Saxon XSLT and XQuery Processor

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Re: [saxon] Using saxon with latest Eclipse (Helios)

From: RB45F <rlb.south@gm...> - 2010-08-28 20:03

Glad to help if I can.

I am running 9.2.1.2 and confirmed the same problem occurs with 9.2.1.1. The
exact error I get is:
java.lang.NoClassDefFoundError: net/sf/saxon/s9api/SaxonApiException

This is when the saxon jar is in the WebContent/WEB-INF/lib folder. As noted
earlier this same project runs properly on tomcat 5.5 / Ubuntu Linux and an
identical project runs properly in earlier versions of eclipse, so it's not
something simple like a bad class path.

Also note that I package saxon with apache jackrabbit database jars and
those jars are picked up correctly in the problematic environment even
though they are deployed identically. The database starts up, my application
starts serving html, and only when I try to run something with saxon do I
get the above error.

Sorry about the incomplete information in my first message. The bug I
mentioned is 3043783 which is just a couple of weeks old. It mentions that
you have a patch in the works so I assumed it would be top of mind.

The problematic environment is the standard amazon EC2 VPS image (linux)
that contains nothing but tomcat. This image is selected by the amazon
eclipse plugin and I have done nothing to customize or modify it. Note the
same amazon EC2 image works fine with saxon if I deploy through an older
eclipse. I suspect the problem lies in the WTP code base of eclipse and
their new version, since their code is in charge of deploying the war to
whatever server you are using.

When searching I found 2 threads that include (I think) a WTP project member
Dave Carver who mentions that he might have to work with you to OSGI enable
saxon:
https://bugs.eclipse.org/bugs/show_bug.cgi?ctype=xml&id=300480
http://www.eclipse.org/forums/index.php?t=msg&goto=536530&;

That's all I can think of at the moment to tell you. Please let me know if
more information would be helpful or if you want me to test a patch for you.

I hope this helps - this sounds like a tricky one to address.

Thanks Michael for your always prompt support. I am a big fan of saxon and
have been for some time.

Michael Kay wrote:
> 
> 
> A number of users have reported class loading issues, but none in terms 
> that are specific enough for me to be confident that I understand the 
> problem and have fixed it. I'm afraid simply reporting that Saxon "will 
> not run" on some particular environment doesn't really help me to 
> identify and investigate the problem. Which Saxon version are you 
> running, anyway? And if you're aware of a logged bug, it helps to cite 
> it. It might have been fixed, it might not - I simply can't tell from 
> this information.
> 
> Problems that only manifest themselves in particular environments are 
> always hard to bottom out, which makes it even more important to provide 
> precise information about what you were doing and how it failed. Please 
> help me fix this one!
> 
> Michael Kay
> Saxonica
> 
> 
> 
> On 27/08/2010 10:58 PM, RB45F wrote:
>> Hello,
>>
>> I am aware of a logged bug regarding class loader issues in eclipse and
>> some
>> other tools. I just upgraded to the Helios (latest) version of Eclipse
>> and
>> found that my saxon-enabled app will no longer run within a standard
>> Amazon
>> EC2 virtual machine. It does still work on other servers that just run
>> tomcat, but EC2 is our production environment and is mandatory in this
>> case.
>>
>> After doing some searching I found the most common workaround is to
>> revert
>> to 9.1 and wait for the bug to get resolved in due course. My problem is
>> that I use the integrated extension function which I think was introduced
>> in
>> 9.2.
>>
>> Is this correct and if so is there another workaround I can try? I'm also
>> curious if the proper fix has an ETA yet. If I can't resolve this I guess
>> I'll have to revert to an older version of eclipse for the time being.
>>
>> Many thanks,
>> Rob
> 
> 
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users 
> worldwide. Take advantage of special opportunities to increase revenue and 
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> 

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Thread	Author	Date
[saxon] Using saxon with latest Eclipse (Helios)	RB45F <rlb.south@gm...>

Re: [saxon] Using saxon with latest Eclipse (Helios)

From: Michael Kay <mike@sa...> - 2010-08-28 19:26

A number of users have reported class loading issues, but none in terms 
that are specific enough for me to be confident that I understand the 
problem and have fixed it. I'm afraid simply reporting that Saxon "will 
not run" on some particular environment doesn't really help me to 
identify and investigate the problem. Which Saxon version are you 
running, anyway? And if you're aware of a logged bug, it helps to cite 
it. It might have been fixed, it might not - I simply can't tell from 
this information.

Problems that only manifest themselves in particular environments are 
always hard to bottom out, which makes it even more important to provide 
precise information about what you were doing and how it failed. Please 
help me fix this one!

Michael Kay
Saxonica

On 27/08/2010 10:58 PM, RB45F wrote:
> Hello,
>
> I am aware of a logged bug regarding class loader issues in eclipse and some
> other tools. I just upgraded to the Helios (latest) version of Eclipse and
> found that my saxon-enabled app will no longer run within a standard Amazon
> EC2 virtual machine. It does still work on other servers that just run
> tomcat, but EC2 is our production environment and is mandatory in this case.
>
> After doing some searching I found the most common workaround is to revert
> to 9.1 and wait for the bug to get resolved in due course. My problem is
> that I use the integrated extension function which I think was introduced in
> 9.2.
>
> Is this correct and if so is there another workaround I can try? I'm also
> curious if the proper fix has an ETA yet. If I can't resolve this I guess
> I'll have to revert to an older version of eclipse for the time being.
>
> Many thanks,
> Rob

Re: [saxon] Using saxon with latest Eclipse (Helios)

From: RB45F <rlb.south@gm...> - 2010-08-28 20:03

Glad to help if I can.

I am running 9.2.1.2 and confirmed the same problem occurs with 9.2.1.1. The
exact error I get is:
java.lang.NoClassDefFoundError: net/sf/saxon/s9api/SaxonApiException

This is when the saxon jar is in the WebContent/WEB-INF/lib folder. As noted
earlier this same project runs properly on tomcat 5.5 / Ubuntu Linux and an
identical project runs properly in earlier versions of eclipse, so it's not
something simple like a bad class path.

Also note that I package saxon with apache jackrabbit database jars and
those jars are picked up correctly in the problematic environment even
though they are deployed identically. The database starts up, my application
starts serving html, and only when I try to run something with saxon do I
get the above error.

Sorry about the incomplete information in my first message. The bug I
mentioned is 3043783 which is just a couple of weeks old. It mentions that
you have a patch in the works so I assumed it would be top of mind.

The problematic environment is the standard amazon EC2 VPS image (linux)
that contains nothing but tomcat. This image is selected by the amazon
eclipse plugin and I have done nothing to customize or modify it. Note the
same amazon EC2 image works fine with saxon if I deploy through an older
eclipse. I suspect the problem lies in the WTP code base of eclipse and
their new version, since their code is in charge of deploying the war to
whatever server you are using.

When searching I found 2 threads that include (I think) a WTP project member
Dave Carver who mentions that he might have to work with you to OSGI enable
saxon:
https://bugs.eclipse.org/bugs/show_bug.cgi?ctype=xml&id=300480
http://www.eclipse.org/forums/index.php?t=msg&goto=536530&;

That's all I can think of at the moment to tell you. Please let me know if
more information would be helpful or if you want me to test a patch for you.

I hope this helps - this sounds like a tricky one to address.

Thanks Michael for your always prompt support. I am a big fan of saxon and
have been for some time.

Michael Kay wrote:
> 
> 
> A number of users have reported class loading issues, but none in terms 
> that are specific enough for me to be confident that I understand the 
> problem and have fixed it. I'm afraid simply reporting that Saxon "will 
> not run" on some particular environment doesn't really help me to 
> identify and investigate the problem. Which Saxon version are you 
> running, anyway? And if you're aware of a logged bug, it helps to cite 
> it. It might have been fixed, it might not - I simply can't tell from 
> this information.
> 
> Problems that only manifest themselves in particular environments are 
> always hard to bottom out, which makes it even more important to provide 
> precise information about what you were doing and how it failed. Please 
> help me fix this one!
> 
> Michael Kay
> Saxonica
> 
> 
> 
> On 27/08/2010 10:58 PM, RB45F wrote:
>> Hello,
>>
>> I am aware of a logged bug regarding class loader issues in eclipse and
>> some
>> other tools. I just upgraded to the Helios (latest) version of Eclipse
>> and
>> found that my saxon-enabled app will no longer run within a standard
>> Amazon
>> EC2 virtual machine. It does still work on other servers that just run
>> tomcat, but EC2 is our production environment and is mandatory in this
>> case.
>>
>> After doing some searching I found the most common workaround is to
>> revert
>> to 9.1 and wait for the bug to get resolved in due course. My problem is
>> that I use the integrated extension function which I think was introduced
>> in
>> 9.2.
>>
>> Is this correct and if so is there another workaround I can try? I'm also
>> curious if the proper fix has an ETA yet. If I can't resolve this I guess
>> I'll have to revert to an older version of eclipse for the time being.
>>
>> Many thanks,
>> Rob
> 
> 
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users 
> worldwide. Take advantage of special opportunities to increase revenue and 
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________
> saxon-help mailing list archived at http://saxon.markmail.org/
> saxon-help@...
> https://lists.sourceforge.net/lists/listinfo/saxon-help 
> 
> 

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Re: [saxon] Using saxon with latest Eclipse (Helios)

From: Michael Kay <mike@sa...> - 2010-08-29 23:51

This doesn't feel to me like something related to bug 3043783. That 
bug involves situation where the Saxon JAR file is successfully loaded, 
and having been loaded, the Configuration fails to initialize properly 
because it fails to find resources or classes within the JAR file itself 
by dynamic loading. Saxon doesn't attempt to do a dynamic load on 
SaxonApiException, so this doesn't feel like the same problem.

Is there any evidence that any Saxon classes have been successfully 
loaded? Is there Saxon code on the stack trace? If there is, then this 
could be a similar problem to 3043783. If not, it looks like a much more 
straightforward situation - the Saxon JAR file itself could not be found 
(by whatever class loader is trying to find it).

Of course, "straightforward" is relative! But it's relatively 
straightforward for me, because if no Saxon code has been loaded, then 
by definition the problem doesn't lie with Saxon code. You say that 
you're "packaging" Saxon, and from the evidence you've given me so far, 
I would say that you've packaged it incorrectly.

 >I suspect the problem lies in the WTP code base of eclipse and their 
new version, since their code is in charge of deploying the war to 
whatever server you are using.

That might well be the case.
> When searching I found 2 threads that include (I think) a WTP project member
> Dave Carver who mentions that he might have to work with you to OSGI enable
> saxon:
> https://bugs.eclipse.org/bugs/show_bug.cgi?ctype=xml&id=300480
> http://www.eclipse.org/forums/index.php?t=msg&goto=536530&;
>
The problems Dave Carver is referring to there are indeed related to 
3043783. The current situation on that bug is that I have produced what 
I hope is a fix, and it's in a trial build which hasn't been generally 
released; I'm hoping to get feedback on it but it's difficult because I 
don't have a test environment that replicates the reported problem.

I have to claim severe ignorance when it comes to OSGi. I've read 
articles that claim to simplify it to the bare essentials, but I have 
great difficulty seeing exactly (a)  what I need to do to Saxon to make 
it work well in an OSGi world, (b) how to test whether I've done it 
right, and (c) how to explain to Saxon users what they should do 
differently as a result. If any OSGi experts on the list would like to 
enlighten me, I'd be very grateful.

Michael Kay
Saxonica

Re: [saxon] Using saxon with latest Eclipse (Helios)

From: RB45F <rlb.south@gm...> - 2010-08-30 05:49

>>You say that you're "packaging" Saxon, and from the evidence you've given
me so far, 
I would say that you've packaged it incorrectly.<<

Poor choice of words. All I meant to say is I put the saxon jar with my
database jars in the WEB-INF/lib folder and the database jars are getting
found properly. Eclipse generates and publishes a war for me. This is how
I've successfully run saxon in (several) earlier versions of eclipse.

Fortunately I can reliably reproduce the problem and can catch the exception
at runtime using an eclipse debugger.

Here is part of the stack trace when ClassNotFoundException is thrown:

Launcher$ExtClassLoader(ClassLoader).findBootstrapClass0(String) line: 891	
Launcher$ExtClassLoader(ClassLoader).loadClass(String, boolean) line: 301	
Launcher$AppClassLoader(ClassLoader).loadClass(String, boolean) line: 299	
Launcher$AppClassLoader.loadClass(String, boolean) line: 276	
Launcher$AppClassLoader(ClassLoader).loadClass(String) line: 251	
WebappClassLoader.loadClass(String, boolean) line: 1275	
WebappClassLoader.loadClass(String) line: 1206	
WebappClassLoader(ClassLoader).loadClassInternal(String) line: 319	
GcStatusUtils.readStatus(String, String, Document, UserRequest) line: 141	

GcStatusUtils.readStatus() is my class and has the following code - this is
where the debugger is positioned for a call to WebappClassLoader with a
param of "net.sf.saxon.s9api.SaxonApiException".

		Node statusNode = XpathXsltUtils.xpathToFirstNode(
				name, 
				gcdoc.getDocumentElement(), 
				null, 
				logger);

The method xpathToFirstNode() does not explicitly reference
SaxonApiException, but SaxonApiException is referenced within an internal
method and is in the class imports.

Note that if I use intellisense to locate a class in the source code editor
net.sf.saxon is not available.

Interestingly, if I inspect the WebappClassLoader instance it does contain a
reference to the saxon jar, as part of a list of all jars in the jarPath
"/WEB-INF/lib". Although I can't confirm it in the debugger, the class
loader appears to be a tomcat class:
http://tomcat.apache.org/tomcat-6.0-doc/api/org/apache/catalina/loader/WebappClassLoader.html

This is from the inspector:

this	WebappClassLoader  (id=76)	
	acc	AccessControlContext  (id=3281)	
	allPermission	AllPermission  (id=3282)	
	antiJARLocking	false	
	classAssertionStatus	null	
	classes	Vector<E>  (id=3285)	
	defaultAssertionStatus	false	
	defaultDomain	null	
	delegate	false	
	domains	HashSet<E>  (id=3292)	
	files	File[1]  (id=3293)	
	hasExternalRepositories	false	
	initialized	true	
	initialized	true	
	jarFiles	JarFile[53]  (id=3295)	
	jarNames	String[53]  (id=3300)	
	jarPath	"/WEB-INF/lib" (id=3301)	
	jarRealFiles	File[53]  (id=3302)	
	lastJarAccessed	1283144670478	
	lastModifiedDates	 (id=3361)	
	loaderDir	File  (id=3362)	
	loaderPC	HashMap<K,V>  (id=3363)	
	nativeLibraries	Vector<E>  (id=3364)	
	needConvert	false	
	nocerts	Certificate[0]  (id=3365)	
	notFoundResources	HashMap<K,V>  (id=3367)	
	package2certs	Hashtable<K,V>  (id=3369)	
	packageAssertionStatus	null	
	packages	HashMap<K,V>  (id=3370)	
	parent	StandardClassLoader  (id=77)	
	parent	StandardClassLoader  (id=77)	
	paths	String[54]  (id=3373)	
	pdcache	HashMap<K,V>  (id=3374)	
	permissionList	ArrayList<E>  (id=3375)	
	repositories	String[1]  (id=3376)	
	repositoryURLs	URL[54]  (id=3377)	
	resourceEntries	HashMap<K,V>  (id=3378)	
	resources	ProxyDirContext  (id=3379)	
	securityManager	null	
	started	true	
	system	Launcher$AppClassLoader  (id=3267)	
	ucp	URLClassPath  (id=3382)	
arg0	"net.sf.saxon.s9api.SaxonApiException" (id=3273)	

At position 44 of jarRealFiles there is a File instance that looks ok like
all the others, which has a path of
"/env/tomcat/webapps/BCW/WEB-INF/lib/saxon9he.jar.jar"

Also interesting is the notFoundResources field, which has 60 entries, b/c
one is for saxon. Here is a copy of all the keys in that map:

{com/sun/org/apache/xml/internal/serializer/Encodings.properties=com/sun/org/apache/xml/internal/serializer/Encodings.properties,
org/apache/derby/loc/m25_en_US.properties=org/apache/derby/loc/m25_en_US.properties,
org/apache/derby/loc/m16_en_US.properties=org/apache/derby/loc/m16_en_US.properties,
org.apache.log4j.LayoutBeanInfo=org.apache.log4j.LayoutBeanInfo,
org/apache/derby/loc/m2.properties=org/apache/derby/loc/m2.properties,
org.apache.derby.loc.m22_en_US=org.apache.derby.loc.m22_en_US,
org/apache/derby/loc/m22_en_US.properties=org/apache/derby/loc/m22_en_US.properties,
net.sf.saxon.s9api.SaxonApiException=net.sf.saxon.s9api.SaxonApiException,
org.apache.derby.loc.m25_en_US=org.apache.derby.loc.m25_en_US,
org.apache.derby.loc.m16_en_US=org.apache.derby.loc.m16_en_US,
org.apache.derby.loc.m25_en=org.apache.derby.loc.m25_en,
org.apache.derby.loc.m16=org.apache.derby.loc.m16,
org/apache/derby/loc/m26_en_US.properties=org/apache/derby/loc/m26_en_US.properties,
javax.servlet.http.HttpServletRequest=javax.servlet.http.HttpServletRequest,
org.apache.derby.loc.m18=org.apache.derby.loc.m18,
org.apache.derby.loc.m2_en=org.apache.derby.loc.m2_en,
org.apache.derby.loc.m13=org.apache.derby.loc.m13,
org/apache/derby/loc/m16.properties=org/apache/derby/loc/m16.properties,
org/apache/derby/loc/m25.properties=org/apache/derby/loc/m25.properties,
org.apache.derby.loc.m26_en=org.apache.derby.loc.m26_en,
org.apache.log4j.PatternLayoutBeanInfo=org.apache.log4j.PatternLayoutBeanInfo,
org/apache/derby/loc/m13.properties=org/apache/derby/loc/m13.properties,
org.apache.derby.loc.m2_en_US=org.apache.derby.loc.m2_en_US,
org.apache.derby.loc.m34_en=org.apache.derby.loc.m34_en,
org.apache.derby.loc.m26_en_US=org.apache.derby.loc.m26_en_US,
logging.properties=logging.properties,
org.apache.derby.loc.m2=org.apache.derby.loc.m2,
org.apache.catalina.servlets.DefaultServlet=org.apache.catalina.servlets.DefaultServlet,
org/apache/derby/loc/m34_en_US.properties=org/apache/derby/loc/m34_en_US.properties,
META-INF/services/org.apache.xerces.xni.parser.XMLParserConfiguration=META-INF/services/org.apache.xerces.xni.parser.XMLParserConfiguration,
org.apache.derby.loc.m25=org.apache.derby.loc.m25,
org.apache.derby.loc.m26=org.apache.derby.loc.m26,
org/apache/derby/loc/m22.properties=org/apache/derby/loc/m22.properties,
org/apache/derby/loc/m13_en_US.properties=org/apache/derby/loc/m13_en_US.properties,
org.apache.derby.loc.m22=org.apache.derby.loc.m22,
org.apache.jasper.servlet.JspServlet=org.apache.jasper.servlet.JspServlet,
javax.servlet.ServletException=javax.servlet.ServletException,
org.apache.derby.loc.m22_en=org.apache.derby.loc.m22_en,
javax.servlet.http.HttpServlet=javax.servlet.http.HttpServlet,
org.apache.log4j.AppenderSkeletonBeanInfo=org.apache.log4j.AppenderSkeletonBeanInfo,
org.apache.derby.loc.m34_en_US=org.apache.derby.loc.m34_en_US,
org.apache.derby.loc.m13_en=org.apache.derby.loc.m13_en,
org/apache/derby/loc/m18.properties=org/apache/derby/loc/m18.properties,
org/apache/derby/loc/m2_en_US.properties=org/apache/derby/loc/m2_en_US.properties,
org/apache/derby/loc/m18_en_US.properties=org/apache/derby/loc/m18_en_US.properties,
org.apache.derby.loc.m34=org.apache.derby.loc.m34,
javax.servlet.http.HttpSession=javax.servlet.http.HttpSession,
com.ibm.uvm.tools.DebugSupport=com.ibm.uvm.tools.DebugSupport,
org.apache.derby.loc.m16_en=org.apache.derby.loc.m16_en,
org.apache.log4j.WriterAppenderBeanInfo=org.apache.log4j.WriterAppenderBeanInfo,
org.apache.log4j.FileAppenderBeanInfo=org.apache.log4j.FileAppenderBeanInfo,
org/apache/derby/loc/m34.properties=org/apache/derby/loc/m34.properties,
META-INF/services/javax.xml.transform.TransformerFactory=META-INF/services/javax.xml.transform.TransformerFactory,
javax.servlet.http.HttpServletResponse=javax.servlet.http.HttpServletResponse,
javax.servlet.ServletInputStream=javax.servlet.ServletInputStream,
org.apache.derby.loc.m18_en_US=org.apache.derby.loc.m18_en_US,
org/apache/derby/loc/m26.properties=org/apache/derby/loc/m26.properties,
META-INF/services/com.sun.org.apache.xalan.internal.xsltc.dom.XSLTCDTMManager=META-INF/services/com.sun.org.apache.xalan.internal.xsltc.dom.XSLTCDTMManager,
org.apache.derby.loc.m18_en=org.apache.derby.loc.m18_en,
org.apache.derby.loc.m13_en_US=org.apache.derby.loc.m13_en_US}

Can you think of anything else I can test?

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Re: [saxon] Using saxon with latest Eclipse (Helios)

From: RB45F <rlb.south@gm...> - 2010-09-01 02:57

Michael,

I was wondering if there has been any progress on this issue. Should I be
waiting for a patch to test or planning on how I might get back to an
earlier saxon release?

Thanks,
Rob
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Re: [saxon] Using saxon with latest Eclipse (Helios)

From: Michael Kay <mike@sa...> - 2010-09-01 08:06

> I was wondering if there has been any progress on this issue. Should I be
> waiting for a patch to test or planning on how I might get back to an
> earlier saxon release?

No progress at my end: as I explained, if Saxon code hasn't been 
successfully loaded, then no change to the Saxon code is going to change 
that; we have to look at whatever it is that is trying to load Saxon to 
find out why it's failing.

It's possible that this failure is related to other reported problems 
where Saxon itself is failing to load classes. There's a patch in the 
pipeline to address that, though I'm waiting for evidence of whether it 
works or not (it's not a problem I know how to reproduce, so I can't 
test it). But there's no evidence that your problem is in any way 
related to this: from all the evidence you've shown me, Saxon has not 
been loaded at all, and it could therefore be a completely 
straightforward classpath problem.

If a straight substitution of the saxon 9.1 jar files in place of saxon 
9.2 solves the problem, then that's a useful data point to start further 
investigation. For example, one possible explanation would be that Saxon 
9.1 works with JDK 1.4, while 9.2 doesn't. But I would expect that to 
show up very clearly in the error logs.

Michael Kay
Saxonica