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bioperl / bioperl-live

Core BioPerl 1.x code
http://bioperl.org
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Fix bsml_sax.t by using lax SAX parser #381

Closed zmughal closed 1 year ago

zmughal commented 1 year ago

The test t/SeqIO/bsml_sax.t may fail on systems with older versions of XML::LibXML due to a 404 for the external BSML DTD's URL. This gives the error:

http error : Unknown IO error
t/SeqIO/bsml_sax.t ..................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 14/15 subtests

Uses lax parser XML::SAX::PurePerl within the test which does not try to fetch the external DTD.

Fixes https://github.com/bioperl/bioperl-live/issues/376.

Connects with https://github.com/bioperl/bioperl-live/pull/379.

zmughal commented 1 year ago

I only did the change here within the test. I don't know where BSML is being used, but perhaps this should also be noted in the documentation?

zmughal commented 1 year ago

CC: @hyphaltip, @cjfields

Thoughts in particular about where the specific SAX parser should be chosen (either just the test file or within the .pm)?

cjfields commented 1 year ago

@zmughal did you want to have a crack at the conflict resolution on this one too? It looks like a simple conflict in the Changes file, you're probably the best judge on how to resolve it among the different pull requests.