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New archival descriptions showing up as "Part of"

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Crystal Gamradt

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Jun 24, 2020, 9:31:43 AM6/24/20
to AtoM Users
Good morning,

I am using version 2.5.4 - 172 of AtoM.

I have been importing our finding aids to AtoM and things have been going well. However, yesterday I imported a few records and the archival desciption page doesn't come up correctly. It looks like it's messing up the heirarchy. It's kind of hard to explain but I'll show you some screenshots.

This is what things usually look like:



But now every record I import or create new looks like this:



The browse screen states that it is "Part of Record:"



I cannot move the box to the archival description. UA045 is grayed out. When I select the box to delete it the entire finding aid is deleted.

Does anyone have any idea what is happenning?  Am I doing something wrong? Is it a server problem.

Confused in SD,

Crystal Gamradt, Archivist
Archives and Special Collections
South Dakota State University

Dan Gillean

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Jun 24, 2020, 11:17:16 AM6/24/20
to ICA-AtoM Users
Hi Crystal, 

It's hard to say exactly what's happening here without more information on the import itself, but I'll suggest a few things to try at first - at the very least, they might rule out some possibilities. 

First, I suggest starting by running some of the common AtoM maintenance tasks listed on our Troubleshooting page - specifically, rebuilding the nested set, clearing the application cache, restarting PHP-FPM, and re-indexing. See: 
My first guess is that the nested set is corrupted. This is something we use to help manage hierarchical relations in a table-based relational database. When it gets corrupted, then records can appear in the wrong place. Fortunately, it's easy to rebuild. 

The other tasks will make sure we are seeing the most recent version of the record (and not a cached version), and that all records are properly indexed. I'd also recommend either clearing your browser cache, or testing in an incognito browser (where the browser cache is typically disabled by default) after running the tasks. Let us know if it helps! 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him


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Gamradt, Crystal

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Jun 24, 2020, 3:56:29 PM6/24/20
to AtoM Users, Julius, Chad
Thank you for your reply. I  had my IT guy run through all of your suggestions (See thread below) but I am still having problems.  I have attached the CSV for my import but the issue also occurs when I create a new archival description through the interface. If there is more information that would help us figure this out just let me know.  I have CC'd Chad Julius on this email. He's my IT guy.

Thanks !

Crystal J. Gamradt, Archivist
SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241
South Dakota State University, Box 2115 | Brookings, South Dakota, 57006

From: Gamradt, Crystal <Crystal...@SDSTATE.EDU>
Sent: Wednesday, June 24, 2020 2:46 PM
To: Julius, Chad <Chad....@sdstate.edu>
Subject: Re: [atom-users] New archival descriptions showing up as "Part of"
 
Still problems.  I'll continue to work with Dan from AtoM to find a solution.

Crystal J. Gamradt, Archivist
SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241
South Dakota State University, Box 2115 | Brookings, South Dakota, 57006
From: Gamradt, Crystal <Crystal...@SDSTATE.EDU>
Sent: Wednesday, June 24, 2020 12:52 PM
To: Julius, Chad <Chad....@sdstate.edu>
Subject: Re: [atom-users] New archival descriptions showing up as "Part of"
 
OK. I'll check it in a bit then.

Crystal J. Gamradt, Archivist
SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241
South Dakota State University, Box 2115 | Brookings, South Dakota, 57006
From: Julius, Chad <Chad....@sdstate.edu>
Sent: Wednesday, June 24, 2020 12:51 PM
To: Gamradt, Crystal <Crystal...@SDSTATE.EDU>
Subject: RE: [atom-users] New archival descriptions showing up as "Part of"
 

I have completed their troubleshooting steps and restarted the services.  I am doing one last search index population so wait 30 minutes before you do anything but here is the information from those steps:

 

Common Maintenance Items:

 

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo php symfony search:status

[sudo] password for sdsuadmin:

Elasticsearch server information:

- Host: localhost

- port: 9200

- Index name: atom

 

Document indexing status:

- Accession: 68/68

- Actor: 563/563

- Aip: 0/0

- Function: 0/0

- Information object: 71663/72817

- Repository: 3/3

- Term: 788/788

 

 

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo php symfony search:populate

Index populated with 74239 documents in 1193.38 seconds.

 

php symfony cc

No errors

 

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo systemctl restart php7.2-fpm

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo systemctl restart memcached

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo systemctl status php7.2-fpm

● php7.2-fpm.service - The PHP 7.2 FastCGI Process Manager

   Loaded: loaded (/lib/systemd/system/php7.2-fpm.service; enabled; vendor preset: enabled)

   Active: active (running) since Wed 2020-06-24 17:48:00 UTC; 20s ago

     Docs: man:php-fpm7.2(8)

Main PID: 6673 (php-fpm7.2)

   Status: "Processes active: 0, idle: 10, Requests: 0, slow: 0, Traffic: 0req/sec"

    Tasks: 11 (limit: 4915)

   CGroup: /system.slice/php7.2-fpm.service

           ├─6673 php-fpm: master process (/etc/php/7.2/fpm/php-fpm.conf)

           ├─6686 php-fpm: pool atom

           ├─6689 php-fpm: pool atom

           ├─6690 php-fpm: pool atom

           ├─6691 php-fpm: pool atom

           ├─6693 php-fpm: pool atom

           ├─6694 php-fpm: pool atom

           ├─6695 php-fpm: pool atom

           ├─6696 php-fpm: pool atom

           ├─6697 php-fpm: pool atom

           └─6698 php-fpm: pool atom

 

Jun 24 17:48:00 libapp001 systemd[1]: Starting The PHP 7.2 FastCGI Process Manager...

Jun 24 17:48:00 libapp001 systemd[1]: Started The PHP 7.2 FastCGI Process Manager.

 

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo systemctl status memcached

● memcached.service - memcached daemon

   Loaded: loaded (/lib/systemd/system/memcached.service; enabled; vendor preset: enabled)

   Active: active (running) since Wed 2020-06-24 17:48:12 UTC; 31s ago

     Docs: man:memcached(1)

Main PID: 6723 (memcached)

    Tasks: 10 (limit: 4915)

   CGroup: /system.slice/memcached.service

           └─6723 /usr/bin/memcached -m 64 -p 11211 -u memcache -l 127.0.0.1 -P /var/run/memcached/memcached.pid

 

Jun 24 17:48:12 libapp001 systemd[1]: Started memcached daemon.

 

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo php symfony propel:build-nested-set

>> propel    Build nested set for information_object...

>> propel    Build nested set for actor...

>> propel    Build nested set for term...

>> propel    Done!

 

sdsuadmin@libapp001:/usr/share/nginx/atom$ sudo php symfony propel:generate-slugs

>> propel    Generate accession slugs...

>> propel    Generate actor slugs...

>> propel    Generate deaccession slugs...

>> propel    Generate digital_object slugs...

>> propel    Generate event slugs...

>> propel    Generate function slugs...

>> propel    Generate information_object slugs...

>> propel    Generate physical_object slugs...

>> propel    Generate relation slugs...

>> propel    Generate rights slugs...

>> propel    Generate static_page slugs...

>> propel    Generate taxonomy slugs...

>> propel    Generate term slugs...

>> propel    Note: you will need to rebuild your search index for slug changes to show up in search results.

>> propel    Done!

 

 

From: Gamradt, Crystal <Crystal...@SDSTATE.EDU>
Sent: Wednesday, June 24, 2020 12:28 PM
To: Julius, Chad <Chad....@sdstate.edu>
Subject: Re: [atom-users] New archival descriptions showing up as "Part of"

 

Thanks Chad.

 

Crystal J. Gamradt, Archivist

SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241

South Dakota State University, Box 2115 | Brookings, South Dakota, 57006

From: Julius, Chad <Chad....@sdstate.edu>
Sent: Wednesday, June 24, 2020 12:27 PM
To: Gamradt, Crystal <Crystal...@SDSTATE.EDU>
Subject: RE: [atom-users] New archival descriptions showing up as "Part of"

 

Working through those tasks now.  I will let you know what/if something comes up.

 

 

From: Gamradt, Crystal <Crystal...@SDSTATE.EDU>
Sent: Wednesday, June 24, 2020 12:10 PM
To: Julius, Chad <Chad....@sdstate.edu>
Subject: Fw: [atom-users] New archival descriptions showing up as "Part of"

 

Chad,

 

I received a reply from the forums.  Can you take a look at their suggestions and see if there is a solution?

 

Thanks!

 

Crystal J. Gamradt, Archivist

SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241

South Dakota State University, Box 2115 | Brookings, South Dakota, 57006

isad_0000000001.csv
Message has been deleted

Dan Gillean

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Jun 24, 2020, 5:28:17 PM6/24/20
to ICA-AtoM Users, Julius, Chad
Hi Crystal, 

Strange. I don't see anything immediately obvious in the CSV that would lead to the outcome you're describing - the legacyID and parentID values all seem to make sense to me. 

This might seem a bit obvious, but just trying to rule out all possibilities: when you add new descriptions via the user interface, are you using the Add menu in the header bar, or are you clicking "Add new" while on the view page of a description? The latter will add your new description as a child of the description on the view page...

Is your AtoM site publicly visible?

I can tell from the logs shared that you're using Nginx and PHP 7.2 - is this an Ubuntu installation as well - as in, have you followed the recommended installation instructions, or are there some deviations - and if so, what? If Ubuntu, is this a 16.04 or an 18.04 installation?

The only other suggestion I can think of for now would be to have Chad try out some of the queries we have on our Troubleshooting page to check for data corruption. 
In the meantime, I'll share this thread with some of our team, and see if anyone else has suggestions. 

Cheers, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/CH2PR06MB6536C2E0149AA06F40AC57F8E4950%40CH2PR06MB6536.namprd06.prod.outlook.com.

Gamradt, Crystal

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Jun 25, 2020, 9:03:45 AM6/25/20
to ica-ato...@googlegroups.com
Thanks for all your help. I'll pass the information on to Chad.

We are not public yet. I was working on getting things all set up during the quarantine and I am SO close to being done.  I hope we can find a resolution.  We've started over once before, I'd hate to have to do that again.

Crystal J. Gamradt, Archivist
SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241
South Dakota State University, Box 2115 | Brookings, South Dakota, 57006
Sent: Wednesday, June 24, 2020 4:27 PM
To: ICA-AtoM Users <ica-ato...@googlegroups.com>
Cc: Julius, Chad <Chad....@sdstate.edu>

Gamradt, Crystal

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Jun 25, 2020, 9:22:35 AM6/25/20
to ica-ato...@googlegroups.com
Dan,


I don’t know if you offer that kind of support but would you be willing to talk with Chad Juilius directly?  He said he  would be more than happy to get you access to the server to get to the bottom of this.  IHe can Zoom/skype etc. with you to work on this.

 

His contact information is:


Chad....@sdstate.edu

605-688-5767



Thank you!!

Crystal

Crystal J. Gamradt, Archivist
SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241
South Dakota State University, Box 2115 | Brookings, South Dakota, 57006
From: ica-ato...@googlegroups.com <ica-ato...@googlegroups.com> on behalf of Gamradt, Crystal <Crystal...@SDSTATE.EDU>
Sent: Thursday, June 25, 2020 8:03 AM
To: ica-ato...@googlegroups.com <ica-ato...@googlegroups.com>

Dan Gillean

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Jun 25, 2020, 10:23:14 AM6/25/20
to ICA-AtoM Users
Hi Crystal, 

I don't think that you'll have to restart all your work for us to get to the bottom of this. I do hope that your IT team is making regular database backups just in case!

We can't offer one-on-one troubleshooting as part of the free support we provide our community via this forum, unfortunately. If you might be interested in paid support, please forward this email thread to in...@artefactual.com, and someone on our team can follow up on available support options. 

In the meantime, I have asked one of our developers to take a look at this thread and see if he has any further suggestions for you. 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/CH2PR06MB653675AC513662F46D5ABFA8E4920%40CH2PR06MB6536.namprd06.prod.outlook.com.

Dan Gillean

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Jun 26, 2020, 12:39:34 PM6/26/20
to ICA-AtoM Users
Hi again Crystal, 

I've looked this over with one of our developers, and we're a bit stumped as to what to suggest next. We also successfully imported the sample CSV that you sent with no errors or nesting issues: 

Screen Shot 2020-06-26 at 8.54.26 AM.png

Just to make sure they are not lost in the thread, I'm copying a couple outstanding suggestions you can try from one of my previous posts: 

This might seem a bit obvious, but just trying to rule out all possibilities: when you add new descriptions via the user interface, are you using the Add menu in the header bar, or are you clicking "Add new" while on the view page of a description? The latter will add your new description as a child of the description on the view page...

And:

The only other suggestion I can think of for now would be to have Chad try out some of the queries we have on our Troubleshooting page to check for data corruption. 

One small thought, though the chances of this are slim: do you have a custom theme in place? If yes, have you tried rebuilding the CSS for your custom theme plugin? Doing so for the default Dominion theme involves making sure that lessc is installed, and then running the "make" command against the theme plugin, like so:
  • sudo apt install nodejs npm make
  • sudo npm install -g "less@<2.0.0"
  • sudo make -C /usr/share/nginx/atom/plugins/arDominionPlugin
A couple quick notes on this:
  • You only need to do the first 2 steps once, to make sure that lessc is installed
  • If you haven't followed our recommended installation instructions, then your path to the root AtoM installation directory might be different. But from the root AtoM installation directory, the path to the Dominion theme plugin is just  plugins/arDominionPlugin. Modify as needed for your installation environment. 
  • If you have a custom theme, you can repeat this process for the custom theme plugin, using the plugin's name. An example:
    •   sudo make -C /usr/share/nginx/atom/plugins/aYourCustomThemePlugin
  • Remember to clear your browser cache, and possibly the application cache and PHP-FPM, before re-testing

A few other general reminders:
  • Make sure you test in an incognito / private browser window, and/or clear your browser cache before re-testing anything, so you are seeing the latest version!
  • Use the import button in the AtoM header to import your records as new. The Import options on a view page of a description will bring in your records as children of the current record.
  • If you are importing from the command-line, don't use the --default-parent-slug or --default-legacy-id options - these will also import your records as children of a target description
  • When in the interface, create new top-level records by using the Add menu in the header - using the "Add new" button on a description view page will create a child record of the current description
  • Perhaps you could try using the Move module to move your record out from under the "Records" record, to become its own top-level record? Then if needed, you could do the same thing to move the "Records" record as a child of your new top-level record. When using the Move module, if you don't select a parent in the first screen, it will move the target description out of a hierarchy to the top level. See:  https://www.accesstomemory.org/docs/latest/user-manual/add-edit-content/archival-descriptions/#method-2-move-a-description-to-a-different-level
Beyond this, without accessing your site and knowing more about your installation environment, it's tough to know what to suggest! I've not seen this happen before in a way that rebuilding the nested set didn't immediately resolve, and so far we haven't been able to reproduce the issue internally. As I mentioned, accessing your site is beyond the level of free support we can offer, but you can always follow up with us off-list if you are interested in paid options. 

I hope this helps!

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him

Gamradt, Crystal

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Jun 30, 2020, 8:21:52 AM6/30/20
to ica-ato...@googlegroups.com
Dan,

Thanks for your diligence in trying to find an answer.  We ended up rolling back to the last snapshot.  Fortunately I didn't have to reimport very much. 

Crystal J. Gamradt, Archivist
SDSU Archives & Special Collections | Hilton M. Briggs Library, Room 241
South Dakota State University, Box 2115 | Brookings, South Dakota, 57006
Sent: Friday, June 26, 2020 11:39 AM
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