Error on index with latest version of cpath code

[Ruth]

Hi,
I keep getting the following error when I try and index my instance of
cpath. It indexes to 89% and then I get the following error:

Fatal Error: org.jdom.input.JDOMParseException: Error on line 1:
Content is not allowed in prolog. There is no stack trace just this
line.

Thanks,
Ruth

[Ethan Cerami]

What data sources have you imported? Looks like it could be something
with the biopax input files...?

--
Ethan Cerami
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org

[Ruth Isserlin]

Mint, Intact, HPRD, Biogrd, Mips (all converted from PSI to Biopax), and
Kegg, Reactome, NCI, Biocarta, Humancyc, Cellmap, Netpath and INOH.
Is there anyway to fix it without re-building?
Ruth

[Ethan Cerami]

My suggestion would be to modify the indexing code to print out the cpath ID for each record as it is indexed, so that you can find the offending record.

Then, look up the XML_BLOB for that offending record, and see which data source it is.  It *might* be possible to update the XML_BLOB directly, w/o having to rebuild everything, but I would not get your hopes up.

Ethan

[Ruth Isserlin]

Hi Ethan,

Thanks for the suggestion.  I found the offending record and the XML_BLOB actually only contained “[PLACE HOLDER]”.  I removed the record and the indexing worked.

Thanks.

Ruth

 

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