[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


mdehoon at ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #8 from mdehoon at ims.u-tokyo.ac.jp  2010-10-03 09:51 EST -------
(In reply to comment #7)
> Does the current funny XML file have anything useful in it?

Yes, but I doubt that many people (if any) are using the Journals database. If
they do, we could make a straightforward parser for plain-text output from the
Journals database, which is supported by NCBI. See this discussion on the
mailing list:

http://lists.open-bio.org/pipermail/biopython-dev/2010-September/008239.html

To resolve this bug, I have modified the parser such that an error is raised
whenever the XML data do not start with the XML declaration (<!xml... ).
Marking this bug as fixed.


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