[Swift-user] gsiftp filesystem mapper removes leading slash

[Allan Espinosa]

Oh i see.  now I'm getting NullPointExceptions:
database pir[] <filesys_mapper;location="gsiftp://gridftp.ranger.tacc.teragrid.org//work/01035/tg802895/pir",
pattern="UNIPROT_for_blast_14.0.seq*">;

$
Swift svn swift-r2490 cog-r2271

RunID: 20090203-1610-usa9ur25
Progress:
Execution failed:
        java.lang.RuntimeException: java.lang.NullPointerException
Caused by:
        java.lang.NullPointerException
        at org.griphyn.vdl.mapping.AbsFile.initDirAndName(AbsFile.java:60)
        at org.griphyn.vdl.mapping.AbsFile.<init>(AbsFile.java:77)
        at org.griphyn.vdl.mapping.AbsFile.listFiles(AbsFile.java:124)
        at org.griphyn.vdl.mapping.file.AbstractFileMapper.existing(AbstractFileMapper.java:166)
        at org.griphyn.vdl.mapping.RootDataNode.checkInputs(RootDataNode.java:96)
        at org.griphyn.vdl.mapping.RootArrayDataNode.checkInputs(RootArrayDataNode.java:64)
        at org.griphyn.vdl.mapping.RootArrayDataNode.innerInit(RootArrayDataNode.java:52)
        at org.griphyn.vdl.mapping.RootArrayDataNode.handleClosed(RootArrayDataNode.java:77)
        at org.griphyn.vdl.mapping.AbstractDataNode.notifyListeners(AbstractDataNode.java:486)
        at org.griphyn.vdl.mapping.AbstractDataNode.closeShallow(AbstractDataNode.java:364)
        at org.griphyn.vdl.mapping.AbstractDataNode.setValue(AbstractDataNode.java:322)
        at org.griphyn.vdl.mapping.RootDataNode.setValue(RootDataNode.java:214)
        at org.griphyn.vdl.karajan.lib.SetFieldValue.deepCopy(SetFieldValue.java:64)
        at org.griphyn.vdl.karajan.lib.SetFieldValue.function(SetFieldValue.java:47)
        at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
        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.Argument.post(Argument.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.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)


So I am guessing this is now a CoG bug right?


On Tue, Feb 3, 2009 at 3:52 PM, Ben Clifford <benc at hawaga.org.uk> wrote:
>
> On Tue, 3 Feb 2009, Allan Espinosa wrote:
>
>> location="gsiftp://gridftp.ranger.tacc.teragrid.org/work/01035/tg802895/pir",
>
>> But gridftp internals in swift reports that it cannot get a directory
>> listing of "work/01035/tg802895/pir".  I was thinking that maybe the
>> leading slashes were removed.  Below is the program output:
>
> CoG's gsiftp handling has an unconventional (as in different to the Globus
> Toolkit) understanding of gsiftp URLs; you need to use two slashes after
> the hostname in gsiftp URLs that are given to CoG.
>
> Globus Toolkit gsiftp URLs implicitly start at /
>
> CoG URLs start in pwd, and need an extra / to get to root.
>
> Both interpretations violate my understand of the ftp:// URI scheme on
> which I understand the gsiftp:// scheme to be modelled.
>
> (to be even more picky, its a violation to use gsiftp:// as a URI scheme
> as it neither begins with x- nor is registered with IANA... ho ho ho)
>