Possible memory leak and failure to restore the observation scope when using a JPA repository from a GraphQL controller

[nikb1tamerfdp]

The context

In my application (Spring Boot 3.2.6), I'm using the GraphQL, Web and JPA starters.
I have created a GraphQL controller, in which I interact with a JPA repository.
I have also enabled observability with Micrometer.

The issue

When I query my controller, everything executes successfully, but I can find this log line (formatted for clarity purpose) :

[...] WARN [...] --- [nio-8080-exec-3] [app=My Application, traceId=7f1a080fea0a3662e74ce0f85d00664b, spanId=3f4b468cb5bccffd] i.m.o.c.ObservationThreadLocalAccessor :
Observation <{
	name=http.server.requests(null),
	error=null,
	context=name='http.server.requests',
	contextualName='null',
	error='null',
	lowCardinalityKeyValues=[
		exception='none',
		method='POST',
		outcome='SUCCESS',
		status='200',
		uri='UNKNOWN'
	],
	highCardinalityKeyValues=[
		http.url='/graphql'
	],
	map=[
		class io.micrometer.tracing.handler.TracingObservationHandler$TracingContext='TracingContext{
			span=ImmutableSpanContext{
				traceId=7f1a080fea0a3662e74ce0f85d00664b,
				spanId=6664922c03ad4f85,
				traceFlags=01,
				traceState=ArrayBasedTraceState{entries=[]}, 
				remote=false, 
				valid=true
			}
		}',
		class io.micrometer.core.instrument.LongTaskTimer$Sample='SampleImpl{
			duration(seconds)=0.0147542, 
			duration(nanos)=1.47542E7, 
			startTimeNanos=29155328641800
		}',
		class io.micrometer.core.instrument.Timer$Sample='io.micrometer.core.instrument.Timer$Sample@3b0b7fc2'
	],
	parentObservation=null
}>
to which we're restoring is not the same as the one set as this scope's parent observation
<{
	name=graphql.datafetcher(null), 
	error=null, 
	context=name='graphql.datafetcher', 
	contextualName='null', 
	error='null', 
	lowCardinalityKeyValues=[
		graphql.error.type='NONE', 
		graphql.field.name='retrieveBookById', 
		graphql.outcome='SUCCESS'
	], 
	highCardinalityKeyValues=[
		graphql.field.path='/retrieveBookById'
	],
	map=[
		class io.micrometer.tracing.handler.TracingObservationHandler$TracingContext='TracingContext{
			span=ImmutableSpanContext{
				traceId=7f1a080fea0a3662e74ce0f85d00664b, 
				spanId=a4204ff90062fd5a, 
				traceFlags=01, 
				traceState=ArrayBasedTraceState{entries=[]}, 
				remote=false, 
				valid=true
			}
		}', 
		class io.micrometer.core.instrument.LongTaskTimer$Sample='SampleImpl{
			duration(seconds)=0.0108987, 
			duration(nanos)=1.08987E7, 
			startTimeNanos=29155332569100
		}', 
		class io.micrometer.core.instrument.Timer$Sample='io.micrometer.core.instrument.Timer$Sample@48ad6d4a'
	], 
	parentObservation={
		name=graphql.request(null), 
		error=null, 
		context=name='graphql.request', 
		contextualName='null', 
		error='null', 
		lowCardinalityKeyValues=[
			graphql.operation='query', 
			graphql.outcome='INTERNAL_ERROR'
		], 
		highCardinalityKeyValues=[
			graphql.execution.id='3bb1672e-660d-bb96-d7c5-4bd6ceb56cd6'
		], 
		map=[
			class io.micrometer.tracing.handler.TracingObservationHandler$TracingContext='TracingContext{
				span=ImmutableSpanContext{
					traceId=7f1a080fea0a3662e74ce0f85d00664b, 
					spanId=deeb0dd86af7c990, 
					traceFlags=01, 
					traceState=ArrayBasedTraceState{entries=[]}, 
					remote=false, 
					valid=true
				}
			}', 
			class io.micrometer.core.instrument.LongTaskTimer$Sample='SampleImpl{
				duration(seconds)=0.0138164, 
				duration(nanos)=1.38164E7, 
				startTimeNanos=29155329694600
			}', 
			class io.micrometer.core.instrument.Timer$Sample='io.micrometer.core.instrument.Timer$Sample@3930f5ed'
		], 
		parentObservation={
			name=http.server.requests(null), 
			error=null, 
			context=name='http.server.requests', 
			contextualName='null', 
			error='null', 
			lowCardinalityKeyValues=[
				exception='none', 
				method='POST', 
				outcome='SUCCESS', 
				status='200', 
				uri='UNKNOWN'
			], 
			highCardinalityKeyValues=[
				http.url='/graphql'
			], 
			map=[
				class io.micrometer.tracing.handler.TracingObservationHandler$TracingContext='TracingContext{
					span=ImmutableSpanContext{
						traceId=7f1a080fea0a3662e74ce0f85d00664b, 
						spanId=6664922c03ad4f85, 
						traceFlags=01, 
						traceState=ArrayBasedTraceState{entries=[]}, 
						remote=false, valid=true
					}
				}',
				class io.micrometer.core.instrument.LongTaskTimer$Sample='SampleImpl{
					duration(seconds)=0.0149397, 
					duration(nanos)=1.49397E7, 
					startTimeNanos=29155328641800
				}', 
				class io.micrometer.core.instrument.Timer$Sample='io.micrometer.core.instrument.Timer$Sample@3b0b7fc2'
			], 
			parentObservation=null
		}
	}
}>.
Most likely a manually created Observation has a scope opened that was never closed. This may lead to thread polluting and memory leaks.

When I connect my application to an Open Telemetry with a Jaeger backend, just to check if everything is ok in terms of trace and spans, it seems that yeah, everything is ok :

This log is not generated if I remove interaction with my JPA repository.
It's also not generated if I annotate the method of my controller (the one annotated with @QueryMapping) with @Observed, or if I set the property spring.jpa.open-in-view to false (something I prefer not to do).

How to reproduce

You can find a sample application right here.

You can query the controller with these information :

• URL : http://localhost:8080/graphql
• Query :

  retrieveBookById(id: "book-1") {
    id
    name
  }

Additional comments

In the original ticket that I've created on Spring Boot project side, @bclozel added this comment, maybe it can give more info :

I'm not sure about the actual source of the problem, but I think that the JPA instrumentation assumes something that is invalid in this case here. First, a bit a background:

• Spring for GraphQL instruments your controller methods by setting/restoring thread locals before/after calling it. Around this method execution, things can be executed asynchronously on various threads, so we don't rely on threadlocals but we store the current observation in the GraphQL context. I have checked that this behavior is correct.
• when a controller method is executed, child observations can be started and they will be shown in the resulting traces

In this case, I think that a specific observation is started with the call to the JPA repository and that somehow this child observation is not closed before the GraphQL data fetching observation (your controller call) is ended. I think this observation is stopped later. While this probably won't cause leaks, the trace might look strange.

I suspect this is due to the datasource observation, keeping things opened as long as the JPA session is opened.

[mp911de]

I'm not sure where the trace is being created at. Generally, all JDBC/JPA instrumentation is happening outside of Spring Data JPA as this project expects an already configured EntityManager with a potentially decorated DataSource.

Paging @rstoyanchev (and @jonatan-ivanov). It could well be that the issue has its origin in Spring GraphQL or Spring Web. After poking a bit on the reproducer, wrapping the repository call within a TransactionTemplate doesn't change anything, however, not calling the repository doesn't reproduce the issue.

I assume an issue somewhere between GraphQL and the DataSource instrumentation.

[bclozel]

I think this issue should be closed in favor of jdbc-observations/datasource-micrometer#41

[mp911de]

Alright, thanks for the pointer.