Unknown collation 2.6 installation

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Bob Higgie

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Jan 22, 2024, 8:15:59 AMJan 22
to AtoM Users
Hi Dan, 
I run Ubuntu 18.04 and Atom 2.6 on a production machine. 
Prior to upgrading I am installing the same configuration on a development  machine so that I can test the upgrade process. I am following the installation instructions exactly, as I did for the production installation. 

The command to create the database is giving the following error:

sudo mysql -h localhost -u root -p -e "CREATE DATABASE atom CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci;"

Enter password: 

ERROR 1273 (HY000) at line 1: Unknown collation: 'utf8mb4_0900_ai_ci'


If I remove the collation the command executes OK, but the installation gives a 500 error at any attempt to interact with the database.


Any ideas?


Thanks Bob. 

Dan Gillean

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Jan 22, 2024, 8:35:19 AMJan 22
to ica-ato...@googlegroups.com
Hi Bob, 

Did you try running the DROP DATABASE command first, to clear out any failed previous attempts? Otherwise...

Let's start by checking some basics - AtoM 2.7 and 2.8 assume you are using MySQL 8 - can you run the following just so we can fully confirm the version you have, the current character set, and some other details? This should be run once you have accessed the MySQL command prompt (instructions on how to do so can be found here): 
  • STATUS;
Additionally, the following should allow us to see what collation is currently set: 
  • SHOW VARIABLES LIKE 'collation%';
If everything looks as expected in the above outputs, and you are able to create the database without the collation command, I wonder if you can apply it afterwards? Bit of a long shot, but we can try: 
  • ALTER DATABASE atom CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci;
Hopefully with a bit more information, I can gather further suggestions from our developers on next steps if nothing above helped to resolve the issue. 

Cheers, 

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


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Bob Higgie

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Jan 22, 2024, 9:24:20 AMJan 22
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Hi Dan,
Thanks for the very prompt reply.
I probably wasn't clear enough in my description.
This is a completely fresh install, first of Ubuntu 18.04 (on the complete hard drive) then following the Linux instructions for Bionic Beaver. (which install MySQL 8).
This error occurs at this point in the installation:

Create the database

Assuming that you are running MySQL in localhost, please create the database by running the following command using the password you created earlier:

sudo mysql -h localhost -u root -p -e "CREATE DATABASE atom CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci;"

At this point there is no database from previous installations. so I can't run any of your suggested checks.   
I am perplexed because this all worked perfectly well last year. 
Bob. 


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Dan Gillean

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Jan 22, 2024, 9:41:29 AMJan 22
to ica-ato...@googlegroups.com
Hi Bob, 

Thanks for the clarification - I am sure that much of the misunderstanding is on my part, not yours!

So, to be totally clear: which version are you installing on your dev server right now - 2.6? or a newer version? 

I know you said you want to test the upgrade process, but.... if you look at our upgrade instructions, they essentially say to install a fresh version of AtoM alongside your old version, and then provide instructions for how to load your data and upgrade the database schema. Therefore, if you already have a production 2.6 instance, and want to test the upgrade process, I am assuming that you should be: 
  • Taking a dump from the production 2.6 instance, and
  • Attempting to install version 2.8 on your development server for testing the upgrade process. 
I am not sure if this is correct or not, since you mention Ubuntu 18.04. One of the reasons our installation process is essentially to install a fresh version alongside the old one is so we can manage the upgrade of underlying dependencies at the same time, including the Ubuntu version. We do NOT recommend attempting to upgrade in place around an existing installation. Since both AtoM 2.7 and 2.8 expect Ubuntu 20.04, I suspect this may be the start of our issues. 

You also mention letting Bionic Beaver handle the MySQL installation... but if I recall correctly, MySQL 5.7 was the default version available to 18.04, so that might be the issue - the collation AtoM expects is not available in that version. In our installation docs for 2.6 (which use MySQL 8 on Ubuntu 18.04), we manually fetch the correct package version using wget: 

Is this what you did, or something different?

Either way, we can check the MySQL version outside of the MySQL command prompt with: 
  • mysql -v
Let's make sure we sort out this remaining confusion before we go any further with suggestions... and apologies in advance if the confusion is all mine! 

Cheers, 

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

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Bob Higgie

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Jan 22, 2024, 9:44:53 AMJan 22
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Hi Dan,
Will get back to you later today.
Bob. 
Sent from my iPhone

Bob Higgie

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Jan 22, 2024, 4:40:34 PMJan 22
to ica-ato...@googlegroups.com
HI Dan,
Thanks for your patience and apologies for the length of this.
As background, I am the only IT person at a small, all volunteer run, museum in the UK. We only open 1 day a week and the production server is currently only on the intranet.
So I'm doing this build at home.
My plan is to install 18.04 and Atom 2.6 from scratch, then upload the CSV file with the 5k records that was used to populate the production server. 
When I have done this I will have a replica of the production server and can then practice the upgrade to 20.04 and Atom 2.7. 
I have followed the Bionic instructions you reference, including:
After installing MySQL I go through the Elasticsearch, nginx, PHP, Gearman and Atom installs. 
It is at this point, Create the Database, that I get the collation error. 
This is what I got as the mysql version:
:~$  mysql --version

mysql  Ver 14.14 Distrib 5.7.42, for Linux (x86_64) using  EditLine wrapper


Which is the wrong version, so I started again with a fresh install of Ubuntu 18.04 then just the MySQL installation followed by checking the version, and still got 5.7. 

This is what happened. It says. I am configuring 8.0 and I get 5.7


Bob. 


Welcome to Ubuntu 18.04.6 LTS (GNU/Linux 4.15.0-213-generic x86_64)


$ wget https://dev.mysql.com/get/mysql-apt-config_0.8.22-1_all.deb

--2024-01-22 21:17:00--  https://dev.mysql.com/get/mysql-apt-config_0.8.22-1_all.deb

Resolving dev.mysql.com (dev.mysql.com)... 104.103.202.230, 2a02:26f0:5700:6a2::2e31, 2a02:26f0:5700:688::2e31

Connecting to dev.mysql.com (dev.mysql.com)|104.103.202.230|:443... connected.

HTTP request sent, awaiting response... 302 Moved Temporarily

Location: https://repo.mysql.com//mysql-apt-config_0.8.22-1_all.deb [following]

--2024-01-22 21:17:00--  https://repo.mysql.com//mysql-apt-config_0.8.22-1_all.deb

Resolving repo.mysql.com (repo.mysql.com)... 23.194.9.197, 2a02:26f0:5d00:1184::1d68, 2a02:26f0:5d00:1191::1d68

Connecting to repo.mysql.com (repo.mysql.com)|23.194.9.197|:443... connected.

HTTP request sent, awaiting response... 200 OK

Length: 18012 (18K) [application/x-debian-package]

Saving to: ‘mysql-apt-config_0.8.22-1_all.deb’


mysql-apt-config_0. 100%[===================>]  17.59K  --.-KB/s    in 0s      


2024-01-22 21:17:00 (73.1 MB/s) - ‘mysql-apt-config_0.8.22-1_all.deb’ saved [18012/18012]


$ sudo dpkg -i mysql-apt-config_0.8.22-1_all.deb

Selecting previously unselected package mysql-apt-config.

(Reading database ... 67750 files and directories currently installed.)

Preparing to unpack mysql-apt-config_0.8.22-1_all.deb ...

Unpacking mysql-apt-config (0.8.22-1) ...

Setting up mysql-apt-config (0.8.22-1) ...

Warning: apt-key should not be used in scripts (called from postinst maintainerscript of the package mysql-apt-config)

OK


$ sudo apt update

Hit:1 http://gb.archive.ubuntu.com/ubuntu bionic InRelease

Hit:2 http://gb.archive.ubuntu.com/ubuntu bionic-updates InRelease             

Hit:3 http://gb.archive.ubuntu.com/ubuntu bionic-backports InRelease           

Hit:4 http://gb.archive.ubuntu.com/ubuntu bionic-security InRelease            

Get:5 http://repo.mysql.com/apt/ubuntu bionic InRelease [20.0 kB]              

Err:5 http://repo.mysql.com/apt/ubuntu bionic InRelease       

  The following signatures couldn't be verified because the public key is not available: NO_PUBKEY B7B3B788A8D3785C

Reading package lists... Done

W: GPG error: http://repo.mysql.com/apt/ubuntu bionic InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY B7B3B788A8D3785C

E: The repository 'http://repo.mysql.com/apt/ubuntu bionic InRelease' is not signed.

N: Updating from such a repository can't be done securely, and is therefore disabled by default.

N: See apt-secure(8) manpage for repository creation and user configuration details.


$ sudo apt install mysql-server


$ sudo apt install mysql-server



image.png



Reading package lists... Done

Building dependency tree       

Reading state information... Done

The following additional packages will be installed:

  libaio1 libcgi-fast-perl libcgi-pm-perl libencode-locale-perl

  libevent-core-2.1-6 libfcgi-perl libhtml-parser-perl libhtml-tagset-perl

  libhtml-template-perl libhttp-date-perl libhttp-message-perl libio-html-perl

  liblwp-mediatypes-perl libtimedate-perl liburi-perl mysql-client-5.7

  mysql-client-core-5.7 mysql-common mysql-server-5.7 mysql-server-core-5.7

Suggested packages:

  libdata-dump-perl libipc-sharedcache-perl libwww-perl mailx tinyca

The following NEW packages will be installed:

  libaio1 libcgi-fast-perl libcgi-pm-perl libencode-locale-perl

  libevent-core-2.1-6 libfcgi-perl libhtml-parser-perl libhtml-tagset-perl

  libhtml-template-perl libhttp-date-perl libhttp-message-perl libio-html-perl

  liblwp-mediatypes-perl libtimedate-perl liburi-perl mysql-client-5.7

  mysql-client-core-5.7 mysql-common mysql-server mysql-server-5.7

  mysql-server-core-5.7

0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.

Need to get 20.1 MB of archives.

After this operation, 157 MB of additional disk space will be used.

Do you want to continue? [Y/n] Y

Get:1 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 mysql-common all 5.8+1.0.4 [7,308 B]

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Get:3 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-client-core-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [6,752 kB]

Get:4 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-client-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [2,028 kB]

Get:5 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-server-core-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [7,542 kB]

Get:6 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4build1 [85.9 kB]

Get:7 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-server-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [3,011 kB]

Get:8 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-tagset-perl all 3.20-3 [12.1 kB]

Get:9 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 liburi-perl all 1.73-1 [77.2 kB]

Get:10 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-parser-perl amd64 3.72-3build1 [85.9 kB]

Get:11 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libcgi-pm-perl all 4.38-1 [185 kB]

Get:12 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libfcgi-perl amd64 0.78-2build1 [32.8 kB]

Get:13 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libcgi-fast-perl all 1:2.13-1 [9,940 B]

Get:14 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libencode-locale-perl all 1.05-1 [12.3 kB]

Get:15 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-template-perl all 2.97-1 [59.0 kB]

Get:16 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB]

Get:17 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-date-perl all 6.02-1 [10.4 kB]

Get:18 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libio-html-perl all 1.001-1 [14.9 kB]

Get:19 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 liblwp-mediatypes-perl all 6.02-1 [21.7 kB]

Get:20 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-message-perl all 6.14-1 [72.1 kB]

Get:21 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-server all 5.7.42-0ubuntu0.18.04.1 [9,944 B]

Fetched 20.1 MB in 27s (751 kB/s)                                              

Preconfiguring packages ...

Selecting previously unselected package mysql-common.

(Reading database ... 67755 files and directories currently installed.)

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Unpacking mysql-common (5.8+1.0.4) ...

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Setting up mysql-common (5.8+1.0.4) ...

update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode

Selecting previously unselected package mysql-server-5.7.

(Reading database ... 67923 files and directories currently installed.)

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Setting up libhtml-tagset-perl (3.20-3) ...

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Setting up libtimedate-perl (2.3000-2) ...

Setting up libio-html-perl (1.001-1) ...

Setting up liblwp-mediatypes-perl (6.02-1) ...

Setting up libaio1:amd64 (0.3.110-5ubuntu0.1) ...

Setting up liburi-perl (1.73-1) ...

Setting up libhtml-parser-perl (3.72-3build1) ...

Setting up libcgi-pm-perl (4.38-1) ...

Setting up mysql-client-core-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Setting up libfcgi-perl (0.78-2build1) ...

Setting up libhttp-date-perl (6.02-1) ...

Setting up libhtml-template-perl (2.97-1) ...

Setting up mysql-server-core-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Setting up libcgi-fast-perl (1:2.13-1) ...

Setting up libhttp-message-perl (6.14-1) ...

Setting up mysql-client-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Setting up mysql-server-5.7 (5.7.42-0ubuntu0.18.04.1) ...

update-alternatives: using /etc/mysql/mysql.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode

Renaming removed key_buffer and myisam-recover options (if present)

Created symlink /etc/systemd/system/multi-user.target.wants/mysql.service → /lib/systemd/system/mysql.service.

Setting up mysql-server (5.7.42-0ubuntu0.18.04.1) ...

Processing triggers for libc-bin (2.27-3ubuntu1.6) ...

Processing triggers for systemd (237-3ubuntu10.57) ...

Processing triggers for man-db (2.8.3-2ubuntu0.1) ...

Processing triggers for ureadahead (0.100.0-21) ...


Reading package lists... Done

Building dependency tree       

Reading state information... Done

The following additional packages will be installed:

  libaio1 libcgi-fast-perl libcgi-pm-perl libencode-locale-perl

  libevent-core-2.1-6 libfcgi-perl libhtml-parser-perl libhtml-tagset-perl

  libhtml-template-perl libhttp-date-perl libhttp-message-perl libio-html-perl

  liblwp-mediatypes-perl libtimedate-perl liburi-perl mysql-client-5.7

  mysql-client-core-5.7 mysql-common mysql-server-5.7 mysql-server-core-5.7

Suggested packages:

  libdata-dump-perl libipc-sharedcache-perl libwww-perl mailx tinyca

The following NEW packages will be installed:

  libaio1 libcgi-fast-perl libcgi-pm-perl libencode-locale-perl

  libevent-core-2.1-6 libfcgi-perl libhtml-parser-perl libhtml-tagset-perl

  libhtml-template-perl libhttp-date-perl libhttp-message-perl libio-html-perl

  liblwp-mediatypes-perl libtimedate-perl liburi-perl mysql-client-5.7

  mysql-client-core-5.7 mysql-common mysql-server mysql-server-5.7

  mysql-server-core-5.7

0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.

Need to get 20.1 MB of archives.

After this operation, 157 MB of additional disk space will be used.

Do you want to continue? [Y/n] Y

Get:1 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 mysql-common all 5.8+1.0.4 [7,308 B]

Get:2 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libaio1 amd64 0.3.110-5ubuntu0.1 [6,476 B]

Get:3 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-client-core-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [6,752 kB]

Get:4 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-client-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [2,028 kB]

Get:5 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-server-core-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [7,542 kB]

Get:6 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4build1 [85.9 kB]

Get:7 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-server-5.7 amd64 5.7.42-0ubuntu0.18.04.1 [3,011 kB]

Get:8 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-tagset-perl all 3.20-3 [12.1 kB]

Get:9 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 liburi-perl all 1.73-1 [77.2 kB]

Get:10 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-parser-perl amd64 3.72-3build1 [85.9 kB]

Get:11 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libcgi-pm-perl all 4.38-1 [185 kB]

Get:12 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libfcgi-perl amd64 0.78-2build1 [32.8 kB]

Get:13 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libcgi-fast-perl all 1:2.13-1 [9,940 B]

Get:14 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libencode-locale-perl all 1.05-1 [12.3 kB]

Get:15 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhtml-template-perl all 2.97-1 [59.0 kB]

Get:16 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB]

Get:17 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-date-perl all 6.02-1 [10.4 kB]

Get:18 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libio-html-perl all 1.001-1 [14.9 kB]

Get:19 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 liblwp-mediatypes-perl all 6.02-1 [21.7 kB]

Get:20 http://gb.archive.ubuntu.com/ubuntu bionic/main amd64 libhttp-message-perl all 6.14-1 [72.1 kB]

Get:21 http://gb.archive.ubuntu.com/ubuntu bionic-updates/main amd64 mysql-server all 5.7.42-0ubuntu0.18.04.1 [9,944 B]

Fetched 20.1 MB in 27s (751 kB/s)                                              

Preconfiguring packages ...

Selecting previously unselected package mysql-common.

(Reading database ... 67755 files and directories currently installed.)

Preparing to unpack .../0-mysql-common_5.8+1.0.4_all.deb ...

Unpacking mysql-common (5.8+1.0.4) ...

Selecting previously unselected package libaio1:amd64.

Preparing to unpack .../1-libaio1_0.3.110-5ubuntu0.1_amd64.deb ...

Unpacking libaio1:amd64 (0.3.110-5ubuntu0.1) ...

Selecting previously unselected package mysql-client-core-5.7.

Preparing to unpack .../2-mysql-client-core-5.7_5.7.42-0ubuntu0.18.04.1_amd64.deb ...

Unpacking mysql-client-core-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Selecting previously unselected package mysql-client-5.7.

Preparing to unpack .../3-mysql-client-5.7_5.7.42-0ubuntu0.18.04.1_amd64.deb ...

Unpacking mysql-client-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Selecting previously unselected package mysql-server-core-5.7.

Preparing to unpack .../4-mysql-server-core-5.7_5.7.42-0ubuntu0.18.04.1_amd64.deb ...

Unpacking mysql-server-core-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Selecting previously unselected package libevent-core-2.1-6:amd64.

Preparing to unpack .../5-libevent-core-2.1-6_2.1.8-stable-4build1_amd64.deb ...

Unpacking libevent-core-2.1-6:amd64 (2.1.8-stable-4build1) ...

Setting up mysql-common (5.8+1.0.4) ...

update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode

Selecting previously unselected package mysql-server-5.7.

(Reading database ... 67923 files and directories currently installed.)

Preparing to unpack .../00-mysql-server-5.7_5.7.42-0ubuntu0.18.04.1_amd64.deb ...

Unpacking mysql-server-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Selecting previously unselected package libhtml-tagset-perl.

Preparing to unpack .../01-libhtml-tagset-perl_3.20-3_all.deb ...

Unpacking libhtml-tagset-perl (3.20-3) ...

Selecting previously unselected package liburi-perl.

Preparing to unpack .../02-liburi-perl_1.73-1_all.deb ...

Unpacking liburi-perl (1.73-1) ...

Selecting previously unselected package libhtml-parser-perl.

Preparing to unpack .../03-libhtml-parser-perl_3.72-3build1_amd64.deb ...

Unpacking libhtml-parser-perl (3.72-3build1) ...

Selecting previously unselected package libcgi-pm-perl.

Preparing to unpack .../04-libcgi-pm-perl_4.38-1_all.deb ...

Unpacking libcgi-pm-perl (4.38-1) ...

Selecting previously unselected package libfcgi-perl.

Preparing to unpack .../05-libfcgi-perl_0.78-2build1_amd64.deb ...

Unpacking libfcgi-perl (0.78-2build1) ...

Selecting previously unselected package libcgi-fast-perl.

Preparing to unpack .../06-libcgi-fast-perl_1%3a2.13-1_all.deb ...

Unpacking libcgi-fast-perl (1:2.13-1) ...

Selecting previously unselected package libencode-locale-perl.

Preparing to unpack .../07-libencode-locale-perl_1.05-1_all.deb ...

Unpacking libencode-locale-perl (1.05-1) ...

Selecting previously unselected package libhtml-template-perl.

Preparing to unpack .../08-libhtml-template-perl_2.97-1_all.deb ...

Unpacking libhtml-template-perl (2.97-1) ...

Selecting previously unselected package libtimedate-perl.

Preparing to unpack .../09-libtimedate-perl_2.3000-2_all.deb ...

Unpacking libtimedate-perl (2.3000-2) ...

Selecting previously unselected package libhttp-date-perl.

Preparing to unpack .../10-libhttp-date-perl_6.02-1_all.deb ...

Unpacking libhttp-date-perl (6.02-1) ...

Selecting previously unselected package libio-html-perl.

Preparing to unpack .../11-libio-html-perl_1.001-1_all.deb ...

Unpacking libio-html-perl (1.001-1) ...

Selecting previously unselected package liblwp-mediatypes-perl.

Preparing to unpack .../12-liblwp-mediatypes-perl_6.02-1_all.deb ...

Unpacking liblwp-mediatypes-perl (6.02-1) ...

Selecting previously unselected package libhttp-message-perl.

Preparing to unpack .../13-libhttp-message-perl_6.14-1_all.deb ...

Unpacking libhttp-message-perl (6.14-1) ...

Selecting previously unselected package mysql-server.

Preparing to unpack .../14-mysql-server_5.7.42-0ubuntu0.18.04.1_all.deb ...

Unpacking mysql-server (5.7.42-0ubuntu0.18.04.1) ...

Setting up libhtml-tagset-perl (3.20-3) ...

Setting up libevent-core-2.1-6:amd64 (2.1.8-stable-4build1) ...

Setting up libencode-locale-perl (1.05-1) ...

Setting up libtimedate-perl (2.3000-2) ...

Setting up libio-html-perl (1.001-1) ...

Setting up liblwp-mediatypes-perl (6.02-1) ...

Setting up libaio1:amd64 (0.3.110-5ubuntu0.1) ...

Setting up liburi-perl (1.73-1) ...

Setting up libhtml-parser-perl (3.72-3build1) ...

Setting up libcgi-pm-perl (4.38-1) ...

Setting up mysql-client-core-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Setting up libfcgi-perl (0.78-2build1) ...

Setting up libhttp-date-perl (6.02-1) ...

Setting up libhtml-template-perl (2.97-1) ...

Setting up mysql-server-core-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Setting up libcgi-fast-perl (1:2.13-1) ...

Setting up libhttp-message-perl (6.14-1) ...

Setting up mysql-client-5.7 (5.7.42-0ubuntu0.18.04.1) ...

Setting up mysql-server-5.7 (5.7.42-0ubuntu0.18.04.1) ...

update-alternatives: using /etc/mysql/mysql.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode

Renaming removed key_buffer and myisam-recover options (if present)

Created symlink /etc/systemd/system/multi-user.target.wants/mysql.service → /lib/systemd/system/mysql.service.

Setting up mysql-server (5.7.42-0ubuntu0.18.04.1) ...

Processing triggers for libc-bin (2.27-3ubuntu1.6) ...

Processing triggers for systemd (237-3ubuntu10.57) ...

Processing triggers for man-db (2.8.3-2ubuntu0.1) ...

Processing triggers for ureadahead (0.100.0-21) ...


$ sudo mysql -v

Welcome to the MySQL monitor.  Commands end with ; or \g.

Your MySQL connection id is 2

Server version: 5.7.42-0ubuntu0.18.04.1 (Ubuntu)








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Jim Adamson

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Jan 23, 2024, 7:36:42 AMJan 23
to ica-ato...@googlegroups.com
Hi Bob,

The key lines in your helpful paste from the terminal are as follows:

Err:5 http://repo.mysql.com/apt/ubuntu bionic InRelease       

  The following signatures couldn't be verified because the public key is not available: NO_PUBKEY B7B3B788A8D3785C

Reading package lists... Done

W: GPG error: http://repo.mysql.com/apt/ubuntu bionic InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY B7B3B788A8D3785C

E: The repository 'http://repo.mysql.com/apt/ubuntu bionic InRelease' is not signed.


I would suggest running the following commands to remove MySQL 5 and pave the way for installing MySQL 8:


sudo apt purge mysql-server

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys B7B3B788A8D3785C 

sudo apt update

sudo apt install mysql-server


Keep an eye on the output from the sudo apt update command - if it returns the same errors as above then I suggest you check this solution and see if it works for you.

BTW, you might consider using Ubuntu 20.04 with AtoM 2.7. Ubuntu 18.04 went end-of-life last year.

Thanks, Jim

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--
Jim Adamson
Systems Administrator/Developer
Facilities Management Systems
IT Services
LFA/023 | Harry Fairhurst building | University of York | Heslington | York | YO10 5DD

Dan Gillean

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Jan 23, 2024, 8:43:06 AMJan 23
to ica-ato...@googlegroups.com
Thanks so much for jumping in, Jim! 

Bob: 

In addition to Jim's helpful suggestions, I would strongly urge you to fully review our installation and upgrade docs. If you try to migrate your content by exporting a CSV from one instance and importing it to another, you will potentially lose all information about other entities (such as the related repository record, authority records, terms, accessions, rightsholders, etc) other than the authorized form of name that would be included in the CSV export. You would also lose all your existing user accounts, likely many of your digital objects, and more. 

The official upgrade documentation describes a process of taking the entire MySQL database (as a sqldump), loading it into a new version of AtoM (which can be a higher version - e.g. it's possible to load a 2.6 production instance sqldump into a new 2.8 installation), and then running a few tasks to update the database schema, load the data, and restart all services. This way will preserve ALL data, and be easier to manage as well. 

In short, if you have a 2.6 production instance, then there's no need to install 2.6 elsewhere to "practice" your upgrade - you will want to set up a new 2.8 installation, and practice taking a sqldump and a copy of your uploads directory from the 2.6 instance, and then running all the steps described in the upgrading documentation. 

See: 
Good luck!

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

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Bob Higgie

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Jan 23, 2024, 9:13:20 AMJan 23
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Thanks Jim and Dan,
This very much newbie really appreciates your help. 
I'll act on your advice Dan.
Bob. 

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