Bpipe run fails

[GoogleCodeExporter]

I have an issue with testing pipelines:
$ bpipe test test.groovy 
================================================================================
====================
|                                 Starting Pipeline at 2012-08-01               
                   |
================================================================================
====================

============================================= Stage ll 
=============================================
Caught: groovy.lang.MissingPropertyException: No such property: input for 
class: script_from_command_line
groovy.lang.MissingPropertyException: No such property: input for class: 
script_from_command_line
    at script_from_command_line$_run_closure1.doCall(script_from_command_line:2)
    at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
    at bpipe.PipelineStage$_run_closure4.doCall(PipelineStage.groovy:174)
    at bpipe.PipelineStage$_run_closure4.doCall(PipelineStage.groovy)
    at bpipe.PipelineStage.run(PipelineStage.groovy:173)
    at bpipe.Pipeline.runSegment(Pipeline.groovy:274)
    at bpipe.Pipeline$_execute_closure2.doCall(Pipeline.groovy:337)
    at bpipe.Pipeline$_execute_closure2.doCall(Pipeline.groovy)
    at bpipe.Pipeline.execute(Pipeline.groovy:329)
    at bpipe.Pipeline.this$2$execute(Pipeline.groovy)
    at bpipe.Pipeline.execute(Pipeline.groovy)
    at bpipe.Pipeline.this$2$execute(Pipeline.groovy)
    at bpipe.Pipeline$this$2$execute.call(Unknown Source)
    at bpipe.Pipeline.run(Pipeline.groovy:248)
    at bpipe.Pipeline$run.callStatic(Unknown Source)
    at bpipe.Pipeline.run(Pipeline.groovy:221)
    at script_from_command_line.run(script_from_command_line:4)
    at bpipe.Runner.main(Runner.groovy:203)

Where test.groovy is a very simple pipeline:
ll = {
   exec "ls -alh $input"
}
Bpipe.run {
   ll
}

This happened with every pipeline I have tried. Any idea what the matter is?

Florent

Original issue reported on code.google.com by florent....@gmail.com on 1 Aug 2012 at 3:35

[GoogleCodeExporter]

I think you should just specify input, like:

bpipe test test.groovy test.txt

In a new (not yet available) version Bpipe will be actually saying:

================== Stage ll ==================
Pipeline failed!

Input expected but not provided

Cheers,

Maciej

Original comment by maciek.k...@gmail.com on 1 Aug 2012 at 3:34

[GoogleCodeExporter]

Thanks Maciek. Actually, I should have mentioned that I running 'test' both 
with and without specifying an input. Here is the  error message when 
specifying an input:

$ bpipe test test.groovy test.groovy 
================================================================================
====================
|                                 Starting Pipeline at 2012-08-02               
                   |
================================================================================
====================

============================================= Stage ll 
=============================================
Caught: java.lang.IncompatibleClassChangeError: the number of constructors 
during runtime and compile time for java.lang.RuntimeException do not match. 
Expected 4 but got 5
java.lang.IncompatibleClassChangeError: the number of constructors during 
runtime and compile time for java.lang.RuntimeException do not match. Expected 
4 but got 5
    at bpipe.PipelineTestAbort.<init>(PipelineTestAbort.groovy:43)
    at bpipe.CommandManager.start(CommandManager.groovy:165)
    at bpipe.PipelineContext.async(PipelineContext.groovy:800)
    at bpipe.PipelineContext.exec(PipelineContext.groovy:685)
    at bpipe.PipelineContext.exec(PipelineContext.groovy)
    at bpipe.PipelineContext.exec(PipelineContext.groovy:648)
    at bpipe.PipelineContext.invokeMethod(PipelineContext.groovy)
    at bpipe.PipelineDelegate.methodMissing(PipelineDelegate.groovy:41)
    at bpipe.PipelineDelegate.invokeMethod(PipelineDelegate.groovy)
    at script_from_command_line$_run_closure1.doCall(script_from_command_line:2)
    at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
    at bpipe.PipelineStage$_run_closure4.doCall(PipelineStage.groovy:174)
    at bpipe.PipelineStage$_run_closure4.doCall(PipelineStage.groovy)
    at bpipe.PipelineStage.run(PipelineStage.groovy:173)
    at bpipe.Pipeline.runSegment(Pipeline.groovy:274)
    at bpipe.Pipeline$_execute_closure2.doCall(Pipeline.groovy:337)
    at bpipe.Pipeline$_execute_closure2.doCall(Pipeline.groovy)
    at bpipe.Pipeline.execute(Pipeline.groovy:329)
    at bpipe.Pipeline.this$2$execute(Pipeline.groovy)
    at bpipe.Pipeline.execute(Pipeline.groovy)
    at bpipe.Pipeline.this$2$execute(Pipeline.groovy)
    at bpipe.Pipeline$this$2$execute.call(Unknown Source)
    at bpipe.Pipeline.run(Pipeline.groovy:248)
    at bpipe.Pipeline$run.callStatic(Unknown Source)
    at bpipe.Pipeline.run(Pipeline.groovy:221)
    at script_from_command_line.run(script_from_command_line:4)
    at bpipe.Runner.main(Runner.groovy:203)

Looking at it again, I realize that the error message is not the same as when 
omitting the input.

Best,

Florent

Original comment by florent....@gmail.com on 2 Aug 2012 at 12:10

[GoogleCodeExporter]

Hi Florent, I think this is actually a separate bug which I've been meaning to 
log but haven't got around to yet.  This happens in some instances when running 
Bpipe with JDK 1.7.  

Unfortunately compiled groovy code isn't portable between Java 1.6 and Java 
1.7, which is most annoying - it means we may have to create separate 
distributions for the two versions of Java.

Can you confirm for me if you're using Java 1.7 here?

If possible, can you try it with 1.6?

Original comment by ssade...@gmail.com on 3 Aug 2012 at 1:13

[GoogleCodeExporter]

Here you go. The same command was tested with Java 5, 6 and 7. It worked only 
in Java 6. Both Java 5 and 7 generated an exception.

Original comment by florent....@gmail.com on 3 Aug 2012 at 3:39

Attachments:

• java_1.6.0_33.log
• java_1.5.0_22.log
• java_1.7.0.log

[GoogleCodeExporter]

See Issue 61 for some followup on the problem mentioned in Comment #2 above.

http://code.google.com/p/bpipe/issues/detail?id=61

Original comment by ssade...@gmail.com on 24 Aug 2012 at 2:00