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Update how measurements are processed #196

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Update how measurements are processed #196

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2629b20
Streaming measurements, and no longer using DeepCopy
rogordon01 Jun 3, 2022
e82da7a
Capturing time taken to generate a normalized event
rogordon01 Jun 3, 2022
fc505e7
Reuse clone when evaluating matched tokens
rogordon01 Jun 3, 2022
e39b7ca
Cleaning up code
rogordon01 Jun 3, 2022
86adc82
Removing comment
rogordon01 Jun 3, 2022
8864425
Create JToken directly from event data versus first creating a String
rogordon01 Jun 6, 2022
34f7b7c
PR comments
rogordon01 Jun 7, 2022
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10 changes: 9 additions & 1 deletion src/lib/Microsoft.Health.Fhir.Ingest.Template/MeasurementExtractor.cs
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Expand Up @@ -126,15 +126,23 @@ protected virtual IEnumerable<JToken> MatchTypeTokens(JObject token)
EnsureArg.IsNotNull(token, nameof(token));
var evaluator = CreateRequiredExpressionEvaluator(Template.TypeMatchExpression, nameof(Template.TypeMatchExpression));

JObject tokenClone = null;

foreach (var extractedToken in evaluator.SelectTokens(token))
{
// Add the extracted data as an element of the original data.
// This allows subsequent expressions access to data from the original event data
if (tokenClone == null)
{
tokenClone = new JObject(token);
}

var tokenClone = token.DeepClone() as JObject;
tokenClone.Add(MatchedToken, extractedToken);
yield return tokenClone;
tokenClone.Remove(MatchedToken);
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Does this work? We are returning the tokenClone and them updating the same reference to remove the property. I don't think we can do the remove. Anything downstream of this will potentially be missing the MatchedToken.

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This should work as intended as this is a synchronous IEnumerable. We first yield the cloned JToken and then produce a Measurement from it. Finally we return here to remove the MatchedToken property and start the loop again. The code producing the Measurement does not hold onto a reference for the token it was given.

We have various unit tests which should be testing out this scenario, such as: https://github.com/microsoft/iomt-fhir/blob/main/test/Microsoft.Health.Fhir.Ingest.Template.UnitTests/CalculatedFunctionContentTemplateTests.cs#L79

}

tokenClone = null;
}

protected IExpressionEvaluator CreateRequiredExpressionEvaluator(TemplateExpression expression, string expressionName)
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28 changes: 23 additions & 5 deletions src/lib/Microsoft.Health.Fhir.Ingest/Data/EventDataWithJsonBodyToJTokenConverter.cs
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Expand Up @@ -3,24 +3,42 @@
// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
// -------------------------------------------------------------------------------------------------

using System.IO;
using System.Text;
using EnsureThat;
using Microsoft.Azure.EventHubs;
using Newtonsoft.Json;
using Newtonsoft.Json.Linq;

namespace Microsoft.Health.Fhir.Ingest.Data
{
public class EventDataWithJsonBodyToJTokenConverter : IConverter<EventData, JToken>
{
private const string BodyAttr = "Body";
private const string PropertiesAttr = "Properties";
private const string SystemPropertiesAttr = "SystemProperties";
private readonly JsonSerializer jsonSerializer = JsonSerializer.CreateDefault();

public JToken Convert(EventData input)
{
EnsureArg.IsNotNull(input, nameof(input));
JToken token = new JObject();
JToken body = null;

if (input.Body.Count > 0)
{
using (var stream = new MemoryStream(input.Body.Array))
using (StreamReader sr = new StreamReader(stream, Encoding.UTF8))
using (JsonReader reader = new JsonTextReader(sr))
{
body = JToken.ReadFrom(reader);
}
}

var body = input.Body.Count > 0
? JToken.Parse(Encoding.UTF8.GetString(input.Body.Array, input.Body.Offset, input.Body.Count))
: null;
var data = new { Body = body, input.Properties, input.SystemProperties };
var token = JToken.FromObject(data);
token[BodyAttr] = body;
token[PropertiesAttr] = JToken.FromObject(input.Properties, jsonSerializer);
token[SystemPropertiesAttr] = JToken.FromObject(input.SystemProperties, jsonSerializer);

return token;
}
}
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85 changes: 69 additions & 16 deletions src/lib/Microsoft.Health.Fhir.Ingest/Service/MeasurementEventNormalizationService.cs
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Expand Up @@ -6,6 +6,7 @@
using System;
using System.Collections.Concurrent;
using System.Collections.Generic;
using System.Diagnostics;
using System.Linq;
using System.Threading;
using System.Threading.Tasks;
Expand Down Expand Up @@ -45,7 +46,7 @@ public MeasurementEventNormalizationService(
Data.IConverter<EventData, JToken> converter,
IExceptionTelemetryProcessor exceptionTelemetryProcessor,
int maxParallelism,
int asyncCollectorBatchSize = 200)
int asyncCollectorBatchSize = 25)
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Do we have any data on the impact of this change?

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No hard numbers. I had originally put in 200 as a starting point, though. With the intent on tweaking it as needed. I can revert this change.

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That might be good for now. If we have enough time to compare just this change with out the others and we see a benefit then we can include.

{
_log = EnsureArg.IsNotNull(log, nameof(log));
_contentTemplate = EnsureArg.IsNotNull(contentTemplate, nameof(contentTemplate));
Expand Down Expand Up @@ -99,7 +100,6 @@ private async Task StartConsumer(ISourceBlock<EventData> producer, IEnumerableAs
var transformingConsumer = new TransformManyBlock<EventData, (string, IMeasurement)>(
async evt =>
{
var createdMeasurements = new List<(string, IMeasurement)>();
try
{
string partitionId = evt.SystemProperties.PartitionKey;
Expand All @@ -115,19 +115,7 @@ private async Task StartConsumer(ISourceBlock<EventData> producer, IEnumerableAs

var token = _converter.Convert(evt);

try
{
foreach (var measurement in _contentTemplate.GetMeasurements(token))
{
measurement.IngestionTimeUtc = evt.SystemProperties.EnqueuedTimeUtc;
createdMeasurements.Add((partitionId, measurement));
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Is there a reason we can't just yield return here?

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@rogordon01 rogordon01 Jun 3, 2022 •
edited
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Unfortunately a yield statement cannot existing inside of a try block if there is a catch block. That is the original reason why I create the custom IEnumerable.

https://docs.microsoft.com/en-us/archive/msdn-magazine/2017/june/essential-net-custom-iterators-with-yield#yield-statement-requirements

}
}
catch (Exception ex)
{
// Translate all Normalization Mapping exceptions into a common type for easy identification.
throw new NormalizationDataMappingException(ex);
}
return CreateMeasurementIterator(token, partitionId, exceptions, errorConsumer, evt);
}
catch (Exception ex)
{
Expand All @@ -137,7 +125,7 @@ private async Task StartConsumer(ISourceBlock<EventData> producer, IEnumerableAs
}
}

return createdMeasurements;
return Enumerable.Empty<(string, IMeasurement)>();
});

var asyncCollectorConsumer = new ActionBlock<(string, IMeasurement)[]>(
Expand Down Expand Up @@ -201,5 +189,70 @@ private Task<bool> ProcessErrorAsync(Exception ex, EventData data)
var handled = _exceptionTelemetryProcessor.HandleException(ex, _log);
return Task.FromResult(!handled);
}

private IEnumerable<(string, IMeasurement)> CreateMeasurementIterator(JToken token, string partitionId, ConcurrentBag<Exception> exceptions, Func<Exception, EventData, Task<bool>> errorConsumer, EventData evt)
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Previously, we batched all Measurements per DeviceEvent before sending down the processing pipeline. If there was an error with one Measurement we wouldn't send any Measurements for that DeviceEvent.

This change streams each Measurement onto the processing pipeline as soon as it is generated

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So one consequence of this is we have bad data and spin, we could be now sending more repeat/duplicate messages down stream?

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That is true if we were to spin. But I had thought that we decided not to spin, and simply discard bad data? Until we could send it over to the EMS?

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We will continue to spin by default though I did add the ability to change the strategy if desired.

{
IEnumerator<Measurement> enumerable = null;
Action<Exception> storeNormalizedException = ex =>
{
var normalizationException = new NormalizationDataMappingException(ex);
if (errorConsumer(normalizationException, evt).ConfigureAwait(false).GetAwaiter().GetResult())
{
exceptions.Add(normalizationException);
}
};

try
{
enumerable = _contentTemplate.GetMeasurements(token).GetEnumerator();
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Shouldn't be we able to remove the lower while loop and just yield return as we iterate through each element here?

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We may also want to look at simplifying this class completely. I don't know if using the TPL adds much value. We can also at switching over to async enumerables https://docs.microsoft.com/en-us/archive/msdn-magazine/2019/november/csharp-iterating-with-async-enumerables-in-csharp-8

https://docs.microsoft.com/en-us/dotnet/csharp/whats-new/tutorials/generate-consume-asynchronous-stream

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See my comment about yield statements inside of try/catch blocks.

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Switching this to an AsyncEnumberable could be a good idea. At the very least it would simplify things. I did make use of the pipelines ability to batch, though. But we could see if that could be refactored.

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In the other perf PR we are no longer using this class. Thoughts on reverting this change? It will still be used for the Azure Function implementation but we wouldn't be taking the risk of potentially introducing a new bug for that path. The new metric is great, and we can work to port it over to the new implementation.

}
catch (Exception ex)
{
storeNormalizedException(ex);
yield break;
}

(string, IMeasurement) currentValue = (partitionId, null);
var shouldLoop = true;
var stopWatch = new Stopwatch();

while (shouldLoop)
{
try
{
stopWatch.Start();
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We have some helper classes that simplify this. We may need to port them from PaaS to OSS.

shouldLoop = enumerable.MoveNext();
stopWatch.Stop();

_log.LogMetric(
IomtMetrics.NormalizedEventGenerationTimeMs(partitionId),
stopWatch.ElapsedMilliseconds);

stopWatch.Reset();

if (shouldLoop)
{
var measurement = enumerable.Current;
measurement.IngestionTimeUtc = evt.SystemProperties.EnqueuedTimeUtc;
currentValue = (partitionId, measurement);
}
else
{
break;
}
}
catch (Exception ex)
{
// Translate all Normalization Mapping exceptions into a common type for easy identification.
storeNormalizedException(ex);
shouldLoop = false;
}

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@dustinburson Do we skip processing the remainder of the DeviceEvent now that one Measurement produced an Exception? Or do we simply skip this Measurement, and allow the remaining Measurements to be generated?

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I think it we would keep processing but we would need to discuss further.

if (shouldLoop)
{
yield return currentValue;
}
}
}
}
}
2 changes: 2 additions & 0 deletions src/lib/Microsoft.Health.Fhir.Ingest/Telemetry/Metrics/IomtMetricDefinition.cs
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Expand Up @@ -24,6 +24,8 @@ private IomtMetricDefinition(string metricName)

public static IomtMetricDefinition NormalizedEvent { get; } = new IomtMetricDefinition(nameof(NormalizedEvent));

public static IomtMetricDefinition NormalizedEventGenerationTimeMs { get; } = new IomtMetricDefinition(nameof(NormalizedEventGenerationTimeMs));

public static IomtMetricDefinition Measurement { get; } = new IomtMetricDefinition(nameof(Measurement));

public static IomtMetricDefinition MeasurementGroup { get; } = new IomtMetricDefinition(nameof(MeasurementGroup));
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11 changes: 11 additions & 0 deletions src/lib/Microsoft.Health.Fhir.Ingest/Telemetry/Metrics/IomtMetrics.cs
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Expand Up @@ -159,5 +159,16 @@ public static Metric HandledException(string exceptionName, string connectorStag
{
return exceptionName.ToErrorMetric(connectorStage, ErrorType.GeneralError, ErrorSeverity.Critical);
}

/// <summary>
/// The time it takes to generate a Normalized Event.
/// </summary>
/// <param name="partitionId">The partition id of the events being consumed from the event hub partition </param>
public static Metric NormalizedEventGenerationTimeMs(string partitionId = null)
{
return IomtMetricDefinition.NormalizedEventGenerationTimeMs
.CreateBaseMetric(Category.Traffic, ConnectorOperation.Normalization)
.AddDimension(_partitionDimension, partitionId);
}
}
}
1 change: 1 addition & 0 deletions test/Microsoft.Health.Fhir.Ingest.UnitTests/Microsoft.Health.Fhir.Ingest.UnitTests.csproj
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Expand Up @@ -36,6 +36,7 @@
<AdditionalFiles Include="..\..\stylecop.json" Link="stylecop.json" />
</ItemGroup>
<ItemGroup>
<ProjectReference Include="..\..\src\lib\Microsoft.Health.Expressions\Microsoft.Health.Expressions.csproj" />
<ProjectReference Include="..\..\src\lib\Microsoft.Health.Fhir.Ingest\Microsoft.Health.Fhir.Ingest.csproj" />
<ProjectReference Include="..\Microsoft.Health.Tests.Common\Microsoft.Health.Tests.Common.csproj" />
</ItemGroup>
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2 changes: 1 addition & 1 deletion ...crosoft.Health.Fhir.Ingest.UnitTests/Service/MeasurementEventNormalizationServiceTests.cs
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Expand Up @@ -43,7 +43,7 @@ public async Task GivenMultipleEventsWithOneResultPer_WhenProcessAsync_ThenEachE
_template.GetMeasurements(null).ReturnsForAnyArgs(new[] { Substitute.For<Measurement>() });
var events = Enumerable.Range(0, 10).Select(i => BuildEvent(i)).ToArray();

var srv = new MeasurementEventNormalizationService(_logger, _template, _exceptionTelemetryProcessor);
var srv = new MeasurementEventNormalizationService(_logger, _template, _converter, _exceptionTelemetryProcessor, 3, 25);
await srv.ProcessAsync(events, _consumer);

_template.ReceivedWithAnyArgs(events.Length).GetMeasurements(null);
Expand Down