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Error uploading xars created via "SimpleFractionationProtocolTemplate"

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Error uploading xars created via "SimpleFractionationProtocolTemplate" wongch  2006-06-24 09:28
Status: Closed
 
Starting with Pipeline tab's "Process and Upload data" and perform the "serach peptide" for 2 or more .mzXML files. If one create a MS2 protocol with SimpleFractionationProtocolTemplate and specify that the same protocol was used to create all files (i.e. shared protocol), the uploading of the first .xar.xml will be completed successfully, but the remaining will all error with
"FATAL: Exception during load
org.fhcrc.cpas.exp.XarFormatException: Protocol actions for protocol urn:lsid:localhost:Protocol.Folder-27:MS2.PreSearch.Fractions.fraction do not match those that have already been loaded. The existing protocol has 4 actions but the file contains 6 actions.

Is this 'illegal'? Any other combination does not generate this error. (I have attached the .xar.log and 2 .xar.xml files.)
 
 
jeckels responded:  2006-06-26 14:11
This should be a legal to load into the a single folder. I was just able to load both XARs into the same folder on my machine.

After the first XAR has been imported, go to the Experiment tab for that folder. Click on the relevant protocol, which should be "fraction (LCMS2 with Fractions)". What do you see in the Protocol Steps section? You should have five entries (see below), but I suspect you will have fewer.

fraction Sample Prep fraction Fractionation fraction LC MS2 Convert to mzXml Mark Run Outputs

Josh
 
wongch responded:  2006-06-26 16:57
Hi Josh,

There are 5 entries. However, when I imported B02.xar.xml, I still get the same error.

Any idea on why the log says "The existing protocol has 4 actions but the file contains 6 actions. " as compared to 5 actions but contains 6 actions? How could I confirm these numbers?

I have also tried re-installed CPAS v1.4, but I still get the same error.

Cheers, Chee-Hong.
 
jeckels responded:  2006-06-27 10:10
The first action in a protocol action set always refers to the back to the parent protocol. We filter this out in the UI, which is why the XAR has 6 actions but the UI only shows 5.

I'm not sure why CPAS, when it compares the protocol in the database with the one in the XAR, thinks that the one in the database has only 4 actions. I did a diff of the two XARs you uploaded and they have exactly the same protocol definition.

Can you go to the Experiment tab, click on the relevant experiment, and export a XAR for the run that loaded successfully? We can look at the protocol actions in the exported XML file and compare with the source file, which might provide some clues.
 
wongch responded:  2006-06-28 09:19
Hi Josh,

That's a good idea… approaching it from another angle. I tried that but got an expcetion. I have attached the log.

I did a quick trace of the code and found that while importing B02.xar.xml, the code will remove some of the existing entries in the database (from B01.xar.xml) to prepare for upload of B02.xar.xml. This leaves 4 entries behind, and the comparison with new information (from B02.xar.xml) does not tally.

Will look futher into this while waiting for your advice.

Thanks! Chee-Hong.
 
jeckels responded:  2006-06-28 10:41
Good catch - I failed to notice that when I looked at your log file. That's certainly the problem, but I'm not sure what might cause it.

Loading these XARs locally, CPAS does not try to delete any of the protocols are part of uploading the second XAR. It should only try to upload them if they aren't referenced by another run. I was also unable to repro the problem with exporting the XAR.

Does the graph for the first experiment run look normal? I'm attaching what I see when I click on the "Run for B01" node to get the full details. If that looks good, I think you're on the right track trying to debug why CPAS thinks it can delete those two protocols.
 
adam responded:  2007-01-04 09:08