define.xml generation error

April 20, 2010

Attempting to generate a define.xml, I get the following error:

java.lang.NullPointerException
 at org.opencdisc.validator.DefineDocumentGenerator.close(DefineDocumentGenerator.java:379)
 at org.opencdisc.validator.DefineDocumentGenerator.generate(DefineDocumentGenerator.java:374)
 at org.opencdisc.validator.DefaultValidator.generate(DefaultValidator.java:154)
 at org.opencdisc.validator.gui.ValidatorClient$ProcessMonitor.run(ValidatorClient.java:1527)

I've not had any issue running SDTM validation on these data. Ideas?

Thanks!

Forums

Hi,

 

Was a define.xml document created in the location that you had specified? Also, please verify your version of the Validator by going to Help -> About OpenCDISC Validator. I think that I have an idea of what the issue might be, so we'll narrow it down and hopefully get everything working for you.

 

Regards,

Tim

OK...I think the original email was a share security issue, but now I get the following:

java.lang.NullPointerException
 at net.sf.saxon.event.XMLEmitter.attribute(XMLEmitter.java:381)
 at net.sf.saxon.event.ProxyReceiver.attribute(ProxyReceiver.java:152)
 at net.sf.saxon.event.XMLIndenter.attribute(XMLIndenter.java:90)
 at net.sf.saxon.event.ProxyReceiver.attribute(ProxyReceiver.java:152)
 at net.sf.saxon.event.ReceivingContentHandler.startElement(ReceivingContentHandler.java:265)
 at org.opencdisc.validator.DefineDocumentGenerator.startElement(DefineDocumentGenerator.java:589)
 at org.opencdisc.validator.DefineDocumentGenerator.startElement(DefineDocumentGenerator.java:581)
 at org.opencdisc.validator.DefineDocumentGenerator.printItemGroupDef(DefineDocumentGenerator.java:426)
 at org.opencdisc.validator.DefineDocumentGenerator.generate(DefineDocumentGenerator.java:345)
 at org.opencdisc.validator.DefaultValidator.generate(DefaultValidator.java:154)
 at org.opencdisc.validator.gui.ValidatorClient$ProcessMonitor.run(ValidatorClient.java:1527)

Here's the Release info:

Validator Version - 1.0.1

Java Runtime - 1.6.0_03

OS - Windows 2003 5.2 x86

This run DID create a define.xml. ItemRefs appear to have been created; ITEMDEFs were not. Let me know if and how to send the incomplete XML.

Thanks for the help! Very much appreciated!

Hi,

 

This is a known issue that will be fixed in our next release, and we apologise for the inconvenience. You'll experience this behaviour when the define.xml generator can't find an exact match for your dataset in our configuration template, since not all of the the information it tries to print out is available to it. In the future, it will just use blanks for this missing information (it's some attributes on your ItemGroupDef) like it does for other information it cannot determine in advance.

 

Regards,

Tim

OK - Thanks for the heads up...if there's a workaround you can directly me to, that would be great. In the meantime, I'll try to figure out a workaround, and share if I come up with one.

Best,

Sean

Hi Sean,

 

The only real workaround that I can think of is to exclude the datasets that are causing the exception to be thrown, and then manually enter the ItemGroupDef for that domain (Alternatively you can create a definition for it in a custom configuration document; this ends up being essentially the same thing). The dataset(s) which are causing the issue should have a Configuration Unavailable error if you perform a SDTM validation on them, which is related to the reason that they cause this exception to be thrown by the generator.

 

That being said, this is definitely fixed in the next release (which we're working hard on right now), so once that comes out you won't have to worry about it anymore.

 

Regards,

Tim

I created a define file and found that a lot of the standard ItemDef Length values for dates such as AESTDTC were defined as - Length="". This created some errors when submitted for checking. Is this a problem with the program. I was using validator 1.0.

Here is a sample of the error messages:

**Parsing Error**  Line: 829  Message: cvc-pattern-valid: Value '' is not facet-valid with respect to pattern '-?[0-9]+' for type 'integer'.
**Parsing Error**  Line: 829  Message: cvc-attribute.3: The value '' of attribute 'Length' on element 'ItemDef' is not valid with respect to its type, 'integer'.
Line 829: <ItemDef OID="AE.AEENDTC" Name="AEENDTC" DataType="datetime" Length="" Origin="" Comment="" def:Label="End Date/Time of Adverse Event"/>

 

Hi David,

 

The Length attribute should not show up with DataType="datetime", so this is a bug in the Validator. We've previously identified this issue, and it will be fixed in the upcoming release. Thanks for your feedback, and we apologise for the inconvenience.

 

Regards,

Tim