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HL7 EU Lab Structured Report Alignment#157

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omarisgreat merged 36 commits intomainfrom
Issue-2663
Sep 8, 2025
Merged

HL7 EU Lab Structured Report Alignment#157
omarisgreat merged 36 commits intomainfrom
Issue-2663

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@omarisgreat omarisgreat commented Feb 10, 2025

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omarisgreat and others added 27 commits February 10, 2025 14:56
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HL7 EU Lab Structured Report Alignment
d95340d
@omarisgreat
Fixes to Examples and updated dependencies
d80be2a
@omarisgreat
Correction to composition resource
641cba7
@omarisgreat
Typo fixes
82420ba
@omarisgreat
Testing fixes for EU Lab
32ea369
@omarisgreat
Testing adding meta profiles
a99c29f
@omarisgreat
Correction to canonical URLs
221ce03
@omarisgreat
Changes to canonicals for testing
98b311d
@omarisgreat
Changes to capabilitystatement for testing
0a27298
@omarisgreat
Revert "Changes to capabilitystatement for testing"
82413a8 
This reverts commit 0a27298.
@omarisgreat
Revert "Changes to canonicals for testing"
04ea0e3 
This reverts commit 98b311d.
@omarisgreat
Changes to capabilitystatement for testing
26465a7
@omarisgreat
Revert "Changes to capabilitystatement for testing"
7b3fb16 
This reverts commit 26465a7.
@omarisgreat
Changes to fullUrls
6e1632d
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Update Bundle-EULabGenomicReport-Example.json
43ed3d4
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Revert "Update Bundle-EULabGenomicReport-Example.json"
2eb959e 
This reverts commit 43ed3d4.
@omarisgreat
Replacing URLs with example
c20b1ee
@omarisgreat
Updating references to URLs
760ba11
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Revert "Updating references to URLs"
1233096 
This reverts commit 760ba11.
@omarisgreat
Merge branch 'main' into Issue-2663
798afe0
@omarisgreat
Update to Package.json
ff7790e
@KazeemHamzat
Update package.json
5f05a7f 
Update package.json
@KazeemHamzat
Added hl7.fhir.eu.extensions.r4
0e6d0f4 
Added hl7.fhir.eu.extensions.r4
@KazeemHamzat
Merge branch 'main' of https://github.com/NHSDigital/NHSDigital-FHIR-…
e0f5b6a 
…Genomics-ImplementationGuide into Issue-2663
@KazeemHamzat
Update package.json
1223f6e 
Removing "hl7.fhir.eu.laboratory": "0.1.1",
@KazeemHamzat
Updated the EU Lab to 0.1.0-balot
9be582f 
hl7.fhir.eu.laboratory": "0.1.0-ballot
@KazeemHamzat
Update Observation-GenomicsVariantSLC52A2
15e57f4 
CodeSystem: "system": "http://purl.obolibrary.org/obo",
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KazeemHamzat commented Sep 4, 2025

1.The "hl7.fhir.eu.laboratory": "0.1.1", is required to validate some examples but the problem seem to be the version '0.1.1'
I have changed it to a balloted version "hl7.fhir.eu.laboratory": "0.1.0-ballot", the error is now resolved but some syntax errors are now required to be fixed in one of the Bundle Examples.. Validator issue is now resolved.
2 CodeSystem, http://www.sequenceontology.org, currently mapped to the element Observation.component:variation-code is also failing validation but I have replaced it with a code I found here, missense_variant [SO_0001583], presently flagged with warning by the validator. We may have to apply the rule for validator to ignore it like the code for genes: http://varnomen.hgvs.org if codesystem-http://www.sequenceontology.org is mandatory.

@omarisgreat
Removal of size for attachment and bundle meta
6c57543 
should allow validation of resources against any package in dependencies (not a fix but issues in Bundle are not useful)
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Removal of Composition profile
467a579
@omarisgreat
Removing Bundle as it will not validate
dd3be43 
Not adding anything material to the package as Composition validates fine
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omarisgreat commented Sep 5, 2025

Hi @KazeemHamzat, I am done with the Bundle, it does not want to Validate no matter what changes are made, even though the other resources are validating against EU Lab just fine. I've decided to cut it as it is not contributing much to the IG.

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Removed EU Extensions
66ac9d6 
Removed EU Extensions
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KazeemHamzat commented Sep 8, 2025

@ryma2fhir , there is need to make exception rule on the validator to ignore CodeSystem-http://www.sequenceontology.org
The same rule that was applied to http://varnomen.hgvs.org/

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omarisgreat commented Sep 8, 2025

@KazeemHamzat, I've made the update to the validation repo to ignore the SequenceOntology CS issues. The PR should now be ready to review

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KazeemHamzat requested changes Sep 8, 2025
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  1. Minor issues to be corrected,
  2. Are the ServiceRequest and Task instance not expected to conform to EU-Lab profiles?

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Corrected issues
dce8590 
Updated Observation reference
Updated date on NamingSystem
Added EU Profiles to ServiceRequest
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omarisgreat commented Sep 8, 2025

@KazeemHamzat, addressed comments, and added profile to ServiceRequest. There is no Task profile in EU Lab so I've left that as is.

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KazeemHamzat approved these changes Sep 8, 2025
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Ok

@KazeemHamzat KazeemHamzat mentioned this pull request Sep 8, 2025
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@omarisgreat omarisgreat merged commit 027f435 into main Sep 8, 2025
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@omarisgreat omarisgreat deleted the Issue-2663 branch September 8, 2025 13:39
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