TechQA.

Hapi Fhir importing Snomed-CT

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I am a newbie in Hapi Fhir, in Fhir also. I'm trying to import Snomed-CT / US version on Hapi Fhir. I'm using the client to do this, this way:

To run the server:

java -jar hapi-fhir-cli.jar run-server

to upload snomed-ct

java -jar hapi-fhir-cli.jar upload-terminology -d SnomedCT_RF2Release_INT_20160131.zip -t http://localhost:8080/baseDstu3 -u http://snomed.info/sct

Code system is uploaded succesfully:

{
  "resourceType": "Bundle",
  "id": "948f4c4b-2e28-475b-a629-3d5122d5e103",
  "meta": {
    "lastUpdated": "2017-09-11T11:47:56.941+02:00"
  },
  "type": "searchset",
  "total": 1,
  "link": [
    {
      "relation": "self",
      "url": "http://localhost:8080/baseDstu3/CodeSystem?_pretty=true"
    }
  ],
  "entry": [
    {
      "fullUrl": "http://localhost:8080/baseDstu3/CodeSystem/1",
      "resource": {
        "resourceType": "CodeSystem",
        "id": "1",
        "meta": {
          "versionId": "1",
          "lastUpdated": "2017-09-11T10:25:43.282+02:00"
        },
        "url": "http://snomed.info/sct",
        "content": "not-present"
      },
      "search": {
        "mode": "match"
      }
    }
  ]
}

But I can't find the codes! This is my ValueSet:

{
  "resourceType": "Bundle",
  "id": "37fff235-1229-4491-a3ab-9bdba2333d57",
  "meta": {
    "lastUpdated": "2017-09-11T11:49:35.553+02:00"
  },
  "type": "searchset",
  "total": 0,
  "link": [
    {
      "relation": "self",
      "url": "http://localhost:8080/baseDstu3/ValueSet?_pretty=true"
    }
  ]
}

This is extracted from my logs:

/hapi-fhir-cli/hapi-fhir-cli-app/target$ java -jar hapi-fhir-cli.jar run-server
------------------------------------------------------------
 HAPI FHIR 3.0.0-SNAPSHOT - Command Line Tool
------------------------------------------------------------
Max configured JVM memory (Xmx): 1.7GB
Detected Java version: 1.8.0_144
------------------------------------------------------------
10:20:49 INFO  ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [DSTU3]
10:20:49 INFO  ca.uhn.fhir.cli.RunServerCommand - Preparing HAPI FHIR JPA server on port 8080
10:20:51 INFO  ca.uhn.fhir.cli.RunServerCommand - Starting HAPI FHIR JPA server in DSTU3 mode
10:21:22 INFO  ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [DSTU3]
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - SQL Warning Code: 10000, SQLState: 01J01
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - Database 'directory:target/jpaserver_derby_files' not created, connection made to existing database instead.
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - SQL Warning Code: 10000, SQLState: 01J01
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - Database 'directory:target/jpaserver_derby_files' not created, connection made to existing database instead.
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - SQL Warning Code: 10000, SQLState: 01J01
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - Database 'directory:target/jpaserver_derby_files' not created, connection made to existing database instead.
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - SQL Warning Code: 10000, SQLState: 01J01
10:21:46 WARN  o.h.e.jdbc.spi.SqlExceptionHelper - Database 'directory:target/jpaserver_derby_files' not created, connection made to existing database instead.
10:21:47 INFO  ca.uhn.fhir.cli.RunServerCommand - Server started on port 8080
10:21:47 INFO  ca.uhn.fhir.cli.RunServerCommand - Web Testing UI : http://localhost:8080/
10:21:47 INFO  ca.uhn.fhir.cli.RunServerCommand - Server Base URL: http://localhost:8080/baseDstu3/
10:22:09 INFO  ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [DSTU3]
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 95ms for query 93e6a047-b93f-4e6c-8ee9-03b51d08bd45
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 96ms for query 93e6a047-b93f-4e6c-8ee9-03b51d08bd45
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
10:22:10 INFO  c.u.f.j.d.d.SearchParamRegistryDstu3 - Refreshed search parameter cache in 108ms
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 67ms for query 60cc4f7c-887c-4fe6-9ca5-32f24017f91a
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 67ms for query 60cc4f7c-887c-4fe6-9ca5-32f24017f91a
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 2ms for query a1ff7c92-b273-4ef4-8898-870c0377a161
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 3ms for query a1ff7c92-b273-4ef4-8898-870c0377a161
10:22:10 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
10:22:10 INFO  c.uhn.fhir.rest.server.RestfulServer - Initializing HAPI FHIR restful server running in DSTU3 mode
10:22:10 INFO  c.uhn.fhir.rest.server.RestfulServer - Added 117 resource provider(s). Total 117
10:22:10 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.jpa.rp.dstu3.AccountResourceProvider
....
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.jpa.rp.dstu3.TestScriptResourceProvider
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.jpa.rp.dstu3.ValueSetResourceProvider
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.jpa.rp.dstu3.VisionPrescriptionResourceProvider
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Added 2 plain provider(s). Total 2
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class org.hl7.fhir.dstu3.hapi.rest.server.ServerProfileProvider
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - Scanning type for RESTful methods: class ca.uhn.fhir.rest.server.PageProvider
10:22:11 INFO  c.uhn.fhir.rest.server.RestfulServer - A FHIR has been lit on this server
10:22:12 INFO  c.u.f.n.BaseThymeleafNarrativeGenerator - Initializing narrative generator
10:22:13 INFO  ca.uhn.fhir.to.Controller - Request(GET //localhost:8080/)@70976daf
10:22:20 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 3ms for query fad4433e-825c-41ae-b22e-9bbb0a1624a0
10:22:20 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 3ms for query fad4433e-825c-41ae-b22e-9bbb0a1624a0
10:22:20 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
...
10:23:50 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 3ms for query f0b25957-c166-4b23-be6e-0d06274da565
10:23:50 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 3ms for query f0b25957-c166-4b23-be6e-0d06274da565
10:23:50 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
10:23:52 INFO  c.u.f.jpa.term.TerminologyLoaderSvc - Beginning SNOMED CT processing
10:23:59 INFO  c.u.f.jpa.term.TerminologyLoaderSvc - Processing file SnomedCT_RF2Release_INT_20160131/Full/Terminology/sct2_Concept_Full_INT_20160131.txt
10:23:59 INFO  c.u.f.jpa.term.TerminologyLoaderSvc -  * Processed 1 records in SnomedCT_RF2Release_INT_20160131/Full/Terminology/sct2_Concept_Full_INT_20160131.txt
10:23:59 INFO  c.u.f.jpa.term.TerminologyLoaderSvc -  * Processed 100000 records in SnomedCT_RF2Release_INT_20160131/Full/Terminology/sct2_Concept_Full_INT_20160131.txt
10:24:00 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 2ms for query 6393e886-2878-4c3a-b50a-a19139c01dd4
10:24:00 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 9ms for query 6393e886-2878-4c3a-b50a-a19139c01dd4
10:24:00 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
...
10:25:29 INFO  c.u.f.jpa.term.TerminologyLoaderSvc -  * Processed 4700000 records in SnomedCT_RF2Release_INT_20160131/Full/Terminology/sct2_Relationship_Full_INT_20160131.txt
10:25:30 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 2ms for query df9f1505-e381-4eda-a04b-934293c54721
10:25:30 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 2ms for query df9f1505-e381-4eda-a04b-934293c54721
10:25:30 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
10:25:40 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 2ms for query 1961cfd8-b2b0-4626-a397-6a7b925e4547
10:25:40 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 2ms for query 1961cfd8-b2b0-4626-a397-6a7b925e4547
10:25:40 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
10:25:41 INFO  c.u.f.jpa.term.TerminologyLoaderSvc - Looking for root codes
10:25:41 INFO  c.u.f.jpa.term.TerminologyLoaderSvc - Done loading SNOMED CT files - 3 root codes, 319446 total codes
10:25:41 INFO  c.u.f.jpa.term.TerminologyLoaderSvc -  * Scanning for circular refs - have scanned 0 / 3 codes (0.0%)
...
10:25:43 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 81ms for query 9aa7c541-8dfa-4176-8621-046c7ba886e4
10:25:43 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 82ms for query 9aa7c541-8dfa-4176-8621-046c7ba886e4
10:25:46 INFO  ca.uhn.fhir.jpa.dao.BaseHapiFhirDao - Saving history entry CodeSystem/1/_history/1
10:25:46 INFO  c.u.f.j.dao.BaseHapiFhirResourceDao - Successfully created resource "CodeSystem/1/_history/1" in 3.314ms
10:25:46 INFO  c.u.f.j.term.HapiTerminologySvcDstu3 - CodeSystem resource has ID: CodeSystem/1
10:25:46 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Storing code system
10:25:46 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Deleting old code system versions
10:25:46 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Flushing...
10:25:46 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Done flushing
10:25:47 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Validating all codes in CodeSystem for storage (this can take some time for large sets)
10:25:47 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Have validated 1000 concepts
...
10:25:49 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Have validated 319000 concepts
10:25:49 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Saving version containing 319446 concepts
10:25:49 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Saving code system
10:25:50 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Setting codesystemversion on 319446 concepts...
10:25:50 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Saving 319446 concepts...
10:25:50 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Have processed 1/319446 concepts (0%)
10:25:56 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Have processed 10000/319446 concepts (3%)
...
10:25:56 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Have processed 310000/319446 concepts (97%)
10:25:56 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Done saving concepts, flushing to database
10:25:57 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Done deleting old code system versions
10:25:57 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Note that some concept saving was deferred - still have 317446 concepts and 472410 relationships
10:25:57 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 7003ms for query a94cc0f2-b99e-4cce-9ba1-16b0b3ce70bb
10:25:57 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 7003ms for query a94cc0f2-b99e-4cce-9ba1-16b0b3ce70bb
10:25:57 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty
10:26:00 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Saving 2000 deferred concepts...
10:26:04 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Saved 2000 deferred concepts (315645 codes remain and 472410 relationships remain) in 3936ms (1ms / code)
...
10:26:25 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Saving 2000 deferred concepts...
10:26:26 INFO  c.u.f.j.term.BaseHapiTerminologySvc - Saved 2000 deferred concepts (305504 codes remain and 472410 relationships remain) in 852ms (0ms / code)
10:26:27 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Initial query result returned in 1ms for query c71cfc5b-02a4-4f16-a47f-15a947611b71
10:26:27 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - Query found 0 matches in 2ms for query c71cfc5b-02a4-4f16-a47f-15a947611b71
10:26:27 INFO  ca.uhn.fhir.jpa.dao.SearchBuilder - The include pids are empty

UPDATE Ok, I see those concepts on database table TRM_CONCEPT and TRM_CONCEPT_LINK. But, Is there a way to query those concepts?

hapi hapi-fhir snomed-ct
Original Q&A
1

There are 1 answers

0
Rodrigo Pio On

There are several ways to query concepts in a FHIR Terminology Server. The simplest one is via $lookup operation of the CodeSystem resource.

Example:

http://<your-fhir-server>/CodeSystem/$lookup?system=http://snomed.info/sct&code=767906009

This should return a Parameters as response with details for the 767906009 concept from SNOMED-CT.

Another operation that can check the presence of a certain code is the $validate-code operation, also from the CodeSystem resource.

Example:

http://<your-fhir-server>/CodeSystem/$validate-code?url=http://snomed.info/sct&code=420247005

It is worth clarifying that concepts are stored in CodeSystem resources, but you were querying a ValueSet, which is not necessarily created when you import a terminology.

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