PHP message: Unsupported taxonomy

[Juan Cruz Amusategui]

Hi,

I'm currently running Atom 2.6.2 - 184. Whenever I go to Manage > Taxonomies and click in "Genre" I get a "500 Internal Server Error" page.

This is what i find in the error log (var/log/nginx/error.log):

FastCGI sent in stderr: "PHP message: Unsupported taxonomy" while reading response header from upstream ... request: "GET /index.php/genre HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:"

I have been able to open the "Genre" page before and add new terms there. In fact those terms work when I click on them. But at some point I lost the ability to add new terms under "Genre" because of this 500 error.

Any ideas how to troubleshoot this ?

Regards,

Juan

[José Raddaoui]

Hi Juan,

This seems like an integrity issue in your database or search index. The error is thrown here, where we look for each term taxonomy's id in a set of expected ids. My impression is that somehow, one of the terms belongs to the genre taxonomy in the search index but it doesn't in the database. A couple of suggestions to troubleshoot this further:

• Check if the issue is only happening for some of the terms with the page and limit parameters (on your site): https://demo.accesstomemory.org/genre?page=1&limit=1
• Try to re-populate the search index from the database: https://www.accesstomemory.org/en/docs/2.6/admin-manual/maintenance/populate-search-index/#maintenance-populate-search-index

Best,

Radda.

[Juan Cruz]

Hi, José.

Thank you very much for your reply. I've re-populated the search index as you suggested. I can access the Genre page now but search isn't working.

When I run "php symfony search:populate --update" I get a long list of errors like this:

Error in one or more bulk request actions:                                                          
  index: /atom/QubitTerm/111 caused type[QubitInformationObject] missing [index: atom]                
  index: /atom/QubitTerm/113 caused type[QubitInformationObject] missing [index: atom]                
  index: /atom/QubitTerm/114 caused type[QubitInformationObject] missing [index: atom]                
  index: /atom/QubitTerm/115 caused type[QubitInformationObject] missing [index: atom]      

...

This is the output for "php symfony search:status":

Elasticsearch server information:
 - Version: 5.6.16
 - Host: localhost
 - Port: 9200
 - Index name: atom

Document indexing status:
 - Accession: 0/0
 - Actor: 5/5
 - Aip: 0/0
 - Function object: 0/0
 - Information object: 0/424
 - Repository: 1/1
 - Term: 430/430

Regards,

Juan

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[José Raddaoui]

Hi again Juan,

Try it without the '--update' flag, it looks like the index needs to be fully recreated.

Best,

Radda.

[Juan Cruz]

Thank you José.

I tried without the flag before but I get this:

Defining mapping QubitAip...
Defining mapping QubitTerm...
Defining mapping QubitActor...
Defining mapping QubitAccession...
Defining mapping QubitRepository...
Defining mapping QubitFunctionObject...
Defining mapping QubitInformationObject...

                                                                 
  Limit of total fields [3000] in index [atom] has been exceeded  
                                                                 

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[José Raddaoui]

Hi Juan,

That's a bit unexpected for me, maybe you have multiple languages enabled (which adds extra fields to the index) in your instance, but I never saw it going over that limit. If you are not using those languages in your site, I'd try to remove them from settings/languages to see if that solves the issue. If that's not an option, you can change that limit through configuration:

https://github.com/artefactual/atom/blob/qa/2.x/plugins/arElasticSearchPlugin/config/search.yml#L32

You'll probably have a file overwriting this configuration in your AtoM folder already, in 'config/search.yaml', the format to overwrite just that property could be something like:

all:

  index:
    configuration:
      index.mapping.total_fields.limit: 10000

Make sure to clear the application cache before running the re-indexing task with:

php symfony cc

Best,

Radda.

[Juan Cruz]

José,

I removed all languages in settings except for english and spanish.

Cleared cache with "php symfony cc".

When I run "php symfony search:populate" I get:

Defining mapping QubitAip...

  name cannot be empty string            
                                         

If I run "php symfony search:status" it returns:

Elasticsearch server information:
 - Version: 5.6.16
 - Host: localhost
 - Port: 9200
 - Index name: atom

Document indexing status:
 - Accession: 0/0

 - Actor: 0/5

 - Aip: 0/0
 - Function object: 0/0
 - Information object: 0/424

 - Repository: 0/1
 - Term: 0/430

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[José Raddaoui]

Hi again Juan,

That issue actually rings a bell, it's possible that there is an empty language row in the settings. Check the following Redmine ticket (that was fixed in 2.6.3) and forum thread:

https://projects.artefactual.com/issues/13465

https://groups.google.com/g/ica-atom-users/c/A--wCn1eMAA/m/R2isOByIAAAJ

Best,

Radda.

[Juan Cruz]

Thank you very much José, everything seems to be working again.

Regards,

Juan

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