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Posted to issues@beam.apache.org by "ASF GitHub Bot (Jira)" <ji...@apache.org> on 2020/05/02 02:23:00 UTC
[jira] [Work logged] (BEAM-9856) HL7v2IO.ListHL7v2Messages should
be refactored to support more parallelization
[ https://issues.apache.org/jira/browse/BEAM-9856?focusedWorklogId=429760&page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel#worklog-429760 ]
ASF GitHub Bot logged work on BEAM-9856:
----------------------------------------
Author: ASF GitHub Bot
Created on: 02/May/20 02:22
Start Date: 02/May/20 02:22
Worklog Time Spent: 10m
Work Description: jaketf opened a new pull request #11596:
URL: https://github.com/apache/beam/pull/11596
This PR is an experiment to illustrate a potential strategy for implementing HL7v2IO.ListMessages as a splittable DoFn that carves the sendTime dimension up into time ranges and uses the Messages.List API.
## DISCLAIMER
This PR is currently a discussion piece to help drive the decision of the future of HL7v2IO.ListMessages.
It has excessive logging for demonstrating behavior / debugging and is currently broken.
CC: @pabloem
## Questions
- What are the prototypical tests for validating splitable DoFn's various methods (e.g. SplitRestriction) stability?
## Current Status: Broken
Currently get confusing NPE with OffsetRangeTracker when running
`./gradlew :sdks:java:io:google-cloud-platform:integrationTest --tests "org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOReadIT.testHL7v2IO_ListHL7v2Messages_filtered"`
I seem to get the expected initial daily splits:
```
WARNING: splitting initial sendTime restriction of [minSendTime, now): [2019-03-09T13:24:44.000Z,2020-05-02T02:18:51.850Z), or [1552137884000, 1588385931850).
total days: 419
into 420 splits.
Last split: [1588339484000, 1588385931850)
```
NPE Error:
```
java.lang.NullPointerException
org.apache.beam.sdk.Pipeline$PipelineExecutionException: java.lang.NullPointerException
at org.apache.beam.runners.direct.DirectRunner$DirectPipelineResult.waitUntilFinish(DirectRunner.java:348)
at org.apache.beam.runners.direct.DirectRunner$DirectPipelineResult.waitUntilFinish(DirectRunner.java:318)
at org.apache.beam.runners.direct.DirectRunner.run(DirectRunner.java:213)
at org.apache.beam.runners.direct.DirectRunner.run(DirectRunner.java:67)
at org.apache.beam.sdk.Pipeline.run(Pipeline.java:317)
at org.apache.beam.sdk.Pipeline.run(Pipeline.java:303)
at org.apache.beam.sdk.io.gcp.healthcare.HL7v2IOReadIT.testHL7v2IO_ListHL7v2Messages_filtered(HL7v2IOReadIT.java:135)
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.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.apache.beam.sdk.testing.TestPipeline$1.evaluate(TestPipeline.java:319)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:305)
at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:365)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:330)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:78)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:328)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:65)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:292)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:305)
at org.junit.runners.ParentRunner.run(ParentRunner.java:412)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecutor.runTestClass(JUnitTestClassExecutor.java:110)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecutor.execute(JUnitTestClassExecutor.java:58)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecutor.execute(JUnitTestClassExecutor.java:38)
at org.gradle.api.internal.tasks.testing.junit.AbstractJUnitTestClassProcessor.processTestClass(AbstractJUnitTestClassProcessor.java:62)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:51)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
at com.sun.proxy.$Proxy2.processTestClass(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:118)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:175)
at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:157)
at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404)
at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException
at org.apache.beam.sdk.transforms.splittabledofn.OffsetRangeTracker.checkDone(OffsetRangeTracker.java:98)
at org.apache.beam.repackaged.direct_java.sdk.fn.splittabledofn.RestrictionTrackers$RestrictionTrackerObserver.checkDone(RestrictionTrackers.java:77)
at org.apache.beam.repackaged.direct_java.runners.core.OutputAndTimeBoundedSplittableProcessElementInvoker.invokeProcessElement(OutputAndTimeBoundedSplittableProcessElementInvoker.java:234)
at org.apache.beam.repackaged.direct_java.runners.core.SplittableParDoViaKeyedWorkItems$ProcessFn.processElement(SplittableParDoViaKeyedWorkItems.java:524)
```
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Issue Time Tracking
-------------------
Worklog Id: (was: 429760)
Remaining Estimate: 0h
Time Spent: 10m
> HL7v2IO.ListHL7v2Messages should be refactored to support more parallelization
> ------------------------------------------------------------------------------
>
> Key: BEAM-9856
> URL: https://issues.apache.org/jira/browse/BEAM-9856
> Project: Beam
> Issue Type: Improvement
> Components: io-java-gcp
> Reporter: Jacob Ferriero
> Assignee: Jacob Ferriero
> Priority: Minor
> Time Spent: 10m
> Remaining Estimate: 0h
>
> Currently the List Messages API paginates through in a single ProcessElement Call.
> However we could get a restriction based on createTime using Messages.List filter and orderby.
>
> This is inline with the future roadmap of HL7v2 bulk export API becomes available that should allow splitting on (e.g. create time dimension). Leveraging this bulk export might be a future optimization to explore.
>
> This could take one of two forms:
> 1. dyanmically splitable via splitable DoFn (sexy, beam idiomatic: make optimization the runner's problem, potentially unnecessarily complex for this use case )
> 2. static splitting on some time partition e.g. finding the earliest createTime and emitting a PCollection of 1 hour partitions and paginating through each hour of data w/ in the time frame that the store spans, in a separate ProcessElement. (easy to implement but will likely have hot keys / stragglers based on "busy hours")
>
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