Failed to load conformance resource in HAPI FHIR 2.2

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Shlomy Reinstein

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Feb 7, 2017, 8:21:45 AM2/7/17
to HAPI FHIR
Hi,

Last week we switched from HAPI 1.4 to HAPI 2.2, mainly for performance reasons.
Since this switch, we've been experiencing sudden breaks of the FHIR server; a few hours after starting up, it stops responding to client requests. When loading the admin website (which provides the UI for the CRUD operations etc), it says that it failed to load the conformance resource. Any idea what the problem may be?

Exception:

2017-02-07 09:28:53.556 [http-nio-8080-exec-5] INFO  ca.uhn.fhir.context.FhirContext [FhirContext.java:235] Creating new FHIR context for FHIR version [DSTU2]
2017-02-07 09:29:03.946 [http-nio-8080-exec-5] WARN  ca.uhn.fhir.to.BaseController [BaseController.java:400] Failed to load conformance statement
ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException: Encountered IOException when performing GET to URL http://ilqhfaatc1vw152:8080/onco-fhir-server/baseDstu2/metadata - java.net.SocketTimeoutException: Read timed out
at ca.uhn.fhir.rest.client.BaseClient.invokeClient(BaseClient.java:332)
at ca.uhn.fhir.rest.client.BaseClient.invokeClient(BaseClient.java:183)
at ca.uhn.fhir.rest.client.GenericClient.conformance(GenericClient.java:105)
at ca.uhn.fhir.to.BaseController.loadAndAddConfDstu2(BaseController.java:398)
at ca.uhn.fhir.to.BaseController.loadAndAddConf(BaseController.java:325)
at ca.uhn.fhir.to.BaseController.addCommonParams(BaseController.java:101)
at ca.uhn.fhir.to.Controller.actionResource(Controller.java:331)

In addition, we get messages like the following from the hosting Tomcat server, I don't know if it's related:

07-Feb-2017 09:33:29.767 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [onco-fhir-server] is still processing a request that has yet to finish. This is very likely to create a memory leak. You can control the time allowed for requests to finish by using the unloadDelay attribute of the standard Context implementation. Stack trace of request processing thread:
 ca.uhn.fhir.narrative.BaseThymeleafNarrativeGenerator.initialize(BaseThymeleafNarrativeGenerator.java:144)
 ca.uhn.fhir.narrative.BaseThymeleafNarrativeGenerator.generateNarrative(BaseThymeleafNarrativeGenerator.java:85)
 ca.uhn.fhir.parser.JsonParser.encodeCompositeElementChildrenToStreamWriter(JsonParser.java:577)
 ca.uhn.fhir.parser.JsonParser.encodeCompositeElementToStreamWriter(JsonParser.java:765)
 ca.uhn.fhir.parser.JsonParser.encodeResourceToJsonStreamWriter(JsonParser.java:913)
 ca.uhn.fhir.parser.JsonParser.encodeResourceToJsonStreamWriter(JsonParser.java:816)
 ca.uhn.fhir.parser.JsonParser.doEncodeResourceToJsonLikeWriter(JsonParser.java:203)
 ca.uhn.fhir.parser.JsonParser.doEncodeResourceToWriter(JsonParser.java:193)
 ca.uhn.fhir.parser.BaseParser.encodeResourceToWriter(BaseParser.java:402)
 ca.uhn.fhir.rest.server.RestfulServerUtils.streamResponseAsResource(RestfulServerUtils.java:702)
 ca.uhn.fhir.rest.server.RestfulResponse.streamResponseAsResource(RestfulResponse.java:96)
 ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor.handleException(ExceptionHandlingInterceptor.java:94)
 ca.uhn.fhir.rest.server.interceptor.ExceptionHandlingInterceptor.handleException(ExceptionHandlingInterceptor.java:55)
 ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:759)
 ca.uhn.fhir.rest.server.RestfulServer.doGet(RestfulServer.java:1226)
 ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1202)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:729)

We did not have such problems with 1.4, it started shortly after the switch to 2.2.

Thanks!
Shlomy

Shlomy Reinstein

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Feb 21, 2017, 2:18:07 AM2/21/17
to HAPI FHIR
I haven't found the reason for this problem yet. I found, however, that disabling paging on the HAPI server caused this problem to be a lot less frequent, but it still happens from time to time. Any idea what I should look for? We're hosting the HAPI FHIR war file in a Tomcat container. I don't see anything in the Tomcat logs when this happens, except for the client exception. Is there a deeper level of debug messages that I can enable in the FHIR server to catch the problem? Thanks! 

qazy...@gmail.com

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Mar 1, 2017, 1:57:22 PM3/1/17
to HAPI FHIR

Hi,

I also see this error every time connectingsave image to the base URL:
Running FHIR on a Docker container. However the API is working correctly with all CRUD operations?


hapi       | 18:45:19 INFO  ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [DSTU3]
hapi       | 18:45:39 WARN  ca.uhn.fhir.to.BaseController - Failed to load conformance statement
hapi       | ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException: Encountered IOException when performing GET to URL http://172.28.46.83:8001/baseDstu3/metadata - org.apache.http.conn.ConnectTimeoutException: Connect to 172.28.46.83:8001 [/172.28.46.83] failed: connect timed out
hapi       | at ca.uhn.fhir.rest.client.BaseClient.invokeClient(BaseClient.java:332)
hapi       | at ca.uhn.fhir.rest.client.GenericClient$BaseClientExecutable.invoke(GenericClient.java:637)
hapi       | at ca.uhn.fhir.rest.client.GenericClient$FetchConformanceInternal.execute(GenericClient.java:929)
hapi       | at ca.uhn.fhir.to.BaseController.loadAndAddConfDstu3(BaseController.java:462)
hapi       | at ca.uhn.fhir.to.BaseController.loadAndAddConf(BaseController.java:327)
hapi       | at ca.uhn.fhir.to.BaseController.addCommonParams(BaseController.java:101)
hapi       | at ca.uhn.fhir.to.Controller.actionHome(Controller.java:234)
hapi       | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
hapi       | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
hapi       | at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
hapi       | at java.lang.reflect.Method.invoke(Method.java:498)
hapi       | at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221)
hapi       | at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
hapi       | at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:114)
hapi       | at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
hapi       | at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
hapi       | at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
hapi       | at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:963)
hapi       | at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:897)
hapi       | at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
hapi       | at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:861)
hapi       | at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
hapi       | at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
hapi       | at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
hapi       | at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:837)
hapi       | at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:584)
hapi       | at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
hapi       | at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)
hapi       | at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)
hapi       | at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180)
hapi       | at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:512)
hapi       | at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
hapi       | at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112)
hapi       | at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
hapi       | at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
hapi       | at org.eclipse.jetty.server.Server.handle(Server.java:534)
hapi       | at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:320)
hapi       | at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251)
hapi       | at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273)
hapi       | at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:95)
hapi       | at org.eclipse.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)
hapi       | at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303)
hapi       | at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148)
hapi       | at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136)
hapi       | at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671)
hapi       | at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589)
hapi       | at java.lang.Thread.run(Thread.java:745)
hapi       | Caused by: org.apache.http.conn.ConnectTimeoutException: Connect to 172.28.46.83:8001 [/172.28.46.83] failed: connect timed out
hapi       | at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:150)
hapi       | at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:353)
hapi       | at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:380)
hapi       | at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:236)
hapi       | at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:184)
hapi       | at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:88)
hapi       | at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
hapi       | at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:184)
hapi       | at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
hapi       | at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:107)
hapi       | at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:55)
hapi       | at ca.uhn.fhir.rest.client.apache.ApacheHttpRequest.execute(ApacheHttpRequest.java:62)
hapi       | at ca.uhn.fhir.rest.client.BaseClient.invokeClient(BaseClient.java:240)
hapi       | ... 46 common frames omitted
hapi       | Caused by: java.net.SocketTimeoutException: connect timed out
hapi       | at java.net.PlainSocketImpl.socketConnect(Native Method)
hapi       | at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
hapi       | at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
hapi       | at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
hapi       | at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
hapi       | at java.net.Socket.connect(Socket.java:589)
hapi       | at org.apache.http.conn.socket.PlainConnectionSocketFactory.connectSocket(PlainConnectionSocketFactory.java:74)
hapi       | at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:141)
hapi       | ... 58 common frames omitted
hapi       | 18:45:39 INFO  ca.uhn.fhir.to.Controller - Request(GET //172.28.46.83:8001/)@46a5b8a7
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left...@gmail.com

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Mar 31, 2017, 9:59:48 PM3/31/17
to HAPI FHIR
It happens to me too. Any Suggestion?

BTW, can you visit {baseUrl}/metadata to get the conformance?

Somesh Kumar

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Apr 28, 2017, 5:35:48 AM4/28/17
to HAPI FHIR

Hi,

Did you found solution to your problem.If yes please guide me. I am also having the same issue

Shlomy Reinstein

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Apr 28, 2017, 5:38:10 AM4/28/17
to Somesh Kumar, HAPI FHIR
Seems to be a deadlock in HAPI FHIR. One of my colleagues communicated his findings to the HAPI team earlier this week, hopefully to be resolved soon. The deadlock was easily discovered using JProfiler.

Shlomy

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James Agnew

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May 1, 2017, 7:18:45 AM5/1/17
to Shlomy Reinstein, Kamal....@philips.com, Somesh Kumar, HAPI FHIR
Hi All,

A fix for the regression in the 2.5-SNAPSHOT build which was causing deadlocks under load has been checked in.

After spending a bunch of time poring over both the thread dumps provided by Kamal and the profiling tools provided by Shlomy (thanks guys!) we actually found a few things that needed to be cleaned up, including one spot where the search facility was asking for a second database connection in the middle of a search (leading to the deadlock). The latest 2.5-SNAPSHOT code and Maven artifacts contain fixes to all of this.

If everyone could try the new build out to make sure they don't see any of these issues I'd appreciate it.

Cheers,
James


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Othman, Kamal

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May 2, 2017, 6:05:57 AM5/2/17
to James Agnew, Shlomy Reinstein, Somesh Kumar, HAPI FHIR, Rawashdeh, Nasser

Hi James,

 

This is very good news J

 

I have run my usual tests and seems pretty stable, will keep running tests in the next few days and will let you know if we find issues .

 

One more thing which I mentioned to you before, It doesn’t apply schema on its own on empty DB

I have to invoke the schema SQL statements manually , up till 2.2 the server manage to do that seamlessly

 

If you could look into that as well , would be great

 

Regards

Kamal

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Othman, Kamal

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May 3, 2017, 2:29:23 AM5/3/17
to James Agnew, Shlomy Reinstein, Somesh Kumar, HAPI FHIR, Rawashdeh, Nasser

Hi James,

 

Any idea when the final release is going to be ready ?

 

We would like to work with this version already, but prefer to work with final or at least frozen version

 

Kamal

 

From: Othman, Kamal
Sent: 2017 May 02 1:06 PM
To: 'James Agnew' <james...@gmail.com>; 'Shlomy Reinstein' <srei...@gmail.com>
Cc: 'Somesh Kumar' <somesh...@gmail.com>; 'HAPI FHIR' <hapi...@googlegroups.com>; Rawashdeh, Nasser <Nasser.R...@philips.com>
Subject: RE: Failed to load conformance resource in HAPI FHIR 2.2

 

Hi James,

 

This is very good news J

 

I have run my usual tests and seems pretty stable, will keep running tests in the next few days and will let you know if we find issues .

 

One more thing which I mentioned to you before, It doesn’t apply schema on its own on empty DB

I have to invoke the schema SQL statements manually , up till 2.2 the server manage to do that seamlessly

 

If you could look into that as well , would be great

 

Regards

Kamal

 

From: James Agnew [mailto:james...@gmail.com]
Sent: 2017 May 01 2:18 PM
To: Shlomy Reinstein <srei...@gmail.com>; Othman, Kamal <kamal....@philips.com>
Cc: Somesh Kumar <somesh...@gmail.com>; HAPI FHIR <hapi...@googlegroups.com>
Subject: Re: Failed to load conformance resource in HAPI FHIR 2.2

 

Hi All,

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James Agnew

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May 3, 2017, 10:04:29 AM5/3/17
to Othman, Kamal, Shlomy Reinstein, Somesh Kumar, HAPI FHIR, Rawashdeh, Nasser
Hi Kamal,

This is a pretty big set of changes, so we definitely need a bit of time for testing across lots of platforms (we actually just discovered this morning that it has an issue on Oracle because of Oracle's ridiculous column length limits) but I also do want to get it released ASAP as I think it's a pretty massive improvement over the current release. 

I guess I'd also really like to get to the bottom of this issue where the tables aren't being automatically being created for you, which reminds me: what database platform and version are you using? I'd like to try and reproduce that.

I'm going to guess probably 2 weeks from now should be when 2.5 gets released?

Cheers,
James



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Othman, Kamal

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May 3, 2017, 3:26:34 PM5/3/17
to James Agnew, Shlomy Reinstein, Somesh Kumar, HAPI FHIR, Rawashdeh, Nasser

Hi James,

Thanks for the reply,

 

We are using MySQL server 5.7

Using this same server installation, all versions 1.4 – 2.4 working fine, only using 2.5-SNAPSHOT we are facing this issue

 

Regarding the missing artifacts, we tried from couple machines including mine which managed before to fetch them

Will try again tomorrow

 

But I think either way we are going to wait for the Release, two weeks should be fine

 

Thanks Again

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Othman, Kamal

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May 28, 2017, 3:58:06 AM5/28/17
to James Agnew, Shlomy Reinstein, Somesh Kumar, HAPI FHIR, Rawashdeh, Nasser

Hi James,

 

Just wanted to check if we have a date for the release

 

p.s: The snapshot version is still unavailable for us, when I say unavailable I mean in maven repository

 

Regards

Kamal

 

From: Othman, Kamal
Sent: 2017 May 03 10:26 PM
To: 'James Agnew' <james...@gmail.com>
Cc: Shlomy Reinstein <srei...@gmail.com>; Somesh Kumar <somesh...@gmail.com>; HAPI FHIR <hapi...@googlegroups.com>; Rawashdeh, Nasser <Nasser.R...@philips.com>
Subject: RE: Failed to load conformance resource in HAPI FHIR 2.2

 

Hi James,

Thanks for the reply,

 

We are using MySQL server 5.7

Using this same server installation, all versions 1.4 – 2.4 working fine, only using 2.5-SNAPSHOT we are facing this issue

 

Regarding the missing artifacts, we tried from couple machines including mine which managed before to fetch them

Will try again tomorrow

 

But I think either way we are going to wait for the Release, two weeks should be fine

 

Thanks Again

Regards

Kamal

 

From: James Agnew [mailto:james...@gmail.com]

Sent: 2017 May 03 5:04 PM
To: Othman, Kamal <kamal....@philips.com>

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Othman, Kamal

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Jun 19, 2017, 5:11:48 AM6/19/17
to James Agnew, Shlomy Reinstein, Somesh Kumar, HAPI FHIR, Rawashdeh, Nasser

Hi James,

 

We would like to report new issue, this one is recurring 100% , very easy to reproduce , happens instantly , also a deadlock

Using our test suit, if we increase the number of writers to 8 , and immediate lock occurs , and server becomes unresponsive.

HAPI gui throws this error :

Failed to load conformance statement, error was: ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException: Failed to parse response from server when performing GET to URL http://localhost:8080/onco-fhir-server/baseDstu2/metadata - java.net.SocketTimeoutException: Read timed out

 

Specifically we are running test suit : FhirPerformance_ThreeWriteThreeRead_ParallelFlowTest_515726 with numberOfWriters=8

 

Attached screen shots from JProfiler and thread dump (added two thread dumps from two fresh executions that lead to lock)

 

This is very much on high alert on our side, if you could have a look would be great

 

Regards

Kamal

 

From: Othman, Kamal

Sent: 2017 May 28 10:58 AM
To: 'James Agnew' <james...@gmail.com>

Cc: 'Shlomy Reinstein' <srei...@gmail.com>; 'Somesh Kumar' <somesh...@gmail.com>; 'HAPI FHIR' <hapi...@googlegroups.com>; Rawashdeh, Nasser <Nasser.R...@philips.com>
Subject: RE: Failed to load conformance resource in HAPI FHIR 2.2

 

Hi James,

 

Just wanted to check if we have a date for the release

 

p.s: The snapshot version is still unavailable for us, when I say unavailable I mean in maven repository

 

Regards

Kamal

 

From: Othman, Kamal
Sent: 2017 May 03 10:26 PM
To: 'James Agnew' <james...@gmail.com>
Cc: Shlomy Reinstein <srei...@gmail.com>; Somesh Kumar <somesh...@gmail.com>; HAPI FHIR <hapi...@googlegroups.com>; Rawashdeh, Nasser <Nasser.R...@philips.com>
Subject: RE: Failed to load conformance resource in HAPI FHIR 2.2

 

Hi James,

Thanks for the reply,

 

We are using MySQL server 5.7

Using this same server installation, all versions 1.4 – 2.4 working fine, only using 2.5-SNAPSHOT we are facing this issue

 

Regarding the missing artifacts, we tried from couple machines including mine which managed before to fetch them

Will try again tomorrow

 

But I think either way we are going to wait for the Release, two weeks should be fine

 

Thanks Again

Regards

Kamal

 

From: James Agnew [mailto:james...@gmail.com]

Sent: 2017 May 03 5:04 PM
To: Othman, Kamal <kamal....@philips.com>

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JProfiler_GeneralView.jpg
ThreadDump.txt
JProfiler_ThreadLockGraph.jpg
ThreadDump2.txt

James Agnew

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Jun 19, 2017, 2:23:04 PM6/19/17
to Othman, Kamal, Shlomy Reinstein, Somesh Kumar, HAPI FHIR, Rawashdeh, Nasser
Hi Kamal,

I'm still looking into what we can do about this, but this issue looks to me like a bug with Hibernate. I've logged a ticket in their tracker here: https://hibernate.atlassian.net/browse/HHH-11825

Hopefully more to come on this soon.

Cheers,
James

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