<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
<p>Hi both,</p>
<p>I thought I should provide a bit if context to the introduction
of the deprecation warning. <br>
</p>
<p>I have been trying to extend the acceptance testing for the
EPrints codebase as part of my CI framework. This means testing
of different EPrints setups. At the moment I run separate daily
testing for the zero and publication flavours of EPrints 3.4.
Having three potential XML libraries (XML::LibXML, XML::GDOME and
XML::DOM) used by EPrints would require running separate testing
against each library. <br>
</p>
<p>Therefore, I did some investigation into the status of all three
libraries. My conclusions were that LibXML is effectively the
industry standard. It is easily available across all platforms
EPrints is supported and looks the best supported going forward.
The latter of these is very important as XML import/export for
EPrints is a critical feature and also a potent vector for
cyberattacks. So I want to make sure the underlying library will
be patched for vulnerabilities and these will be rolled out in a
way that it is easy for those deploying EPrints to upgrade, (i.e.
through OS package management).</p>
<p>As John has identified, EPrints 3.4 (and 3.3) will try to use
LibXML unless it is explicitly disabled (slightly confusingly by
setting enable_libxml to 0). If it is not disabled and
XML::LibXML is not installed, then XML initialisation will fail
rather than try to see if XML::GDOME is installed. Therefore, as
he suggests grepping for 'enable_libxml' through the directory he
lists should help you find the config line you need to comment
out. I would also added ~/site_lib/ to that list, if it exists on
your EPrints repository server.</p>
<p>Regards</p>
<p>David Newman<br>
</p>
<div class="moz-cite-prefix">On 17/01/2022 10:52, John Salter via
Eprints-tech wrote:<br>
</div>
<blockquote type="cite" cite="mid:EMEW3|835ee9f8cc11b7f48837a4eb836e18d5y0GAwP14eprints-tech-bounces|ecs.soton.ac.uk|DU2PR03MB7895EA301F1054687BE0C4E3C4579@DU2PR03MB7895.eurprd03.prod.outlook.com">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]-->
<style>@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}@font-face
{font-family:"Segoe UI";
panose-1:2 11 5 2 4 2 4 2 2 3;}@font-face
{font-family:Menlo;}p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}p.xmsonormal, li.xmsonormal, div.xmsonormal
{mso-style-name:x_msonormal;
margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}p.xxmsonormal, li.xxmsonormal, div.xxmsonormal
{mso-style-name:x_xmsonormal;
margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}p.xp1, li.xp1, div.xp1
{mso-style-name:x_p1;
margin:0cm;
margin-bottom:.0001pt;
font-size:9.0pt;
font-family:Menlo;
color:black;}p.xmsochpdefault, li.xmsochpdefault, div.xmsochpdefault
{mso-style-name:x_msochpdefault;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:10.0pt;
font-family:"Times New Roman",serif;}span.xmsohyperlink
{mso-style-name:x_msohyperlink;
color:#0563C1;
text-decoration:underline;}span.xemailstyle25
{mso-style-name:x_emailstyle25;
font-family:"Calibri",sans-serif;
color:windowtext;}span.xs1
{mso-style-name:x_s1;}span.xapple-converted-space
{mso-style-name:x_apple-converted-space;}span.xxapple-converted-space
{mso-style-name:x_xapple-converted-space;}span.EmailStyle27
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}div.WordSection1
{page:WordSection1;}</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div style="padding-bottom: 10px; padding-top: 5px;">
<div style="padding:12px; border:1px solid #8D3970;
background-color:#F7F9FA; color:#8D3970; font-size:14px;
line-height:22px; font-family: Calibri, Arial, Helvetica,
sans-serif;">
<strong>CAUTION:</strong> This e-mail originated outside the
University of Southampton.
</div>
</div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=k03pxT8JIHNgGShfhm%2FZlalnkgIpEehLkJVUex52BOA%3D&reserved=0" originalSrc="https://github.com/eprints/eprints3.4/blob/master/perl_lib/EPrints/XML.pm#L65-L86" shash="knkBxSd69igpXMonzfn2CKmpRO09nTOwDG0BfNonOG8ICR1dsV+ookS2lHWNc/ZxAyfbbLgJEix8ziyVyqFwFaMgxL7zBV5jBAvEPOkP/pKRhbXLHYyNNyW2tCfWGl3GX1b5G1ax7mtGO1XjxtG5MDePaMvNifAsTtSHmtKmghY=" originalsrc="https://github.com/eprints/eprints3.4/blob/master/perl_lib/EPrints/XML.pm#L65-L86" shash="iEpQhvm7WcApRTR263je3IQMkj0WikD4hB1nF/VwiQVp72di9i0bu9m6optlID4hk9wfCgTn8pStQosomCPwFxIgsPbqubZvqdZ8Z62hMzk3/kD26AlS1DK2cCICwB04HH+9VdWNPdDwMRTFkzHGBMzoUxpQ7XdJPoe2TIf5YAE=" 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"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The
option to select which XML library to use is:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">$c->{enable_libxml}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">From
the above, EPrints will try to use LibXML if:<br>
$c->{enable_libxml} *<b>does not</b>* exist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">$c->{enable_libxml}
exists and is set to 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">If
either:<br>
- 'enable_libxml' is set to 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">-
the module EPrints::XML::LibXML produces errors<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">then
the deprecation warning message is produced.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">So,
try grepping for 'enable_libxml' in
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">~/lib/<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">~/archives/ARCHIVEID/cfg/<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">~/cfg/<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">perl
-e 'use XML::LibXML::SAX;'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Secondly,
I'd try grepping for 'enable_libxml' in:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">
[EPRINTS_ROOT]/lib/<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">
[EPRINTS_ROOT]/cfg/<br>
[EPRINTS_ROOT]/archives/[ARCHIVE_ID]/cfg/<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">To
see if things look happy.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">John<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"> 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"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Hi Jim,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">If memory serves me correctly,
somewhere* in the EPrints config, there is an option to
use either DOM, or LibXML.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">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></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">*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></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">If you try grepping for 'DOM' in:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">~/lib/cfg<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Segoe
UI",sans-serif;background:white">~/perl_lib/SystemSettings.pl</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Segoe
UI",sans-serif;background:white">~/cfg/</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Segoe
UI",sans-serif;background:white">~/archives/ARCHIVE_ID/cfg/</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Segoe
UI",sans-serif;background:white">do you find any
options that say 'use XML::DOM' in some way (although
not a literal perl 'use XML::DOM' statement)?</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Segoe
UI",sans-serif;background:white">Cheers,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Segoe
UI",sans-serif;background:white">John</span><o:p></o:p></p>
</div>
<div class="MsoNormal" style="text-align:center" align="center">
<hr width="98%" size="2" align="center">
</div>
<div id="divRplyFwdMsg">
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;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>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> <o:p></o:p></p>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="xmsonormal"><span lang="EN-US">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></span></p>
<p class="xmsonormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="xmsonormal"><span lang="EN-US"> <o:p></o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="xmsonormal" style="margin-left:36.0pt"><b><span style="font-size:12.0pt;color:black" lang="EN-US">From:
</span></b><span style="font-size:12.0pt;color:black" lang="EN-US">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><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:36.0pt"><span lang="EN-US"> <o:p></o:p></span></p>
</div>
<p class="xmsonormal" style="margin-left:36.0pt"><span lang="EN-US">John,<o:p></o:p></span></p>
<p class="xmsonormal" style="margin-left:72.0pt"><span lang="EN-US"> 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></span></p>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">[EPRINTS_ROOT]/bin/generate_views
[ARCHIVE_ID] --view subjects
</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">as
you suggested, and got the following output:</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">eprints@synapse:/opt/eprints3$
bin/generate_views sigpubs --view subjects</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">*** DEPRECATION WARNING
***</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">In future versions,
EPrints will be standardising to only support the
LibXML library for providing XML functionality.</span></span><span class="xapple-converted-space"><span lang="EN-US">
</span></span><span class="xs1"><span lang="EN-US">Please
ensure LibXML is installed before upgrading EPrints.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine
parse_xml_string redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 119.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine _parse_url
redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 144.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine parse_xml
redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 164.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine event_parse
redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 211.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine _dispose
redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 248.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine
clone_and_own redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 261.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine
document_to_string redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 276.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine
make_document redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 286.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Subroutine version
redefined at
/opt/eprints3/bin/../perl_lib/EPrints/XML/DOM.pm
line 295.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Can't use an undefined
value as an ARRAY reference at
/opt/eprints3/bin/../perl_lib/XML/DOM/NamedNodeMap.pm
line 142.</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">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></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">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></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xp1" style="margin-left:36.0pt"><span class="xs1"><span lang="EN-US">Jim</span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xmsonormal" style="margin-left:36.0pt"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="xmsonormal" style="margin-left:36.0pt"><span lang="EN-US"> <o:p></o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="xmsonormal" style="margin-left:72.0pt"><b><span style="font-size:12.0pt;color:black" lang="EN-US">From:
</span></b><span style="font-size:12.0pt;color:black" lang="EN-US">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><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span lang="EN-US"> <o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">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><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">If
you have access to the server, and run:</span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">[EPRINTS_ROOT]/bin/generate_views
[ARCHIVE_ID] --view subjects</span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">does
it give any additional warnings/errors?</span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">Cheers,</span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US">John</span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span style="font-size:12.0pt;color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
</div>
<div style="margin-left:36.0pt">
<div style="margin-left:36.0pt">
<div class="MsoNormal" style="text-align:center" align="center"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">
<hr width="100%" size="1" align="center">
</span></div>
</div>
</div>
<div id="x_divRplyFwdMsg">
<p class="xmsonormal" style="margin-left:72.0pt"><b><span style="color:black" lang="EN-US">From:</span></b><span style="color:black" lang="EN-US">
<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><span lang="EN-US">
<o:p></o:p></span></p>
<div>
<p class="xmsonormal" style="margin-left:72.0pt"><span lang="EN-US"> <o:p></o:p></span></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:72.0pt;line-height:16.5pt;background:#F7F9FA">
<strong><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:#8D3970" lang="EN-US">CAUTION:</span></strong><span style="font-size:10.5pt;color:#8D3970" lang="EN-US"> This e-mail originated outside the
University of Southampton.
</span><span lang="EN-US"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="xxmsonormal" style="margin-left:72.0pt"><span style="color:black" lang="EN-US">Hi,</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">
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><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">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><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">I looked in the
apache server log and find this error whenever I
get the Internal Server Error:</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">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%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=fzOIf9fe9Wiu1wKd72gvIsviy760%2BhnBOJ0vzJrxOMA%3D&reserved=0" originalSrc="http://sigpubs.si.washington.edu/view/subjects/" shash="UP8r49OR8P50GK+aeVp01wMzmRtxwAw9XWy9clgFbuihtWQfGe0YHKq90bBGaT7naXtDp37REBNd44i644AKm+nVp13+eB+AQBpkVjPx4cN0AtTC6gYE8/CF+eUt/vyTOAcR1trzDzTpwVBpWSB42llzyR39cx4OxigOLCDpCjU=" originalsrc="http://sigpubs.si.washington.edu/view/subjects/" shash="KEYwDFDiQvs/cP+/cPL4ln/yGZ2nhmplRoHeIz7nLDYdAgKVOJ3dryvdx+8K0/pM6v2BwX5Db/WM+DEobYPAR5lZqQFI+sLeYzJMlyarowkygJbGc1Q1Woz6rH1TgXFqZb8kbs4Lux1EZQtWz+ziNjjgz19wJyyK9qWhFSpvzgY=" title="http://sigpubs.si.washington.edu/view/subjects/" moz-do-not-send="true">http://sigpubs.si.washington.edu/view/subjects/</a></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">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><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">I've searched
the web and this mailing list and can't find
this particular situation. Any suggestions?
Thanks.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US"> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">Jim Brinkley</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">Structural
Informatics Group</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">University of
Washington</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">Seattle USA</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt;font-variant-caps:normal;orphans:auto;text-align:start;widows:auto;word-spacing:0px"><span style="color:black" lang="EN-US">http//:si.washington.edu</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="xxmsonormal" style="margin-left:72.0pt"><span lang="EN-US"> <o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<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>
*** Archive: <a class="moz-txt-link-freetext" href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.eprints.org%2Ftech.php%2F&data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rkAnx7lt9Cry7Elj4fIjl4NIxScNh7x%2Frw0S6QwPJHw%3D&reserved=0" originalSrc="http://www.eprints.org/tech.php/" shash="Ze18KOLt2JUne0eLR62J1OWEPe2N7SXlRVX4gegvGEKEJlixK4twir7unQTUtingRjAPVJ5+KjYX69tA9nyYsKl+/mvCnevtDaLWLlhFaNaYYz1W3N90BalqPxA5xxrLujq/Yd0RzsM2WAIIRhBlRgAo4lq3R8f4DVtWrHN9Xyk=">http://www.eprints.org/tech.php/</a>
*** EPrints community wiki: <a class="moz-txt-link-freetext" href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwiki.eprints.org%2F&data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=dMn%2BJNG4okZBadguZsNF7slspWhtYofAWPpYM8MyWd8%3D&reserved=0" originalSrc="http://wiki.eprints.org/" shash="sXpm3/yxC1bjtJR6FFbL3JVrpaFEzVDXmjxzPp4jm/2z+IGdrNz2FSnKkzK0+1pVQZizrzOLEpn/BJNCHi2lWhH6Jw4BPJfoo5CoWpbXNxSQyxLjKvWVGguw8ElDqTN23sa7UpJ/4GmRSOaTY8Yyr8++4LsCxnR0mQinWqyNrpw=">http://wiki.eprints.org/</a></pre>
</blockquote>
<div id="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><br>
<table style="border-top: 1px solid #D3D4DE;">
<tr>
<td style="width: 55px; padding-top: 13px;"><a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.avg.com%2Femail-signature%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Demailclient&data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Bch6rTU%2BYSNQ0kST8zCHw1QZnHl2Tk%2BCarcwaBvsdjo%3D&reserved=0" originalSrc="http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient" shash="vUS5mk+GOyGn2JY4lm4h2gN6pRGjhlu8IG1Ri429QgUMJMmT5qXGP/51dVagYOftiqsjxdPl58wdxXiuc6VZ75ssJj2xhb+lshFpUJ0+MBiWG1wVq+xPY7p3sExYgXc3yl0Q0y/G66KSIf6fUZu5uhuQGKnnBReUVITxAJiv6q4=" target="_blank"><img src="https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png" alt="" width="46" height="29" style="width: 46px; height: 29px;"></a></td>
<td style="width: 470px; padding-top: 12px; color: #41424e; font-size: 13px; font-family: Arial, Helvetica, sans-serif; line-height: 18px;">Virus-free. <a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.avg.com%2Femail-signature%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Demailclient&data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Bch6rTU%2BYSNQ0kST8zCHw1QZnHl2Tk%2BCarcwaBvsdjo%3D&reserved=0" originalSrc="http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient" shash="vUS5mk+GOyGn2JY4lm4h2gN6pRGjhlu8IG1Ri429QgUMJMmT5qXGP/51dVagYOftiqsjxdPl58wdxXiuc6VZ75ssJj2xhb+lshFpUJ0+MBiWG1wVq+xPY7p3sExYgXc3yl0Q0y/G66KSIf6fUZu5uhuQGKnnBReUVITxAJiv6q4=" target="_blank" style="color: #4453ea;">www.avg.com</a>
</td>
</tr>
</table><a href="#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2" width="1" height="1"> </a></div></body>
</html>