ORMInvalidArgumentException on Numeric data types when importing via CSV, using date/time types

[C-Norton]

Fatal error: Uncaught Doctrine\ORM\ORMInvalidArgumentException: A new entity was found through the relationship 'NumericDataTypes\Entity\NumericDataTypesTimestamp#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@6325. 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 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/ORMInvalidArgumentException.php:97
Stack trace:
#0 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(3521): Doctrine\ORM\ORMInvalidArgumentException::newEntitiesFoundThroughRelationships()
#1 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(390): Doctrine\ORM\UnitOfWork->assertThatThereAreNoUnintentionallyNonPersistedAssociations()
#2 /var/www/html/vendor/doctrine/orm
in /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/ORMInvalidArgumentException.php on line 97

[C-Norton]

System information

Omeka S

4.1.1

8.1.34
fpm-fcgi
512M
512M
512M
Yes
calendar, cgi-fcgi, Core, ctype, curl, date, dom, exif, FFI, fileinfo, filter, ftp, gd, gettext, hash, iconv, intl, json, libxml, mbstring, mysqli, mysqlnd, openssl, pcre, PDO, pdo_mysql, Phar, posix, readline, Reflection, session, shmop, SimpleXML, sockets, sodium, SPL, standard, sysvmsg, sysvsem, sysvshm, tokenizer, xml, xmlreader, xmlwriter, xsl, Zend OPcache, zip, zlib

8.0.45-0ubuntu0.24.04.1
mysqlnd 8.1.34
ONLY_FULL_GROUP_BY, STRICT_TRANS_TABLES, NO_ZERO_IN_DATE, NO_ZERO_DATE, ERROR_FOR_DIVISION_BY_ZERO, NO_ENGINE_SUBSTITUTION

Linux 6.8.0-101-generic x86_64

Advanced Search (3.4.23), Analytics Snippet (3.4.4), Archive Repertory (3.15.16), Block Plus (3.4.42), Blocks Disposition (3.4.3), Bulk Edit (3.4.20), Bulk Export (3.4.36), CSSEditor (1.3.1), CSV Import (2.6.2), Common (3.4.76), Custom Ontology (3.4.6), Custom Vocab (2.0.1), Data Type RDF (3.4.7), Data Visualization (1.1.0), Faceted Browse (1.8.0), File Sideload (1.7.1), Generic module (3.4.43), Google Analytics (1.3), Hide Properties (1.3.1), Hierarchy (1.2.1), IIIF Server (3.6.24), Image Server (3.6.19), Item Carousel Block (1.3.0), Item Sets Tree (0.7.5), Log (3.4.31), Mapping (1.9.0), Metadata Browse (1.6.0), Mirador Viewer (3.4.8), Numeric Data Types (1.11.3), Omeka Classic Importer (1.5.1), Omeka S Item Importer (1.2.1), Page Blocks (1.2), Reference (3.4.57), Show More (1.4), Timeline (3.4.18), Transcript (4.1.1), Value Suggest (1.16.1), XML Viewer (3.4.10)
Extract Text (2.0.0)
XML TEI Viewer (1.0), XML TEI Viewer (1.0)
Wikidata (1.4.0)

9.9 GiB
71.5 GiB
1.9 GiB

/usr/bin/php7.4
/usr/bin/

[zerocrates]

There should be more lines to that error message, specifically more of those numbered lines. The full thing could be helpful to see.

[C-Norton]

Sorry, thought I got all of it

Doctrine\ORM\ORMInvalidArgumentException: Multiple non-persisted new entities were found through the given association graph:

* A new entity was found through the relationship 'NumericDataTypes\Entity\NumericDataTypesTimestamp#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@1852. 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.
* A new entity was found through the relationship 'NumericDataTypes\Entity\NumericDataTypesTimestamp#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@2027. 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.
* A new entity was found through the relationship 'NumericDataTypes\Entity\NumericDataTypesTimestamp#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@2104. 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.
* A new entity was found through the relationship 'NumericDataTypes\Entity\NumericDataTypesTimestamp#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@2119. 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.
* A new entity was found through the relationship 'NumericDataTypes\Entity\NumericDataTypesTimestamp#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@2053. 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.
* A new entity was found through the relationship 'NumericDataTypes\Entity\NumericDataTypesTimestamp#resource' that was not configured to cascade persist operations for entity: Omeka\Entity\Item@2145. 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 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/ORMInvalidArgumentException.php:100
Stack trace:
#0 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(3521): Doctrine\ORM\ORMInvalidArgumentException::newEntitiesFoundThroughRelationships()
#1 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(390): Doctrine\ORM\UnitOfWork->assertThatThereAreNoUnintentionallyNonPersistedAssociations()
#2 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/EntityManager.php(392): Doctrine\ORM\UnitOfWork->commit()
#3 /var/www/html/application/src/Api/Adapter/AbstractEntityAdapter.php(418): Doctrine\ORM\EntityManager->flush()
#4 /var/www/html/application/src/Api/Manager.php(227): Omeka\Api\Adapter\AbstractEntityAdapter->batchCreate()
#5 /var/www/html/application/src/Api/Manager.php(97): Omeka\Api\Manager->execute()
#6 /var/www/html/modules/CSVImport/src/Job/Import.php(364): Omeka\Api\Manager->batchCreate()
#7 /var/www/html/modules/CSVImport/src/Job/Import.php(266): CSVImport\Job\Import->create()
#8 /var/www/html/modules/CSVImport/src/Job/Import.php(205): CSVImport\Job\Import->processBatchData()
#9 /var/www/html/application/src/Job/DispatchStrategy/Synchronous.php(34): CSVImport\Job\Import->perform()
#10 /var/www/html/modules/Log/src/Job/Dispatcher.php(82): Omeka\Job\DispatchStrategy\Synchronous->send()
#11 /var/www/html/application/data/scripts/perform-job.php(66): Log\Job\Dispatcher->send()
#12 {main} 

[jimsafley]

This may be a conflict with another module. We have had issues with the Log module in a related problem, so I'd deactivate that one and run an import. If the problem persists, you'll need to deactivate all modules but NumericDataTypes and CSVImport. If that works, you'll need to reactivate them one-by-one to determine which one is at fault.

[C-Norton]

So I deactivated all the modules except Numeric Data Types, Data Type RDF (needed for this import job), and CSVImport, and got the following. I've checked with the stakeholder to see if I can share the actual import data; waiting to hear back.

I've also started the conversation of upgrading this server to 4.2 so that we can be on the latest version of NDT

Stack trace:
#0 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(3521): Doctrine\ORM\ORMInvalidArgumentException::newEntitiesFoundThroughRelationships()
#1 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/UnitOfWork.php(390): Doctrine\ORM\UnitOfWork->assertThatThereAreNoUnintentionallyNonPersistedAssociations()
#2 /var/www/html/vendor/doctrine/orm/lib/Doctrine/ORM/EntityManager.php(392): Doctrine\ORM\UnitOfWork->commit()
#3 /var/www/html/application/src/Api/Adapter/AbstractEntityAdapter.php(418): Doctrine\ORM\EntityManager->flush()
#4 /var/www/html/application/src/Api/Manager.php(227): Omeka\Api\Adapter\AbstractEntityAdapter->batchCreate()
#5 /var/www/html/application/src/Api/Manager.php(97): Omeka\Api\Manager->execute()
#6 /var/www/html/modules/CSVImport/src/Job/Import.php(364): Omeka\Api\Manager->batchCreate()
#7 /var/www/html/modules/CSVImport/src/Job/Import.php(266): CSVImport\Job\Import->create()
#8 /var/www/html/modules/CSVImport/src/Job/Import.php(205): CSVImport\Job\Import->processBatchData()
#9 /var/www/html/application/src/Job/DispatchStrategy/Synchronous.php(34): CSVImport\Job\Import->perform()
#10 /var/www/html/modules/Common/src/Job/Dispatcher.php(27): Omeka\Job\DispatchStrategy\Synchronous->send()
#11 /var/www/html/application/data/scripts/perform-job.php(66): Common\Job\Dispatcher->send()
#12 {main}

[jimsafley]

To completely rule out conflicts with other modules, could you deactivate DataTypeRdf and try the import again? I've looked at its code and found nothing obvious that would account for the error, but it would be nice to be certain.

A reminder to back up your database before upgrading to the latest versions of Omeka and NumericDataTypes.