Merge branch 'engagement/hl7data-improvements' of https://github.com/…

…CDCgov/prime-reportstream into engagement/hl7data-improvements
CDCgov · Feb 27, 2025 · 75876bd · 75876bd
2 parents 17fd137 + 26a5eb9
commit 75876bd
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diff --git a/prime-router/src/main/resources/metadata/fhir_transforms/common/adjust-ordering-provider.yml b/prime-router/src/main/resources/metadata/fhir_transforms/common/adjust-ordering-provider.yml
@@ -18,11 +18,11 @@ elements:
   - name: set-obr-16-13-if-not-practitioner
     resource: 'Bundle.entry.resource.ofType(Practitioner)'
     condition: '%npiResource.value.exists().not()'
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/xcn-practitioner").extension("XCN.13").value[x]'
+    bundleProperty: '%resource.identifier.type.coding.code'
     value: [ '"U"' ]
 
   - name: set-obr-16-13-if-practitioner
     resource: 'Bundle.entry.resource.ofType(Practitioner)'
     condition: '%npiResource.value.exists()'
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/xcn-practitioner").extension("XCN.13").value[x]'
+    bundleProperty: '%resource.identifier.type.coding.code'
     value: [ '"NPI"' ]
diff --git a/prime-router/src/main/resources/metadata/fhir_transforms/common/modify-aoe-values.yml b/prime-router/src/main/resources/metadata/fhir_transforms/common/modify-aoe-values.yml
@@ -7,19 +7,20 @@ elements:
     value: ['""']
     bundleProperty: '%resource.code.text'
 
+# TODO if new ORU extension move all the commented sections over
   #OBX-15(1).2 Producer's ID [CWE] > Text (ST)
-  - name: suppress-producers-id-text
-    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value.join(",").contains("OBX.15")).extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-organization").value.coding.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding").value = "coding")'
-    condition: '%resource.exists()'
-    value: [ '""' ]
-    bundleProperty: '%resource.display'
-
-  #OBX-15(1).3 Producer's ID [CWE] > Name of Coding System (ID)
-  - name: suppress-producers-id-coding-system
-    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value.join(",").contains("OBX.15")).extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-organization").value.coding.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding").value = "coding").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system")'
-    condition: '%resource.value.exists()'
-    value: [ '""' ]
-    bundleProperty: '%resource.value[x]'
+#  - name: suppress-producers-id-text
+#    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value.join(",").contains("OBX.15")).extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-organization").value.coding.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding").value = "coding")'
+#    condition: '%resource.exists()'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.display'
+#
+#  #OBX-15(1).3 Producer's ID [CWE] > Name of Coding System (ID)
+#  - name: suppress-producers-id-coding-system
+#    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field").value.join(",").contains("OBX.15")).extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-organization").value.coding.where(extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding").value = "coding").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system")'
+#    condition: '%resource.value.exists()'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.value[x]'
 
   #OBX-19(1).1.1 Date/Time of the Analysis [DTM] > Date/Time (DTM)
   - name: aoe-analysis-date
@@ -34,34 +35,35 @@ elements:
     value: [ 'Bundle.entry.resource.ofType(Observation).first().issued' ]
 
   #OBX-23(1).2 Performing Organization Name [XON~] > Organization Name Type Code (IS)
-  - name: suppress-performing-organization-name-type-code
-    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).extension("https://reportstream.cdc.gov/fhir/StructureDefinition/organization-name-type")[0].value.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding")'
-    condition: '%resource.value.coding.code.exists()'
-    value: [ '""' ]
-    bundleProperty: '%resource.value.coding.code'
-
-  #OBX-23(1).6 Performing Organization Name [XON~] > Assigning Authority (HD)
-  - name: suppress-performing-organization-assigning-authority-universal-id
-    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).identifier.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority")'
-    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").exists()'
-    value: [ '""' ]
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").value[x]'
-
-  - name: suppress-performing-organization-assigning-authority-id-type
-    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).identifier.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority")'
-    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type").exists()'
-    value: [ '""' ]
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type").value[x]'
+#  - name: suppress-performing-organization-name-type-code
+#    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).extension("https://reportstream.cdc.gov/fhir/StructureDefinition/organization-name-type")[0].value.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding")'
+#    condition: '%resource.value.coding.code.exists()'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.value.coding.code'
+#
+#  #OBX-23(1).6 Performing Organization Name [XON~] > Assigning Authority (HD)
+#  - name: suppress-performing-organization-assigning-authority-universal-id
+#    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).identifier.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority")'
+#    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").exists()'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").value[x]'
 
-  - name: suppress-performing-organization-assigning-authority-namespace-id
-    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).identifier.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority")'
-    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").exists()'
-    value: [ '""' ]
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").value[x]'
+#  - name: suppress-performing-organization-assigning-authority-id-type
+#    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).identifier.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority")'
+#    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type").exists()'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id-type").value[x]'
+#
+#  - name: suppress-performing-organization-assigning-authority-namespace-id
+#    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization).identifier.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority")'
+#    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").exists()'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").value[x]'
 
   #OBX-24(1).6 Performing Organization Address [XAD~] > Country (ID)
-  - name: suppress-performing-organization-address-country
-    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization)'
-    condition: '%resource.address.country.exists()'
-    value: [ '""' ]
-    bundleProperty: '%resource.address.country'
+  # TODO can we remove this?
+#  - name: suppress-performing-organization-address-country
+#    resource: 'Bundle.entry.resource.ofType(ServiceRequest).supportingInfo.resolve().performer.resolve().ofType(Organization)'
+#    condition: '%resource.address.country.exists()'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.address.country'
diff --git a/...router/src/main/resources/metadata/fhir_transforms/common/suppress-device-information.yml b/...router/src/main/resources/metadata/fhir_transforms/common/suppress-device-information.yml
@@ -1,24 +1,25 @@
 ## Suppresses Device information OBX-18-1,OBX-18-2,OBX-18-3
 elements:
-  ##OBX-18-1
-  - name: suppress-device-name
-    resource: 'Bundle.entry.resource.ofType(Device).identifier'
-    value: [ '""' ]
-    bundleProperty: '%resource.value'
-
-    ##OBX-18-2
-  - name: suppress-device-namespace_id
-    resource: 'Bundle.entry.resource.ofType(Device).identifier'
-    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").exists()'
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").value[x]'
-    value: [ '""' ]
+# TODO figure out what to do with OBX-18 since some files may need the field values?
+#  ##OBX-18-1
+#  - name: suppress-device-name
+#    resource: 'Bundle.entry.resource.ofType(Device).identifier'
+#    value: [ '""' ]
+#    bundleProperty: '%resource.value'
+
+#    ##OBX-18-2
+#  - name: suppress-device-namespace_id
+#    resource: 'Bundle.entry.resource.ofType(Device).identifier'
+#    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").exists()'
+#    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/namespace-id").value[x]'
+#    value: [ '""' ]
 
     ##OBX-18-3
-  - name: suppress-device-universal-id
-    resource: 'Bundle.entry.resource.ofType(Device).identifier'
-    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").exists()'
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").value[x]'
-    value: [ '""' ]
+#  - name: suppress-device-universal-id
+#    resource: 'Bundle.entry.resource.ofType(Device).identifier'
+#    condition: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").exists()'
+#    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/assigning-authority").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/universal-id").value[x]'
+#    value: [ '""' ]
 
     ##OBX-18-3 different mappings
   - name: suppress-device-type-id
@@ -35,9 +36,9 @@ elements:
 
   ##PID-10-9
   - name: suppress-patient-pid-10-9-value
-    resource: 'Bundle.entry.resource.ofType(Patient)'
-    condition: '%resource.extension("http://ibm.com/fhir/cdm/StructureDefinition/local-race-cd").exists()'
-    bundleProperty: '%resource.extension("http://ibm.com/fhir/cdm/StructureDefinition/local-race-cd").value.text'
+    resource: 'Bundle.entry.resource.ofType(Patient).extension("http://ibm.com/fhir/cdm/StructureDefinition/local-race-cd")'
+    condition: '%resource.exists()'
+    bundleProperty: '%resource.value.text'
     value: [ '""' ]
 
   ##PID-22-ethnic-value (Hispanic or Latino)
@@ -54,9 +55,9 @@ elements:
     bundleProperty: '%resource.code.text'
     value: [ '""' ]
 
-  #SPM-4-9
-  - name: suppress-patient-spm-4-9
-    resource: 'Bundle.entry.resource.ofType(Specimen).type'
+  #SPM-1-8
+  - name: suppress-specimen-spm-1-8
+    resource: 'Bundle.entry.resource.ofType(Specimen).collection.bodySite'
     condition: '%resource.text.exists()'
     value: [ '""' ]
     bundleProperty: '%resource.text'
diff --git a/...esources/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml b/...esources/metadata/fhir_transforms/senders/SimpleReport/simple-report-sender-transform.yml
@@ -420,22 +420,22 @@ elements:
     bundleProperty: '%resource.collection.bodySite.coding[0].display'
     value: [ '%resource.collection.bodySite.text' ]
 
-  - name: sr-observation-producer-id-identifier
-    resource: 'Bundle.entry.resource.ofType(Observation)'
-    condition: '%resource.performer.exists().not()'
-    bundleProperty: '%resource.performer'
-    value: [ '%diagnosticReport.basedOn.resolve().performer' ]
-
   - name: sr-observation-producer-id-hl7use
     resource: 'Bundle.entry.resource.ofType(Observation).performer.resolve()'
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field")[1].value[x]'
+    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field")[0].value[x]'
     value: [ '"OBX.15"' ]
 
   - name: sr-observation-performing-org-hl7use
     resource: 'Bundle.entry.resource.ofType(Observation).performer.resolve()'
-    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field")[0].value[x]'
+    bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2Field")[1].value[x]'
     value: [ '"OBX.25"' ]
 
+  - name: sr-observation-producer-id-identifier
+    resource: 'Bundle.entry.resource.ofType(Observation)'
+    condition: '%resource.performer.exists().not()'
+    bundleProperty: '%resource.performer'
+    value: [ '%diagnosticReport.basedOn.resolve().performer' ]
+
   - name: sr-observation-producer-id-cwe-identifier
     resource: 'Bundle.entry.resource.ofType(Observation).performer.resolve()'
     bundleProperty: '%resource.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-organization").valueCodeableConcept.coding.code'
@@ -598,6 +598,10 @@ elements:
     bundleProperty: 'Bundle.entry.resource.ofType(ServiceRequest).requester.resolve().practitioner.resolve().address.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/xad-address").extension("https://reportstream.cdc.gov/fhir/StructureDefinition/sad-address-line").extension("SAD.1").value[x]'
     value: [ 'Bundle.entry.resource.ofType(ServiceRequest).requester.resolve().practitioner.resolve().address.line[0]' ]
 
+  - name: sr-service-request-requester-address-street-2
+    bundleProperty: 'Bundle.entry.resource.ofType(ServiceRequest).requester.resolve().practitioner.resolve().address.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/xad-address").extension("XAD.2").value[x]'
+    value: [ 'Bundle.entry.resource.ofType(ServiceRequest).requester.resolve().practitioner.resolve().address.line[1]' ]
+
   # order-effective-date
   - name: sr-service-request-orc-order-effective-date
     bundleProperty: 'Bundle.entry.resource.ofType(ServiceRequest).extension("https://reportstream.cdc.gov/fhir/StructureDefinition/orc-common-order").extension("ORC.15").value[x]'

diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/OBX-shadow.yml b/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/OBX-shadow.yml
@@ -0,0 +1,43 @@
+constants:
+  hl7ObservationPath: '/PATIENT_RESULT/ORDER_OBSERVATION/OBSERVATION(%{resultIndex})'
+
+elements:
+  # OBX 15.2
+  - name: obx-producer-text
+    condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.where(code in ("AOE")).exists()'
+    value: [ '""' ]
+    hl7Spec: [ '%{hl7ObservationPath}/OBX-15-2' ]
+
+  # OBX 15.3
+  - name: obx-producer-coding-system-name
+    condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.where(code in ("AOE")).exists()'
+    value: [ '""' ]
+    hl7Spec: [ '%{hl7ObservationPath}/OBX-15-3' ]
+
+  # OBX 23-2
+  - name: obx-organization-name-type-code
+    condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.where(code in ("AOE")).exists().not()'
+    value: [ '"L"' ]
+    hl7Spec: [ '%{hl7ObservationPath}/OBX-23-2' ]
+
+  # OBX 23-2 - Remove tag if AOE
+  - name: obx-organization-name-type-code-aoe
+    condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.where(code in ("AOE")).exists()'
+    value: [ '""' ]
+    hl7Spec: [ '%{hl7ObservationPath}/OBX-23-2' ]
+
+  # OBX 23-6.1-3
+  - name: obx-assigning-authority-namespace-id
+    condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.where(code in ("AOE")).exists().not()'
+    value: [ '"CLIA"' ]
+    hl7Spec: [ '%{hl7ObservationPath}/OBX-23-6-1' ]
+
+  - name: obx-assigning-authority-universal-id
+    condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.where(code in ("AOE")).exists().not()'
+    value: [ '"2.16.840.1.113883.4.7"' ]
+    hl7Spec: [ '%{hl7ObservationPath}/OBX-23-6-2' ]
+
+  - name: obx-assigning-authority-universal-id-type
+    condition: '%resource.code.coding.extension("https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code").value.where(code in ("AOE")).exists().not()'
+    value: [ '"ISO"' ]
+    hl7Spec: [ '%{hl7ObservationPath}/OBX-23-6-3' ]
diff --git a/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/ORU_R01-shadow.yml b/prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/ORU_R01-shadow.yml
@@ -0,0 +1,16 @@
+# $schema: ./../../../../../../metadata/json_schema/fhir/fhir-to-hl7-mapping.json
+
+hl7Class: ca.uhn.hl7v2.model.v27.message.ORU_R01
+extends: classpath:/metadata/hl7_mapping/ORU_R01/ORU_R01-base.yml
+
+elements:
+  - name: obx-shadow
+    resource: 'Bundle.entry.resource.ofType(Observation)'
+    condition: '%resource.count() > 0'
+    schema: classpath:/metadata/hl7_mapping/ORU_R01/OBX-shadow.yml
+    resourceIndex: resultIndex
+
+  # ORC 21.7
+  - name: orc-identifier-type-code
+    value: [ '""' ]
+    hl7Spec: [ /PATIENT_RESULT/ORDER_OBSERVATION/ORC-21-7 ]
diff --git a/...uter/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MS/MS-receiver-transform.yml b/...uter/src/main/resources/metadata/hl7_mapping/receivers/STLTs/MS/MS-receiver-transform.yml
@@ -1,6 +1,6 @@
 hl7Class: ca.uhn.hl7v2.model.v251.message.ORU_R01
 
-extends: classpath:/metadata/hl7_mapping/ORU_R01/ORU_R01-base.yml
+extends: classpath:/metadata/hl7_mapping/ORU_R01/ORU_R01-shadow.yml
 
 elements:
   - name: ms-name-of-the-sender-application-Namespace-Id
@@ -18,12 +18,11 @@ elements:
     value: [ '"MSDOH"' ]
     hl7Spec: [ 'MSH-6-1' ]
 
-  - name: ms-receiving-facility-universal-ID
-    condition: 'true'
-    value: [ '"2.16.840.1.114222.1.3645"' ]
-    hl7Spec: [ 'MSH-6-2' ]
-
-  - name: ms-receiving-facility-universal-ID-Type
-    condition: 'true'
-    value: [ '"ISO"' ]
-    hl7Spec: [ 'MSH-6-3' ]
+  # Suppress the XON.10 value in Organization
+  # prime-router/src/main/resources/metadata/hl7_mapping/receivers/Common/remove-orc-21-10/remove-orc-21-10.yml
+  # TODO remove if new extension for ORU-R01 base
+  - name: suppress-organization-orc-21-10
+    resource: 'Bundle.entry.resource.ofType(ServiceRequest).requester.resolve().organization.resolve().extension("https://reportstream.cdc.gov/fhir/StructureDefinition/xon-organization").extension("XON.10")'
+    condition: '%resource.value.exists()'
+    value: [ '""' ]
+    hl7Spec: [ '/PATIENT_RESULT/ORDER_OBSERVATION/ORC-21-10' ]