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add stub for HLA nomenclature terminology upload #1330

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@jschneid-nmdp
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commented May 31, 2019

This is an initial step toward adding support for upload of HLA nomenclature via the $upload-external-code-system operation.

Currently seeking comments and feedback, or, if this looks like a reasonable start, would welcome having it merged into the main hapi-fhir repo.

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commented May 31, 2019

Coverage Status

Coverage decreased (-0.2%) to 75.572% when pulling 86b0ac0 on nmdp-bioinformatics:imgthla-terminology-upload into f6c7ff1 on jamesagnew:master.

Remove allele_id property. (If needed, a CodeSystem supplement could …
…define it. Defining a separate allele_id CodeSystem, and related ConceptMap, may also be a reasonable option.) Trying to keep the list of concept properties as straightforward as possible for now.
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commented Jun 4, 2019

The imgthla.xml file in this pull request describes attributes of the HLA nomenclature CodeSystem resource, including "IMGTHLA concept properties" such as expression_suffix, is_dna_concept, is_protein_concept, etc.

For now, I've made an effort to limit the list of properties to include only those which appear to be the most straightforward.

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commented Jun 27, 2019

HI @jschneid-nmdp - This is great, looks awesome!

My only one request: Would you be able to add a simple test along the lines of the LOINC One. It doesn't need to be fancy, but having a test like this will ensure that any future changes to the framework don't break your work.

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commented Jun 28, 2019

I've added a very basic TerminologyLoaderSvcImgthlaTest, patterned after TerminologyLoaderSvcLoincTest, and made some related minor modifications to the TerminologyLoaderSvcImpl.processImgthlaFiles method (to allow for files located in subdirectories of the zipfile).

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commented Jun 28, 2019

Fantastic, thanks! Will merge now.

@jamesagnew jamesagnew merged commit 5c55133 into jamesagnew:master Jun 28, 2019

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jamesagnew added a commit that referenced this pull request Jun 28, 2019

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commented Jun 28, 2019

Thanks!

@jschneid-nmdp jschneid-nmdp deleted the nmdp-bioinformatics:imgthla-terminology-upload branch Jun 28, 2019

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