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From "Eroma (JIRA)" <j...@apache.org>
Subject [jira] [Comment Edited] (AIRAVATA-2219) With groovey scripts some of the post job commands with special characters are failing
Date Wed, 04 Jan 2017 19:40:58 GMT

    [ https://issues.apache.org/jira/browse/AIRAVATA-2219?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15785958#comment-15785958
] 

Eroma edited comment on AIRAVATA-2219 at 1/4/17 7:40 PM:
---------------------------------------------------------

with latest even with the / the abaqus application is failing in dev.seagrid.org.
Abinit application execution also fails with error [1]
2017-01-04 14:29:13 [pool-7-thread-41] ERROR o.a.a.g.i.t.DefaultJobSubmissionTask - JobSubmission
failed
groovy.lang.MissingPropertyException: No such property: MODULEPATH 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.GStringTemplateScript34$_getTemplate_closure1.doCall(GStringTemplateScript34.groovy:2)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
        at groovy.lang.Closure.call(Closure.java:414)
        at groovy.lang.Closure$WritableClosure.writeTo(Closure.java:844)
        at groovy.lang.Closure$WritableClosure.toString(Closure.java:970)
        at org.apache.airavata.gfac.core.GFacUtils.parseCommands(GFacUtils.java:764)
        at org.apache.airavata.gfac.core.GFacUtils.lambda$createGroovyMap$3(GFacUtils.java:595)
        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:596)
        at org.apache.airavata.gfac.impl.task.DefaultJobSubmissionTask.execute(DefaultJobSubmissionTask.java:74)
        at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:816)
        at org.apache.airavata.gfac.impl.GFacEngineImpl.executeJobSubmission(GFacEngineImpl.java:512)
        at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:388)




was (Author: eroma_a):
with latest even with the / the abaqus application is failing in dev.seagrid.org.



> With groovey scripts some of the post job commands with special characters are failing
> --------------------------------------------------------------------------------------
>
>                 Key: AIRAVATA-2219
>                 URL: https://issues.apache.org/jira/browse/AIRAVATA-2219
>             Project: Airavata
>          Issue Type: Bug
>         Environment: https://dev.seagrid.org
>            Reporter: Eroma
>            Assignee: Shameera Rathnayaka
>             Fix For: 0.17
>
>
> when running application Abaqus which has pre job command
> abq_job=${baseinp%.*}
> job submission fails with error  [1] in gfac log.
> [1]
> 2016-11-09 14:46:40 [pool-7-thread-41] ERROR o.a.airavata.gfac.core.GFacUtils - Error
while creating groovy map
> groovy.lang.GroovyRuntimeException: Failed to parse template script (your template may
contain an error or be trying to use expressions not currently supported): startup failed:
> GStringTemplateScript74.groovy: 2: unexpected token: . @ line 2, column 66.
>    > out << """abq_job=${baseinp%.*}"""}}
>                                  ^
> 1 error
>         at groovy.text.GStringTemplateEngine$GStringTemplate.<init>(GStringTemplateEngine.java:198)
>         at groovy.text.GStringTemplateEngine.createTemplate(GStringTemplateEngine.java:110)
>         at groovy.text.TemplateEngine.createTemplate(TemplateEngine.java:41)
>         at org.apache.airavata.gfac.core.GFacUtils.parseCommands(GFacUtils.java:788)
>         at org.apache.airavata.gfac.core.GFacUtils.lambda$createGroovyMap$3(GFacUtils.java:599)
>         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$ReduceOp.evaluateSequential(ReduceOps.java:708)
>         at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
>         at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
>         at org.apache.airavata.gfac.core.GFacUtils.createGroovyMap(GFacUtils.java:600)
>         at org.apache.airavata.gfac.impl.task.DefaultJobSubmissionTask.execute(DefaultJobSubmissionTask.java:75)
>         at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:773)
>         at org.apache.airavata.gfac.impl.GFacEngineImpl.executeJobSubmission(GFacEngineImpl.java:469)
>         at org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:345)
>         at org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:245)
>         at org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
>         at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
>         at org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:21)
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>         at java.lang.Thread.run(Thread.java:745)
> 2016-11-09 14:46:40 [pool-7-thread-41] ERROR o.a.a.g.i.t.DefaultJobSubmissionTask - JobSubmission
failed



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