Issues with uploading LOINC codessytem to HAPI Server

Vivek Namboothiri

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Oct 13, 2021, 5:40:06 AM10/13/21

to HAPI FHIR

Hi ,

I have downloaded the latest version of HAPI FHIR server(version "5.5.1") and was trying to import the LOINC code system in to the FHIR server using the hapi-fhir-cli tool. I have used LOINC version 2.71 and getting the error as shown below:

ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method: java.lang.IllegalArgumentException: Value exceeds maximum length (2000): 2313

at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:272)

at ca.uhn.fhir.rest.server.method.OperationMethodBinding.invokeServer(OperationMethodBinding.java:332)

at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.doInvokeServer(BaseResourceReturningMethodBinding.java:326)

at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.invokeServer(BaseResourceReturningMethodBinding.java:434)

at ca.uhn.fhir.rest.server.method.OperationMethodBinding.invokeServer(OperationMethodBinding.java:307)

at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:1152)

at ca.uhn.fhir.rest.server.RestfulServer.doPost(RestfulServer.java:423)

at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1861)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)

at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:799)

at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:550)

at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)

at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:602)

at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)

at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)

at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)

at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)

at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)

at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)

at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)

at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)

at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)

at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)

at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)

at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)

at org.eclipse.jetty.server.Server.handle(Server.java:516)

at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:388)

at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:633)

at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:380)

at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)

at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)

at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)

at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)

at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)

at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)

at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)

at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)

at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:386)

Any idea/reference on what is going wrong here?

Regards,

Vivek

Vivek Namboothiri

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Oct 13, 2021, 1:21:52 PM10/13/21

to HAPI FHIR

It's the same issue with hapi-fhir-cli version 5.5.2 as well. The command used is :

hapi-fhir-cli upload-terminology -v r4 -u http://loinc.org -t http://localhost:8080/baseR4 -d Loinc_2.71.zip

Basically, it`s unable to upload LOINC terminology data for LOINC version 2.71 in the latest HAPI FHIR server using the CLI tool.

Regards,

Vivek

kalyan pamula

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Jan 12, 2022, 12:43:02 PM1/12/22

to HAPI FHIR

Anyone able to load LONIC 2.71.

Paul Jones

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Jan 12, 2022, 2:16:07 PM1/12/22

to HAPI FHIR

I solved it locally by changing the loinc archive as follows (assumes you do not need this linguistic variant):

removing file AccessoryFiles/LinguisticVariants/zhCN5LinguisticVariant.csv
removing the first line (containing "5","zh","CN","Chinese (CHINA)","Lin Zhang, A LOINC volunteer from China") from file AccessoryFiles/LinguisticVariants/LinguisticVariants.csv