Update OML mappings (#15910)

* Update OML FHIR -> HL7 Mappings * Update OML HL7 -> FHIR mappings * Add OML mapping integration tests * Removing unused FHIR -> HL7 mappings * Adding OML to CWE/CE override * Adjusting existing tests * Adding tests for new misc mappings * Update existing OML integration tests * Fixing integration tests after rebase * expected oru changes * Specimen.collection conditional update * Updating formatting for cleaner diff * Missed e2e test updates * PRT <-> Device mappings will be taken care of in the next PR * Changed line endings from CRLF to LF * Removing OML use of HL7v2Name url
CDCgov · Oct 8, 2024 · 9ae7f66 · 9ae7f66
1 parent 1bf38e8
commit 9ae7f66
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Showing 64 changed files with 8,200 additions and 2,695 deletions.
diff --git a/prime-router/metadata/HL7/catchall/hl7/message/OML_O21.yml b/prime-router/metadata/HL7/catchall/hl7/message/OML_O21.yml
@@ -8,27 +8,48 @@ resources:
     repeats: false
     isReferenced: false
 
+  - resourceName: Provenance
+    segment: MSH
+    resourcePath: segments/MSH/Provenance-Source
+
+  - resourceName: Provenance
+    segment: MSH
+    resourcePath: segments/MSH/Provenance-Transformation
+
   - resourceName: Patient
     segment: .PID
     group: PATIENT
     resourcePath: segments/PID/Patient
     isReferenced: true
     repeats: false
+    additionalSegments:
+      - .PD1
+      - MSH
+      - .NTE
+      - .NK1
 
-  - resourceName: ServiceRequest
-    segment: .ORC
-    group: ORDER
-    resourcePath: segments/ORC/ServiceRequest
+  - resourceName: Provenance
+    segment: .PID
+    group: PATIENT
+    resourcePath: segments/PID/Provenance-Patient
+
+  - resourceName: RelatedPerson
+    segment: .NK1
+    group: PATIENT
+    resourcePath: segments/NK1/RelatedPerson
+    isReferenced: false
     repeats: true
+
+  - resourceName: Encounter
+    segment: .PV1
+    group: PATIENT.PATIENT_VISIT
+    resourcePath: segments/PV1/Encounter
     isReferenced: true
     additionalSegments:
-      - .OBSERVATION_REQUEST.OBR
-      - .OBSERVATION_REQUEST.NTE
-      - PATIENT.PATIENT_VISIT.PV1
+      - .PV2
       - MSH
-      - PATIENT.PID
 
-  - resourceName: Observation
+  - resourceName: OMLObservation
     segment: .OBSERVATION_REQUEST.OBSERVATION.OBX
     group: ORDER
     resourcePath: segments/OBX/Observation
@@ -40,11 +61,32 @@ resources:
       - .OBSERVATION_REQUEST.OBSERVATION.NTE
       - MSH
 
-  - resourceName: Specimen
-    segment: SPECIMEN.SPM
-    group: ORDER.OBSERVATION_REQUEST
+  - resourceName: OMLSpecimenSource
+    segment: .OBSERVATION_REQUEST.OBR
+    group: ORDER
+    resourcePath: segments/ORC/Specimen
+    isReferenced: true
+    repeats: true
+
+  - resourceName: OMLSpecimen
+    segment: .OBSERVATION_REQUEST.SPECIMEN.SPM
+    group: ORDER
     resourcePath: segments/SPM/Specimen
     repeats: true
     isReferenced: true
     additionalSegments:
-      - MSH
+      - MSH
+
+  - resourceName: ServiceRequest
+    segment: .ORC
+    group: ORDER
+    resourcePath: segments/ORC/ServiceRequest
+    repeats: true
+    isReferenced: true
+    additionalSegments:
+      - .OBSERVATION_REQUEST.OBR
+      - .OBSERVATION_REQUEST.NTE
+      - PATIENT.PATIENT_VISIT.PV1
+      - MSH
+      - PATIENT.PID
+      - .OBSERVATION_REQUEST.OBSERVATION.OBX
diff --git a/prime-router/metadata/HL7/catchall/hl7/message/ORU_R01.yml b/prime-router/metadata/HL7/catchall/hl7/message/ORU_R01.yml
@@ -28,8 +28,8 @@ resources:
       - .NK1
 
   - resourceName: Provenance
-    group: PATIENT_RESULT.PATIENT
     segment: .PID
+    group: PATIENT_RESULT.PATIENT
     resourcePath: segments/PID/Provenance-Patient
 
   - resourceName: RelatedPerson
@@ -45,7 +45,7 @@ resources:
     resourcePath: segments/PV1/Encounter
     isReferenced: true
     additionalSegments:
-      - .PATIENT.VISIT.PV2
+      - .VISIT.PV2
       - MSH
 
   - resourceName: Observation

diff --git a/prime-router/metadata/HL7/catchall/hl7/segments/ORC/ServiceRequest.yml b/prime-router/metadata/HL7/catchall/hl7/segments/ORC/ServiceRequest.yml
@@ -348,6 +348,27 @@ subject:
   expressionType: resource
   specs: $Patient
 
+specimen:
+  generateList: true
+  expressionType: nested
+  expressions:
+    - valueOf: datatype/Reference
+      generateList: true
+      expressionType: resource
+      specs: $OMLSpecimen
+      useGroup: true
+    - valueOf: datatype/Reference
+      expressionType: resource
+      specs: $OMLSpecimenSource
+      useGroup: true
+
+supportingInfo:
+  generateList: true
+  valueOf: datatype/Reference
+  expressionType: resource
+  specs: $OMLObservation
+  useGroup: true
+
 note:
   valueOf: segments/NTE/Annotation
   expressionType: resource

diff --git a/prime-router/metadata/HL7/catchall/hl7/segments/ORC/Specimen.yml b/prime-router/metadata/HL7/catchall/hl7/segments/ORC/Specimen.yml
@@ -29,9 +29,15 @@ container:
               expressionType: HL7Spec
 
 collection:
-  condition: $spm7 NOT_NULL
+  condition: $obr7 NOT_NULL || $obr8 NOT_NULL || $obr9 NOT_NULL || $obr10 NOT_NULL || $obr15 NOT_NULL
   expressionType: nested
   generateList: true
+  vars:
+    obr7: OBR.7
+    obr8: OBR.8
+    obr9: OBR.9
+    obr10: OBR.10
+    obr15: OBR.15
   expressionsMap:
     bodySite:
       valueOf: datatypes/CWE/CodeableConcept
@@ -62,6 +68,24 @@ collection:
           type: STRING
           valueOf: "GeneralUtils.dateTimeWithZoneId(dateTimeIn,ZONEID)"
           expressionType: JEXL
+    _collectedDateTime:
+      condition: $dateTimeIn NOT_NULL && $end NULL
+      expressionType: nested
+      vars:
+        dateTimeIn: OBR.7
+        end: OBR.8
+      expressionsMap:
+        extension_1:
+          generateList: true
+          expressionType: nested
+          expressionsMap:
+            url:
+              type: SYSTEM_URL
+              value: hl7v2-date-time
+            valueString:
+              type: STRING
+              valueOf: $dateTimeIn
+              expressionType: HL7Spec
     collector:
       condition: $obr10 NOT_NULL
       vars:
@@ -87,10 +111,10 @@ note_specimen-source:
       expressionsMap:
         url:
           type: SYSTEM_URL
-          value: hl7v2Name
+          value: hl7v2Component
         valueString:
           type: STRING
-          valueOf: specimen-source
+          valueOf: OBR.15.3
 
 note_collectors-comment:
   condition: $obr39 NOT_NULL

diff --git a/prime-router/metadata/HL7/catchall/hl7/segments/PID/Patient.yml b/prime-router/metadata/HL7/catchall/hl7/segments/PID/Patient.yml
@@ -91,9 +91,15 @@ contact:
           vars:
             nk141: STRING, NK1.41
     relationship:
-      valueOf: datatypes/CWE/CodeableConcept
-      expressionType: resource
-      specs: NK1.7
+      generateList: true
+      expressionType: nested
+      expressions:
+      - valueOf: datatypes/CWE/CodeableConcept
+        expressionType: resource
+        specs: NK1.3
+      - valueOf: datatypes/CWE/CodeableConcept
+        expressionType: resource
+        specs: NK1.7
     period:
       vars:
         startDate: NK1.8

diff --git a/prime-router/src/main/kotlin/fhirengine/utils/HL7Reader.kt b/prime-router/src/main/kotlin/fhirengine/utils/HL7Reader.kt
@@ -24,6 +24,7 @@ import java.util.Date
 import ca.uhn.hl7v2.model.v251.message.OML_O21 as v251_OML_O21
 import ca.uhn.hl7v2.model.v251.message.ORU_R01 as v251_ORU_R01
 import ca.uhn.hl7v2.model.v251.segment.MSH as v251_MSH
+import ca.uhn.hl7v2.model.v27.message.OML_O21 as v27_OML_O21
 import ca.uhn.hl7v2.model.v27.message.ORU_R01 as v27_ORU_R01
 import ca.uhn.hl7v2.model.v27.segment.MSH as v27_MSH
 import fhirengine.translation.hl7.structures.nistelr251.message.ORU_R01 as NIST_ELR_ORU_R01
@@ -141,6 +142,7 @@ class HL7Reader(private val actionLogger: ActionLogger) : Logging {
                     }
                     "OML" -> {
                         return listOf(
+                            v27_OML_O21::class.java,
                             v251_OML_O21::class.java
                         )
                     }
@@ -301,6 +303,12 @@ class HL7Reader(private val actionLogger: ActionLogger) : Logging {
                         ValidationContextFactory.noValidation(),
                         ReportStreamCanonicalModelClassFactory(ORU_R01::class.java),
                     )
+                } else if (hl7MessageType?.msh93 == "OML_O21") {
+                        DefaultHapiContext(
+                            ParserConfiguration(),
+                            ValidationContextFactory.noValidation(),
+                            ReportStreamCanonicalModelClassFactory(v27_OML_O21::class.java),
+                        )
                 } else {
                     DefaultHapiContext(ValidationContextFactory.noValidation())
                 }

diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/OML_O21/OML_O21-base.yml b/prime-router/src/main/resources/metadata/hl7_mapping/OML_O21/OML_O21-base.yml
@@ -1,9 +1,11 @@
 # $schema: ./../../../../../../metadata/json_schema/fhir/fhir-to-hl7-mapping.json
 
-hl7Class: ca.uhn.hl7v2.model.v251.message.OML_O21
+hl7Class: ca.uhn.hl7v2.model.v27.message.OML_O21
+
 constants:
   # Prefix for RS custom extension URLs
   rsext: '"https://reportstream.cdc.gov/fhir/StructureDefinition/"'
+
 elements:
   - name: message-headers
     condition: >
@@ -15,63 +17,25 @@ elements:
     schema: classpath:/metadata/hl7_mapping/resources/MessageHeader/MSH.yml
 
   - name: software-segment
-    condition: 'Bundle.entry.resource.ofType(MessageHeader).exists()'
+    resource: 'Bundle.entry.resource.ofType(Provenance).where(entity.exists()).entity.what.resolve()'
+    schema: classpath:/metadata/hl7_mapping/resources/Device/SFT.yml
+
+  - name: software-segment-legacy
+    condition: >
+      Bundle.entry.resource.ofType(MessageHeader).exists() and
+      (Bundle.entry.resource.ofType(MessageHeader).source.extension(%`rsext-software-vendor-org`).exists() or
+       Bundle.entry.resource.ofType(Provenance).exists().not())
     resource: 'Bundle.entry.resource.ofType(MessageHeader)'
     schema: classpath:/metadata/hl7_mapping/resources/MessageHeader/SFT.yml
 
-  - name: patient-information
-    resource: 'Bundle.entry.resource.ofType(Patient)'
-    condition: '%resource.count() = 1'
-    required: true
-    constants:
-      hl7SegmentGroup: '/PATIENT'
-    schema: classpath:/metadata/hl7_mapping/common/patient.yml
-
-  - name: patient-contact
-    resource: 'Bundle.entry.resource.ofType(Patient).contact'
-    condition: '%resource.exists()'
-    constants:
-      hl7SegmentGroup: '/PATIENT'
-    schema: classpath:/metadata/hl7_mapping/common/patient-contact.yml
-
-  - name: patient-visit
-    resource: 'Bundle.entry.resource.ofType(Encounter)'
+  - name: patient-base
     condition: '%resource.count() = 1'
-    constants:
-      hl7SegmentGroup: '/PATIENT/PATIENT_VISIT'
-    schema: classpath:/metadata/hl7_mapping/common/patient-visit.yml
-
-  - name: order
-    resource: Bundle.entry.resource.ofType(ServiceRequest)
-    condition: '%resource.count() > 0'
-    required: true
-    schema: classpath:/metadata/hl7_mapping/OML_O21/base/service-request-order.yml
-    constants:
-      hl7SegmentGroup: '/ORDER'
+    resource: 'Bundle.entry.resource.ofType(Patient)'
+    resourceIndex: patientIndex
+    schema: classpath:/metadata/hl7_mapping/OML_O21/base/patient/patient-base.yml
 
-  - name: order-observation-request
-    resource: Bundle.entry.resource.ofType(ServiceRequest)
-    condition: '%resource.count() > 0'
-    required: true
-    constants:
-      hl7SegmentGroup: '/ORDER/OBSERVATION_REQUEST'
-    schema: classpath:/metadata/hl7_mapping/OML_O21/base/service-request-order-observation.yml
+  - name: order-base
+    resource: 'Bundle.entry.resource.ofType(ServiceRequest).where(subject.resolve().id = %resource.entry.resource.ofType(Patient).id)'
     resourceIndex: orderIndex
-
-  - name: order-observation-result
-    resource: Bundle.entry.resource.ofType(Observation)
-    condition: '%resource.count() > 0'
-    required: true
-    schema: classpath:/metadata/hl7_mapping/common/observation-result.yml
-    constants:
-      hl7SegmentGroup: '/ORDER/OBSERVATION_REQUEST/OBSERVATION(%{resultIndex})'
-      hl7OBXField: '%{hl7SegmentGroup}/OBX'
-    resourceIndex: resultIndex
-
-  - name: order-specimen
-    resource: Bundle.entry.resource.ofType(Specimen)
-    condition: '%resource.count() = 1'
     required: true
-    schema: classpath:/metadata/hl7_mapping/common/specimen.yml
-    constants:
-      hl7SpecimenFieldPath: /ORDER/OBSERVATION_REQUEST/SPECIMEN/SPM
+    schema: classpath:/metadata/hl7_mapping/OML_O21/base/order/order-base.yml
diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/OML_O21/OML_O21-test.yml b/prime-router/src/main/resources/metadata/hl7_mapping/OML_O21/OML_O21-test.yml
@@ -0,0 +1,8 @@
+# $schema: ./../../../../../../metadata/json_schema/fhir/fhir-to-hl7-mapping.json
+
+hl7Class: ca.uhn.hl7v2.model.v27.message.OML_O21
+
+extends: classpath:/metadata/hl7_mapping/OML_O21/OML_O21-base.yml
+elements:
+  - name: message-headers
+    condition: 'true'
diff --git a/.../metadata/hl7_mapping/OML_O21/base/order/observation-request/observation-request-base.yml b/.../metadata/hl7_mapping/OML_O21/base/order/observation-request/observation-request-base.yml
@@ -0,0 +1,15 @@
+# $schema: ./../../../../../../../../../metadata/json_schema/fhir/fhir-to-hl7-mapping.json
+
+elements:
+
+  - name: observation-request
+    required: true
+    schema: classpath:/metadata/hl7_mapping/OML_O21/base/order/observation-request/observation-request.yml
+
+  - name: observation-request-observation
+    schema: classpath:/metadata/hl7_mapping/OML_O21/base/order/observation-request/observation/observation.yml
+
+  - name: observation-request-specimen
+    resource: '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "SPM") | %resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).exists().not())'
+    resourceIndex: specimenIndex
+    schema: classpath:/metadata/hl7_mapping/OML_O21/base/order/observation-request/specimen/specimen.yml
diff --git a/...urces/metadata/hl7_mapping/OML_O21/base/order/observation-request/observation-request.yml b/...urces/metadata/hl7_mapping/OML_O21/base/order/observation-request/observation-request.yml
@@ -0,0 +1,14 @@
+# $schema: ./../../../../../../../../../metadata/json_schema/fhir/fhir-to-hl7-mapping.json
+
+elements:
+
+  - name: observation-request-service-request
+    required: true
+    schema: classpath:/metadata/hl7_mapping/resources/ServiceRequest/OBR.yml
+    constants:
+      obrFieldPath: '/ORDER(%{orderIndex})/OBSERVATION_REQUEST/OBR'
+
+#  - name: observation-request-note
+# todo in second pass, for ORU this is mapped through Observation.note; OML maps through ServiceRequest.note
+# this is already mapped into fhir via ORC/ServiceRequest... where is fhir -> hl7?
+# todo add scearnio in full oml test for an OBSERVATION_REQUEST.NTE