FHIR feature updates #285

joeflack4 · 2022-07-11T21:46:55Z

Partially addresses:

SSSOM on FHIR: small bugfixes / updates timsbiomed/issues#85

Overview

Minor bug fixes
Dev updates (comments, etc)
Added test(s)

Updates

7b91d57da9a5143c5ce8335897ad2542424797c6

    - Add: _test_to_fhir_json()

157ae226921891feeaa38b4329c98b762b2b8727

    - Refactored 3 JSON writer functions to a state that they were probably intended to be in: 1 json function with branching logic depending on 'serialization' param.

0ab8625887a1d57adeadd5ad6d3c47dd08524839

    - Update: Minor codestyle updates, comments, todo's
    - Delete: Unused schema/fhir_json.csv. Mappings will continue to be done via pure Python
    - Bugfix: extension.ValueString -> extension.valueString
    - Delete: Comments about spec field mappings

0dd0772dc7bc4a263fa8e8f8e5c02c6f6c3264bf

    - Added: schema/fhir_json.csv: For automation of conversion by utilizing CSV export from curated GoogleSheet.
    - Update: Comments: Added state of mappings between SSSOM and FHIR ConceptMap

sssom/writers.py

schema/fhir_json.csv

sssom/writers.py

joeflack4 · 2023-09-04T00:50:12Z

src/sssom/writers.py

@@ -450,7 +520,7 @@ def to_fhir_json(msdf: MappingSetDataFrame) -> Dict:
                                        #  ...that is, if I happen to know the categories/codes for this categorical variable
                                        #  ...if i do that, do i also need to upload that coding as a (i) `ValueSet` resource? (or (ii) codeable concept? prolly (i))
                                        "url": "http://example.org/fhir/StructureDefinition/mapping_justification",
-                                        "ValueString": row.get(
+                                        "valueString": row.get(


Capitalization bugfix

Partially addresses:

SSSOM on FHIR: small bugfixes / updates timsbiomed/issues#85

@matentzn This is an FYI, although this is the main reason I think I started this PR. It's the only bug fix.

@ShahimEssaid This is a main reason of this PR. But I wanna get this one merged first to get a flow going; more updates will come in subsequent PRs.

src/sssom/writers.py

tests/test_cli.py

src/sssom/writers.py

tests/test_conversion.py

joeflack4 · 2024-05-05T04:56:11Z

tests/test_writers.py

+        self.assertEqual(d["url"], mapping_set_id)
+        self.assertIn(d["identifier"][0]["system"], mapping_set_id)
+        self.assertEqual(d["identifier"][0]["value"], mapping_set_id)
+        self.assertEqual(d["identifier"][0]["value"], d["url"])


Update: test_write_sssom_fhir()

@ShahimEssaid Review my assertions

Added more assertions. @ShahimEssaid could you maybe review my assertions and, for whichever you can easily understand, can you confirm if my expectations of what I should be seeing in the output are valid / ideal? Feel free to suggest any other assertions I might want to add.

Note that I don't have any outputs for you to review yet. When I do, they will be in: https://github.com/timsbiomed/sssom-on-fhir-content/

FYI here's the actual output file that I'm testing here: basic.fhir.json

tests/test_writers.py

matentzn

Nice changes! Some comments, but its close

src/sssom/writers.py

tests/test_cli.py

matentzn

I did not do a detailed code review, just looked out for breaking changes. If you want me to merge and run a release, ping me on slack.

src/sssom/writers.py

- Added: schema/fhir_json.csv: For automation of conversion by utilizing CSV export from curated GoogleSheet. - Update: Comments: Added state of mappings between SSSOM and FHIR ConceptMap

- Update: Minor codestyle updates, comments, todo's - Delete: Unused schema/fhir_json.csv. Mappings will continue to be done via pure Python - Bugfix: extension.ValueString -> extension.valueString - Delete: Comments about spec field mappings

- Refactored 3 JSON writer functions to a state that they were probably intended to be in: 1 json function with branching logic depending on 'serialization' param.

- Add: _test_to_fhir_json() - Update: test_write_sssom_fhir(): More assertions - Update: Fixed some typos - Update: model mappings: exporter: title --> title (was previously name --> title) - Update: Drepecated these functions instead of deleting: write_fhir_json(), write_ontoportal_json()

joeflack4 self-assigned this Jul 11, 2022

joeflack4 marked this pull request as draft July 11, 2022 21:46

joeflack4 requested a review from matentzn July 11, 2022 21:47

joeflack4 added the enhancement New feature or request label Jul 11, 2022

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joeflack4 force-pushed the fhir-extension branch from 81734f0 to 8a63397 Compare July 14, 2022 16:43

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joeflack4 changed the title ~~FHIR Feature~~ FHIR feature updates Aug 10, 2022

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cmungall reviewed Aug 30, 2023

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matentzn requested review from hrshdhgd and removed request for matentzn September 19, 2023 13:53

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Ontoportal CLI test #529

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joeflack4 added 3 commits May 13, 2024 16:36

FHIR Feature

7f647df

- Added: schema/fhir_json.csv: For automation of conversion by utilizing CSV export from curated GoogleSheet. - Update: Comments: Added state of mappings between SSSOM and FHIR ConceptMap

FHIR Feature

52b97ba

- Update: Minor codestyle updates, comments, todo's - Delete: Unused schema/fhir_json.csv. Mappings will continue to be done via pure Python - Bugfix: extension.ValueString -> extension.valueString - Delete: Comments about spec field mappings

Refactor JSON writer functions

ea2a407

- Refactored 3 JSON writer functions to a state that they were probably intended to be in: 1 json function with branching logic depending on 'serialization' param.

joeflack4 dismissed matentzn’s stale review via 8003e19 May 13, 2024 20:36

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matentzn approved these changes May 14, 2024

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matentzn merged commit 91d08b8 into master May 14, 2024
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FHIR feature updates #285

FHIR feature updates #285

joeflack4 commented Jul 11, 2022 •

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joeflack4 Sep 4, 2023 •

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joeflack4 May 5, 2024

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FHIR feature updates #285

FHIR feature updates #285

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joeflack4 commented Jul 11, 2022 • edited Loading

Overview

Updates

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joeflack4 Sep 4, 2023 • edited Loading

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Capitalization bugfix

joeflack4 May 5, 2024

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Update: test_write_sssom_fhir()

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joeflack4 commented Jul 11, 2022 •

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joeflack4 Sep 4, 2023 •

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Update: `test_write_sssom_fhir()`