Torch V1.0.0-alpha.7: Redact Resource Without Meta Error
Hey everyone,
I'm running into a bit of a snag with Torch v1.0.0-alpha.7 and hoping someone can lend a hand. I've got Torch deployed using feasibility-deploy, and I'm using the execute-crtdl.sh script from the repo (link here). If this isn't the right place for this question, please let me know!
The Issue
So, when I run:
./execute-crtdl.sh -f queries/example-crtdl.json
with this example-crtdl.json, a link is generated just fine. But, here's the kicker: when I try to resolve that link, I get hit with this RuntimeException:
[reactor-http-epoll-1] ERROR d.m.torch.rest.FhirController - Job 0fa19252-89bc-44c1-acb2-ec7036914ad0 failed: java.lang.RuntimeException: Trying to redact Resource without Meta
java.lang.RuntimeException: java.lang.RuntimeException: Trying to redact Resource without Meta
at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(Unknown Source)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Unknown Source)
at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.reportException(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.invoke(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateParallel(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateParallel(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source)
at java.base/java.util.stream.ReferencePipeline$Head.forEach(Unknown Source)
at de.medizininformatikinitiative.torch.service.BatchCopierRedacter.transformBatch(BatchCopierRedacter.java:50)
at de.medizininformatikinitiative.torch.service.CrtdlProcessingService.lambda$processBatch$12(CrtdlProcessingService.java:142)
at reactor.core.publisher.FluxMapFuseable$MapFuseableSubscriber.onNext(FluxMapFuseable.java:113)
at reactor.core.publisher.FluxMapFuseable$MapFuseableSubscriber.onNext(FluxMapFuseable.java:129)
at reactor.core.publisher.MonoFlatMap$FlatMapMain.secondComplete(MonoFlatMap.java:245)
at reactor.core.publisher.MonoFlatMap$FlatMapInner.onNext(MonoFlatMap.java:305)
at reactor.core.publisher.FluxMapFuseable$MapFuseableSubscriber.onNext(FluxMapFuseable.java:129)
at reactor.core.publisher.Operators$BaseFluxToMonoOperator.completePossiblyEmpty(Operators.java:2096)
at reactor.core.publisher.MonoCollect$CollectSubscriber.onComplete(MonoCollect.java:145)
at reactor.core.publisher.FluxConcatMapNoPrefetch$FluxConcatMapNoPrefetchSubscriber.onComplete(FluxConcatMapNoPrefetch.java:241)
at reactor.core.publisher.FluxIterable$IterableSubscription.slowPath(FluxIterable.java:357)
at reactor.core.publisher.FluxIterable$IterableSubscription.request(FluxIterable.java:294)
at reactor.core.publisher.FluxConcatMapNoPrefetch$FluxConcatMapNoPrefetchSubscriber.innerComplete(FluxConcatMapNoPrefetch.java:275)
at reactor.core.publisher.FluxConcatMap$ConcatMapInner.onComplete(FluxConcatMap.java:889)
at reactor.core.publisher.FluxMap$MapSubscriber.onComplete(FluxMap.java:144)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.request(MonoIgnoreThen.java:165)
at reactor.core.publisher.FluxMap$MapSubscriber.request(FluxMap.java:164)
at reactor.core.publisher.Operators$MultiSubscriptionSubscriber.request(Operators.java:2330)
at reactor.core.publisher.FluxConcatMapNoPrefetch$FluxConcatMapNoPrefetchSubscriber.request(FluxConcatMapNoPrefetch.java:339)
at reactor.core.publisher.Operators$BaseFluxToMonoOperator.request(Operators.java:2066)
at reactor.core.publisher.FluxMapFuseable$MapFuseableSubscriber.request(FluxMapFuseable.java:171)
at reactor.core.publisher.MonoFlatMap$FlatMapInner.onSubscribe(MonoFlatMap.java:291)
at reactor.core.publisher.FluxMapFuseable$MapFuseableSubscriber.onSubscribe(FluxMapFuseable.java:96)
at reactor.core.publisher.Operators$BaseFluxToMonoOperator.onSubscribe(Operators.java:2050)
at reactor.core.publisher.FluxConcatMapNoPrefetch$FluxConcatMapNoPrefetchSubscriber.onSubscribe(FluxConcatMapNoPrefetch.java:164)
at reactor.core.publisher.FluxIterable.subscribe(FluxIterable.java:201)
at reactor.core.publisher.FluxIterable.subscribe(FluxIterable.java:83)
at reactor.core.publisher.InternalMonoOperator.subscribe(InternalMonoOperator.java:76)
at reactor.core.publisher.MonoFlatMap$FlatMapMain.onNext(MonoFlatMap.java:165)
at reactor.core.publisher.FluxMap$MapSubscriber.onNext(FluxMap.java:122)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.complete(MonoIgnoreThen.java:294)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.onNext(MonoIgnoreThen.java:188)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.subscribeNext(MonoIgnoreThen.java:237)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.onComplete(MonoIgnoreThen.java:204)
at reactor.core.publisher.FluxConcatMapNoPrefetch$FluxConcatMapNoPrefetchSubscriber.innerComplete(FluxConcatMapNoPrefetch.java:287)
at reactor.core.publisher.FluxConcatMap$ConcatMapInner.onComplete(FluxConcatMap.java:889)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.complete(MonoIgnoreThen.java:295)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.onNext(MonoIgnoreThen.java:188)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.subscribeNext(MonoIgnoreThen.java:237)
at reactor.core.publisher.MonoIgnoreThen$ThenIgnoreMain.onComplete(MonoIgnoreThen.java:204)
at reactor.core.publisher.FluxPeekFuseable$PeekFuseableSubscriber.onComplete(FluxPeekFuseable.java:277)
at reactor.core.publisher.FluxPeekFuseable$PeekFuseableSubscriber.onComplete(FluxPeekFuseable.java:277)
at reactor.core.publisher.FluxContextWrite$ContextWriteSubscriber.onComplete(FluxContextWrite.java:126)
at reactor.core.publisher.FluxFilter$FilterConditionalSubscriber.onComplete(FluxFilter.java:300)
at reactor.core.publisher.FluxHandle$HandleConditionalSubscriber.onComplete(FluxHandle.java:440)
at reactor.core.publisher.FluxConcatMapNoPrefetch$FluxConcatMapNoPrefetchSubscriber.onComplete(FluxConcatMapNoPrefetch.java:241)
at reactor.core.publisher.FluxConcatMapNoPrefetch$FluxConcatMapNoPrefetchSubscriber.innerComplete(FluxConcatMapNoPrefetch.java:287)
at reactor.core.publisher.FluxConcatMap$ConcatMapInner.onComplete(FluxConcatMap.java:889)
at reactor.core.publisher.FluxPeek$PeekSubscriber.onComplete(FluxPeek.java:260)
at reactor.core.publisher.FluxPeek$PeekSubscriber.onComplete(FluxPeek.java:260)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.checkTerminated(FluxFlatMap.java:850)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.drainLoop(FluxFlatMap.java:612)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.drain(FluxFlatMap.java:592)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.onComplete(FluxFlatMap.java:469)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.checkTerminated(FluxFlatMap.java:850)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.drainLoop(FluxFlatMap.java:612)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.drain(FluxFlatMap.java:592)
at reactor.core.publisher.FluxFlatMap$FlatMapMain.onComplete(FluxFlatMap.java:469)
at reactor.core.publisher.SerializedSubscriber.onComplete(SerializedSubscriber.java:146)
at reactor.core.publisher.FluxRetryWhen$RetryWhenMainSubscriber.onComplete(FluxRetryWhen.java:204)
at reactor.core.publisher.FluxExpand$ExpandBreathSubscriber.drainQueue(FluxExpand.java:168)
at reactor.core.publisher.FluxExpand$ExpandBreathSubscriber.onComplete(FluxExpand.java:147)
at reactor.core.publisher.FluxMapFuseable$MapFuseableSubscriber.onComplete(FluxMapFuseable.java:152)
at reactor.core.publisher.MonoFlatMap$FlatMapMain.secondComplete(MonoFlatMap.java:246)
at reactor.core.publisher.MonoFlatMap$FlatMapInner.onNext(MonoFlatMap.java:305)
at reactor.core.publisher.FluxOnErrorResume$ResumeSubscriber.onNext(FluxOnErrorResume.java:79)
at reactor.core.publisher.FluxOnAssembly$OnAssemblySubscriber.onNext(FluxOnAssembly.java:539)
at reactor.core.publisher.FluxMapFuseable$MapFuseableSubscriber.onNext(FluxMapFuseable.java:129)
at reactor.core.publisher.FluxContextWrite$ContextWriteSubscriber.onNext(FluxContextWrite.java:107)
at reactor.core.publisher.FluxMapFuseable$MapFuseableConditionalSubscriber.onNext(FluxMapFuseable.java:299)
at reactor.core.publisher.FluxFilterFuseable$FilterFuseableConditionalSubscriber.onNext(FluxFilterFuseable.java:337)
at reactor.core.publisher.Operators$BaseFluxToMonoOperator.completePossiblyEmpty(Operators.java:2096)
at reactor.core.publisher.MonoCollect$CollectSubscriber.onComplete(MonoCollect.java:145)
at reactor.core.publisher.FluxMap$MapSubscriber.onComplete(FluxMap.java:144)
at reactor.core.publisher.FluxPeek$PeekSubscriber.onComplete(FluxPeek.java:260)
at reactor.core.publisher.FluxMap$MapSubscriber.onComplete(FluxMap.java:144)
at reactor.netty.channel.FluxReceive.onInboundComplete(FluxReceive.java:413)
at reactor.netty.channel.ChannelOperations.onInboundComplete(ChannelOperations.java:455)
at reactor.netty.channel.ChannelOperations.terminate(ChannelOperations.java:509)
at reactor.netty.http.client.HttpClientOperations.onInboundNext(HttpClientOperations.java:821)
at reactor.netty.channel.ChannelOperationsHandler.channelRead(ChannelOperationsHandler.java:115)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412)
at io.netty.channel.CombinedChannelDuplexHandler$DelegatingChannelHandlerContext.fireChannelRead(CombinedChannelDuplexHandler.java:436)
at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:346)
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:318)
at io.netty.channel.CombinedChannelDuplexHandler.channelRead(CombinedChannelDuplexHandler.java:251)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:442)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412)
at io.netty.handler.ssl.SslHandler.unwrap(SslHandler.java:1519)
at io.netty.handler.ssl.SslHandler.decodeJdkCompatible(SslHandler.java:1377)
at io.netty.handler.ssl.SslHandler.decode(SslHandler.java:1428)
at io.netty.handler.codec.ByteToMessageDecoder.decodeRemovalReentryProtection(ByteToMessageDecoder.java:530)
at io.netty.handler.codec.ByteToMessageDecoder.callDecode(ByteToMessageDecoder.java:469)
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:290)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:412)
at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:440)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:420)
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:868)
at io.netty.channel.epoll.AbstractEpollStreamChannel$EpollStreamUnsafe.epollInReady(AbstractEpollStreamChannel.java:799)
at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:501)
at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:399)
at io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:998)
at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.RuntimeException: Trying to redact Resource without Meta
at de.medizininformatikinitiative.torch.util.Redaction.redact(Redaction.java:120)
at de.medizininformatikinitiative.torch.service.BatchCopierRedacter.transform(BatchCopierRedacter.java:162)
at de.medizininformatikinitiative.torch.service.BatchCopierRedacter.lambda$transform$7(BatchCopierRedacter.java:129)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source)
at java.base/java.util.HashMap$EntrySpliterator.forEachRemaining(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachTask.compute(Unknown Source)
at java.base/java.util.concurrent.CountedCompleter.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.invoke(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateParallel(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateParallel(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source)
at java.base/java.util.stream.ReferencePipeline$Head.forEach(Unknown Source)
at de.medizininformatikinitiative.torch.service.BatchCopierRedacter.transform(BatchCopierRedacter.java:112)
at de.medizininformatikinitiative.torch.service.BatchCopierRedacter.lambda$transformBatch$0(BatchCopierRedacter.java:51)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source)
at java.base/java.util.Spliterators$ArraySpliterator.forEachRemaining(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.base/java.util.stream.ForEachOps$ForEachTask.compute(Unknown Source)
at java.base/java.util.concurrent.CountedCompleter.exec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinTask.doExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool.scan(Unknown Source)
at java.base/java.util.concurrent.ForkJoinPool.runWorker(Unknown Source)
at java.base/java.util.concurrent.ForkJoinWorkerThread.run(Unknown Source)
Diving Deeper into the Error
The core of the error message, ***
