Failing t/SeqIO/bsml_sax.t due to 404 for DTD URL

[zmughal]

The test failure shows up as

http error : Unknown IO error
# Looks like your test exited with 255 just after 1.
t/SeqIO/bsml_sax.t .................. 
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 14/15 subtests 

This only occurs when older versions of XML::LibXML are installed which is currently the case in Debian (discovered via https://github.com/bioperl/bioperl-live/pull/374#issuecomment-1515090544). Per the changelog at Debian, an older version of XML::LibXML is being used due to security issues with loading an external DTD https://metadata.ftp-master.debian.org/changelogs//main/libx/libxml-libxml-perl/libxml-libxml-perl_2.0207+dfsg+really+2.0134-1_changelog.

There are several workarounds:

• The current DTD could be changed to a working URL which is currently

   t/data/U83300.bsml:<!DOCTYPE Bsml PUBLIC "-//EBI//Labbook, Inc. BSML DTD//EN" "http://www.ebi.ac.uk/xembl/dtd/BSML2_2.DTD">

from http://www.ebi.ac.uk/xembl/dtd/BSML2_2.DTD to one linked from http://xml.coverpages.org/bsml.html.

• Switch the parser used in the test (or library code) to one that does not try to load the external DTD.

$XML::SAX::ParserPackage = "XML::SAX::PurePerl";

Future fix could be to make sure that any XML::SAX parser has a feature to turn off loading the external DTD or supply the DTD locally.

Connects with https://github.com/shlomif/perl-XML-LibXML/issues/71.

[zmughal]

Some more info:

• There is also a BSML 3.1 DTD copy at https://github.com/JCVI-VIRIFX/bsml/blob/master/schema/bsml3_1.dtd. It can not be used however since it is only available via HTTPS and some SAX parsers such as XML::LibXML can only work with HTTP.
• Using the BSML 2.2 DTD from http://xml.coverpages.org/bsml.html works on debian:bullseye but not on debian:bookworm because of a change in libxml where it gives the error:

  tree error : xmlAddEntity: invalid redeclaration of predefined entity
  tree error : xmlAddEntity: invalid redeclaration of predefined entity
  # Looks like your test exited with 255 just after 1.
  t/SeqIO/bsml_sax.t .................. 
  Dubious, test returned 255 (wstat 65280, 0xff00)
  Failed 14/15 subtests 

  More info here https://gitlab.gnome.org/GNOME/libxml2/-/issues/307 (in newer libxml versions, this error will be a warning instead).