Genomic Order Management Service - FHIR Packages

We’re starting to implement this and one of our first steps will be to document and set up testing resources for our local system.

To do this I’m looking at using HL7 igPublisher which will allow us to use open source FHIR Testing tools.

However when I try to use the packages from this service I get this error.

Sushi: info  Attempting to download uk.nhsdigital.genomics.r4#0.4.2 from https://packages.fhir.org/uk.nhsdigital.genomics.r4/0.4.2 (00:00.001 / 00:07.818, 23Mb)
Sushi: info  Attempting to download uk.nhsdigital.genomics.r4#0.4.2 from https://packages2.fhir.org/packages/uk.nhsdigital.genomics.r4/0.4.2 (00:00.186 / 00:08.004, 23Mb)
Sushi: error Failed to load uk.nhsdigital.genomics.r4#0.4.2: Failed to download uk.nhsdigital.genomics.r4#0.4.2 from the registry (00:00.509 / 00:08.514, 23Mb)
Sushi: info  Loaded hl7.fhir.r4.core#4.0.1 with 4581 resources                                       (00:03.117 / 00:11.631, 23Mb)
Sushi: info  Loaded virtual package sushi-local#LOCAL with 0 resources                               (00:00.011 / 00:11.642, 23Mb)
Sushi: info  Converting FSH to FHIR resources...                                                     (00:00.023 / 00:11.666, 23Mb)
Sushi: error Parent https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport not found for DiagnosticReport (00:00.008 / 00:11.675, 23Mb)
Sushi:   File: /Users/kevinmayfield/github/MFT/FHIRGenomics/input/fsh/DiagnosticReport.fsh           (00:00.001 / 00:11.676, 23Mb)
Sushi:   Line: 1 - 75                                                                                (00:00.000 / 00:11.677, 23Mb)
Sushi: error Parent https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest not found for ServiceRequest (00:00.164 / 00:11.842, 23Mb)
Sushi:   File: /Users/kevinmayfield/github/MFT/FHIRGenomics/input/fsh/ServiceRequest.fsh             (00:00.001 / 00:11.843, 23Mb)

I believe the package I should be using is uk.nhsdigital.genomics.r4 version 0.4.2 which is the FHIR IG (FHIR Genomics Implementation Guide) the OAS specification points to.

To work around this I’ve tried

fhir.r4.ukcore.stu2 2.0.1-pre-release

Which finds the package but then gives

Sushi: error Structure Definition https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport is missing a snapshot. Snapshot is required for import. (00:00.009 / 00:16.428, 23Mb)
Sushi:   File: /Users/kevinmayfield/github/MFT/FHIRGenomics/input/fsh/DiagnosticReport.fsh           (00:00.001 / 00:16.430, 23Mb)
Sushi:   Line: 1 - 75                                                                                (00:00.001 / 00:16.432, 23Mb)
Sushi: error Structure Definition https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest is missing a snapshot. Snapshot is required for import. (00:00.157 / 00:16.589, 23Mb)
Sushi:   File: /Users/kevinmayfield/github/MFT/FHIRGenomics/input/fsh/ServiceRequest.fsh             (00:00.001 / 00:16.591, 23Mb)
Sushi:   Line: 1 - 18                                                                                (00:00.001 / 00:16.593, 23Mb)
Sushi: info  Converted 11 FHIR StructureDefinitions.                                                 (00:00.063 / 00:16.656, 23Mb)

To work around this I’ve used

package fhir.r4.ukcore.stu2 version 2.1.0

Could you please advise if this is ok?

Hi Kevin,

Thanks for the question, there are a few workarounds you could try, first, could you try downloading v0.4.3? A new version was released quite recently, which may mean older versions have been removed from the registry: uk.nhsengland.genomics.r4 0.4.3 - SIMPLIFIER.NET

We will update the API Catalog OAS and IG links so the right version is referenced.

If that doesn’t work, I would recommend downloading the STU3 prerelease package for UK Core (fhir.r4.ukcore.stu3.currentbuild 0.0.17-pre-release - SIMPLIFIER.NET), as there have been some updates in STU3 that we are taking advantage of. Please note that this will be missing some Genomic specific CodeSystems etc. which may result warnings during terminology validation.

If you still receive the Snapshot warnings we can attempt to release a package with Snapshots.

Best,
Omar

1 Like

thanks.

Have downloaded the genomics ig and manually added that to my own implementation guide.

2 Likes

So what I did was go to the simplifier link and download with snapshots (HL7 igPublisher needs snapshots).

I’m still using the incorrect version of UKCore, but I could do the same with that (download correct package with snapshots).

Had to make some corrections to the profiles as they were missing an id and igPublisher doesn’t like that.

Have managed to extend UKCore-ServiceRequest to add in accessionNumber slice.
Also extended NHSDigital-DiagnosticReport-Genomics to add in accessionNumber slice and other slices to help support HL7v2 ORU conversion.

This is a bit of a proof of concept (but I’d like to do this).

Code behind IG is here GitHub - FHIR-MFT/FHIRGenomics
Implementation Guide is here Home - MFT Genomics v0.0.1-current

as discussed I’m using

UKCore

fhir.r4.ukcore.stu3.currentbuild#0.0.18-pre-release

and will swap over to genomics package once this contains snapshots.

@omarisgreat As I’m now posting using a non NHS England account many of posts above are going past a spam filter and have been hidden.

If I’ve said anything useful for a wider audience, can you repost?