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Re: [EP-tech] Debian9 full-upgrade to Debian10 likes to remove eprints

  • To: <th.lauke@arcor.de>
  • Subject: Re: [EP-tech] Debian9 full-upgrade to Debian10 likes to remove eprints
  • From: David R Newman <drn@ecs.soton.ac.uk>
  • Date: Mon, 7 Dec 2020 17:30:59 +0000
Hi Thomas,
I am still confused how you got round the problem of EPrints being uninstalled because of the shift from MySQL and MariaDB between Debian 9 and 10.  Maybe, I should wait for your complete instructions when you have got everything working as you want. You could have probably allowed EPrints to have been uninstalled and then re-installed again after the Debian 9 - 10 upgrade has completed.  I think such a removal as part of an OS upgrade should not remove anything that could not be replaced by re-installing post upgrade.  Assuming you have not changed an core code files.
I generally try to avoid installing EPrints from package managers.  EPrints is both complex and has a large number of dependencies and is also liable to be hacked around with in ways that do not always play nicely with package managed upgrades. Also running an EPrints package upgrade is not something that should be done lightly.  To the extent that I would advise you "apt hold" so the package only get upgrade when explicitly requested rather than part of a general upgrade of packages.  I remember when a colleague of mine tried to get EPrints added to the main Debian distribution and the long list dependencies (if you include implicit (i.e. dependencies of dependencies), dependencies and large number of files within the package was one of the reasons it was not accepted.
Regarding MariaDB vs MySQL argument.  I generally install EPrints or RHEL-based Linux operating systems which has been using MariaDB for a while.  Apart from one issue we had with MariaDB, which presented as sorting issues in lists of EPrints [1], I don't have anything negative to say about MariaDB.  I think [1] is only an issue in pre-10.x versions of MariaDB but I have not had a chance to thoroughly test this.  (Also, recent EPrints have a generic fix for this that applies whatever MySQL or MariaDB version is installed).  My colleague who is more of an expert on databases says there are a lot of improvements in the latest (10.x) versions of MariaDB that can help deal with issues that complex EPrints repositories can suffer with such as exceeding the row length for a table.  I also believe later versions of MariaDB 10.x Enterprise comes pre-compiled with a maximum of 128 indexes per table rather than 64, which has been another issue on a number of larger EPrints repositories of which I am aware. 

Regards

David Newman

[1] https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmariadb.com%2Fkb%2Fen%2Fwhy-is-order-by-in-a-from-subquery-ignored%2F&amp;data=04%7C01%7C%7C12702716211d4c8929dc08d89ad5dd1c%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637429590615214324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=gnzzHkSCJcnZm52tZ5n5ftTRGyN7Wy%2Fp%2BfszW%2F8DImw%3D&amp;reserved=0

On 07/12/2020 16:55, th.lauke@arcor.de wrote

CAUTION: This e-mail originated outside the University of Southampton.

Hi David,


It would be useful for clarity if you could detail the exact steps that you had to take ...

yes, for sure, after passing the final goal ... and successful reproduction on our production server;
fortunately `script` helps :)


to keeping/upgrading MySQL between Debian 9 and Debian 10.

as indicated by EPrints status, mariaDB is still running ...
EPrints Release:        3.4.2
Database Driver:        EPrints::Database::mysql [DBI 1.642, DBD::mysql 4.050]
Database Server Version:        MySQL 10.1.47-MariaDB-0+deb9u1
XML Library:    XML::LibXML 2.0134 /usr/lib/x86_64-linux-gnu/perl5/5.28/XML/LibXML.pm


adding MySQL's own APT repository so that it continue to exist according to your operating system ...

obviously mariaDB has to be deactivated in order to allow mysql the operation!


1. Does cfg/cfg.d/10_core.pl exist for you archive and is $c->{host} set
to the hostname for you testing clone and the URL you are accessing
/cgi/users/login on in your web browser?

yes


2. Have you run "epadmin generate_apacheconf --system --replace" before
reloading Apache?

no, but my correct updating was ignored (i.e. overridden by the 'commented' old line): as stated on https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhttpd.apache.org%2Fdocs%2Fcurrent%2Fen%2Fconfiguring.html&amp;data=04%7C01%7C%7C12702716211d4c8929dc08d89ad5dd1c%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637429590615214324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=LyidYbUgmdd3z5pkd6msWyXiSNvx1WG7oPczVxBA6gg%3D&amp;reserved=0
the comment sign has to be the very first sign in the first column ...!


3. Do you have HTTPS enabled on this test clone in 10_core.pl or another
file in your archive's cfg/cfg.d/ directory (e.g. https.pl).  If so what
is $c->{securehost} set to?

fortunately the server is running behind the fire wall, so I don't have to care for this :)

Finally again, I will be back when mysql is really engaged
Thomas

P.S.: What do you think about mariaDB?


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