Hi,
We just did our first Sequest mudpit with 8.2 and are getting the failure below, I have attached the xar file.
Thanks,
Bill
01 Aug 2008 23:53:59,043 FATAL: Exception during import
org.labkey.api.exp.XarFormatException: Could not find Parent protocol with LSID urn:lsid:uky.edu:Protocol.Folder-60:MS2.SequestAnalysis.Fractions:3
at org.labkey.api.exp.XarSource.getProtocol(XarSource.java:204)
at org.labkey.experiment.XarReader.loadActionSet(XarReader.java:1522)
at org.labkey.experiment.XarReader.loadDoc(XarReader.java:268)
at org.labkey.experiment.XarReader.parseAndLoad(XarReader.java:107)
at org.labkey.experiment.api.ExperimentServiceImpl.loadXar(ExperimentServiceImpl.java:565)
at org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:126)
at org.labkey.experiment.pipeline.XarImportTask.run(XarImportTask.java:105)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:464)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:569)
at org.labkey.ms2.pipeline.AbstractMS2SearchPipelineJob.run(AbstractMS2SearchPipelineJob.java:167)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
01 Aug 2008 23:53:59,043 FATAL: XAR import FAILED |
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| jeckels responded: |
2008-08-06 16:59 |
Hi Bill,
It looks like there's a bug in the template XAR file for Sequest fraction searches. I'll open a bug to get this fixed, but you should be able to edit the generated .xar.xml and load it to verify that it fixes the problem.
It looks like the attachment didn't show up, but around line 70 in your .xar.xml file you should see a line that looks like:
<exp:Protocol rdf:about="${FolderLSIDBase}:MS2.SequestAnalysis.Fractions:">
It's missing a trailing '3', so change it to:
<exp:Protocol rdf:about="${FolderLSIDBase}:MS2.SequestAnalysis.Fractions:3">
Then browse to the .xar.xml file using the pipeline and click to import it.
Please let me know if that fixes the problem.
Thanks,
Josh |
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| wnels2 responded: |
2008-08-07 07:09 |
Thanks Josh,
I did add the 3 to that line an was able to re-import the xar.
I also opened the ms2.jar in C:\Program Files\Labkey Server\modules\moduleLibDir\ms2 and changed the org.labkey.ms2.pipeline.sequest.templates.MS2SearchSequestFractions.xml to include the 3 and then restarted Tomcat.
This did not work. Am I doing this correctly?
Thanks,
Bill |
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| jeckels responded: |
2008-08-07 10:47 |
Hi Bill,
At startup the server will look for the ms2.jar inside of ms2.module and make sure that it matches the one in moduleLibDir. If it doesn't, it will overwrite the copy in moduleLibDir.
I'm attaching an updated ms2.module. You should be able to overwrite the one in C:\Program Files\Labkey Server\modules, restart the server, and be all set.
Thanks,
Josh |
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| wnels2 responded: |
2008-08-07 11:29 |
Thank you. |
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ms2.module