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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Oct 28 10:57:42 UTC 2009


------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-10-28 06:57 EST -------
Good point - and hopefully the NCBI will make all their XML consistent.

In the meantime, instead of the white list, how about a blacklist?
i.e. If the data starts "<html" (ignoring case) raise an error?
We could also spot things like FASTA and GenBank files etc, and
as all we want to do is spot non-XML, this should be reliable.

We discussed some of these issues before: I originally suggested
doing an XML check in Bio.Entrez.efetch (etc), and you countered
this saying the format validation should be in the parser (as in
this specific bug report):


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