Error in one or more bulk request actions: index: /atom/QubitInformationObject/188659 caused StrictDynamicMappingException

[Sally-Anne Shearn]

Hi everyone,

My colleague is having some odd problems with an archival description she manually input into our AtoM 2.4 and published.  It keeps appearing and disappearing, sometimes we can find it and other times, even when you type in the exact url, AtoM tells you the page does not exist (regardless of whether you are signed in or not). She has tried exporting the XML, deleting the original, and then reimporting it, and got the following error message.

Exception: Error in one or more bulk request actions: index: /atom/QubitInformationObject/188659 caused StrictDynamicMappingException[mapping set to strict, dynamic introduction of [archivistsNotes] within [QubitInformationObject] is not allowed]

We then discovered AtoM hadn't deleted the original either, the command wasn't even in the active jobs list.  As far as any of us can see the entry looks normal, we tried deleting the archivists notes field (which only has one line of free text in it) and exporting/importing but got the same error message.

When we can see the entry, the authority record is correctly displayed under 'Creator' and when you click on it you are taken through to the linked authority record.  However when you have the authority record open, the archival description does not appear as a linked file.

We're a little baffled as to how we've ended up with a phantom archival description that appears and disappears at random.  Any advice would be appreciated!

Sally

[Dan Gillean]

Hi Sally, 

Some possibilities for you to explore: 

First, what setting do you currently have for the treeview sorting? Are you using the sidebar treeview, or the full-width treeview? There are some known issues with the identifier and identifier-title sort (especially when some descriptions are missing either a title or an identifier) that have caused weird disappearing record behavior in the past. I would strongly recommend setting the treeview sort to "Manual" if it is not already. 

Additionally: was the data in the Archivist's note field cut and pasted from somewhere, such as a Microsoft Word document? It's possible that you've pasted in non-UTF-8 characters that are causing issues when AtoM tries to save the record. Check especially for those curly "smart quote" apostrophes and quotation marks that Microsoft loves to use, and replace them by deleting and typing them in manually. 

Regardless of what you find with the above questions, in general the first thing I'd suggest is that you try running some basic maintenance tasks to see if it can resolve the issue. The following command-line tasks should be run from the root AtoM installation directory - if you have followed our recommended installation instructions, this is typically /usr/share/nginx/atom. If you are not the person responsible for installing and maintaining your AtoM instance, feel free to pass this on to the technical support person. 

First, let's make sure that the nested set (which helps maintain hierarchical relations) isn't corrupted, and that all your descriptions have a proper slug value. Run: 

• php symfony propel:build-nested-set
• php symfony propel:generate-slugs

Now we will clear the application cache: 

• php symfony cc

PHP-FPM also has its own cache, so we'll restart it. The command will depend on the operating system and PHP version you have. Here are the most common options: 

• Ubuntu 14.04 with PHP 5.x: sudo service php5-fpm restart
• Ubuntu 16.04 with PHP 7.0: sudo systemctl restart php7.0-fpm
• Ubuntu 18.04 with PHP 7.2: sudo systemctl restart php7.2-fpm

If you are using Memcached, I would also restart that. If you're not sure, you can try running these anyway - it won't mess up anything if it's not installed, the command just won't work: 

• Ubuntu 14.04: sudo service memcached restart
• Ubuntu 16.04 and 18.04: sudo systemctl restart memcached

Finally, let's reindex your records: 

• php symfony search:populate

Now, when you re-test, make sure you also either clear your web browser cache, and/or test in an incognito/private browser window, where the web browser cache is typically disabled by default. We want to make sure we are seeing an updated version of the page, not a cached one! 

If that doesn't help resolve the issue: 

We'll probably need a bit more information about your installation environment to be able to help. First, what operating system and version is AtoM installed on? What version of PHP are you using? What version of MySQL do you have installed? Did you follow our recommended installation instructions, or have you made any local changes (and if so, what changes)?

Additionally, please check if there are any further details available in the web server error logs. If  you are using Nginx as you webserver as we recommend, you can typically check these with the following command: 

• sudo tail -f /var/log/nginx/error.log
  
• See:  https://www.accesstomemory.org/docs/2.4/admin-manual/maintenance/logging/#web-server-logs

Feel free to share any relevant message you find there. 

One other possibility: we have been seeing some strange behaviors with MySQL 5.7's default STRICT_MODE setting. You can check what modes are in use in your installation with the following: 

• mysql -u root -proot -e "SELECT @@sql_mode, @@GLOBAL.SQL_MODE;"

The last possibility I can think of off the top of my head is that there is some corruption in the database that is causing these issues. I have some suggestions for that as well, but let's start with the above. Let us know how it goes, and what you find! 

Cheers, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056

@accesstomemory

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[Sally-Anne Shearn]

Dear Dan,

Thank you so much for such a detailed reply.  Our treeview sorting is set to manual and my colleague typed all of the text directly into AtoM so I think I will have to pass your email on to our IT support Jim to see if it's any of the other things you mention (unfortunately I don't have access to the command line myself).

I'll let the forum know what we find out just in case anyone else comes across the same problem.

Sally

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[Sally-Anne Shearn]

Dear Dan,

I just wanted to let you know that I passed the solution on to our IT support and he implemented it this week and it works.  The error now appears to be fixed so thank you very much for that!

Sally