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google / fhir-data-pipes

A collection of tools for extracting FHIR resources and analytics services on top of that data.
https://google.github.io/fhir-data-pipes/
Apache License 2.0
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The JSON of FHIR Resource that is not compressed (res_encoding = `JSON`) is stored in `res_text_vc` column, not in `res_text`, caused NPE #925

Closed muhammad-levi closed 5 months ago

muhammad-levi commented 6 months ago

https://github.com/google/fhir-data-pipes/blob/bf9b890a648ed4570f4874243e1c755f0fa3d65e/pipelines/batch/src/main/java/com/google/fhir/analytics/JdbcFetchHapi.java#L90C57-L90C65

I think line 90 should be changed from

jsonResource = new String(resultSet.getBytes("res_text"), Charsets.UTF_8);

to

jsonResource = new String(resultSet.getBytes("res_text_vc"), Charsets.UTF_8);

References:

full pipeline error log:

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Pipeline execution failed
    at com.google.fhir.analytics.EtlUtils.runMultiplePipelines(EtlUtils.java:136)
    at com.google.fhir.analytics.EtlUtils.runMultiplePipelinesWithTimestamp(EtlUtils.java:76)
    at com.google.fhir.analytics.PipelineManager$PipelineThread.run(PipelineManager.java:554)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Pipeline execution failed
    at java.base/java.util.concurrent.CompletableFuture.reportGet(CompletableFuture.java:396)
    at java.base/java.util.concurrent.CompletableFuture.get(CompletableFuture.java:2073)
    at com.google.fhir.analytics.EtlUtils.runMultiplePipelines(EtlUtils.java:123)
    ... 2 more
Caused by: java.lang.RuntimeException: Pipeline execution failed
    at org.apache.beam.runners.flink.FlinkRunner.run(FlinkRunner.java:112)
    at org.apache.beam.sdk.Pipeline.run(Pipeline.java:321)
    at org.apache.beam.sdk.Pipeline.run(Pipeline.java:307)
    at com.google.fhir.analytics.EtlUtils$PipelineSupplier.get(EtlUtils.java:157)
    at com.google.fhir.analytics.EtlUtils$PipelineSupplier.get(EtlUtils.java:147)
    at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1768)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
    at org.apache.flink.runtime.jobmaster.JobResult.toJobExecutionResult(JobResult.java:144)
    at org.apache.flink.runtime.minicluster.MiniClusterJobClient.lambda$getJobExecutionResult$3(MiniClusterJobClient.java:137)
    at java.base/java.util.concurrent.CompletableFuture$UniApply.tryFire(CompletableFuture.java:646)
    at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
    at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
    at org.apache.flink.runtime.rpc.akka.AkkaInvocationHandler.lambda$invokeRpc$1(AkkaInvocationHandler.java:258)
    at java.base/java.util.concurrent.CompletableFuture.uniWhenComplete(CompletableFuture.java:863)
    at java.base/java.util.concurrent.CompletableFuture$UniWhenComplete.tryFire(CompletableFuture.java:841)
    at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
    at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
    at org.apache.flink.util.concurrent.FutureUtils.doForward(FutureUtils.java:1389)
    at org.apache.flink.runtime.concurrent.akka.ClassLoadingUtils.lambda$null$1(ClassLoadingUtils.java:93)
    at org.apache.flink.runtime.concurrent.akka.ClassLoadingUtils.runWithContextClassLoader(ClassLoadingUtils.java:68)
    at org.apache.flink.runtime.concurrent.akka.ClassLoadingUtils.lambda$guardCompletionWithContextClassLoader$2(ClassLoadingUtils.java:92)
    at java.base/java.util.concurrent.CompletableFuture.uniWhenComplete(CompletableFuture.java:863)
    at java.base/java.util.concurrent.CompletableFuture$UniWhenComplete.tryFire(CompletableFuture.java:841)
    at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
    at java.base/java.util.concurrent.CompletableFuture.complete(CompletableFuture.java:2147)
    at org.apache.flink.runtime.concurrent.akka.AkkaFutureUtils$1.onComplete(AkkaFutureUtils.java:47)
    at akka.dispatch.OnComplete.internal(Future.scala:300)
    at akka.dispatch.OnComplete.internal(Future.scala:297)
    at akka.dispatch.japi$CallbackBridge.apply(Future.scala:224)
    at akka.dispatch.japi$CallbackBridge.apply(Future.scala:221)
    at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:60)
    at org.apache.flink.runtime.concurrent.akka.AkkaFutureUtils$DirectExecutionContext.execute(AkkaFutureUtils.java:65)
    at scala.concurrent.impl.CallbackRunnable.executeWithValue(Promise.scala:68)
    at scala.concurrent.impl.Promise$DefaultPromise.$anonfun$tryComplete$1(Promise.scala:284)
    at scala.concurrent.impl.Promise$DefaultPromise.$anonfun$tryComplete$1$adapted(Promise.scala:284)
    at scala.concurrent.impl.Promise$DefaultPromise.tryComplete(Promise.scala:284)
    at akka.pattern.PromiseActorRef.$bang(AskSupport.scala:621)
    at akka.pattern.PipeToSupport$PipeableFuture$$anonfun$pipeTo$1.applyOrElse(PipeToSupport.scala:24)
    at akka.pattern.PipeToSupport$PipeableFuture$$anonfun$pipeTo$1.applyOrElse(PipeToSupport.scala:23)
    at scala.concurrent.Future.$anonfun$andThen$1(Future.scala:532)
    at scala.concurrent.impl.Promise.liftedTree1$1(Promise.scala:29)
    at scala.concurrent.impl.Promise.$anonfun$transform$1(Promise.scala:29)
    at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:60)
    at akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:63)
    at akka.dispatch.BatchingExecutor$BlockableBatch.$anonfun$run$1(BatchingExecutor.scala:100)
    at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
    at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:81)
    at akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:100)
    at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:49)
    at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:48)
    at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:373)
    at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1182)
    at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1655)
    at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1622)
    at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:165)
Caused by: org.apache.flink.runtime.JobException: Recovery is suppressed by NoRestartBackoffTimeStrategy
    at org.apache.flink.runtime.executiongraph.failover.flip1.ExecutionFailureHandler.handleFailure(ExecutionFailureHandler.java:138)
    at org.apache.flink.runtime.executiongraph.failover.flip1.ExecutionFailureHandler.getFailureHandlingResult(ExecutionFailureHandler.java:82)
    at org.apache.flink.runtime.scheduler.DefaultScheduler.handleTaskFailure(DefaultScheduler.java:252)
    at org.apache.flink.runtime.scheduler.DefaultScheduler.maybeHandleTaskFailure(DefaultScheduler.java:242)
    at org.apache.flink.runtime.scheduler.DefaultScheduler.updateTaskExecutionStateInternal(DefaultScheduler.java:233)
    at org.apache.flink.runtime.scheduler.SchedulerBase.updateTaskExecutionState(SchedulerBase.java:684)
    at org.apache.flink.runtime.scheduler.SchedulerNG.updateTaskExecutionState(SchedulerNG.java:79)
    at org.apache.flink.runtime.jobmaster.JobMaster.updateTaskExecutionState(JobMaster.java:444)
    at jdk.internal.reflect.GeneratedMethodAccessor42.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.apache.flink.runtime.rpc.akka.AkkaRpcActor.lambda$handleRpcInvocation$1(AkkaRpcActor.java:316)
    at org.apache.flink.runtime.concurrent.akka.ClassLoadingUtils.runWithContextClassLoader(ClassLoadingUtils.java:83)
    at org.apache.flink.runtime.rpc.akka.AkkaRpcActor.handleRpcInvocation(AkkaRpcActor.java:314)
    at org.apache.flink.runtime.rpc.akka.AkkaRpcActor.handleRpcMessage(AkkaRpcActor.java:217)
    at org.apache.flink.runtime.rpc.akka.FencedAkkaRpcActor.handleRpcMessage(FencedAkkaRpcActor.java:78)
    at org.apache.flink.runtime.rpc.akka.AkkaRpcActor.handleMessage(AkkaRpcActor.java:163)
    at akka.japi.pf.UnitCaseStatement.apply(CaseStatements.scala:24)
    at akka.japi.pf.UnitCaseStatement.apply(CaseStatements.scala:20)
    at scala.PartialFunction.applyOrElse(PartialFunction.scala:123)
    at scala.PartialFunction.applyOrElse$(PartialFunction.scala:122)
    at akka.japi.pf.UnitCaseStatement.applyOrElse(CaseStatements.scala:20)
    at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:171)
    at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
    at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
    at akka.actor.Actor.aroundReceive(Actor.scala:537)
    at akka.actor.Actor.aroundReceive$(Actor.scala:535)
    at akka.actor.AbstractActor.aroundReceive(AbstractActor.scala:220)
    at akka.actor.ActorCell.receiveMessage(ActorCell.scala:580)
    at akka.actor.ActorCell.invoke(ActorCell.scala:548)
    at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:270)
    at akka.dispatch.Mailbox.run(Mailbox.scala:231)
    at akka.dispatch.Mailbox.exec(Mailbox.scala:243)
    ... 5 more
Caused by: org.apache.beam.sdk.util.UserCodeException: java.lang.NullPointerException: Cannot read the array length because "bytes" is null
    at org.apache.beam.sdk.util.UserCodeException.wrap(UserCodeException.java:39)
    at org.apache.beam.sdk.io.jdbc.JdbcIO$ReadFn$DoFnInvoker.invokeProcessElement(Unknown Source)
    at org.apache.beam.runners.core.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:211)
    at org.apache.beam.runners.core.SimpleDoFnRunner.processElement(SimpleDoFnRunner.java:188)
    at org.apache.beam.runners.flink.metrics.DoFnRunnerWithMetricsUpdate.processElement(DoFnRunnerWithMetricsUpdate.java:62)
    at org.apache.beam.runners.flink.translation.functions.FlinkDoFnFunction.flatMap(FlinkDoFnFunction.java:122)
    at org.apache.beam.runners.flink.translation.functions.FlinkDoFnFunction.flatMap(FlinkDoFnFunction.java:59)
    at org.apache.flink.runtime.operators.FlatMapDriver.run(FlatMapDriver.java:113)
    at org.apache.flink.runtime.operators.BatchTask.run(BatchTask.java:519)
    at org.apache.flink.runtime.operators.BatchTask.invoke(BatchTask.java:360)
    at org.apache.flink.runtime.taskmanager.Task.runWithSystemExitMonitoring(Task.java:958)
    at org.apache.flink.runtime.taskmanager.Task.restoreAndInvoke(Task.java:937)
    at org.apache.flink.runtime.taskmanager.Task.doRun(Task.java:766)
    at org.apache.flink.runtime.taskmanager.Task.run(Task.java:575)
    at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.NullPointerException: Cannot read the array length because "bytes" is null
    at java.base/java.lang.String.<init>(String.java:1383)
    at com.google.fhir.analytics.JdbcFetchHapi$ResultSetToRowDescriptor.mapRow(JdbcFetchHapi.java:90)
    at com.google.fhir.analytics.JdbcFetchHapi$ResultSetToRowDescriptor.mapRow(JdbcFetchHapi.java:67)
    at org.apache.beam.sdk.io.jdbc.JdbcIO$ReadFn.processElement(JdbcIO.java:1528)
bashir2 commented 5 months ago

Thanks @muhammad-levi for reporting this issue and fixing it. I made a long comment on your PR here. The TL;DR; is that with that change the JDBC mode won't work for HAPI JPA versions earlier than 5.7.0 (i.e., 2021 and earlier) but we are okay with that because for those versions the FHIR API mode can be used.