Annotation Load fails: Data truncation

Installation Forum (Inactive)
Annotation Load fails: Data truncation greener  2008-04-23 10:47
Status: Closed
 
I went to upload the current swiss and uniprot databases into the new CPAS and received a data truncation error. I have a python script to trim these databases down so they will load more efficently but before I run it I wanted to see if there is something else you would suggest. Thanks again you guys for all your help and support, The new system looks great! Tons of great new features!
-Rich


ERROR AnnotationUploadManager 2008-04-23 10:32:24,575 JobThread-4.1 : Failed to parse file /data/db/200804021/uniprot_trembl.xml
java.sql.DataTruncation: Data truncation
    at org.labkey.ms2.protein.uniprot.uniprot.beginElement(uniprot.java:111)
    at org.labkey.ms2.protein.XMLProteinHandler.startElement(XMLProteinHandler.java:222)
    at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
    at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source)
    at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.labkey.ms2.protein.XMLProteinHandler.parse(XMLProteinHandler.java:297)
    at org.labkey.ms2.protein.XMLProteinLoader.parseFile(XMLProteinLoader.java:74)
    at org.labkey.ms2.protein.AnnotationUploadManager$AnnotationLoadJob.run(AnnotationUploadManager.java:132)
    at java.util.concurrent.Executors$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)
 
 
jeckels responded:  2008-04-28 11:04
Hi Rich,

It's hard to tell from the error output (I just improved the logging for 8.2) but it appears that either the path to the file or the comment for the upload may be longer than the columns allow in the database. Both are currently limited to 200 characters.

Does that match up with what you're trying to upload? If so, does the problem go away if you make either of the values shorter?

Thanks,
Josh
 
greener responded:  2008-04-30 07:08
Thanks Josh, having a smaller path did the trick. Thanks -Rich