Mandatory input files to upload LOINC 2.65 to HAPI FHIR 3.6.0

[ricar...@gmail.com]

Hi everyone,

I managed to import SNOMED CT (2018-07 release) on HAPI FHIR 3.6.0 using the hapi-fhir-cli tool but I'm having some trouble with LOINC (2.65 release). I'm running:

hapi-fhir-cli upload-terminology -d /usr/local/fhir/Loinc_2.65_LoincTableCore.zip -d /usr/local/fhir/Loinc_2.65_MultiAxialHierarchy_2.65.zip -v dstu3 -t http://192.168.61.118:8081/fhir/baseDstu3 -u http://loinc.org

According to the docs (http://hapifhir.io/doc_cli.html#_toc_upload_terminology), it should work, but I get:

Failure during REST processing: ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException: Could not find the following mandatory files in input: [Loinc.csv, loincupload.properties, AnswerList.csv, LoincAnswerListLink.csv, Part.csv, LoincPartLink.csv, PartRelatedCodeMapping.csv, DocumentOntology.csv, LoincRsnaRadiologyPlaybook.csv, Top2000CommonLabResultsUs.csv, Top2000CommonLabResultsSi.csv, LoincUniversalLabOrdersValueSet.csv, LoincIeeeMedicalDeviceCodeMappingTable.csv, ImagingDocumentCodes.csv]

I also checked the Smile CDR docs (https://smilecdr.com/docs/current/fhir_repository/terminology.html) and only two files are listed as mandatory, but I checked the source history on Git (https://github.com/jamesagnew/hapi-fhir/blob/master/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java) and all the files have been asserted to be present for a while. I can't seem to find some of the files required (e.g LOINC Imaging Document Codes). Am I missing something?

Thank you very much.

[James Agnew]

The Loinc 2.65 release uses a slightly different release format from previous releases.

At present you need to use HAPI FHIR 3.7.0-SNAPSHOT in order to upload it.

Note that you don't necessarily need to use the 3.7.0 CLI tool for the actual upload, but the server needs to be be build with that version in order to understand the new format.

Cheers,

James

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[Fredrik Duprez]

I tried this with HAPI FHIR version 3.7.0 and r4 as the fhir version and I get the same error message:

hapi-fhir-cli upload-terminology -d ~/Downloads/Loinc_2.65_LoincTableCore.zip -d ~/Downloads/Loinc_2.65_MultiAxialHierarchy_2.65.zip -d ~/Downloads/Loinc_2.65_Text_2.65.zip -v r4 -t http://localhost:8080/hapi-fhir-jpaserver/fhir -u http://loinc.org

Error:

ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException: HTTP 422 Unprocessable Entity: Could not find the following mandatory files in input: [LoincTable/Loinc.csv, loincupload.properties, AnswerList.csv, LoincAnswerListLink.csv, Part.csv, LoincPartLink.csv, PartRelatedCodeMapping.csv, DocumentOntology.csv, LoincRsnaRadiologyPlaybook.csv, Top2000CommonLabResultsUs.csv, Top2000CommonLabResultsSi.csv, LoincUniversalLabOrdersValueSet.csv, LoincIeeeMedicalDeviceCodeMappingTable.csv, ImagingDocumentCodes.csv]

[James Agnew]

Hi Fredrik,

You need to use the "LOINC Complete Download File" available here: https://loinc.org/downloads/

Cheers,

James

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[Fredrik Duprez]

Thank you,

now I just get one missing file, loincupload.propertes:

hapi-fhir-cli upload-terminology  -d ~/Downloads/Loinc_2.65.zip -v r4 -t http://localhost:8080/hapi-fhir-jpaserver/fhir -u http://loinc.org

ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException: HTTP 422 Unprocessable Entity: Could not find the following mandatory files in input: [loincupload.properties]

Where do I find that one?

[Fredrik Duprez]

To answer my own question I found this piece of documentation:

https://smilecdr.com/docs/current/fhir_repository/terminology.html

In short you need to provide the file yourself, so I tried this:

# This is the version identifier for the AnswerList file

answerlist.version=2.65

# This is the version identifier for uploaded ConceptMap resources

conceptmap.version=2.65

And thus my cli command was:

hapi-fhir-cli upload-terminology  -d ~/Downloads/Loinc_2.65.zip -d ~/Downloads/loincupload.properties -v r4 -t http://localhost:8080/hapi-fhir-jpaserver/fhir -u http://loinc.org

Now it seems to import OK:

2019-03-12 13:47:20 [main] INFO  c.u.f.c.UploadTerminologyCommand Beginning upload - This may take a while...

2019-03-12 13:48:45 [main] INFO  c.u.f.c.UploadTerminologyCommand Upload complete!

2019-03-12 13:48:45 [main] INFO  c.u.f.c.UploadTerminologyCommand Response:

<Parameters xmlns="http://hl7.org/fhir">

   <parameter>

      <name value="conceptCount"/>

      <valueInteger value="183052"/>

   </parameter>

   <parameter>

      <name value="target"/>

      <valueReference>

         <reference value="CodeSystem/loinc"/>

      </valueReference>

   </parameter>

</Parameters>

2019-03-12 13:48:45 [main] INFO  ca.uhn.fhir.cli.App HAPI FHIR is shutting down...