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[Developers] Cannot extract data from a study on an upgraded database

Please, I have an urgent matter:
I have a database coming from OpenClinica 3.0.4.2 on a Postgres 9.0
database, which is now on a OpenClinica 3.1.2-Communiry on a Postgres 8.4
database.
The migration worked fine. The database contains 2 studies.
I can create data sets and extract data with no problems from study A. But
when I do the same on study B, I get the following:
The extract data job failed with the message:
java.io.UTFDataFormatException: Invalid byte 2 of 3-byte UTF-8 sequence.
More information may be available in the log files.
The log in the log files isn't worth much (tomcat6-stdout):
found both id 7 and dataset 16
found odm xml file path C:\Program Files\Apache Software Foundation\Tomcat
6.0\openclinica2.datadatasets\16\2012\10\19\232930271
found xslt file name C:\Program Files\Apache Software Foundation\Tomcat 6.0
\openclinica2.dataxslt\ODMToTAB.xsl
== found job date: Fri Oct 19 23:29:30 CEST 2012
Warning: at xsl:variable on line 735 of :
SXWN9001: A variable with no following sibling instructions has no effect
Warning: at xsl:variable on line 1009 of :
SXWN9001: A variable with no following sibling instructions has no effect
Error
java.io.UTFDataFormatException: Invalid byte 2 of 3-byte UTF-8 sequence.
trying to retrieve status on
16_EXCEL_Urine_24h_2012-10-19-232930266.xls1350682170272 XsltTriggers
found state: -1
adding a message!
net.sf.saxon.trans.DynamicError: java.io.UTFDataFormatException: Invalid
byte 2 of 3-byte UTF-8 sequence.
at net.sf.saxon.event.Sender.sendSAXSource(Sender.java:283)
at net.sf.saxon.event.Sender.send(Sender.java:144)
at net.sf.saxon.event.Sender.send(Sender.java:46)
at net.sf.saxon.Controller.transform(Controller.java:1340)
at
org.akaza.openclinica.job.XsltTransformJob.executeInternal(XsltTransformJob.java:264)
at
org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:199)
at
org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
Caused by: java.io.UTFDataFormatException: Invalid byte 2 of 3-byte UTF-8
sequence.
at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.scanContent(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanContent(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$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.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at net.sf.saxon.event.Sender.sendSAXSource(Sender.java:270)
... 7 more
---------
java.io.UTFDataFormatException: Invalid byte 2 of 3-byte UTF-8 sequence.
at org.apache.xerces.impl.io.UTF8Reader.invalidByte(Unknown Source)
at org.apache.xerces.impl.io.UTF8Reader.read(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.scanContent(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanContent(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at net.sf.saxon.event.Sender.sendSAXSource(Sender.java:270)
at net.sf.saxon.event.Sender.send(Sender.java:144)
at net.sf.saxon.event.Sender.send(Sender.java:46)
at net.sf.saxon.Controller.transform(Controller.java:1340)
at
org.akaza.openclinica.job.XsltTransformJob.executeInternal(XsltTransformJob.java:264)
at
org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
at org.quartz.core.JobRunShell.run(JobRunShell.java:199)
at
org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
File Name?EXCEL_Urine_24h_2012-10-19-230444192.xls
file to deleted:EXCEL_Urine_24h_2012-10-19-230444192.xlsFile Not to
deleted:EXCEL_Urine_24h_2012-10-19-230444192.xls
File Name?Urine_24hD20121019232930+0200.xml
trying to retrieve status on
16_EXCEL_Urine_24h_2012-10-19-232930266.xls1350682170272 XsltTriggers
found state: -1
adding a message!
No matter which extract output format I choose, I get the same error.
Unfortunately, I cannot see which character or line of text that causes
this UTFDataFormatException.
Even when I create datasets containing just a single item, I get the same
error. Please note, that data extracts the other study on the same database
work perfectly.
Does anyone have an idea to what could be wrong?? How do I check which
character or which line this causes the exception to be thrown?
Best regards,
Janus
This discussion has been closed.