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    <p>Hi both,</p>
    <p>I thought I should provide a bit if context to the introduction
      of the deprecation warning.&nbsp; <br>
    </p>
    <p>I have been trying to extend the acceptance testing for the
      EPrints codebase as part of my CI framework.&nbsp; This means testing
      of different EPrints setups.&nbsp; At the moment I run separate daily
      testing for the zero and publication flavours of EPrints 3.4.&nbsp;
      Having three potential XML libraries (XML::LibXML, XML::GDOME and
      XML::DOM) used by EPrints would require running separate testing
      against each library.&nbsp; <br>
    </p>
    <p>Therefore, I did some investigation into the status of all three
      libraries.&nbsp; My conclusions were that LibXML is effectively the
      industry standard.&nbsp; It is easily available across all platforms
      EPrints is supported and looks the best supported going forward.&nbsp;
      The latter of these is very important as XML import/export for
      EPrints is a critical feature and also a potent vector for
      cyberattacks.&nbsp; 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).&nbsp; 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.&nbsp; 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.&nbsp; 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>
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          <strong>CAUTION:</strong> This e-mail originated outside the
          University of Southampton.
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          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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&amp;data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=k03pxT8JIHNgGShfhm%2FZlalnkgIpEehLkJVUex52BOA%3D&amp;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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US">$c-&gt;{enable_libxml}<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US">From
              the above, EPrints will try to use LibXML if:<br>
              $c-&gt;{enable_libxml} *<b>does not</b>* exist<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US">$c-&gt;{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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US">If
              either:<br>
              - &nbsp;'enable_libxml' is set to 0<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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:&quot;Calibri&quot;,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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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:&quot;Calibri&quot;,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:&quot;Calibri&quot;,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:&quot;Calibri&quot;,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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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:&quot;Calibri&quot;,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:&quot;Calibri&quot;,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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US">&nbsp;
              [EPRINTS_ROOT]/lib/<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US">&nbsp;
              [EPRINTS_ROOT]/cfg/<br>
              &nbsp; [EPRINTS_ROOT]/archives/[ARCHIVE_ID]/cfg/<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US">If
              it is explicitly disabled, try commenting-out that line,
              and running:<br>
              &nbsp; [EPRINTS_ROOT]/bin/epadmin test<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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:&quot;Calibri&quot;,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:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span></p>
          <div>
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              1.0pt;padding:3.0pt 0cm 0cm 0cm">
              <p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif" lang="EN-US">From:</span></b><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,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">&lt;brinkley@uw.edu&gt;</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>&nbsp;</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>&nbsp;</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>&nbsp;</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:&quot;Segoe
                UI&quot;,sans-serif;background:white">~/perl_lib/SystemSettings.pl</span><o:p></o:p></p>
          </div>
          <div>
            <p class="MsoNormal"><span style="font-family:&quot;Segoe
                UI&quot;,sans-serif;background:white">~/cfg/</span><o:p></o:p></p>
          </div>
          <div>
            <p class="MsoNormal"><span style="font-family:&quot;Segoe
                UI&quot;,sans-serif;background:white">~/archives/ARCHIVE_ID/cfg/</span><o:p></o:p></p>
          </div>
          <div>
            <p class="MsoNormal"><span style="font-family:&quot;Segoe
                UI&quot;,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>&nbsp;</o:p></p>
          </div>
          <div>
            <p class="MsoNormal"><span style="font-family:&quot;Segoe
                UI&quot;,sans-serif;background:white">Cheers,</span><o:p></o:p></p>
          </div>
          <div>
            <p class="MsoNormal"><span style="font-family:&quot;Segoe
                UI&quot;,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:&quot;Calibri&quot;,sans-serif;color:black">From:</span></b><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,sans-serif;color:black">
                Jim Brinkley &lt;<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>&gt;<br>
                <b>Sent:</b> 14 January 2022 20:13<br>
                <b>To:</b> John Salter &lt;<a href="mailto:J.Salter@leeds.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">J.Salter@leeds.ac.uk</a>&gt;;
                <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>
                &lt;<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>&gt;<br>
                <b>Cc:</b> Jim Brinkley &lt;<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>&gt;<br>
                <b>Subject:</b> Re: Internal server error when
                refreshing views</span> <o:p></o:p></p>
            <div>
              <p class="MsoNormal">&nbsp;<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">&nbsp;<o:p></o:p></span></p>
              <p class="xmsonormal"><span lang="EN-US">&nbsp;<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 &lt;<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>&gt;<br>
                    <b>Date: </b>Friday, January 14, 2022 at 12:07 PM<br>
                    <b>To: </b>John Salter &lt;<a href="mailto:J.Salter@leeds.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">J.Salter@leeds.ac.uk</a>&gt;,
                    &quot;<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>&quot;
                    &lt;<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>&gt;<br>
                    <b>Cc: </b>Jim Brinkley &lt;<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>&gt;<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">&nbsp;<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">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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">&nbsp;</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">&nbsp;
                  </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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</span><span lang="EN-US"><o:p></o:p></span></p>
              <p class="xmsonormal" style="margin-left:36.0pt"><span lang="EN-US">&nbsp;<o:p></o:p></span></p>
              <p class="xmsonormal" style="margin-left:36.0pt"><span lang="EN-US">&nbsp;<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 &lt;<a href="mailto:J.Salter@leeds.ac.uk" moz-do-not-send="true" class="moz-txt-link-freetext">J.Salter@leeds.ac.uk</a>&gt;<br>
                    <b>Date: </b>Friday, January 14, 2022 at 11:27 AM<br>
                    <b>To: </b>&quot;<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>&quot;
                    &lt;<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>&gt;,
                    Jim Brinkley &lt;<a href="mailto:brinkley@uw.edu" moz-do-not-send="true" class="moz-txt-link-freetext">brinkley@uw.edu</a>&gt;<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">&nbsp;<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">&nbsp;</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">&nbsp;</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">&nbsp;</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:&quot;Calibri&quot;,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>
                    &lt;<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>&gt;
                    on behalf of Jim Brinkley via Eprints-tech &lt;<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>&gt;<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>
                    &lt;<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>&gt;<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">&nbsp;<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:&quot;Calibri&quot;,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">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
                        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">&nbsp;</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 &nbsp;menu Browse:Browse by
                        Subjects, then click on any of the subjects in
                        my customized subject list, as for example, my
                        first subject, &quot;3-D Reconstruction&quot;. I then get
                        &quot;Internal Server Error&quot;. 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">&nbsp;</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">&nbsp;</span><a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsigpubs.si.washington.edu%2Fview%2Fsubjects%2F&amp;data=04%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca988862a82514a66fab608d9d9b321c1%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637780185647702009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=fzOIf9fe9Wiu1wKd72gvIsviy760%2BhnBOJ0vzJrxOMA%3D&amp;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">&nbsp;</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&nbsp; 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">&nbsp;</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">&nbsp;</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">&nbsp;<o:p></o:p></span></p>
                  </div>
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      <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>
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