Error 500 when deleting a series

[Roberto Greiner]

Hi,

I have an atom 2.9.0 install, and when I try to delete a series, I got
an error 500 page.  Checking the NGinx error log, I got the following error:


2025/09/16 15:04:52 [error] 312872#312872: *4570 FastCGI sent in stderr:
"PHP message: PHP Fatal error:  Uncaught Error: Call to undefined method
Elastica\Index::deleteById() in
/usr/share/nginx/atom/plugins/arElasticSearchPlugin/lib/arElasticSearchMultiIndexWrapper.class.php:60
Stack trace:
#0
/usr/share/nginx/atom/plugins/arElasticSearchPlugin/lib/arElasticSearchPlugin.class.php(469):
arElasticSearchMultiIndexWrapper->deleteById()
#1 /usr/share/nginx/atom/lib/model/QubitInformationObject.php(373):
arElasticSearchPlugin->delete()
#2 /usr/share/nginx/atom/lib/model/QubitObject.php(605):
QubitInformationObject->delete()
#3
/usr/share/nginx/atom/apps/qubit/modules/informationobject/actions/deleteAction.class.php(43):
QubitObject->deleteFullHierarchy()
#4
/usr/share/nginx/atom/cache/qubit/prod/config/config_core_compile.yml.php(975):
InformationObjectDeleteAction->execute()
#5
/usr/share/nginx/atom/cache/qubit/prod/config/config_core_compile.yml.php(970):
sfExecutionFilter->executeAction()
#6
/usr/share/nginx/atom/cache/qubit/prod/config/config_core_compile.yml.php(956):
s" while reading response header from upstream, client: 2801:88:fd::50,
server: _, request: "POST
/index.php/dossie-de-pagamento-a-fornecedor-pessoa-fisica-ou-pessoa-juridica-v/informationobject/delete
HTTP/1.1", upstream: "fastcgi://unix:/run/php-fpm.atom.sock:", host:
"atom.fundunesp.org.br", referrer:
"https://atom.fundunesp.org.br/index.php/dossie-de-pagamento-a-fornecedor-pessoa-fisica-ou-pessoa-juridica-v/informationobject/delete"


I've restarted elasticsearch, but the error still happens. Any idea of
what could be happening or what else I should do to debug this?

Thank you,

Roberto Greiner

PS:

My setup:
Atom version 2.9.0
VM running in XCP-ng 8.2
Ubuntu 24.04.03
1TB storage for atom, 50GB for root
16GB RAM, 16GB swap

--
-----------------------------------------------------
Marcos Roberto Greiner

Os otimistas acham que estamos no melhor dos mundos
Os pessimistas tem medo de que isto seja verdade
James Branch Cabell
-----------------------------------------------------

[Dan Gillean]

Hi Roberto, 

Just to double-check a few things: 

Are you using PHP 8.x with AtoM 2.9? The error details mention Elastica, but I think it's actually a PHP error (looking for a missing method used by a PHP library that interacts with Elasticsearch). However, it's also worth checking the ES version - are you running Elasticsearch 6.x? You can try running php symfony search:status to check this and other information about your ES instance. See: 

• https://www.accesstomemory.org/docs/latest/admin-manual/maintenance/cli-tools/#check-the-status-of-your-elasticsearch-index

If that suggestion doesn't uncover anything, we can check the database schema version next. If you look in Admin > Settings at the full version number listed, is the second number after the dash 193 (i.e. is the full version number listed as 2.9.0 - 193, or something else)? This second number is the database schema version, which for the 2.9.0 release should be v193 (per the release notes on the wiki) - if this number doesn't match it often means that a step might have been missed during an upgrade (generally, either dropping and then recreating the database BEFORE loading your sqldump, or else running the sql upgrade task AFTER loading your data).

You can always check for data corruption as well - this can cause unexpected errors in some cases. There is now a command-line task in AtoM that will check for the most common forms of it: 

• https://www.accesstomemory.org/docs/latest/admin-manual/maintenance/cli-tools/#find-data-integrity-issues

And if that doesn't work....

Here is a general troubleshooting suggestions thread I made a while ago - perhaps something there will help. It's always a good idea to try some of AtoM's other common maintenance tasks as well, just in case (like restarting services, clearing the application cache, rebuilding the nested set, etc). See: 

• https://groups.google.com/g/ica-atom-users/c/wVrhL-TAaDY/m/Isu3jUY-AAAJ
• This thread also has more suggestions for diagnosing and troubleshooting ES issues: https://groups.google.com/g/ica-atom-users/c/tzvQRtkGMto/m/ezUvRyQHAQAJ

Good luck! 

Dan Gillean, MAS, MLIS
Business & User Experience Analyst
Artefactual Systems, Inc.
604-527-2056

he / him

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[Roberto Greiner]

About the PH version, I'm running PHP 8.3:
root@atom:/usr/share/nginx/atom# php --version
PHP 8.3.6 (cli) (built: Jul 14 2025 18:30:55) (NTS)
Copyright (c) The PHP Group
Zend Engine v4.3.6, Copyright (c) Zend Technologies
    with Zend OPcache v8.3.6, Copyright (c), by Zend Technologies

Elasticsearch status:

root@atom:/usr/share/nginx/atom# php symfony search:status
Elasticsearch server information:
 - Version: 6.8.23
 - Host: localhost
 - Port: 9200
 - Index name: atom

Document indexing status:
 - Accession: 0/0
 - Actor: 522/522
 - Aip: 99/99
 - Function object: 0/0
 - Information object: 10526/10526
 - Repository: 2/2
 - Term: 327/327

Also, it can't be an upgrade problem, because this is a new install, I did not upgrade from a previous version.

To view this discussion visit https://groups.google.com/d/msgid/ica-atom-users/CAC1FhZLRfmUY3MUXs6WUVAhbBKrGFt19%2BKffvyR98aqnXw5hyw%40mail.gmail.com.