[Swift-devel] Trunk failing with provenance.log=true

[Mihael Hategan]

While that is true, schema checking of the sites file is optional.
You'll get the warning seen below and swift should continue.

I believe that the other error is due to the run-time. I'll take a look
when I can.

Mihael

On Tue, 2013-09-03 at 07:43 -0500, Michael Wilde wrote:
> Luiz, in trunk, stricter XML parsing is used now.  You need to start sites.xml with these two lines:
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <config xmlns="http://swift-lang.org/sites">
> 
> We need to start using the README and Download pages to make people aware of changes like this.
> 
> - Mike
> 
> 
> ----- Original Message -----
> > From: "Luiz Gadelha" <lgadelha at lncc.br>
> > To: swift-devel at ci.uchicago.edu
> > Sent: Tuesday, September 3, 2013 6:33:09 AM
> > Subject: [Swift-devel] Trunk failing with provenance.log=true
> > 
> > Hi,
> > 
> > I'm getting the error message below when setting the provenance.log
> > parameter to true in the latest trunk version. Both scripts I tested
> > work with provenance.log disabled.
> > 
> > Regards,
> > 
> > Luiz
> > 
> > $ swift -sites.file sites-vortex.xml -tc.file tc-vortex.data
> > blast.swift
> > -d=genes.pep -i=seq3.seq -n=64
> > Swift trunk swift-r7023 cog-r3768
> > RunID: 20130903-0731-gg3aup4d
> > Warning: The @ syntax for function invocation is deprecated
> > [Error] sites-vortex.xml, line 1, col 9: cvc-elt.1: Cannot find the
> > declaration of element 'config'.
> > 
> > Execution failed:
> > java.lang.UnsupportedOperationException
> > 	k:concat @ swift.k, line: 29
> > Caused by: java.lang.UnsupportedOperationException
> > 	at k.rt.Sink.getAll(Sink.java:45)
> > 	at org.globus.cog.karajan.util.TypeUtil.toString(TypeUtil.java:201)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.functions.Misc$Concat.function(Misc.java:448)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.functions.AbstractFunction.runBody(AbstractFunction.java:38)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:154)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:147)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.user.Function.runBody(Function.java:99)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:245)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:69)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.FramedInternalFunction.run(FramedInternalFunction.java:63)
> > 	at org.globus.cog.karajan.compiled.nodes.Main.run(Main.java:79)
> > 	at k.thr.LWThread.run(LWThread.java:228)
> > 	at
> > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
> > 	at
> > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> > 	at java.lang.Thread.run(Thread.java:679)
> > 
> > 
> > $ swift foreach.swift
> > Swift trunk swift-r7023 cog-r3768
> > RunID: 20130903-0755-r4lxbb67
> > Warning: The @ syntax for function invocation is deprecated
> > [Error] sites.xml, line 1, col 9: cvc-elt.1: Cannot find the
> > declaration
> > of element 'config'.
> > 
> > Execution failed:
> > java.lang.UnsupportedOperationException
> > 	k:concat @ swift.k, line: 29
> > Caused by: java.lang.UnsupportedOperationException
> > 	at k.rt.Sink.getAll(Sink.java:45)
> > 	at org.globus.cog.karajan.util.TypeUtil.toString(TypeUtil.java:201)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.functions.Misc$Concat.function(Misc.java:448)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.functions.AbstractFunction.runBody(AbstractFunction.java:38)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:154)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.InternalFunction.run(InternalFunction.java:147)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > 	org.globus.cog.karajan.compiled.nodes.Sequential.run(Sequential.java:22)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.user.Function.runBody(Function.java:99)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.runBody(InvocationWrapper.java:245)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.user.InvocationWrapper.run(InvocationWrapper.java:69)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.CompoundNode.runChild(CompoundNode.java:87)
> > 	at
> > org.globus.cog.karajan.compiled.nodes.FramedInternalFunction.run(FramedInternalFunction.java:63)
> > 	at org.globus.cog.karajan.compiled.nodes.Main.run(Main.java:79)
> > 	at k.thr.LWThread.run(LWThread.java:228)
> > 	at
> > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
> > 	at
> > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> > 	at java.lang.Thread.run(Thread.java:679)
> > 
> > --
> > Luiz Gadelha
> > http://www.lncc.br/~lgadelha
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> > https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> > 
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