Docker test version, removed log statements

ga4gh · Sep 30, 2024 · ac3b9d6 · ac3b9d6
1 parent da8aae4
commit ac3b9d6
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Showing 4 changed files with 13 additions and 36 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,6 +1,6 @@
 name: Standard Tests
-#on: [push, pull_request, workflow_dispatch] #workflow_dispatch works only if its active in the main branch
-on: [pull_request, workflow_dispatch] #workflow_dispatch works only if its active in the main branch
+on: [push, pull_request, workflow_dispatch] #workflow_dispatch works only if its active in the main branch
+#on: [pull_request, workflow_dispatch] #workflow_dispatch works only if its active in the main branch
 jobs:
   Unit-Test:
     runs-on: ubuntu-latest

diff --git a/build.gradle b/build.gradle
@@ -38,7 +38,7 @@ configurations.all {
 
 archivesBaseName = 'ga4gh-starter-kit-drs'
 group 'org.ga4gh'
-version '0.3.2'
+version '0.3.3-test'
 
 repositories {
     // Use jcenter for resolving dependencies.

diff --git a/src/main/java/org/ga4gh/starterkit/drs/app/DrsServerSpringConfig.java b/src/main/java/org/ga4gh/starterkit/drs/app/DrsServerSpringConfig.java
@@ -1,8 +1,9 @@
 package org.ga4gh.starterkit.drs.app;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
+import org.apache.catalina.connector.Connector;
+import org.apache.commons.cli.Options;
+import org.ga4gh.starterkit.common.config.DatabaseProps;
+import org.ga4gh.starterkit.common.config.ServerProps;
 import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
 import org.ga4gh.starterkit.common.util.CliYamlConfigLoader;
 import org.ga4gh.starterkit.common.util.DeepObjectMerger;
@@ -11,19 +12,9 @@
 import org.ga4gh.starterkit.common.util.webserver.AdminEndpointsFilter;
 import org.ga4gh.starterkit.common.util.webserver.CorsFilterBuilder;
 import org.ga4gh.starterkit.common.util.webserver.TomcatMultiConnectorServletWebServerFactoryCustomizer;
-import org.apache.catalina.connector.Connector;
-import org.apache.commons.cli.Options;
-import org.ga4gh.starterkit.common.config.DatabaseProps;
-import org.ga4gh.starterkit.common.config.ServerProps;
 import org.ga4gh.starterkit.drs.config.DrsServiceProps;
 import org.ga4gh.starterkit.drs.exception.DrsCustomExceptionHandling;
-import org.ga4gh.starterkit.drs.model.AwsS3AccessObject;
-import org.ga4gh.starterkit.drs.model.Checksum;
-import org.ga4gh.starterkit.drs.model.DrsObject;
-import org.ga4gh.starterkit.drs.model.DrsServiceInfo;
-import org.ga4gh.starterkit.drs.model.FileAccessObject;
-import org.ga4gh.starterkit.drs.model.PassportBroker;
-import org.ga4gh.starterkit.drs.model.PassportVisa;
+import org.ga4gh.starterkit.drs.model.*;
 import org.ga4gh.starterkit.drs.utils.cache.AccessCache;
 import org.ga4gh.starterkit.drs.utils.hibernate.DrsHibernateUtil;
 import org.ga4gh.starterkit.drs.utils.passport.UserPassportMapVerifier;
@@ -45,6 +36,10 @@
 import org.springframework.web.context.annotation.RequestScope;
 import org.springframework.web.filter.CorsFilter;
 
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Contains Spring bean definitions that are to be loaded for the DRS service
  * under all deployment contexts (ie as part of both standalone and GA4GH
@@ -283,7 +278,7 @@ public AccessRequestHandler accessRequestHandler() {
         return new AccessRequestHandler();
     }
 
-    @Bean
+        @Bean
     @RequestScope
     public AuthInfoRequestHandler authInfoRequestHandler() {
         return new AuthInfoRequestHandler();

diff --git a/src/main/java/org/ga4gh/starterkit/drs/utils/hibernate/DrsHibernateUtil.java b/src/main/java/org/ga4gh/starterkit/drs/utils/hibernate/DrsHibernateUtil.java
@@ -270,52 +270,39 @@ private List<FileAccessObject> createAndReturnFileObjects(DrsObject drsObject, S
     public <I extends Serializable, T extends HibernateEntity<I>> List<DrsObject> performBulkInsertWithExecutor(
             List<DrsObject> objectList, int numThreads, int batchSize, List<DrsObject> failedRecords) throws Exception {
 
-        //loggingUtil.info("1");
         ExecutorService executor = Executors.newFixedThreadPool(numThreads);
         List<Future<List<DrsObject>>> futures = new ArrayList<>();
         int totalSize = objectList.size();
 
         try {
-            //loggingUtil.info("2");
             for (int i = 0; i < totalSize; i += batchSize) {
-                //loggingUtil.info("3");
                 List<DrsObject> batch = objectList.subList(i, Math.min(i + batchSize, totalSize));
 
                 futures.add(executor.submit(() -> {
-                    //loggingUtil.info("4");
                     List<DrsObject> failedBatch = new ArrayList<>();
 
                     Session session = null;
                     Transaction tx = null;
 
                     try {
-                        // Use reflection to access the private getSessionFactory() method
                         Method method = HibernateUtil.class.getDeclaredMethod("getSessionFactory");
                         method.setAccessible(true);  // Bypass private access
                         SessionFactory sessionFactory = (SessionFactory) method.invoke(hibernateUtil);
 
                         session = sessionFactory.openSession();
                         tx = session.beginTransaction();
-                        //loggingUtil.info("5");
-                        //loggingUtil.info("7");
                         for (DrsObject object : batch) {
                             try {
-                                //loggingUtil.info("8");
                                 session.save(object);
-                                //loggingUtil.info("9");
                             } catch (HibernateException ex) {
-                                //loggingUtil.info("10");
                                 loggingUtil.error("HibernateException occurred: " + ex);
                                 failedBatch.add(object);
                             }
                         }
-                        //loggingUtil.info("11");
                         session.flush();
                         session.clear();
                         tx.commit();
-                        //loggingUtil.info("12");
                     } catch (Exception ex) {
-                        //loggingUtil.info("13");
                         if (tx != null) {
                             tx.rollback();
                         }
@@ -327,21 +314,16 @@ public <I extends Serializable, T extends HibernateEntity<I>> List<DrsObject> pe
                             session.close();
                         }
                     }
-
-                    //loggingUtil.info("14");
                     return failedBatch;
                 }));
             }
-            //loggingUtil.info("15");
 
             List<DrsObject> allFailedRecords = new ArrayList<>();
             for (Future<List<DrsObject>> future : futures) {
                 allFailedRecords.addAll(future.get());
             }
-            //loggingUtil.info("16");
             return allFailedRecords;
         } finally {
-            //loggingUtil.info("17");
             executor.shutdown();
         }
     }