FHIR Chat · Terminology - Unable to load SNOMED Codes · hapi

Stream: hapi

Topic: Terminology - Unable to load SNOMED Codes


view this post on Zulip Shreshta Balachandar (Jan 12 2021 at 12:56):

Hi all!

I am trying to load SNOMED codes using the CLI but am currently having some issues regarding the entry size. I have included the console snippet below. Has anyone else seen this issue?

Thanks,
Shreshta

$ hapi-fhir-cli upload-terminology -d $DIR/pocs/snomed/SnomedCT_InternationalRF2_PRODUCTION_20190731T120000Z.zip -v r4 -t http://localhost:8080/fhir -u http://snomed.info/sct
------------------------------------------------------------
?  HAPI FHIR 5.2.0 - Command Line Tool
------------------------------------------------------------
Process ID                      : 20288@$COMPUTER_NAME
Max configured JVM memory (Xmx) : 2.0GB
Detected Java version           : 11.0.8
------------------------------------------------------------
2021-01-08 11:08:21.197 [main] INFO  c.u.f.c.UploadTerminologyCommand Adding ZIP file: $DIR/pocs/snomed/SnomedCT_InternationalRF2_PRODUCTION_20190731T120000Z.zip
2021-01-08 11:08:23.265 [main] INFO  c.u.f.c.UploadTerminologyCommand File size is greater than 10 MB - Going to use a local file reference instead of a direct HTTP transfer. Note that this will only work when executing this command on the same server as the FHIR server itself.
2021-01-08 11:08:26.502 [main] INFO  c.u.f.c.UploadTerminologyCommand Beginning upload - This may take a while...
2021-01-08 11:08:27.474 [main] ERROR c.u.f.c.UploadTerminologyCommand Received the following response:
{
  "resourceType": "OperationOutcome",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><h1>Operation Outcome</h1><table border=\"0\"><tr><td style=\"font-weight: bold;\">ERROR</td><td>[]</td><td><pre>invalid entry size (expected 0 but got 607159 bytes)</pre></td>\n\t\t\t\t\t\n\t\t\t\t\n\t\t\t</tr>\n\t\t</table>\n\t</div>"
  },
  "issue": [ {
    "severity": "error",
    "code": "processing",
    "diagnostics": "invalid entry size (expected 0 but got 607159 bytes)"
  } ]
}
2021-01-08 11:08:27.482 [main] ERROR ca.uhn.fhir.cli.App Error during execution:
ca.uhn.fhir.rest.server.exceptions.InternalErrorException: HTTP 500 Server Error: invalid entry size (expected 0 but got 607159 bytes)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
        at ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException.newInstance(BaseServerResponseException.java:302)
        at ca.uhn.fhir.rest.client.impl.BaseClient.invokeClient(BaseClient.java:351)
        at ca.uhn.fhir.rest.client.impl.GenericClient$BaseClientExecutable.invoke(GenericClient.java:540)
        at ca.uhn.fhir.rest.client.impl.GenericClient$OperationInternal.execute(GenericClient.java:1314)
        at ca.uhn.fhir.cli.UploadTerminologyCommand.invokeOperation(UploadTerminologyCommand.java:204)
        at ca.uhn.fhir.cli.UploadTerminologyCommand.run(UploadTerminologyCommand.java:113)
        at ca.uhn.fhir.cli.BaseApp.run(BaseApp.java:268)
        at ca.uhn.fhir.cli.App.main(App.java:43)
2021-01-08 11:08:27.500 [Thread-0] INFO  ca.uhn.fhir.cli.App HAPI FHIR is shutting down...

view this post on Zulip Lin Zhang (Jan 12 2021 at 13:35):

increase the max memory size to say 16GB or more? just my guess.


Last updated: Apr 12 2022 at 19:14 UTC