Upgrade/jnj fixes

src/main/java/org/ohdsi/webapi/Constants.java

@@ -22,18 +22,18 @@ public interface Constants {
   Float DEFAULT_THRESHOLD = 0.01f;
 
   ImmutableList<String> ALLOWED_JOB_EXECUTION_PARAMETERS = ImmutableList.of(
-          "jobName",
-          "jobAuthor",
-          "cohort_definition_id",
+          Params.JOB_NAME,
+          Params.JOB_AUTHOR,
+          Params.COHORT_DEFINITION_ID,
           "cohortId",
           "cohortDefinitionIds",
-          "source_id",
-          "source_key",
+          Params.SOURCE_ID,
+          Params.SOURCE_KEY,
           "scriptType",
-          "analysis_id",
+          Params.ANALYSIS_ID,
           "concept_set_id",
-          "estimation_analysis_id",
-          "prediction_analysis_id"
+          Params.PATHWAY_ANALYSIS_ID,
+          Params.COHORT_CHARACTERIZATION_ID
   );
 
   String SESSION_ID = "sid";

src/main/java/org/ohdsi/webapi/JobConfig.java

@@ -5,28 +5,25 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.ohdsi.webapi.audittrail.listeners.AuditTrailJobListener;
-import org.ohdsi.webapi.common.generation.AutoremoveJobListener;
-import org.ohdsi.webapi.common.generation.CancelJobListener;
+import org.ohdsi.webapi.job.JdbcSearchableJobExecutionDao;
 import org.ohdsi.webapi.job.JobTemplate;
+import org.ohdsi.webapi.job.SearchableJobExecutionDao;
 import org.ohdsi.webapi.security.authz.AuthorizationService;
-import org.ohdsi.webapi.service.JobService;
 import org.ohdsi.webapi.util.ManagedThreadPoolTaskExecutor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.ohdsi.webapi.batch.JdbcSearchableJobExecutionDao;
-import org.ohdsi.webapi.batch.SearchableJobExecutionDao;
 import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.explore.JobExplorer;
+import org.springframework.batch.core.explore.support.JobExplorerFactoryBean;
 import org.springframework.batch.core.launch.JobLauncher;
 import org.springframework.batch.core.launch.support.TaskExecutorJobLauncher;
 import org.springframework.batch.core.repository.JobRepository;
 import org.springframework.batch.core.repository.support.JobRepositoryFactoryBean;
-import org.springframework.jdbc.datasource.DataSourceTransactionManager;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.DependsOn;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.context.annotation.Primary;
 import org.springframework.core.task.TaskExecutor;
@@ -37,6 +34,12 @@
 
 /**
  * Spring Batch 5.x configuration for Java 21 / Spring Boot 3.2
+ *
+ * IMPORTANT: Spring Batch and JPA share the same DataSource, so they MUST use
+ * the same PlatformTransactionManager (the primary JpaTransactionManager).
+ * Using a separate DataSourceTransactionManager for batch would cause
+ * "Already value [ConnectionHolder] bound to thread" errors whenever a
+ * batch step touches JPA repositories.
  */
 @Configuration
 @Lazy(false)
@@ -77,25 +80,32 @@ private void init() {
         log.info("Batch table prefix: {}", this.tablePrefix);
     }
 
-    // Spring Batch transaction manager (separate from JPA)
-    @Bean("batchTransactionManager")
-    public DataSourceTransactionManager batchTransactionManager(DataSource dataSource) {
-        return new DataSourceTransactionManager(dataSource);
-    }
-
     // JobRepository configuration for Spring Batch 5
+    // Uses the primary JpaTransactionManager (shared DataSource rule)
     @Bean
     public JobRepository jobRepository(DataSource dataSource, 
-                                       @Qualifier("batchTransactionManager") DataSourceTransactionManager batchTransactionManager) throws Exception {
+                                       PlatformTransactionManager transactionManager) throws Exception {
         JobRepositoryFactoryBean factory = new JobRepositoryFactoryBean();
         factory.setDataSource(dataSource);
-        factory.setTransactionManager(batchTransactionManager);
+        factory.setTransactionManager(transactionManager);
         factory.setTablePrefix(this.tablePrefix);
         factory.setIsolationLevelForCreate(isolationLevelForCreate);
         factory.afterPropertiesSet();
         return factory.getObject();
     }
 
+    // JobExplorer configuration for Spring Batch 5 - CRITICAL: Must use same table prefix as JobRepository
+    @Bean
+    public JobExplorer jobExplorer(DataSource dataSource,
+                                   PlatformTransactionManager transactionManager) throws Exception {
+        JobExplorerFactoryBean factory = new JobExplorerFactoryBean();
+        factory.setDataSource(dataSource);
+        factory.setTransactionManager(transactionManager);
+        factory.setTablePrefix(this.tablePrefix);
+        factory.afterPropertiesSet();
+        return factory.getObject();
+    }
+
     @Bean
     public TaskExecutor batchTaskExecutor() {
         ManagedThreadPoolTaskExecutor taskExecutor = new ManagedThreadPoolTaskExecutor();
@@ -127,33 +137,34 @@ public JobLauncher asyncJobLauncher(JobRepository jobRepository, @Qualifier("bat
 
     @Bean
     public JobTemplate jobTemplate(JobLauncher jobLauncher, JobRepository jobRepository, AuthorizationService authorizationService,
-                                   @Qualifier("batchTransactionManager") PlatformTransactionManager batchTransactionManager) {
-        return new JobTemplate(jobLauncher, jobRepository, authorizationService, batchTransactionManager);
+                                   PlatformTransactionManager transactionManager) {
+        return new JobTemplate(jobLauncher, jobRepository, authorizationService, transactionManager);
     }
 
     /**
-     * TransactionTemplate for batch tasklets using batchTransactionManager.
-     * This ensures tasklets use the same transaction manager as the Spring Batch step,
-     * preventing conflicts when creating nested transactions.
+     * TransactionTemplate for batch tasklets.
+     * Uses the same JpaTransactionManager as the step transaction,
+     * so nested PROPAGATION_REQUIRED calls participate in the existing transaction.
      */
     @Bean("batchTransactionTemplate")
     public TransactionTemplate batchTransactionTemplate(
-            @Qualifier("batchTransactionManager") PlatformTransactionManager batchTransactionManager) {
+            PlatformTransactionManager transactionManager) {
         TransactionTemplate template = new TransactionTemplate();
-        template.setTransactionManager(batchTransactionManager);
+        template.setTransactionManager(transactionManager);
         return template;
     }
 
     /**
      * TransactionTemplate with PROPAGATION_REQUIRES_NEW for batch tasklets.
-     * Used when tasklets need to commit data immediately (e.g., cache updates)
-     * independent of the step's transaction.
+     * Used when tasklets need to commit data immediately (e.g., status updates)
+     * independent of the step's transaction. JpaTransactionManager properly
+     * suspends the outer transaction (including its ConnectionHolder).
      */
     @Bean("batchTransactionTemplateRequiresNew")
     public TransactionTemplate batchTransactionTemplateRequiresNew(
-            @Qualifier("batchTransactionManager") PlatformTransactionManager batchTransactionManager) {
+            PlatformTransactionManager transactionManager) {
         TransactionTemplate template = new TransactionTemplate();
-        template.setTransactionManager(batchTransactionManager);
+        template.setTransactionManager(transactionManager);
         template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
         return template;
     }

src/main/java/org/ohdsi/webapi/JobInvalidator.java

@@ -1,8 +1,8 @@
 package org.ohdsi.webapi;
 
+import org.ohdsi.webapi.job.SearchableJobExecutionDao;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.ohdsi.webapi.batch.SearchableJobExecutionDao;
 import org.springframework.batch.core.BatchStatus;
 import org.springframework.batch.core.ExitStatus;
 import org.springframework.batch.core.JobExecution;

src/main/java/org/ohdsi/webapi/check/checker/cohort/CohortChecker.java

@@ -1,21 +1,13 @@
 package org.ohdsi.webapi.check.checker.cohort;
 
-import org.ohdsi.analysis.estimation.comparativecohortanalysis.design.CohortMethodAnalysis;
-import org.ohdsi.analysis.estimation.comparativecohortanalysis.design.ComparativeCohortAnalysis;
-import org.ohdsi.webapi.check.builder.DuplicateValidatorBuilder;
-import org.ohdsi.webapi.check.builder.IterableForEachValidatorBuilder;
-import org.ohdsi.webapi.check.builder.NotNullNotEmptyValidatorBuilder;
 import org.ohdsi.webapi.check.builder.ValidatorGroupBuilder;
 import org.ohdsi.webapi.check.checker.BaseChecker;
 import org.ohdsi.webapi.check.checker.tag.helper.TagHelper;
 import org.ohdsi.webapi.cohortdefinition.dto.CohortDTO;
-import org.ohdsi.webapi.service.dto.CommonEntityExtDTO;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 import jakarta.annotation.PostConstruct;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.List;
 
 @Component