Remaining ORM/OML Updates #16539

JFisk42 · 2024-11-14T00:58:34Z

This PR finishes the mappings and related changes for the new OML and ORM mappings.

Test Steps:

Run the full gamut of tests: ./gradlew test, ./gradlew testSmoke, ./gradlew testIntegration.

Changes

The OML and ORM integration tests scenarios now include all supported fields and supported repeated segments/fields.
Mappings for OBR -> Specimen are now fully supported (primarily mappings for OBR-15/SPS were added for FHIR->HL7).
- For ORU and OML these are directly mapped through Specimen.
- For ORM (and when present in ORU/OML) these are preserved through ServiceRequest.extension
Java classes were created for basic OML segment groups to support several mapped fields.

Checklist

Testing

Tested locally?
Ran ./prime test or ./gradlew testSmoke against local Docker ReportStream container?
(For Changes to /frontend-react/...) Ran npm run lint:write?
Added tests?

Process

Are there licensing issues with any new dependencies introduced?
Includes a summary of what a code reviewer should test/verify?
Updated the release notes?
Database changes are submitted as a separate PR?
DevOps team has been notified if PR requires ops support?

Linked Issues

Fixes Finalize OML Mappings #16065

To Be Done

Tickets to log:

There is an issue where OBR.15.1 is not correctly mapped for FHIR->HL7
Documentation/Investigation around the inability to handle multiple order groups for OML messages.

JFisk42 · 2024-11-15T22:57:16Z

prime-router/src/main/kotlin/fhirengine/utils/HL7Reader.kt

@@ -141,12 +140,6 @@ class HL7Reader(private val actionLogger: ActionLogger) : Logging {
                            )
                        }
                    }
-                    "OML" -> {


This was removed as it was pointed out on a previous PR that it is an outdated pattern that shouldn't be followed.

JFisk42 · 2024-11-15T23:13:44Z

prime-router/src/main/resources/metadata/hl7_mapping/resources/ServiceRequest/OBR.yml

@@ -29,21 +29,6 @@ elements:
    value: [ '%resource.occurrence.extension(%`rsext-hl7v2-date-time`).value' ]
    hl7Spec: [ '%{obrFieldPath}-6' ]

-  - name: observation-collected-datetime


These mappings were moved out to both ServiceRequest/OBRExtension and Specimen/OBR for a few different reasons:

The mappings you see here look at %resource.specimen to find the values. ORU is not currently populating ServiceRequest.specimen. (This might be incorrect according to the mapping inventory). Moving these mappings out allow ORU and OML to each access these fields differently.

ORM does not map to a Specimen resource at all, thus to preserve the fields they need to be in OBRExtension.

This might be incorrect according to the mapping inventory - can we ticket this?

JFisk42 · 2024-11-15T23:14:23Z

prime-router/src/test/kotlin/common/UniversalPipelineTestUtils.kt

@@ -67,11 +67,11 @@ SPM|1|0cba76f5-35e0-4a28-803a-2f31308aae9b||258500001^Nasopharyngeal swab^SCT|||

 @Suppress("ktlint:standard:max-line-length")
 const val cleanHL7RecordConverted =


These changes were related to OBR.7 appearing in OBR Extensions now.

JFisk42 · 2024-11-15T23:23:35Z

prime-router/src/testIntegration/resources/datatests/HL7_to_FHIR/sample_oml_20240319-001.fhir

              }
            ]
          }
        },
-        "note" : [
+        "container": [


Lots of formatting changes. The meat of the change is new values coming through. This was happened after adding the OML java classes and new data being returned due to OBR.15 getting represented as SPS instead of a String.

JFisk42 · 2024-11-15T23:28:43Z

.../src/testIntegration/kotlin/datatests/mappinginventory/catchall/orcobr/OBRToSpecimenTests.kt

+import gov.cdc.prime.router.datatests.mappinginventory.verifyHL7ToFHIRToHL7Mapping
+import org.junit.jupiter.api.Test
+
+class OBRToSpecimenTests {


I'm open to different names/locations for these tests. They made sense at the time. These tests specifically test that

FHIR->HL7 OBR/Specimen mappings work despite being linked in the FHIR through different paths in ORU/OML.

HL7->FHIR->HL7 OBR/Specimen mappings work for ORM despite not having the Specimen resource.

...pinginventory/catchall/orcobr/orc_obr-to-servicerequest_diagnosticreport-obr8-populated.fhir

prime-router/metadata/HL7/catchall/hl7/segments/ORC/OBRExtension.yml

prime-router/src/main/resources/metadata/hl7_mapping/resources/ServiceRequest/OBRExtension.yml

...outer/src/main/java/fhirengine/translation/hl7/structures/fhirinventory/message/OML_O21.java

arnejduranovic

Looks good! Can we also please:

update the PR description to include links or ticket numbers in the TODO section?
remember to open a PR merging this feature branch into main? We're ready for that now, right?

arnejduranovic · 2024-11-21T16:11:49Z

prime-router/src/main/resources/metadata/hl7_mapping/resources/ServiceRequest/OBR.yml

@@ -29,21 +29,6 @@ elements:
    value: [ '%resource.occurrence.extension(%`rsext-hl7v2-date-time`).value' ]
    hl7Spec: [ '%{obrFieldPath}-6' ]

-  - name: observation-collected-datetime


This might be incorrect according to the mapping inventory - can we ticket this?

JFisk42 · 2024-11-21T21:56:24Z

Squashing and merging now to unblock others, will create and link ticket todos asap.

* Add OML Java Classes * Updated tests with repeating fields and segments * OML FHIR->HL7 Updates * OBR -> Specimen Additions and Updates * Missed todos * Populating OBR 7&8 as separate datetime fields when in extension

JFisk42 added 2 commits November 7, 2024 16:56

Add OML Java Classes

65f9b33

Updated tests with repeating fields and segments

318718b

JFisk42 added the platform Platform Team label Nov 15, 2024

JFisk42 added 2 commits November 15, 2024 14:17

OML FHIR->HL7 Updates

4622979

OBR -> Specimen Additions and Updates

25ea2eb

JFisk42 force-pushed the platform/josh/16065-final-OML-mappings branch from eb38dcf to 25ea2eb Compare November 15, 2024 22:28

Missed todos

fa3dc79

JFisk42 changed the title ~~Platform/josh/16065 final oml mappings~~ Remaining ORM/OML Updates Nov 15, 2024

JFisk42 commented Nov 15, 2024

View reviewed changes

JFisk42 marked this pull request as ready for review November 15, 2024 23:32

JFisk42 requested a review from a team as a code owner November 15, 2024 23:32

MichaelEsuruoso assigned jack-h-wang Nov 18, 2024

jack-h-wang reviewed Nov 19, 2024

View reviewed changes

prime-router/metadata/HL7/catchall/hl7/segments/ORC/OBRExtension.yml Outdated Show resolved Hide resolved

prime-router/src/main/resources/metadata/hl7_mapping/resources/ServiceRequest/OBRExtension.yml Outdated Show resolved Hide resolved

jack-h-wang reviewed Nov 20, 2024

View reviewed changes

...outer/src/main/java/fhirengine/translation/hl7/structures/fhirinventory/message/OML_O21.java Show resolved Hide resolved

Populating OBR 7&8 as separate datetime fields when in extension

78009ee

jack-h-wang approved these changes Nov 21, 2024

View reviewed changes

arnejduranovic approved these changes Nov 21, 2024

View reviewed changes

JFisk42 merged commit 39e79a8 into OML-Updates-Base Nov 21, 2024
9 checks passed

JFisk42 deleted the platform/josh/16065-final-OML-mappings branch November 21, 2024 21:56

JFisk42 mentioned this pull request Nov 21, 2024

Finalize OML Mappings #16065

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Remaining ORM/OML Updates #16539

Remaining ORM/OML Updates #16539

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JFisk42 commented Nov 21, 2024

		@@ -67,11 +67,11 @@ SPM\|1\|0cba76f5-35e0-4a28-803a-2f31308aae9b\|\|258500001^Nasopharyngeal swab^SCT\|\|\|

		@Suppress("ktlint:standard:max-line-length")
		const val cleanHL7RecordConverted =

Remaining ORM/OML Updates #16539

Remaining ORM/OML Updates #16539

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JFisk42 commented Nov 14, 2024 • edited Loading

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Checklist

Testing

Process

Linked Issues

To Be Done

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