fix mysql server gone away and dead lock on table

lib/Alchemy/Phrasea/Model/Repositories/WorkerRunningJobRepository.php

@@ -102,4 +102,12 @@ class WorkerRunningJobRepository extends EntityRepository
     {
         return parent::getEntityManager();
     }
+
+    public function reconnect()
+    {
+        if($this->_em->getConnection()->ping() === false) {
+            $this->_em->getConnection()->close();
+            $this->_em->getConnection()->connect();
+        }
+    }
 }

lib/Alchemy/Phrasea/WorkerManager/Subscriber/RecordSubscriber.php

@@ -101,6 +101,9 @@ class RecordSubscriber implements EventSubscriberInterface
 
         $repoWorker = $this->getRepoWorker();
         $em = $repoWorker->getEntityManager();
+        // check connection an re-connect if needed
+        $repoWorker->reconnect();
+
         $workerRunningJob = $repoWorker->findOneBy([
             'databoxId' => $event->getRecord()->getDataboxId(),
             'recordId'  => $event->getRecord()->getRecordId(),
@@ -108,6 +111,7 @@ class RecordSubscriber implements EventSubscriberInterface
             'workOn'    => $event->getSubdefName()
         ]);
 
+        if ($workerRunningJob) {
             $em->beginTransaction();
             try {
                 $em->remove($workerRunningJob);
@@ -116,6 +120,7 @@ class RecordSubscriber implements EventSubscriberInterface
             } catch (\Exception $e) {
                 $em->rollback();
             }
+        }
 
         $this->messagePublisher->publishMessage(
             $payload,
@@ -223,6 +228,9 @@ class RecordSubscriber implements EventSubscriberInterface
 
             $repoWorker = $this->getRepoWorker();
             $em = $repoWorker->getEntityManager();
+            // check connection an re-connect if needed
+            $repoWorker->reconnect();
+
             $workerRunningJob = $repoWorker->findOneBy([
                 'databoxId' => $event->getRecord()->getDataboxId(),
                 'recordId'  => $event->getRecord()->getRecordId(),
@@ -230,6 +238,7 @@ class RecordSubscriber implements EventSubscriberInterface
                 'workOn'    => $event->getSubdefName()
             ]);
 
+            if ($workerRunningJob) {
                 $em->beginTransaction();
                 try {
                     $em->remove($workerRunningJob);
@@ -238,6 +247,7 @@ class RecordSubscriber implements EventSubscriberInterface
                 } catch (\Exception $e) {
                     $em->rollback();
                 }
+            }
 
             $this->messagePublisher->publishMessage(
                 $payload,

lib/Alchemy/Phrasea/WorkerManager/Worker/SubdefCreationWorker.php

@@ -81,6 +81,7 @@ class SubdefCreationWorker implements WorkerInterface
 
                 // tell that a file is in used to create subdef
                 $em = $this->repoWorker->getEntityManager();
+                $this->repoWorker->reconnect();
                 $em->beginTransaction();
 
                 try {
@@ -108,13 +109,13 @@ class SubdefCreationWorker implements WorkerInterface
                 try {
                     $this->subdefGenerator->generateSubdefs($record, $wantedSubdef);
                 } catch (\Exception $e) {
-                    $em->beginTransaction();
                     try {
+                        $this->repoWorker->reconnect();
+                        $em->getConnection()->beginTransaction();
                         $em->remove($workerRunningJob);
                         $em->flush();
                         $em->commit();
                     } catch (\Exception $e) {
-                        $em->rollback();
                     }
                 }
 
@@ -170,7 +171,8 @@ class SubdefCreationWorker implements WorkerInterface
                 $this->indexer->flushQueue();
 
                 // tell that we have finished to work on this file
-                $em->beginTransaction();
+                $this->repoWorker->reconnect();
+                $em->getConnection()->beginTransaction();
                 try {
                     $workerRunningJob->setStatus(WorkerRunningJob::FINISHED);
                     $workerRunningJob->setFinished(new \DateTime('now'));
@@ -178,8 +180,18 @@ class SubdefCreationWorker implements WorkerInterface
                     $em->flush();
                     $em->commit();
                 } catch (\Exception $e) {
+                    try {
+                        $em->getConnection()->beginTransaction();
+                        $workerRunningJob->setStatus(WorkerRunningJob::FINISHED);
+                        $em->persist($workerRunningJob);
+                        $em->flush();
+                        $em->commit();
+                    } catch (\Exception $e) {
+                        $this->messagePublisher->pushLog("rollback on recordID :" . $workerRunningJob->getRecordId());
                         $em->rollback();
                     }
+
+                }
             }
         }
     }

lib/Alchemy/Phrasea/WorkerManager/Worker/WriteMetadatasWorker.php

@@ -82,6 +82,7 @@ class WriteMetadatasWorker implements WorkerInterface
 
             // tell that a file is in used to create subdef
             $em = $this->getEntityManager();
+            $this->repoWorker->reconnect();
             $em->beginTransaction();
 
             try {
@@ -245,6 +246,7 @@ class WriteMetadatasWorker implements WorkerInterface
 
 
             // tell that we have finished to work on this file
+            $this->repoWorker->reconnect();
             $em->beginTransaction();
             try {
                 $workerRunningJob->setStatus(WorkerRunningJob::FINISHED);