You are viewing a plain text version of this content. The canonical link for it is here.
Posted to issues@airavata.apache.org by "Marcus Christie (JIRA)" <ji...@apache.org> on 2017/07/28 13:34:00 UTC
[jira] [Assigned] (AIRAVATA-2494) Groovy templates throw
MissingPropertyException when it doesn't recognize a variable
[ https://issues.apache.org/jira/browse/AIRAVATA-2494?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Marcus Christie reassigned AIRAVATA-2494:
-----------------------------------------
Assignee: (was: Shameera Rathnayaka)
> Groovy templates throw MissingPropertyException when it doesn't recognize a variable
> ------------------------------------------------------------------------------------
>
> Key: AIRAVATA-2494
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2494
> Project: Airavata
> Issue Type: Bug
> Components: GFac
> Reporter: Marcus Christie
> Fix For: 0.19
>
>
> h3. Steps to reproduce
> # Add post job command to deployment
> # For example, for gaussian 09 on comet in seagrid.org we had (approximately)
> {noformat}
> 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* ${PWD}_restart; fi;
> {noformat}
> h3. Expected results
> Since there are no predefined [script variables|https://github.com/apache/airavata/blob/8bc2dcc4eb3a45c09fa32903c38bd97e349b4599/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/Script.java#L43-L43] in this post job command, it should just pass through. I would expect that once the Groovy templating is applied that the post job command is unchanged.
> h3. Actual results
> GFac throws an exception. See the stack trace below.
> h3. Workaround
> For now the workaround is to escape the dollar sign in variables that aren't predefined script variables:
> {noformat}
> mkdir -p "\$PWD"_restart; if (ls ./*.chk 1> /dev/null 2>&1); then cp *.chk \${PWD}_restart; fi; if (ls ./*.rwf* 1> /dev/null 2>&1); then mv *.rwf* \${PWD}_restart; fi;
> {noformat}
> h3. Implementation ideas
> * Change our implementation of GroovyMap so that if a variable is requested that doesn't exist in the map it will just return that variable back, with a dollar sign in front. For example, the following would be true
> {code}
> groovyMap.get("PWD").equals("${PWD}")
> {code}
> 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 {{$PWD}} won't cause errors and will just pass through.
> h3. More information
> Stack trace:
> {noformat}
> 2017-07-27 15:36:44,501 [pool-7-thread-24] INFO o.a.a.gfac.core.GFacUtils process_id=PROCESS_64a60cad-fe27-4f92-a5c5-7
> 7358d4ae93d, token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, experiment_id=Clone_of_Clone_of_Testmvrwf_93b1e30c-c79a-4ff
> 6-8fb6-d76eae96fd16, gateway_id=seagrid - Email list: gw77jobs@scigap.org
> 2017-07-27 15:36:44,515 [pool-7-thread-24] ERROR o.a.a.g.i.t.DefaultJobSubmissionTask process_id=PROCESS_64a60cad-fe27-
> 4f92-a5c5-77358d4ae93d, token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, experiment_id=Clone_of_Clone_of_Testmvrwf_93b1e3
> 0c-c79a-4ff6-8fb6-d76eae96fd16, gateway_id=seagrid - JobSubmission failed
> groovy.lang.MissingPropertyException: No such property: PWD for class: groovy.lang.Binding
> at groovy.lang.Binding.getVariable(Binding.java:63)
> at groovy.lang.Binding.getProperty(Binding.java:105)
> at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:172)
> at groovy.lang.Closure.getPropertyTryThese(Closure.java:312)
> at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:302)
> at groovy.lang.Closure.getProperty(Closure.java:287)
> at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:50)
> at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:307)
> at groovy.tmp.templates.GStringTemplateScript424$_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)
> {noformat}
--
This message was sent by Atlassian JIRA
(v6.4.14#64029)