[AIRAVATA-2494] Groovy templates throw MissingPropertyException when it doesn't recognize a variable

• Type: Bug
• Status: Open
• Priority: Major
• Resolution: Unresolved
• Fix Version/s: 0.19
• Component/s: GFac
• Assignee: Unassigned
• Reporter: Marcus Christie
• Created: 28/Jul/17 13:32
• Updated: 28/Jul/17 13:33

Description

Steps to reproduce

1. Add post job command to deployment
2. For example, for gaussian 09 on comet in seagrid.org we had (approximately)

   mkdir -p "$PWD"_restart; if (ls ./*.chk 1> /dev/null 2>&1); then cp *.chk ${PWD}_restart; fi; if (ls ./*.rwf* 1> /dev/null 2>&1); then mv *.rwf* ${PWD}_restart; fi;
   

Expected results

Since there are no predefined script variables in this post job command, it should just pass through. I would expect that once the Groovy templating is applied that the post job command is unchanged.

Actual results

GFac throws an exception. See the stack trace below.

Workaround

For now the workaround is to escape the dollar sign in variables that aren't predefined script variables:

mkdir -p "\$PWD"_restart; if (ls ./*.chk 1> /dev/null 2>&1); then cp *.chk \${PWD}_restart; fi; if (ls ./*.rwf* 1> /dev/null 2>&1); then mv *.rwf* \${PWD}_restart; fi;

Implementation ideas

• Change our implementation of GroovyMap so that if a variable is requested that doesn't exist in the map it will just return that variable back, with a dollar sign in front. For example, the following would be true

  groovyMap.get("PWD").equals("${PWD}")
  

  The downside to this approach is that it may make typos harder to find. But in any case a typo will cause an error so this approach seems preferable because other environment variables like $PWD won't cause errors and will just pass through.

More information

Stack trace:

2017-07-27 15:36:44,501 [pool-7-thread-24] INFO  o.a.a.gfac.core.GFacUtils process_id=PROCESS_64a60cad-fe27-4f92-a5c5-7
7358d4ae93d, token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, experiment_id=Clone_of_Clone_of_Testmvrwf_93b1e30c-c79a-4ff
6-8fb6-d76eae96fd16, gateway_id=seagrid - Email list: [e-mail]
2017-07-27 15:36:44,515 [pool-7-thread-24] ERROR o.a.a.g.i.t.DefaultJobSubmissionTask process_id=PROCESS_64a60cad-fe27-
4f92-a5c5-77358d4ae93d, token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, experiment_id=Clone_of_Clone_of_Testmvrwf_93b1e3
0c-c79a-4ff6-8fb6-d76eae96fd16, gateway_id=seagrid - JobSubmission failed
groovy.lang.MissingPropertyException: No such property: PWD for class: groovy.lang.Binding
        at groovy.lang.Binding.getVariable(Binding.java:63)
        at groovy.lang.Binding.getProperty(Binding.java:105)
        at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:172)
        at groovy.lang.Closure.getPropertyTryThese(Closure.java:312)
        at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:302)
        at groovy.lang.Closure.getProperty(Closure.java:287)
        at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:50)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:307)
        at groovy.tmp.templates.GStringTemplateScript424$_getTemplate_closure1.doCall(GStringTemplateScript424.groovy:2
)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
        at groovy.lang.Closure.call(Closure.java:414)
        at groovy.lang.Closure$WritableClosure.writeTo(Closure.java:844)
        at groovy.lang.Closure$WritableClosure.toString(Closure.java:970)
        at org.apache.airavata.gfac.core.GFacUtils.parseCommands(GFacUtils.java:715)
        at org.apache.airavata.gfac.core.GFacUtils.lambda$createGroovyMap$5(GFacUtils.java:555)
        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
        at java.util.stream.SortedOps$SizedRefSortingSink.end(SortedOps.java:352)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
        at org.apache.airavata.gfac.core.GFacUtils.createGroovyMap(GFacUtils.java:556)
        at org.apache.airavata.gfac.impl.task.DefaultJobSubmissionTask.execute(DefaultJobSubmissionTask.java:72)
        at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
        at org.apache.airavata.gfac.impl.GFacEngineImpl.executeJobSubmission(GFacEngineImpl.java:510)
        at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:386)
        at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
        at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
        at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
        at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:748)