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<p>Hi Jim,</p>
<p>Regarding installing XML::LibXML on EPrints, I think the page
that you may have seen the guide for how to install this was on
the EPrints installation page for Debian / Ubuntu:</p>
<p><a class="moz-txt-link-freetext" href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.eprints.org%2Fw%2FInstalling_EPrints_on_Debian%2FUbuntu%23Installing_EPrints_from_Source&data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7C5cd12d9afec14cad5d7b08d9d9fdabbc%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780505819830130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Oj2SHyU91DqiN7AL2lh5Gzhjlo9kzOBzkf2EhKwwWo8%3D&reserved=0" originalSrc="https://wiki.eprints.org/w/Installing_EPrints_on_Debian/Ubuntu#Installing_EPrints_from_Source" shash="my1UuzLb/KbKHBpkQd9Pa5fiRnbk/5bsuz9oS74OkUcTdRDVsRlggz9sl3SfMT9S024IS/vCDluMomQKNpYm2BuYUx/81ywImIT0Q07mGKhrx6MNtR8Tyd/glnYbvq8pZ5yIAB/lZC8SFxEhZt+N4u0omRIVuORzciixFMdswyA=">https://wiki.eprints.org/w/Installing_EPrints_on_Debian/Ubuntu#Installing_EPrints_from_Source</a></p>
<p>My general advice would always be to install from the OS's
package manager rather than CPAN. You may get a slightly earlier
version of the Perl module but it will get updated automatically
when you do package upgrades. If you use CPAN there is a good
chance this will never get upgraded until you move server again.</p>
<p>I don't think it matters that the version specified is 1.63. As
I understand the use command will not complain unless the version
installed is earlier than this. I typically run version 2.0018 at
the moment and EPrints does not complain about this not being
1.63. Why 1.63 was specified is a a legacy thing before my time.
I assume there was functionality missing in earlier versions.
However, now no one would be using such an old version it is
probably superfluous. Although it should make no difference with
modern systems, it is probably best to leave the version number to
use alone, to avoid any unintended consequences.</p>
<p>The way that EPrints XML init code works is as follows:</p>
<p>1. Tests if XML::LibXML is installed and returns if yes.</p>
<p>2. If not returned, prints a deprecation warning.<br>
</p>
<p>3. Tests if XML::GDOME is installed and returns if yes.</p>
<p>4. If not returned uses XML::DOM which is provided as part of the
EPrints codebase, so will be initialised for XML as a last
resort. This is what caused you your initial error message, as
this packaged with EPrints version of XML::DOM has not be updated
for quite some time.<br>
</p>
<p>I am looking towards just using XML::LibXML in later versions of
EPrints, probably 3.5.x. This is probably a couple of years off
based on current timescales. At which point EPrints would fail
when you run "epadmin test" and will tell you how to fix (i.e.
install XML::LibXML). As other options will be removed, I don't
think there is much point updating the packaged with EPrints
version of XML::DOM to address the original issue you reported.<br>
</p>
<p>Regards</p>
<p>David Newman<br>
</p>
<div class="moz-cite-prefix">On 17/01/2022 19:32, Jim Brinkley via
Eprints-tech wrote:<br>
</div>
<blockquote type="cite" cite="mid:EMEW3|53b6a816de0c30d39481090ed218fa51y0GJcW14eprints-tech-bounces|ecs.soton.ac.uk|41E856AA-4637-4530-BEE1-6297B3A311F0@uw.edu">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">John,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
That did it! A few more specifics in case someone else has
this problem:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">The
main issue turned out to be that I hadn’t installed
XML::LibXML even though I thought I had. I found that out
when I tried your suggestion:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">perl
-e 'use XML::LibXML 1.63;' which told me the module wasn’t
installed.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">So
in Ubuntu I did apt-get install libxml-libxml-perl, which
I saw somewhere is recommended over installing by CPAN
(don’t remember where). I don’t know whether this
installed 1.63, but the perl <br>
“use..” statement seemed to be OK.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">After
this “epadmin test” had no errors, as did “generate_views.
“, and I no longer get the Internal Server error when I go
to a new view.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">A
little more detail:<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">After
looking at XML.pm I see (as you note) that the system
will try to use LibXML if $c->(enable_libxml) does not
exist (which it doesn’t in my case). Given that I hadn’t
installed LibXML properly the "use EPrints::XML::LibXML;
1"; at line 73 will fail and it will default to requiring
Eprints::XML::DOM at line 85. (Assuming I remember my perl
correctly).<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I
also noted that the $c datastructure comes from
SystemSettings:conf, which I believe is written by the
installer. So somehow the configure script of the
installer must have throught I did have LibXML . That’s
easily possible because I first installed this in 2019 on
CentOS after migrating and upgrading from an earlier
Eprints2 installation, then migrated again to Ubuntu. So
probably I missed some step in the migration process.<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">In
any case it seems to work now. I really appreciate your
taking the time to help me with this. And after looking at
the code more I also appreciate how much effort has gone
into creating this very nice program.<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Jim</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-family:"Calibri",sans-serif;color:black" lang="EN-GB">From:
</span></b><span style="font-family:"Calibri",sans-serif;color:black" lang="EN-GB">John Salter <a class="moz-txt-link-rfc2396E" href="mailto:J.Salter@leeds.ac.uk"><J.Salter@leeds.ac.uk></a><br>
<b>Date: </b>Monday, January 17, 2022 at 2:52 AM<br>
<b>To: </b>Jim Brinkley <a class="moz-txt-link-rfc2396E" href="mailto:brinkley@uw.edu"><brinkley@uw.edu></a>,
<a class="moz-txt-link-rfc2396E" href="mailto:eprints-tech@ecs.soton.ac.uk">"eprints-tech@ecs.soton.ac.uk"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:eprints-tech@ecs.soton.ac.uk"><eprints-tech@ecs.soton.ac.uk></a><br>
<b>Subject: </b>RE: Internal server error when
refreshing views<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-GB"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">Hi Jim,<br>
I've had a better look, and this is the block that checks
which XML modules to use, and also produces the warning
you see:<br>
<a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feprints%2Feprints3.4%2Fblob%2Fmaster%2Fperl_lib%2FEPrints%2FXML.pm%23L65-L86&data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7C5cd12d9afec14cad5d7b08d9d9fdabbc%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780505819830130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=F4G1XMA6dzBdsyoddYRmCV0zKxIo0P7GKQO%2FW36kwyg%3D&reserved=0" originalSrc="https://github.com/eprints/eprints3.4/blob/master/perl_lib/EPrints/XML.pm#L65-L86" shash="MKMk35Ln+st0JDMur+7RDSOnPnVzWL5yomyUp3dRTR5xaJ0AUhL/himuY8wH+OdOlV6BzD97I36d+arLWyhizJFbBsGs+qMIzkE2xcxnDUtxILECFYGcFLKFP5xAhWjninOMYJOsRtpXZXkGnWMvaJ4Axx11tETUWZxFCWzOjaU=" originalsrc="https://github.com/eprints/eprints3.4/blob/master/perl_lib/EPrints/XML.pm#L65-L86" shash="shE0U6WSGyDf2UvvMk+punHjOxZ88tdETnsSMd08AeQQVISx2Y5yZmgXBffhn6VIteP2sDMhXnFlmHyDDu4BOkw7ERRP9OGjt1+96VQu8JZ/bekFNd7Lg6pc8I+jjkDeadpjJ1CRhDdi7pwn/yV9MoyE33lIjncZ861VCzxH2Cg=" moz-do-not-send="true">https://github.com/eprints/eprints3.4/blob/master/perl_lib/EPrints/XML.pm#L65-L86</a><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">The option to select which XML library to use
is:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">$c->{enable_libxml}<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">From the above, EPrints will try to use
LibXML if:<br>
$c->{enable_libxml} *<b>does not</b>* exist<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">$c->{enable_libxml} exists and is set to 1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">If either:<br>
- 'enable_libxml' is set to 0<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">- the module EPrints::XML::LibXML produces
errors<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">then the deprecation warning message is
produced.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">So, try grepping for 'enable_libxml' in
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">~/lib/<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">~/archives/ARCHIVEID/cfg/<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">~/cfg/<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">First I would try checking LibXML is happy.
Try running these on the commandline (as the EPrints
user):<br>
perl -e 'use XML::LibXML 1.63;'<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">perl -e 'use XML::LibXML::SAX;'<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">If either of the above lines produce errors
or warnings, I'd look at fixing them first.
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">Secondly, I'd try grepping for
'enable_libxml' in:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"> [EPRINTS_ROOT]/lib/<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"> [EPRINTS_ROOT]/cfg/<br>
[EPRINTS_ROOT]/archives/[ARCHIVE_ID]/cfg/<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">If it is explicitly disabled, try
commenting-out that line, and running:<br>
[EPRINTS_ROOT]/bin/epadmin test<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">To see if things look happy.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB">John<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D" lang="EN-GB"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
John Salter
<br>
<b>Sent:</b> 14 January 2022 20:38<br>
<b>To:</b> Jim Brinkley <a class="moz-txt-link-rfc2396E" href="mailto:brinkley@uw.edu"><brinkley@uw.edu></a>;
<a class="moz-txt-link-abbreviated" href="mailto:eprints-tech@ecs.soton.ac.uk">eprints-tech@ecs.soton.ac.uk</a><br>
<b>Subject:</b> Re: Internal server error when
refreshing views<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">Hi Jim,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">If memory serves me correctly, somewhere*
in the EPrints config, there is an option to use either
DOM, or LibXML.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">This faint memory ties in with your note
about previous upgrades. It seems like your install
might not be using LibXML, even though you've added the
packages to the server.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">*the 'somewhere' is possibly the crux here.
My v3.4 knowledge isn't as ingrained as v3.3, and I'm
not at my computer at the moment.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">If you try grepping for 'DOM' in:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">~/lib/cfg<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-family:"Segoe
UI",sans-serif;color:black;background:white" lang="EN-GB">~/perl_lib/SystemSettings.pl</span><span lang="EN-GB"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-family:"Segoe
UI",sans-serif;color:black;background:white" lang="EN-GB">~/cfg/</span><span lang="EN-GB"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-family:"Segoe
UI",sans-serif;color:black;background:white" lang="EN-GB">~/archives/ARCHIVE_ID/cfg/</span><span lang="EN-GB"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-family:"Segoe
UI",sans-serif;color:black;background:white" lang="EN-GB">do you find any options that say 'use
XML::DOM' in some way (although not a literal perl 'use
XML::DOM' statement)?</span><span lang="EN-GB"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-family:"Segoe
UI",sans-serif;color:black;background:white" lang="EN-GB">Cheers,</span><span lang="EN-GB"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-family:"Segoe
UI",sans-serif;color:black;background:white" lang="EN-GB">John</span><span lang="EN-GB"><o:p></o:p></span></p>
</div>
<div class="MsoNormal" style="margin-left:.5in;text-align:center" align="center">
<span lang="EN-GB">
<hr width="100%" size="0" align="center">
</span></div>
<div id="divRplyFwdMsg">
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black" lang="EN-GB">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black" lang="EN-GB"> Jim Brinkley <<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>><br>
<b>Sent:</b> 14 January 2022 20:13<br>
<b>To:</b> John Salter <<a href="mailto:J.Salter@leeds.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">J.Salter@leeds.ac.uk</a>>;
<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>
<<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>><br>
<b>Cc:</b> Jim Brinkley <<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>><br>
<b>Subject:</b> Re: Internal server error when
refreshing views</span><span lang="EN-GB">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="xmsonormal" style="margin-left:.5in">PS I just
noticed that the error I see in the Apache server log
whenever I get the Internal Server Error is exactly the
same one I see at the end of the output below.<o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"> <o:p></o:p></p>
<p class="xmsonormal" style="margin-left:.5in"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="xmsonormal" style="margin-left:1.0in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Jim Brinkley
<<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>><br>
<b>Date: </b>Friday, January 14, 2022 at 12:07 PM<br>
<b>To: </b>John Salter <<a href="mailto:J.Salter@leeds.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">J.Salter@leeds.ac.uk</a>>,
"<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>"
<<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>><br>
<b>Cc: </b>Jim Brinkley <<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>><br>
<b>Subject: </b>Re: Internal server error when
refreshing views</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.0in"> <o:p></o:p></p>
</div>
<p class="xmsonormal" style="margin-left:1.0in">John,<o:p></o:p></p>
<p class="xmsonormal" style="margin-left:1.5in">
Thanks for you quick reply. My guess is the problem is
not to do with the specific subject “3-D
Reconconstruction” because it occurs for all subjects in
my list, including single word subjects, such as
“MindSeer”. However I just now ran <o:p></o:p></p>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">[EPRINTS_ROOT]/bin/generate_views
[ARCHIVE_ID] --view subjects
</span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">as you suggested,
and got the following output:</span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black"> </span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">eprints@synapse:/opt/eprints3$
bin/generate_views sigpubs --view subjects</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">***
DEPRECATION WARNING ***</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">In
future versions, EPrints will be standardising to only
support the LibXML library for providing XML
functionality.</span><span class="xapple-converted-space">
</span><span class="xs1">Please ensure LibXML is
installed before upgrading EPrints.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
parse_xml_string redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
119.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
_parse_url redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
144.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
parse_xml redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
164.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
event_parse redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
211.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
_dispose redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
248.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
clone_and_own redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
261.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
document_to_string redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
276.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
make_document redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
286.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Subroutine
version redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm line
295.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Can't
use an undefined value as an ARRAY reference at
/opt/eprints3/bin/../perl_lib/XML/DOM/NamedNodeMap.pm
line 142.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1"> </span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">I’ve
seen something like this everytime I’ve run
generate_views. I thought maybe I should update
LibXML, so in Ubuntu I did apt install libxml-perl,
and similar for some of the other ones in the above
list. But from the message above it looks like the
perl modules in eprints3..perl_lib are redefining
existing ones in Ubuntu, so that last error seems to
be happening in the version of XML::DOM in
eprints3..perl_lib.
</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1"> </span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">I
should also say that the last time I moved sigpubs to
a new server (around 2019) I upgraded from Eprints 2
to 3, and I think this problem has been happening ever
since. I pretty much ignored it until now because I
didn’t have time to deal with it, and I could always
tell people to just refresh the browser, but now I
have a bit more time and it would be nice to fix this.</span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1"> </span><o:p></o:p></p>
<p class="xp1" style="margin-left:1.0in"><span class="xs1">Jim</span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black"> </span><o:p></o:p></p>
<p class="xmsonormal" style="margin-left:1.0in"> <o:p></o:p></p>
<p class="xmsonormal" style="margin-left:1.0in"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="xmsonormal" style="margin-left:1.5in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">John Salter
<<a href="mailto:J.Salter@leeds.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">J.Salter@leeds.ac.uk</a>><br>
<b>Date: </b>Friday, January 14, 2022 at 11:27 AM<br>
<b>To: </b>"<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>"
<<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>>,
Jim Brinkley <<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>><br>
<b>Subject: </b>Re: Internal server error when
refreshing views</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"> <o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">Hi Jim,<br>
At a guess, this sounds like something that is
trying to group records together into a browse view
mis-treating the '3-D ...' text - maybe incorrectly
normalising it to create the A / B / C ... links at
the top of the view page.</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black"> </span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">If you have
access to the server, and run:</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">[EPRINTS_ROOT]/bin/generate_views
[ARCHIVE_ID] --view subjects</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">does it give
any additional warnings/errors?</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black"> </span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">Cheers,</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black">John</span><o:p></o:p></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:1.5in"><span style="font-size:12.0pt;color:black"> </span><o:p></o:p></p>
</div>
<div style="margin-left:.5in">
<div style="margin-left:.5in">
<div class="MsoNormal" style="margin-left:.5in;text-align:center" align="center">
<span style="font-size:11.0pt;font-family:"Calibri",sans-serif">
<hr width="100%" size="0" align="center">
</span></div>
</div>
</div>
<div id="x_divRplyFwdMsg">
<p class="xmsonormal" style="margin-left:1.5in"><b><span style="color:black">From:</span></b><span style="color:black">
<a href="mailto:eprints-tech-bounces@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech-bounces@ecs.soton.ac.uk</a>
<<a href="mailto:eprints-tech-bounces@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech-bounces@ecs.soton.ac.uk</a>>
on behalf of Jim Brinkley via Eprints-tech <<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>><br>
<b>Sent:</b> 14 January 2022 19:02<br>
<b>To:</b> <a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>
<<a href="mailto:eprints-tech@ecs.soton.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">eprints-tech@ecs.soton.ac.uk</a>><br>
<b>Subject:</b> [EP-tech] Internal server error when
refreshing views</span> <o:p>
</o:p></p>
<div>
<p class="xmsonormal" style="margin-left:1.5in"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<div style="border:solid #8D3970 1.0pt;padding:9.0pt
9.0pt 9.0pt 9.0pt">
<p class="xmsonormal" style="margin-left:1.5in;line-height:16.5pt;background:#F7F9FA">
<strong><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:#8D3970">CAUTION:</span></strong><span style="font-size:10.5pt;color:#8D3970"> This
e-mail originated outside the University of
Southampton.
</span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="xxmsonormal" style="margin-left:1.5in"><span style="color:black">Hi,</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black"> I run an
eprints3 site at sigpubs.si.washington.edu. It
generally works fine except when a view
regenerates I get an internal server error.</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black"> </span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">To recreate this issue I can
login, go to Admin:System Tools, and then click
on Regenerate Views, which as I understand it,
causes all views to be regenerated whenever I
request them. For example, I can go to menu
Browse:Browse by Subjects, then click on any of
the subjects in my customized subject list, as
for example, my first subject, "3-D
Reconstruction". I then get "Internal Server
Error". If I then refresh the browser page the
error goes away and the correct view appears.
This view then remains correct for as long as
I've tested it, but I think there may be a
timeout when it gets regenerated again.</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black"> </span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">I looked in the apache
server log and find this error whenever I get
the Internal Server Error:</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">Can't use an undefined value
as an ARRAY reference at
/opt/eprints3/perl_lib/XML/DOM/NamedNodeMap.pm
line 142.\n, referer:<span class="xxapple-converted-space"> </span><a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsigpubs.si.washington.edu%2Fview%2Fsubjects%2F&data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7C5cd12d9afec14cad5d7b08d9d9fdabbc%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780505819830130%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=hs6LxH3ka0TQMbnT42L9QPPOObzryhLpV7ouFevrL4g%3D&reserved=0" originalSrc="http://sigpubs.si.washington.edu/view/subjects/" shash="VAkFneF12etNQOdznxVoG8mT65BaKtm69WZRjKfNNmOFgYh75NGo+W/vCCeE9mBIEH8At4sXVIFKj6jdDdcjNg4PwmwRaIoVOYsjJM7BOAf5kXsIYGONkOXrJ0YG6Pt5sHHh5dDrgOzVlOj9gQ/76Wlik+sNb/krGDngEsHf2+E=" originalsrc="http://sigpubs.si.washington.edu/view/subjects/" shash="HRAEQZ7szte6YTuvS+iMTysFCVm31p4FoBkPfmFbx0LQR5QsjvKDZn7ZmaRc48hQtUxL+4NRIS6mKHrgTOwBZBCi6t0MfpQbIYgY8DnS+rKq6vVQhROMs1HAU/xDX2aC9IDsO0PkrVtGIeNE7aYJnI3Hdctj4rhNvSSNiwMyqDE=" title="http://sigpubs.si.washington.edu/view/subjects/" moz-do-not-send="true">http://sigpubs.si.washington.edu/view/subjects/</a></span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black"> </span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">I am running what I think
is the latest stable version of Eprints: 3.4.3,
on Ubuntu 20.04, perl version 5.30, apache2.
Apache is running as www-data.www-data. The
repository is owned by eprints.eprints, and
www-data is in group eprints so it can write
files to the repository. I don't think
permissions are the issue because once I refresh
the page the view is OK, and the files in the
views directory are changed.</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black"> </span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">I've searched the web and
this mailing list and can't find this particular
situation. Any suggestions? Thanks.</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black"> </span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">Jim Brinkley</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">Structural Informatics Group</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">University of Washington</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">Seattle USA</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black">http//:si.washington.edu</span><o:p></o:p></p>
<p class="xxmsonormal" style="margin-left:1.5in"> <o:p></o:p></p>
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<pre class="moz-quote-pre" wrap="">*** Options: <a class="moz-txt-link-freetext" href="http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech">http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech</a>
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