[Swift-devel] [Bug 152] New: filesys_mapper gives exception

[bugzilla-daemon at mcs.anl.gov]

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=152

           Summary: filesys_mapper gives exception
           Product: Swift
           Version: unspecified
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: wilde at mcs.anl.gov


Running this script throws an exception in the filesys_mapper:

type File;

type Mol2;

(File out) rundock ( Mol2 ligand )
{
  app { echo "rundock debug:" @ligand @out stdout=@out; }
}

Mol2 ligand <filesys_mapper;
location="/disks/gpfs/ligandatlas/databases/KEGG_and_Drugs-test",
suffix="D01995.mol2">;

File out <"dockdb.out">;

out = rundock( ligand );

--

Gives:

Swift script dockdb1.swift starting at Sat Aug 2 09:54:06 CDT 2008
running on sites: localhost

Swift svn swift-r2159 cog-r2122 (CoG modified locally)

RunID: 20080802-0954-qmar4l7d
Progress: 
Execution failed:
        Index: 0

Swift Script dockdb1.swift ended at Sat Aug 2 09:54:09 CDT 2008 with exit code
0
--

Exception in log is:

2008-08-02 09:54:09,209-0500 INFO  New NEW
id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20080802-0954-x2fxvmz5:720000000003
2008-08-02 09:54:09,248-0500 INFO  AbstractDataNode closed
tag:benc at ci.uchicago.edu,2008:swift:dataset:20080802-0954-x2fxvmz5:720000000004
2008-08-02 09:54:09,248-0500 INFO  AbstractDataNode ROOTPATH
dataset=tag:benc at ci.uchicago.edu,2008:swift:dataset:20080802-0954-x2fxvmz5:720000000004
path=$
2008-08-02 09:54:09,249-0500 INFO  AbstractDataNode dataset
tag:benc at ci.uchicago.edu,2008:swift:dataset:20080802-0954-x2fxvmz5:720000000004
exception while mapping path f
rom root
java.lang.IndexOutOfBoundsException: Index: 0
        at java.util.Collections$EmptyList.get(Collections.java:2968)
        at org.griphyn.vdl.mapping.Path.isArrayIndex(Path.java:271)
        at
org.griphyn.vdl.mapping.file.FileSystemArrayMapper.map(FileSystemArrayMapper.java:30)
        at
org.griphyn.vdl.mapping.AbstractDataNode.logContent(AbstractDataNode.java:376)
--

This occurred first when mapping a 4-member test dataset. I shrunk the script
to a smaller example and show it here mapping a single member dataset. 

Script and all logs and output are in:
www.ci.uchicago.edu/~wilde/filesys_mapper_exception.2008.0802.tar.gz


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