Is this LOINC FHIR Terminology Server Implementation FOSS?

Home Forums LOINC FHIR Terminology Server Is this LOINC FHIR Terminology Server Implementation FOSS?

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  • #447540
    Manisha Mantri
    Participant

    Hi,

    Is this LOINC Server implementation a FOSS? I mean can one deploy it locally/regionally for integration?

    #447541
    Manisha Mantri
    Participant

    I can see its a HAPI implementation. But I wanted to know if any changes needed/done to set-up LOINC files in it.

    #447542
    Tim Briscoe
    Keymaster

    Hi, Manisha. Our terminology server uses SmileCDR, the commercial product that uses the open-source HAPI-FHIR as its backend. The tooling we use to update LOINC terminology is available for anyone to use within HAPI-FHIR. Once you stand up your HAPI-FHIR instance, you can use its upload-terminology command in conjunction with the LOINC zip file you download from our site. For example:

    ./hapi-fhir-cli upload-terminology -d Downloads/Loinc_2.68.zip -f dstu3 -t http://localhost:8080/baseDstu3 -u http://loinc.org

    Documentation is available at https://hapifhir.io/hapi-fhir/docs/tools/hapi_fhir_cli.html#upload-terminology

    I hope this helps! Keep us informed of your progress and let us know if you need additional assistance.

    #476726
    Aitor Perez
    Participant

    Hi,

    Just trying to upload the latest LOINC terminology file (Loinc_2.73.zip) to my local HAPI FHIR server using hapi-fhir-cli command but seems Loinc_2.73.zip is missing some needed files (MultiAxialHierarchy.csv)

    This is the error:

    HTTP 422 Unprocessable Entity: HAPI-0862: Could not find the following mandatory files in input: [AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv]

    Checking the ZIP content, this file doesn’t exists.

    I’m doing something wrong? Or latest LOINC releases are not compatible any more with this HAPI FHIR command line tool ?

    Thanks in advance

    #476727
    Tim Briscoe
    Keymaster

    Hello Aitor,

    Yes, we have renamed this hierarchy and its associated artifact. In your HAPI-FHIR server, you should have a file named loincupload.properties. Within it, you should be able to change the file name for this artifact as so:

    # LOINC hierarchy
    ## Default value if key not provided: AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
    ## File must be present
    loinc.hierarchy.file=AccessoryFiles/ComponentHierarchyBySystem/ComponentHierarchyBySystem.csv

    We’ll see if we can have HAPI-FHIR make this change at the source so others do not run into this issue.

    #477068
    Shantanu Banerjee
    Participant

    Hi Team,

    I am using HAPI JPA FHIR server version 6.2.1 (latest pull from master branch).

    I was getting the above issue (about <span style=”background-color: #fbfbfb; font-family: Lato, Helvetica, Arial, Lucida, sans-serif; font-size: 15.6px;”>MultiAxialHierarchy.csv)</span>  and following your instruction created a file

    names loincupdate.properties in src/main/resources folder and built and ran the server.

    However I am still getting the error. Where am I going wrong? Where should I create the file?

     

    Thanks in advance.

    #477070
    Tim Briscoe
    Keymaster

    Hello Shantanu,

    My implementation uses SmileCDR rather than HAPI so the structure may be slightly different. Of course SmileCDR is more or less the same as HAPI but it’s worth noting.

    Here’s the structure we have:

    smilecdr/terminology/loinc/
    – upload-loinc.sh
    – Loinc_2.73.zip
    – loincupload.properties

    Where upload-loinc.sh is a script which calls the smileutil tool. The script passes the necessary parameters to update the terminology based on the input file. Your port number will probably vary.

    ../../bin/smileutil upload-terminology -v r4 -t http://localhost:18999/ -u http://loinc.org -b “user:pass” -l -d Loinc_2.73.zip -d loincupload.properties

    Documentation on smileutil is at https://smilecdr.com/docs/smileutil/upload_terminology.html

    Again, HAPI/Smile doesn’t know to look for the new artifact name so that’s why you need to update the referenced file in loincupload.properties. Should HAPI not have such a properties file, you can alternatively rename the artifact within the zip to MultiAxialHierarchy.csv.

    I hope this helps. Keep us updated on your progress.

    #477535
    Shantanu Banerjee
    Participant

    Thanks Tim,

    Your suggestion above correct . We have to use it with as a parameter (with -d option). I used the below command and it worked. The path names may vary for others

    hapi-fhir-cli upload-terminology -d Loinc_2.73.zip -d loincupload.properties -v r4 -t http://localhost:8080/fhir -u http://loinc.org

    Thanks again

     

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