[Swift-user] swift execution problem
Yue, Chen - BMD
yuechen at bsd.uchicago.edu
Wed Mar 18 18:32:46 CDT 2009
Hi,
I'm new to Swift programming. I was able to run a swift script before, but I couldn't run it now. I'm wondering if someone can help me figure out why. The swift script, sites.xml, tc.data, and all the error messages are copied in this email. Thank you!
Regards,
Chen, Yue
*********************
Swift script
*********************
type Fasta {}
type PTMapOut {}
type Solution {}
type Inputfile {}
app (PTMapOut ofile) PTMap (Solution sfile, Fasta fastafile, Inputfile input, Inputfile parameter)
{
PTMap @filename(sfile) @filename(fastafile) @filename(input) @filename(parameter) stdout=@filename(ofile <mailto:stdout=@filename(ofile> );
}
Fasta texts[] <filesys_mapper;prefix="fasta">;
doall(Fasta texts[])
{
Solution sfile <"BSASolution.mzXML">;
Inputfile input <"inputs.txt">;
Inputfile parameter <"parameters.txt">;
foreach p in texts {
PTMapOut r <regexp_mapper;
source=@p <mailto:source=@p> ,
match="fasta(.*)",
transform="\\1.out <file://\\1.out> "
>;
r = PTMap(sfile, p, input, parameter);
}
}
// Main
doall(texts);
**************
sites.xml
**************
<pool handle="localhost">
<gridftp url="local://localhost" />
<execution provider="local" />
<workdirectory >/var/tmp</workdirectory>
<profile namespace="karajan" key="jobThrottle">0</profile>
</pool>
**************
tc.data
**************
localhost echo /bin/echo INSTALLED INTEL32::LINUX null
localhost cat /bin/cat INSTALLED INTEL32::LINUX null
localhost ls /bin/ls INSTALLED INTEL32::LINUX null
localhost grep /bin/grep INSTALLED INTEL32::LINUX null
localhost sort /bin/sort INSTALLED INTEL32::LINUX null
localhost paste /bin/paste INSTALLED INTEL32::LINUX null
localhost PTMap /home/yuechen/PTMap/PTMap INSTALLED INTEL32::LINUX null
**************
Error messages
**************
[yuechen at communicado PTMap]$ swift PTMap.swift
Execution failed:
java.lang.NullPointerException
at org.globus.cog.abstraction.impl.common.task.ServiceImpl.toString(ServiceImpl.java:156)
at java.lang.String.valueOf(String.java:2577)
at java.lang.StringBuffer.append(StringBuffer.java:220)
at org.globus.cog.karajan.workflow.nodes.grid.GridNode.function(GridNode.java:31)
at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:45)
at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
at org.globus.cog.karajan.workflow.nodes.ExecuteFile.notificationEvent(ExecuteFile.java:163)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
at org.globus.cog.karajan.workflow.nodes.Sequential.childCompleted(Sequential.java:45)
at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
at org.globus.cog.karajan.workflow.nodes.user.UserDefinedElement.childCompleted(UserDefinedElement.java:283)
at org.globus.cog.karajan.workflow.nodes.user.SequentialImplicitExecutionUDE.childCompleted(SequentialImplicitExecutionUDE.java:85)
at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
at org.globus.cog.karajan.workflow.nodes.If.childCompleted(If.java:30)
at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:27)
at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.executeChildren(AbstractFunction.java:40)
at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)
at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:240)
at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:281)
at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:393)
at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:332)
at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)
at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
at org.globus.cog.karajan.workflow.events.EventWorker.run(EventWorker.java:69)
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