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Error on index with latest version of cpath code
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Ruth  
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 More options Jul 27, 1:11 pm
From: Ruth <ruth.isser...@utoronto.ca>
Date: Mon, 27 Jul 2009 10:11:35 -0700 (PDT)
Local: Mon, Jul 27 2009 1:11 pm
Subject: Error on index with latest version of cpath code
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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


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Ethan Cerami  
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 More options Jul 27, 2:34 pm
From: Ethan Cerami <cer...@cbio.mskcc.org>
Date: Mon, 27 Jul 2009 14:34:18 -0400
Local: Mon, Jul 27 2009 2:34 pm
Subject: Re: Error on index with latest version of cpath code
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What data sources have you imported?  Looks like it could be something
with the biopax input files...?

Ruth wrote:
> 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
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org

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Ruth Isserlin  
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 More options Jul 27, 2:47 pm
From: "Ruth Isserlin" <ruth.isser...@utoronto.ca>
Date: Mon, 27 Jul 2009 14:47:21 -0400
Local: Mon, Jul 27 2009 2:47 pm
Subject: RE: Error on index with latest version of cpath code
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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


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Ethan Cerami  
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 More options Jul 27, 3:01 pm
From: Ethan Cerami <cer...@cbio.mskcc.org>
Date: Mon, 27 Jul 2009 15:01:16 -0400
Local: Mon, Jul 27 2009 3:01 pm
Subject: Re: Error on index with latest version of cpath code
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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

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

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Ruth Isserlin  
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 More options Jul 28, 9:03 am
From: "Ruth Isserlin" <ruth.isser...@utoronto.ca>
Date: Tue, 28 Jul 2009 09:03:09 -0400
Local: Tues, Jul 28 2009 9:03 am
Subject: RE: Error on index with latest version of cpath code
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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

  _____  

From: cpath-dev@googlegroups.com [mailto:cpath-dev@googlegroups.com] On
Behalf Of Ethan Cerami
Sent: Monday, July 27, 2009 3:01 PM
To: cpath-dev@googlegroups.com
Cc: gro...@cbio.mskcc.org
Subject: Re: Error on index with latest version of cpath code

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 wrote:

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


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