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Xar XML file import problems after peptide database search

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Xar XML file import problems after peptide database search greg.tyrelle  2006-03-28 00:04
Status: Closed
 
I have successfully installed CPAS 1.1 on a RedHat Enterprise Linux 3.0 system. I am running the recommended version of Tomcat and Postgres 8.0.6.

I have tried uploading example data into the project root directory and then running a database search against UniProt. The Xtandem search seem to execute without any problems (the cpas.log indicates no errors), however after the search completes CPAS attempts to load an Xar file that describes the search run (generated automatically ?). When the Xar file is loaded the following database error occurs:

org.fhcrc.cpas.exp.XarFormatException: java.sql.SQLException: ERROR: insert or update on table "objectproperty" violates foreign key constraint "fk_objectproperty_object"

After browsing the previous support messages I discovered a similar problem with importing Xar files here:

https://cpas.fhcrc.org/announcements/home/support/details.view?rowId=85

See the reload.txt attachment. The database error is the same, however the Xar file that the Xtandem search (pipeline module) generates does not have PropertyObjectDeclaration elements ?

The full output is in the attached search.log file, I have also included the Xar file generated by the search.

Any help would be greatly appreciated as I am not familiar enough with the codebase yet to start debugging this problem myself.

Cheers,

_greg
 
 
Peter responded:  2006-03-28 23:04
Greg,

I think this is caused by a bug in the xar xml template that is used to geneate search.xar.xml. try opening it in a text editor and look for the string

${RunLSIDBase}::MS2.ConvertToPepXml

take out the extra : and try uploading the xar again.

this shows up for me if you try to upload the same xar.xml in 2 different folders, which is why it escaped our testing.

Let me know.

Peter Hussey
 
greg.tyrelle responded:  2006-03-31 01:07
Hello Peter,

I removed the extra : from the experiment template and tried the search again. However I get another error, this one also seems to be a problem with loading the generated Xar file:

org.fhcrc.cpas.exp.XarFormatException: java.sql.SQLException: ERROR: value too long for type character varying(50)

I have attached the log file, which contains the full stack trace.

I now understand why I was getting the previous error. I was running the same search multiple times (with the same parameters) hence uploading the same Xar file to two different folders.
 
greg.tyrelle responded:  2006-04-04 01:27
Doh! The previous error was due to the database encoding being LATIN1. I dropped the database and recreated it with UNICODE encoding which fixed the 'value too long for type character' error.

However upon restarting tomcat, CPAS complained about the "core" schema not being available. Previous problems suggested that I needed to restart tomcat and try to access CPAS again (after which it would load the 'core' schema). I did this and had the same problem with the "core" schema missing.

After restarting both tomcat and postgres, dropping and recreating the cpas database I could not resolve the problem. I ended up running the bootstrap.sql script directly on the CPAS database using psql. Problem solved and everything works fine now.

Thanks for your help.
 
adam responded:  2007-01-03 14:47