executeUpdate();
@@ -780,8 +785,9 @@ AND userid IN (
             WHERE dataelementcategoryid = :targetCategoryId
         )
         """;
-    return getSession()
-        .createNativeQuery(sql)
+    return nativeSynchronizedQuery(sql)
+        // see updateCatDimensionConstraintsCategoryRefs
+        .addSynchronizedEntityClass(Category.class)
         .setParameter("targetCategoryId", targetCategoryId)
         .setParameter("sourceCategoryIds", sourceCategoryIds)
         .setLockOptions(new LockOptions(PESSIMISTIC_WRITE).setTimeOut(5000))