upload failed due to Unexpected '<' in attribute value

CPAS Forum (Inactive)
upload failed due to Unexpected '<' in attribute value wonjong.moon  2007-01-26 06:27
Status: Closed
Assigned To: adam
 
I had the following error message. I attached the log file.
Would you explain what's wrong and how to upload xtandem result without restarting whole process again, please? I tried to upload search.xar.xml file, bud it did not work.

26 Jan 2007 05:35:16,878 INFO : No experiment data handler registered for mime type text/xml on file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.xtan.xml, no special loading will be done on this file.
26 Jan 2007 05:35:16,880 INFO : Finished trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.xtan.xml into the system
26 Jan 2007 05:35:16,881 INFO : Trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml into the system
26 Jan 2007 05:35:16,915 INFO : prepareRun: Starting upload from "MFL25-101906-pl1011.pep.xml"
26 Jan 2007 05:35:16,954 INFO : Clearing out existing MS2 data for MFL25-101906-pl1011.pep.xml
26 Jan 2007 05:35:17,043 INFO : Finished clearing out existing MS2 data for MFL25-101906-pl1011.pep.xml
26 Jan 2007 05:35:17,079 ERROR: XMLStreamException in next()
com.ctc.wstx.exc.WstxParsingException: Unexpected '<' in attribute value
 at [row,col {unknown-source}]: [339,57]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.parseNormalizedAttrValue(WstxStreamReader.java:1834)
    at com.ctc.wstx.sr.WstxStreamReader.handleNsAttrs(WstxStreamReader.java:2862)
    at com.ctc.wstx.sr.WstxStreamReader.handleStartElem(WstxStreamReader.java:2767)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2691)
 
 
jeckels responded:  2007-01-26 13:27
From the error message in the log, CPAS is failing to parse the pep.xml file. There's a problem on line 339. If you take a look, it might give you a pointer as to the cause of the problem. Also, can you attach the file, or at least the first 500 lines if it's very large?
 
brendanx responded:  2007-01-26 13:41
Yes, line 339 is:

<parameter name="pipeline, protocol description" value="<note type=" input" label="protein, cleavage semi">

which is not valid XML. You can fix this file by changing it to:

<parameter name="pipeline, protocol description" value="protein, cleavage semi"/>

You should also edit /protocols/xtandem/Partial.xml to change:

  <note label="pipeline, protocol description" type="input">&lt;note type="input" label="protein, cleavage semi"&gt;yes&lt;/note&gt;</note>

to:

  <note label="pipeline, protocol description" type="input">protein, cleavage semi</note>

Or this will happen every time you use that protocol. Apparently the pipeline doesn't like it when you put XML tags in your protocol description.

I will post a bug here, but try to stay away from <> in your protocol description until you get our next release.
 
wonjong.moon responded:  2007-01-26 15:28
Thank you very much.

Here's the link to the whole files xtan.xml. pep.xml. prot.xml

http://binf.gmu.edu/wmoon/MF-pl1011-Dec05.zip

I will fix that line, try to load again. Thank you.
 
wonjong.moon responded:  2007-01-26 16:52
I fixed the line 339 and partial.xml as you said, but another error message I got.
I checked the line 59262 in pep.xml and prot.xml. I don't see something wrong. You can find the lines if you download the files from the link in my previous post. Thank you.

26 Jan 2007 16:36:19,107 INFO : Finished trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml into the system
26 Jan 2007 16:36:19,109 INFO : Trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml into the system
26 Jan 2007 16:36:19,139 INFO : Finished trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml into the system
26 Jan 2007 16:36:19,142 INFO : Trying to load data file file:/proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.prot.xml into the system
26 Jan 2007 16:36:19,151 INFO : Starting to load ProteinProphet file /proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.prot.xml
26 Jan 2007 16:36:19,157 INFO : Resolved referenced PepXML file to /proteomics/Duffy/CPAS/3550_3/MF-pl1011-Dec05/xtandem/Partial/MFL25-101906-pl1011.pep.xml
26 Jan 2007 16:36:19,166 INFO : MFL25-101906-pl1011.pep.xml has already been loaded so it does not need to be reloaded
26 Jan 2007 16:36:55,919 INFO : Loaded 50 protein groups...
26 Jan 2007 16:37:11,204 INFO : Loaded 100 protein groups...
26 Jan 2007 16:37:21,184 INFO : Loaded 150 protein groups...
26 Jan 2007 16:37:30,941 INFO : Loaded 200 protein groups...
26 Jan 2007 16:37:34,015 FATAL: Exception during load
org.fhcrc.cpas.exp.XarFormatException: org.fhcrc.cpas.exp.ExperimentException: com.ctc.wstx.exc.WstxParsingException: Unexpected '<' in attribute value
 at [row,col {unknown-source}]: [59262,10]
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:925)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:340)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:164)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:116)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:124)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.run(ExperimentPipelineJob.java:133)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    at java.util.concurrent.FutureTask.run(FutureTask.java:123)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    at java.lang.Thread.run(Thread.java:595)
Caused by: org.fhcrc.cpas.exp.ExperimentException: com.ctc.wstx.exc.WstxParsingException: Unexpected '<' in attribute value
 at [row,col {unknown-source}]: [59262,10]
    at org.fhcrc.cpas.ms2.ProteinProphetExperimentDataHandler.importFile(ProteinProphetExperimentDataHandler.java:36)
    at org.fhcrc.cpas.exp.XarReader.loadDataFile(XarReader.java:921)
    ... 13 more
Caused by: com.ctc.wstx.exc.WstxParsingException: Unexpected '<' in attribute value
 at [row,col {unknown-source}]: [59262,10]
    at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:396)
    at com.ctc.wstx.sr.WstxStreamReader.parseNormalizedAttrValue(WstxStreamReader.java:1834)
    at com.ctc.wstx.sr.WstxStreamReader.handleNsAttrs(WstxStreamReader.java:2862)
    at com.ctc.wstx.sr.WstxStreamReader.handleStartElem(WstxStreamReader.java:2767)
    at com.ctc.wstx.sr.WstxStreamReader.nextFromTree(WstxStreamReader.java:2691)
    at com.ctc.wstx.sr.WstxStreamReader.next(WstxStreamReader.java:971)
    at org.fhcrc.cpas.tools.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.fhcrc.cpas.tools.ProtXmlReader$Protein.loadChildren(ProtXmlReader.java:162)
    at org.fhcrc.cpas.tools.ProtXmlReader$Protein.<init>(ProtXmlReader.java:155)
    at org.fhcrc.cpas.tools.ProteinGroup.getProteins(ProteinGroup.java:109)
    at org.fhcrc.cpas.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:115)
    at org.fhcrc.cpas.ms2.ProteinProphetExperimentDataHandler.importFile(ProteinProphetExperimentDataHandler.java:28)
    ... 14 more
26 Jan 2007 16:37:34,019 FATAL: Upload FAILED
 
brendanx responded:  2007-01-26 17:07
Well, at line 59261 (the line about where the error is reported) I see:

         <annotation protein_description="2" num_tot_proteins="/>

I have no idea why ProteinProphet would write this line. It sure looks corrupted. You might want to see if this happens every time you run this. If so, then report to the Sashimi project.

You should be able to fix this quickly by changing the line to:

         <annotation protein_description="2" num_tot_proteins="1"/>