[Biopython-dev] [Bug 2938] Bio.Entrez.read() returns empty string for HTML (not an error)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2938





------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk  2009-12-18 05:44 EST -------
(In reply to comment #6)
> The offending XML file (the one that does not start with <?xml) is created by
> efetch from the journals database. Upon the EUtils documentation more
> carefully, it seems that XML output from the journals database is not
> officially supported; only text and html output are supported. One option is
> to simply remove the offending XML file from the tests, and raise an error
> whenever Entrez.read is presented with data that do not start with <?xml.
> Additionally, we could add a parser for the text output generated by efetch
> from the journals database.

Hmm - sounds like a plan, but maybe drop the Entrez team a query about this.
Does the current funny XML file have anything useful in it?

Peter


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