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https://issues.apache.org/jira/browse/XALANJ-2365?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=12671176#action_12671176
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Henk Spaan commented on XALANJ-2365:
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I also got this problem on 2.7.1.
Unfortunately it's not consistent.
After a reboot of the appserver, the problem goes away for a few transforms and 
then returns. 
So, it's probably a resource problem that's caught by an dysfunctional catch.

Searching the sources I only see a reference to "SystemId Unknown" in 
DefaultErrorHandler.
DefaultErrorHandler does not throw TransformerExceptions when an error() is 
issued, so I guess that explains the transformer doesn't fail.
However it does throw an exceptions in error(SaxParseException).

So where is the bug?
No idea.
I'll try a custom errorhandler and cross my fingers that we can reproduce it 
after a new release in the customer's test environment.

My advice:
A NPE without stacktrace is not informative and there are probably more 
examples.
Whenever the cause of a TransformerException is a RuntimeException or Error, it 
should be upgraded to fatal.
The question is just: where do check the exception type.
That's for someone else to decide, if anyone still cares to maintain Xalan.

> NPE in DOMSource transformation using xsl:copy-of select
> --------------------------------------------------------
>
>                 Key: XALANJ-2365
>                 URL: https://issues.apache.org/jira/browse/XALANJ-2365
>             Project: XalanJ2
>          Issue Type: Bug
>          Components: transformation
>    Affects Versions: 2.7
>         Environment: Windows XP, running Sun Java 1.5 and IBM Java 1.5
>            Reporter: Andrew Hay
>             Fix For: The Latest Development Code
>
>         Attachments: copy-of_select.xml, XMLValidatorUpdate.xsl
>
>
> We're currently working on moving from Xalan 2.3.1 to Xalan 2.7.0 and have
> encountered a problem with xsl:copy-of.  Using StreamSource transformations,
> the code behaves as expected.  However when using a DOMSource transformation
> (which we mostly do) a NullPointerException is thrown.  The transformation
> is exited at the point reached without any exception being thrown. 
> Unfortunately the resulting XML is missing nodes that had not been reached
> in the transformation.  
> The XSL stylesheet is very similar to many others that we have, with the
> template causing the problem being :-
>    <xsl:template match="/WorkingDocument/Notes/Request" mode="build">
>        <Request>
>          <xsl:copy-of select = "Message"/>
>          <xsl:copy-of select = "Action"/>                     
>          <xsl:copy-of select = "NPQuote"/>
>          ......
>          Some manipulation of data in the Request node
>          .......
>        </Request>
>    </xsl:template>
> The node /WorkingDocument/Notes/Request/NPQuote does not exist.  Xalan
> outputs a warning message "SystemId Unknown; Line #37; Column #37;
> java.lang.NullPointerException" but does not throw an Exception.  No node
> after the completion of the previous line appears in the resulting XML.
> I've tried this in Xalan 2.7.0 unsuccessfully and also recreated the same
> problem this week in Xalan 2.7.1.

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