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Re: [EP-tech] Elements-EPrints Odd Characters stopping upload

Hi James,

Ah, so it looks like the error message is wrong rather than necessarily the code.  I should probably fix that and change it to \\u{%04X}.  If you issue where the first fail_hi is called on the second in teh snippet of code you provided (i.e. which one is line 178).

Symplectic are responsible for the code in eprints3/symplectic/perl_lib/Symplectic/RepoProcess/MetadataManager.pm so I would not want to hack around with it.  This is why I think both us and they are keen for people to move to RT2 as having code that sits on top of EPrints maintained by a third-party is not ideal, as the change management process can be a nightmare.  You could suggest your idea to Symplectic but for such rare border cases (which can be resolved manually) and with RT2 available, I don't think they would be keen or making changes to the RT1 code unless it is a very small change and they can be confident it would not have any side effects.

Regards

David Newman

On 17/02/2021 12:18, James Kerwin wrote:
CAUTION: This e-mail originated outside the University of Southampton.
Hi David,

Thank you for your reply. Unfortunately I don't have access to the Elements database(s) but I've explained this issue to our Elements people and hopefully should get a response. Meanwhile, some time ago Mr Salter gave me the means to extract the Elements xml and transform it via the crosswalks outside of EPrints, so I may do that with the different records and see what we get. Doing this has only just now occurred to me now so I'll give it a go.

On the subject of the character in question... The error code comes from (I think!):

eprints3/perl_lib/URI/Escape.pm

Specifically here in the _fail_hi sub:

"sub uri_escape {
    my($text, $patn) = @_;
    return undef unless defined $text;
    if (defined $patn){
        unless (exists  $subst{$patn}) {
            # Because we can't compile the regex we fake it with a cached sub
            (my $tmp = $patn) =~ s,/,\\/,g;
            eval "\$subst{\$patn} = sub {\$_[0] =~ s/([$tmp])/\$escapes{\$1} || _fail_hi(\$1)/ge; }";
            Carp::croak("uri_escape: $@") if $@;
        }
        &{$subst{$patn}}($text);
    } else {
        $text =~ s/($Unsafe{RFC3986})/$escapes{$1} || _fail_hi($1)/ge;
    }
    $text;
}

sub _fail_hi {
    my $chr = shift;
    Carp::croak(sprintf "Can't escape \\x{%04X}, try uri_escape_utf8() instead", ord($chr));"

The FULL error log line says:

Can't escape \\x{2019}, try uri_escape_utf8() instead at /opt/eprints3/perl_lib/URI/Escape.pm line 178.\n\tURI::Escape::_fail_hi('\xe2\x80\x99') called at /opt/eprints3/perl_lib/URI/Escape.pm line 171\n\tURI::Escape::uri_escape('Published by the American Physical Society under the terms of...') called at (eval 177) line 82\n\tEPrints::Config::uolrepo::__ANON__('dataset', 'EPrints::DataSet=HASH(0x7f21238f9358)', 'repository', 'Symplectic::Wrappers::EPrintsSession=HASH(0x7f2124610710)', 'dataobj', 'EPrints::DataObj::EPrint=HASH(0x7f21285879b0)', 'changed', 'HASH(0x7f212d684f18)') called at /opt/eprints3/perl_lib/EPrints/DataSet.pm line 1517\n\tEPrints::DataSet::run_trigger('EPrints::DataSet=HASH(0x7f21238f9358)', 105, 'dataobj', 'EPrints::DataObj::EPrint=HASH(0x7f21285879b0)', 'changed', 'HASH(0x7f212d684f18)') called at /opt/eprints3/perl_lib/EPrints/DataObj.pm line 669\n\tEPrints::DataObj::commit('EPrints::DataObj::EPrint=HASH(0x7f21285879b0)', undef) called at /opt/eprints3/perl_lib/EPrints/DataObj/EPrint.pm line 1011\n\tEPrints::DataObj::EPrint::commit('EPrints::DataObj::EPrint=HASH(0x7f21285879b0)') called at /opt/eprints3/perl_lib/Symplectic/RepoProcess/MetadataManager.pm line 355\n\tSymplectic::RepoProcess::MetadataManager::add_preferred_bibliographic('Symplectic::RepoProcess::MetadataManager=HASH(0x7f2123858468)', 'eprint', 'EPrints::DataObj::EPrint=HASH(0x7f21285879b0)', 'raw_record', 'XML::LibXML::Document=SCALAR(0x7f212858bb60)', 'types', 'ARRAY(0x7f21254315a0)', 'limit_to', 'ARRAY(0x7f21215fceb8)', ...) called at /opt/eprints3/perl_lib/Symplectic/RepoProcess/MetadataManager.pm line 240\n\tSymplectic::RepoProcess::MetadataManager::add_bibliographic('Symplectic::RepoProcess::MetadataManager=HASH(0x7f2123858468)', 'eprint', 'EPrints::DataObj::EPrint=HASH(0x7f21285879b0)', 'publication', 'Symplectic::PubsModel::Publication=HASH(0x7f212d6b7fe8)') called at /opt/eprints3/perl_lib/Symplectic/RepoProcess/IngestWorkflow.pm line 203\n\tSymplectic::RepoProcess::IngestWorkflow::update_metadata('Symplectic::RepoProcess::IngestWorkflow=HASH(0x7f212858f348)', 'eprint', 'EPrints::DataObj::EPrint=HASH(0x7f21285879b0)', 'publication', 'Symplectic::PubsModel::Publication=HASH(0x7f212d6b7fe8)', 'auth_details', 'Symplectic::PubsModel::AuthDetails=HASH(0x7f212d785c38)', 'record', 'Symplectic::RepoModel::PublicationsRecord=HASH(0x7f212c73f510)', ...) called at /opt/eprints3/perl_lib/Symplectic/RepoProcess/PublicationManager.pm line 65\n\tSymplectic::RepoProcess::PublicationManager::get_deposit_representation('Symplectic::RepoProcess::PublicationManager=HASH(0x7f212d7ac290)', 'publication', 'Symplectic::PubsModel::Publication=HASH(0x7f212d6b7fe8)', 'auth_details', 'Symplectic::PubsModel::AuthDetails=HASH(0x7f212d785c38)') called at /opt/eprints3/perl_lib/Symplectic/Process/FileDepositProcessor.pm line 148\n\tSymplectic::Process::FileDepositProcessor::handle('Symplectic::Process::FileDepositProcessor=HASH(0x7f212d6d73b0)', 'pid', 485375, 'auth_details', 'Symplectic::PubsModel::AuthDetails=HASH(0x7f212d785c38)', 'deposit_props', 'Symplectic::PubsModel::DepositProperties=HASH(0x7f212e8a0440)', 'atom', 'CGI::File::Temp=GLOB(0x7f212d7fae08)', ...) called at /opt/eprints3/perl_lib/Symplectic/Handlers/RepositoryHandler.pm line 235\n\tSymplectic::Handlers::RepositoryHandler::post_handler('session', 'Symplectic::Wrappers::EPrintsSession=HASH(0x7f2124610710)', 'request', 'Apache2::RequestRec=SCALAR(0x7f212e8a77a8)', 'auth_details', 'Symplectic::PubsModel::AuthDetails=HASH(0x7f212d785c38)') called at /opt/eprints3/perl_lib/Symplectic/Handlers/RepositoryHandler.pm line 109\n\tSymplectic::Handlers::RepositoryHandler::handler_multi('Apache2::RequestRec=SCALAR(0x7f212e8a77a8)', undef) called at /opt/eprints3/perl_lib/Symplectic/Apache/Rewrite.pm line 98\n\tSymplectic::Apache::Rewrite::__ANON__('Apache2::RequestRec=SCALAR(0x7f212e8a77a8)') called at -e line 0\n\teval {...} called at -e line 0\n

I'm making some big assumptions, but I THINK the "\\x{%04X}" is saying "take 4 characters from the result of ord($chr) and put them here". I'm possibly very wrong. I think any solution for this needs to belong in the Symplectic code on the repo server. I don't fancy altering core EPrints code for the sake of this. I'll be in a whole world of hell before I know it. Yesterday when tracing this I ended up at:

eprints3/symplectic/perl_lib/Symplectic/RepoProcess/MetadataManager.pm

Reading through the code it appears to identify the preferred record and start processing it. Perhaps this is a good opportunity to intervene and either swap bad characters for good ones or encode/decode "properly" (as if I know what I'm talking about). Complicated slightly by not being able to thoroughly test it. I suppose another option would be to see what XSLT etc. can do with regard to this and so catch the problem within the crosswalks.

If we verify the manual record in Elements it gets a higher precedence than the Scopus record and so the problem disappears.

Regarding the other problem with the file link I will need to refamiliarise myself with it and I'll reply later. Plus this email is already wordy enough as it is!

Thanks,
James



On Wed, Feb 17, 2021 at 10:31 AM David R Newman <drn@ecs.soton.ac.uk> wrote:

Hi James,

I think you would need to look at this field in the Elements record in its database to look how it is being stored differently when there is an import compared to where there is manual entry.  As you said I think the problem is in part that text box entries get parsed and encoded before going into the database but imports do not (or at very least the process between input and output to the Elements database is different).  It would be useful to know how they look different in the Elements database as they may assist making EPrints more resilient to unexpected encodings in future. 

However "\\x{2019}" looks like an escaped version of something that is not particularly valid.  If this was "\\u{2019}" this would probably work better as \x I think can only be used to represent a standard ASCII character that can be only two hex digits like \x3a is a colon ":". \u is used for the extended character set (i.e. UTF-16).  \u{2019} in UTF-8 would be \xE2\x80\x99.

It would be interesting to get a bit more information about your other issue with regular quote marks and semi-colons that are part of the standard ASCII set rather than an extended characters.  These really should not be causing a problem.

Regards

David Newman

On 17/02/2021 09:44, James Kerwin via Eprints-tech wrote:
CAUTION: This e-mail originated outside the University of Southampton.
Hi All,

This is an Elements/EPrints question. Apologies that it isn't purely EPrints, but this is probably the best place to get an answer. I want to know if others experience this or it's some oddity to our setup.

We are using RT1 (for now) and EPrints 3.3.14 (also for now until upgrade). Occasionally we get an Elements record that is from Scopus, PubMed etc. that has an odd character in it that prevents upload. When I look in the Apache logs it tells me the problem. Yesterday's one was the presence of:

 "Unicode Character “’” (U+2019)"

Which showed in the logs as:

"Can't escape \\x{2019}, try uri_escape_utf8() instead at /opt/eprints3/perl_lib/URI/Escape.pm"

Importantly if I copy the problem characters to the manual elements record it doesn't pose a problem. There appears some processing to properly encode characters entered via text box, but not characters dragged in from other sources into Elements.

I've also had the issue with the files containing "'" or" ";" etc not being accessible via Elements (a very similar, but different problem).

I found where I COULD fix the former issue, but it involves changing EPrints code when I SHOULD be altering the Symplectic connector code on the repo server.

Anyway, I'm not specifically looking for a solution, but has anybody else experienced anything similar? If so, does it stop with RT2? I hope to raise a ticket with Symplectic over this eventually.

Thanks,
James



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