Following the MySQL Upgrade path killed MySQL completely

[cand...@kingscollege.qld.edu.au]

I know this is a mysql issue and not an atom issue, but I was hoping someone could shed some light - I started following the upgrade details to move to 2.6, and the first step was MySQL 8 - so I started following the instructions to install it on the Atom documentation but when it finishes installing I get this error:

dpkg: error processing package mysql-community-server (--configure):

 installed mysql-community-server package post-installation script subprocess returned error exit status 1

I've tried backing up the databases and then completely purging everything MySQL related from the server, but no matter what, when I try to reinstall MySQL I get the same error. The last time we changed MySQL on the atom server I ended up needing to create a new atom server because it wasn't working but I don't really want to do that again. 

If anyone has seen something similar and can give some suggestions that would be amazing.

Thanks!

[Karl Goetz]

Hi,

Please include the full dpkg error; it will provide more clues as to where the problem lies.

Please also expand on how you're doing the upgrade - are they official Ubuntu(?) packages, third party?

thanks,

Karl.

---

From: ica-ato...@googlegroups.com <ica-ato...@googlegroups.com> on behalf of cand...@kingscollege.qld.edu.au <cand...@kingscollege.qld.edu.au>
Sent: Thursday, 17 June 2021 8:19 AM
To: AtoM Users <ica-ato...@googlegroups.com>
Subject: [atom-users] Following the MySQL Upgrade path killed MySQL completely

 

      

This e-mail message may contain confidential or legally privileged information and is intended only for the use of the intended recipient(s). Any unauthorised disclosure, dissemination, distribution, copying or the taking of any action in reliance on the information herein is prohibited. E-mails are not secure and cannot be guaranteed to be error-free as they can be intercepted, amended, or contain viruses. Anyone who communicates with us by e-mail is deemed to have accepted these risks. King's Christian College is not responsible for errors or omissions in this message and denies any responsibility for any damage arising from the use of e-mail. Any opinion and other statement contained in this message and any attachment are solely those of the author and do not necessarily represent those of the College.

--
You received this message because you are subscribed to the Google Groups "AtoM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ica-atom-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/a2fa0433-9e2d-4a52-8cbf-0c64f4f6267bn%40googlegroups.com.

This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.

[cand...@kingscollege.qld.edu.au]

Hey Karl,

dpkg: error processing package mysql-community-server (--configure):

 installed mysql-community-server package post-installation script subprocess returned error exit status 1

Errors were encountered while processing:

mysql-community-server

E: Sub-process /usr/bin/dpkg returned an error code (1)

I am upgrading following the instructions here for installing MySQL 8 - so if the Atom docs are using the official Ubuntu packages, then so am I. 

[Karl Goetz]

Hi Caleb

I know this doesn't help you per se, but for what its worth I followed the mysql installing instructions and didn't encounter an issue so it appears to be something specific to your environment and we'd need more information to help diagnose that.

Looking back at a previous mail you said "I upgraded to 16.04 and 2.5.1 today". If you are still running Ubuntu 16.04 then you'll need to upgrade. Atom 2.6 and 2.7 are only supported on Ubuntu 18.04.

thanks,

Karl.

---

From: ica-ato...@googlegroups.com <ica-ato...@googlegroups.com> on behalf of cand...@kingscollege.qld.edu.au <cand...@kingscollege.qld.edu.au>

Sent: Thursday, 17 June 2021 10:26 AM
To: AtoM Users <ica-ato...@googlegroups.com>
Subject: Re: [atom-users] Following the MySQL Upgrade path killed MySQL completely

 

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/58ccc0dd-23a4-4ab4-9c0c-ad3069662684n%40googlegroups.com.

[Lalie Lapleni]

Good day everyone,

can ATOM manage many record centers from different locations? A kind of union catalog?

Maybe another system that can manage different record centers in various locations in the country or outside?  That system allows you to search simultaneously in different directories.  Thanks

Rosalie Ndejuru

Expert National Archives- Rwanda

      

This e-mail message may contain confidential or legally privileged information and is intended only for the use of the intended recipient(s). Any unauthorised disclosure, dissemination, distribution, copying or the taking of any action in reliance on the information herein is prohibited. E-mails are not secure and cannot be guaranteed to be error-free as they can be intercepted, amended, or contain viruses. Anyone who communicates with us by e-mail is deemed to have accepted these risks. King's Christian College is not responsible for errors or omissions in this message and denies any responsibility for any damage arising from the use of e-mail. Any opinion and other statement contained in this message and any attachment are solely those of the author and do not necessarily represent those of the College.

--
You received this message because you are subscribed to the Google Groups "AtoM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ica-atom-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/a2fa0433-9e2d-4a52-8cbf-0c64f4f6267bn%40googlegroups.com.

--

Rosalie Ndejuru

[Dan Gillean]

Hello Lalie, 

AtoM does have basic multi-repository support - by which I mean that you can create more than one archival institution record, and link descriptions and authority records to different institution records. The public demo site is multi-repository, for example. 

There are also some settings that can be used to potentially enhance the ability for public users to explore within the context of just one institution at a time - see for example: 

• https://www.accesstomemory.org/docs/latest/user-manual/administer/settings/#enable-institutional-scoping
  

As AtoM requires only an internet connection and a web browser to be able to access, there is theoretically no reason why multiple users from different institutions in geographically separate locations couldn't share one installation.

That said, it is also important to understand the limitations of AtoM's multi-repository support. It was designed with access in mind - so AtoM could be used as a portal site for many different institutions for example, but the original assumption was that each institution would have their own archival management system and would be contributing records to a shared portal for access, typically managed by a single administrator or small team. 

Because of these early design decisions, this means that AtoM does NOT currently have full multi-repository support. By this I mean:

• There is no way to use separate access points, such as subjects, places, genres, or any other controlled vocabularies. All users would need to agree to use the same vocabularies, which would mean that unless a plan to coordinate a controlled vocabulary is put in place by an administrator, you might end up with duplicate terms with minor spelling variations, etc. 
• There is no way to associate accessions, donors, rightsholder records, or physical storage containers with a specific institution. Once again, all users would need to be comfortable sharing these elements, and being able to see each other's work - or else agree not to use these modules for the shared access portal. 
• There are some known scalability issues with AtoM's permissions module, so we don't recommend trying to add a lot of complex group permissions so that users of one institution can't see the draft records of another, etc. I can point you to other previous threads in the forum where I have discussed this in greater detail, but for now just know that a shared site will work best if there is trust and mutual respect among participants, so you don't need to apply complex permissions to hide works in progress from each other. 

Despite these limitations, this is a common practice in Canada - you can find many provincial and territorial portal sites, many of which are used as the primary or only catalog from some of the smaller participating institutions. Some examples: 

• Archeion
• MemorySask
• MemoryNS 

Finally, AtoM does not currently have the ability to act as a public front end for a number of other archival management systems or catalogs, even if they are AtoM sites. Right now, you'd need to actually import a copy of the data you want from each separate site into the AtoM union catalog. Long term, we hope to see a separation of the public front end from the staff edit interface so we can support exactly this kind of scenario, but it doesn't exist yet. Note that people have developed their own solutions however - for example, this simple search interface provides results from two different AtoM catalogs used by St. John's College at the University of Westminster: 

• https://www.sjcarchives.org.uk/
  

Hope this helps!

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/CAPL2zgAW8HYN-cGTs_7ziH6iE0%3DKS2UDx3NePB4ZoDVbe5Q5Kg%40mail.gmail.com.

[pcol...@gmail.com]

Hi:    Thank you for your ‘help’ although your message is ‘Greek’ to me.   I was looking to confirm the spelling of a person’s name who graduated in the 1954 electrical class but have found other ways of doing so.   Paul.

 

From: ica-ato...@googlegroups.com <ica-ato...@googlegroups.com> On Behalf Of Dan Gillean
Sent: June 22, 2021 9:57 AM
To: ICA-AtoM Users <ica-ato...@googlegroups.com>
Subject: Re: [atom-users] Following the MySQL Upgrade path killed MySQL completely

 

Hello Lalie, 

 

      

This e-mail message may contain confidential or legally privileged information and is intended only for the use of the intended recipient(s). Any unauthorised disclosure, dissemination, distribution, copying or the taking of any action in reliance on the information herein is prohibited. E-mails are not secure and cannot be guaranteed to be error-free as they can be intercepted, amended, or contain viruses. Anyone who communicates with us by e-mail is deemed to have accepted these risks. King's Christian College is not responsible for errors or omissions in this message and denies any responsibility for any damage arising from the use of e-mail. Any opinion and other statement contained in this message and any attachment are solely those of the author and do not necessarily represent those of the College.

--
You received this message because you are subscribed to the Google Groups "AtoM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ica-atom-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/a2fa0433-9e2d-4a52-8cbf-0c64f4f6267bn%40googlegroups.com.

 

--

Rosalie Ndejuru

--
You received this message because you are subscribed to the Google Groups "AtoM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ica-atom-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/CAPL2zgAW8HYN-cGTs_7ziH6iE0%3DKS2UDx3NePB4ZoDVbe5Q5Kg%40mail.gmail.com.

--
You received this message because you are subscribed to the Google Groups "AtoM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ica-atom-user...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/ica-atom-users/CAC1FhZ%2BA7c91oK%2B%2BUeMyokgVeWyEDR%2BxUb4tmr3dxViHJ_-JKw%40mail.gmail.com.

[Lalie Lapleni]

Thank you Dan.  We are looking to upgrade to ATOM.  Have good time

Rosalie Ndejuru

[cand...@kingscollege.qld.edu.au]

So I managed to fix the MySQL problem - but now I have another issue. (Mysql issue was a deleted folder that needed to exist for installation to complete). 

Following the instructions for installing / upgrading seemed to all go with no problems, all the versions of the software were the latest already, all the services were there and enabled, and all the config files that the guide called to manually edit were done - but after rebooting the server and making sure the services are running I get a 500 error when trying to access the localhost to run the webinstaller. Before I rebooted the server it was just a white page.

I checked the Nginx log, as I would assume its a web server issue, and I saw 59 of this particular error today so far:

[error] 1800#1800: *12 FastCGI sent in stderr: "PHP message: Unable to open the log file "/usr/share/nginx/atom/log/qubit_prod.log" for writing" while 

reading response header from upstream, client: (ip address), server: atom.(our link), request: "GET /index.php/informationobject/browse?places=33844&sort=rel

evance&sf_culture=en&showAdvanced=1&topLod=0&sortDir=asc HTTP/1.1", upstream: "fastcgi://unix:/run/php7.2-fpm.atom.sock:", host: "atom.(our link)"

The file didn't actually exist, so I created it and gave ownership to www-data. I reloaded the service and tried hitting the localhost again, but got the same error showing up in the log. I don't know if this error specifically is the only catalyst for it not working or not, but any ideas on what to look for would be great.

Thanks!

[José Raddaoui]

Hi,

As you suspected this may still be a permissions issue. I'd double check that Ningx and PHP-FPM are actually being run by `www-data` and that the configuration path points to the current AtoM folder, then change the permission of the entire AtoM folder, as mentioned in the documentation:

https://www.accesstomemory.org/en/docs/2.6/admin-manual/installation/linux/ubuntu-bionic/#filesystem-permissions

Best regards,

Radda.

[cand...@kingscollege.qld.edu.au]

Thanks José for confirming - I keep forgetting working with Ubuntu that sometimes I need to reboot to see changes take effect properly. I had changed the permissions following the documentation but it wasn't until I rebooted that it started working again.