Doctrine's criteria causing "a new entity was found" error during batch update all

[jimsafley]

Running a batch update all may throw the following exception:

2019-05-08T18:44:31+00:00 ERR (3): Doctrine\ORM\ORMInvalidArgumentException: A new entity was found through the relationship 'Omeka\Entity\Value#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@00000000161f4291000000005cd06bdd. To solve this issue: Either explicitly call EntityManager#persist() on this unknown entity or configure cascade persist  this association in the mapping for example @ManyToOne(..,cascade={"persist"}). If you cannot find out which entity causes the problem implement 'Omeka\Entity\Resource#__toString()' to get a clue. in /mnt/1TB/html/omeka-s/vendor/doctrine/orm/lib/Doctrine/ORM/ORMInvalidArgumentException.php:92
Stack trace:
#0 /mnt/1TB/html/omeka-s/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(852): Doctrine\ORM\ORMInvalidArgumentException::newEntityFoundThroughRelationship(Array, Object(Omeka\Entity\Item))
#1 /mnt/1TB/html/omeka-s/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(740): Doctrine\ORM\UnitOfWork->computeAssociationChanges(Array, Object(Omeka\Entity\Item))
#2 /mnt/1TB/html/omeka-s/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(802): Doctrine\ORM\UnitOfWork->computeChangeSet(Object(Doctrine\ORM\Mapping\ClassMetadata), Object(Omeka\Entity\Value))
#3 /mnt/1TB/html/omeka-s/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(340): Doctrine\ORM\UnitOfWork->computeChangeSets()
#4 /mnt/1TB/html/omeka-s/vendor/doctrine/orm/lib/Doctrine/ORM/EntityManager.php(356): Doctrine\ORM\UnitOfWork->commit(NULL)
#5 /mnt/1TB/html/omeka-s/application/src/Api/Adapter/AbstractEntityAdapter.php(406): Doctrine\ORM\EntityManager->flush()
#6 /mnt/1TB/html/omeka-s/application/src/Api/Manager.php(236): Omeka\Api\Adapter\AbstractEntityAdapter->batchUpdate(Object(Omeka\Api\Request))
#7 /mnt/1TB/html/omeka-s/application/src/Api/Manager.php(146): Omeka\Api\Manager->execute(Object(Omeka\Api\Request))
#8 /mnt/1TB/html/omeka-s/application/src/Job/BatchUpdate.php(30): Omeka\Api\Manager->batchUpdate('items', Array, Array, Array)
#9 /mnt/1TB/html/omeka-s/application/src/Job/DispatchStrategy/Synchronous.php(34): Omeka\Job\BatchUpdate->perform()
#10 /mnt/1TB/html/omeka-s/application/src/Job/Dispatcher.php(105): Omeka\Job\DispatchStrategy\Synchronous->send(Object(Omeka\Entity\Job))
#11 /mnt/1TB/html/omeka-s/application/data/scripts/perform-job.php(43): Omeka\Job\Dispatcher->send(Object(Omeka\Entity\Job), Object(Omeka\Job\DispatchStrategy\Synchronous))
#12 {main}

It seems that three conditions must be met to see this bug:

• The user clears a property value via the form's "Clear property values" control;
• The BatchUpdate job runs batchUpdate() more than once (more than one iteration);
• The values to be cleared do not exist (it works if the values exist)

Our use of Doctrine's criteria is likely the cause here. This patch fixes the problem by removing the offending criteria and filtering manually. Prior to this we attempted to detach the Value after it was used and, while that fixed the issue, it replicated resource titles somehow.

This observation may be helpful diagnosing this problem.

I have two items and I set the BatchUpdate job to iterate one item at a time. I add a dcterms:abstract value to item #1 and run "Clear property values" for dcterms:abstract. The job runs successfully, deleting the value. Then I add a dcterms:abstract value to item #2 and run "Clear property values" for dcterms:abstract. The job results in the "A new entity was found" error.

[jimsafley]

The recent upgrade to Doctrine 2.6 does not fix this bug.