OBR -> Specimen Additions and Updates

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

@@ -34,6 +34,70 @@ extension:
           valueOf: datatypes/EI/Identifier
           expressionType: resource
           specs: OBR.3
+    - expressionType: nested
+      vars:
+        obr8: OBR.8
+      condition: $obr8 NOT_NULL
+      generateList: true
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.7, OBR.8
+        valuePeriod:
+          expressionType: nested
+          vars:
+            start: OBR.7
+            end: OBR.8
+            dateTimeIn: OBR.7
+            dateTimeOut: OBR.8
+          expressions:
+            - valueOf: datatypes/DR/Period
+              expressionType: resource
+    - expressionType: nested
+      vars:
+        obr7: OBR.7
+        obr8: OBR.8
+      condition: $obr7 NOT_NULL && $obr8 NULL
+      generateList: true
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.7
+        valueDateTime:
+          expressionType: nested
+          vars:
+            dateTimeIn: OBR.7
+          expressions:
+            - type: STRING
+              valueOf: "GeneralUtils.dateTimeWithZoneId(dateTimeIn,ZONEID)"
+              expressionType: JEXL
+        _valueDateTime:
+          expressionType: nested
+          expressionsMap:
+            extension_1:
+              generateList: true
+              expressionType: nested
+              expressionsMap:
+                url:
+                  type: SYSTEM_URL
+                  value: hl7v2-date-time
+                valueString:
+                  type: STRING
+                  valueOf: OBR.7
+                  expressionType: HL7Spec
+    - expressionType: nested
+      vars:
+        obr9: STRING, OBR.9
+      condition: $obr9 NOT_NULL
+      specs: OBR.9
+      generateList: true
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.9
+        valueQuantity:
+          expressionType: resource
+          valueOf: datatypes/CQ/Quantity
     - expressionType: nested
       vars:
         obr10: STRING_ALL, OBR.10
@@ -83,6 +147,97 @@ extension:
           expressionType: resource
           valueOf: datatypes/CWE/CodeableConcept
           specs: OBR.13
+    - expressionType: nested
+      vars:
+        obr14: STRING, OBR.14
+      condition: $obr14 NOT_NULL
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.14
+        valueDateTime:
+          type: STRING
+          valueOf: "GeneralUtils.dateTimeWithZoneId(dateTimeIn,ZONEID)"
+          expressionType: JEXL
+          vars:
+            dateTimeIn: OBR.14
+        _valueDateTime:
+          condition: $obr14 NOT_NULL
+          expressionType: nested
+          vars:
+            obr14: OBR.14
+          expressionsMap:
+            extension:
+              generateList: true
+              expressionType: nested
+              expressionsMap:
+                url:
+                  type: SYSTEM_URL
+                  value: hl7v2-date-time
+                valueString:
+                  type: STRING
+                  valueOf: $obr14
+                  expressionType: HL7Spec
+    - expressionType: nested
+      vars:
+        obr151: STRING_ALL, OBR.15.1
+      condition: $obr151 NOT_NULL
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.15.1
+        valueCodeableConcept:
+          valueOf: datatypes/CWE/CodeableConcept
+          expressionType: resource
+          specs: OBR.15.1
+    - expressionType: nested
+      vars:
+        obr152: STRING_ALL, OBR.15.2
+      condition: $obr152 NOT_NULL
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.15.2
+        valueCodeableConcept:
+          valueOf: datatypes/CWE/CodeableConcept
+          expressionType: resource
+          specs: OBR.15.2
+    - expressionType: nested
+      vars:
+        obr153: OBR.15.3
+      condition: $obr153 NOT_NULL
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.15.3
+        valueString:
+          type: STRING
+          valueOf: OBR.15.3
+          expressionType: HL7Spec
+    - expressionType: nested
+      vars:
+        obr154: STRING_ALL, OBR.15.4
+      condition: $obr154 NOT_NULL
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.15.4
+        valueCodeableConcept:
+          valueOf: datatypes/CWE/CodeableConcept
+          expressionType: resource
+          specs: OBR.15.4
+    - expressionType: nested
+      vars:
+        obr156: STRING_ALL, OBR.15.6
+      condition: $obr156 NOT_NULL
+      expressionsMap:
+        url:
+          type: STRING
+          value: OBR.15.6
+        valueCodeableConcept:
+          valueOf: datatypes/CWE/CodeableConcept
+          expressionType: resource
+          specs: OBR.15.6
     - expressionType: nested
       vars:
         obr16: STRING_ALL, OBR.16

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

@@ -12,21 +12,16 @@ type:
   specs: OBR.15.1
 
 container:
-  condition: $obr152
+  condition: $obr152 NOT_NULL
   expressionType: nested
   generateList: true
   vars:
     obr152: OBR.15.2
   expressionsMap:
     additiveCodeableConcept:
-      expressionType: nested
-      expressions:
-        - expressionType: nested
-          expressionsMap:
-            text:
-              type: STRING
-              valueOf: OBR.15.2
-              expressionType: HL7Spec
+      valueOf: datatypes/CWE/CodeableConcept
+      expressionType: resource
+      specs: OBR.15.2
 
 collection:
   condition: $obr7 NOT_NULL || $obr8 NOT_NULL || $obr9 NOT_NULL || $obr10 NOT_NULL || $obr15 NOT_NULL

prime-router/src/main/resources/metadata/hl7_mapping/OML_O21/base/order/observation-request/observation-request.yml

@@ -8,6 +8,12 @@ elements:
     constants:
       obrFieldPath: '/ORDER(%{orderIndex})/OBSERVATION_REQUEST/OBR'
 
+  - name: observation-request-specimen
+    resource: '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR")'
+    schema: classpath:/metadata/hl7_mapping/resources/Specimen/OBR.yml
+    constants:
+      obrFieldPath: '/ORDER(%{orderIndex})/OBSERVATION_REQUEST/OBR'
+
   - name: observation-request-note
     resource: '%resource.note'
     resourceIndex: noteIndex

prime-router/src/main/resources/metadata/hl7_mapping/ORU_R01/base/patient-result/order-observation/order-observation.yml

@@ -20,6 +20,12 @@ elements:
     constants:
       obrFieldPath: '/PATIENT_RESULT(%{patientIndex})/ORDER_OBSERVATION(%{orderIndex})/OBR'
 
+  - name: observation-request-specimen
+    resource: '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR")'
+    schema: classpath:/metadata/hl7_mapping/resources/Specimen/OBR.yml
+    constants:
+      obrFieldPath: '/PATIENT_RESULT(%{patientIndex})/ORDER_OBSERVATION(%{orderIndex})/OBR'
+
   - name: observation-request-diagnostic-report
     resource: '%resource'
     schema: classpath:/metadata/hl7_mapping/resources/DiagnosticReport/OBR.yml

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
-    condition: '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR").collection.collected.is(dateTime)'
-    value: [ '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR").collection.collected.extension(%`rsext-hl7v2-date-time`).value' ]
-    hl7Spec: [ '%{obrFieldPath}-7' ]
-
-  - name: observation-collected-datetime-start
-    condition: '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR").collection.collected.is(Period)'
-    value: [ '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR").collection.collected.start.extension(%`rsext-hl7v2-date-time`).value' ]
-    hl7Spec: [ '%{obrFieldPath}-7' ]
-
-  - name: observation-collected-end-datetime
-    condition: '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR").collection.collected.is(Period)'
-    value: [ '%resource.specimen.resolve().where(extension(%`rsext-hl7v2Segment`).value = "OBR").collection.collected.end.extension(%`rsext-hl7v2-date-time`).value' ]
-    hl7Spec: [ '%{obrFieldPath}-8' ]
-
   - name: ordering-provider-from-practitioner
     condition: '%context.requester.resolve().is(Practitioner) and %context.requester.resolve().extension(%`rsext-hl7v2Field`).value = "OBR.16"'
     schema: classpath:/metadata/hl7_mapping/resources/Practitioner/XCN.yml

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

@@ -16,6 +16,28 @@ elements:
     constants:
       eiFieldPath: '%{obrFieldPath}-3'
 
+  - name: observation-collected-datetime
+    value: [ '%resource.extension.where(url = "OBR.7").value.extension(%`rsext-hl7v2-date-time`).value' ]
+    hl7Spec: [ '%{obrFieldPath}-7' ]
+
+  - name: observation-collected-period-start
+    resource: '%resource.extension.where(url = "OBR.7, OBR.8").value.start'
+    schema: classpath:/metadata/hl7_mapping/datatypes/dateTime/DTMorDT.yml
+    constants:
+      dtmFieldPath: '%{obrFieldPath}-7'
+
+  - name: observation-collected-period-end
+    resource: '%resource.extension.where(url = "OBR.7, OBR.8").value.end'
+    schema: classpath:/metadata/hl7_mapping/datatypes/dateTime/DTMorDT.yml
+    constants:
+      dtmFieldPath: '%{obrFieldPath}-8'
+
+  - name: specimen-collection-volume
+    resource: '%resource.extension.where(url = "OBR.9").value'
+    schema: classpath:/metadata/hl7_mapping/datatypes/Quantity/CQ.yml
+    constants:
+      cqFieldPath: '%{obrFieldPath}-9'
+
   - name: collector-identifier
     resource: '%resource.extension.where(url = "OBR.10").value.resolve()'
     schema: classpath:/metadata/hl7_mapping/resources/Practitioner/XCN.yml
@@ -39,6 +61,38 @@ elements:
     constants:
       cweField: '%{obrFieldPath}-13'
 
+  - name: specimen-received-datetime
+    value: [ '%resource.extension.where(url = "OBR.14").value.extension(%`rsext-hl7v2-date-time`).value' ]
+    hl7Spec: [ '%{obrFieldPath}-14' ]
+
+  - name: specimen-source-name
+    resource: '%resource.extension.where(url = "OBR.15.1").value'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-1'
+
+  - name: specimen-source-additives
+    resource: '%resource.extension.where(url = "OBR.15.2").value'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-2'
+
+  - name: specimen-source-collection-method-freetext
+    value: [ '%resource.extension.where(url = "OBR.15.3").value' ]
+    hl7Spec: [ '%{obrFieldPath}-15-3' ]
+
+  - name: specimen-source-body-site
+    resource: '%resource.extension.where(url = "OBR.15.4").value'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-4'
+
+  - name: specimen-source-collection-method-code
+    resource: '%resource.extension.where(url = "OBR.15.6").value'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-6'
+
   - name: call-back-phone-number-obr-from-extension
     condition: '%context.requester.where(extension(%`rsext-callback-number`).value.extension(%`rsext-hl7v2Field`).value[%telecomIndex] = "OBR.17").exists().not()'
     resource: '%resource.extension.where(url = "https://reportstream.cdc.gov/fhir/StructureDefinition/callback-number").value'
@@ -128,7 +182,6 @@ elements:
       cneFieldPath: '%{obrFieldPath}-45(%{cweIndex})'
     resourceIndex: cweIndex
 
-
   - name: medically-necessary-duplicate-procedure
     resource: '%resource.extension.where(url = "OBR.48").value'
     schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml

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

@@ -0,0 +1,56 @@
+# $schema: ./../../../../../../../metadata/json_schema/fhir/fhir-to-hl7-mapping.json
+
+elements:
+
+  - name: observation-collected-datetime
+    condition: '%resource.collection.collected.is(dateTime)'
+    value: [ '%resource.collection.collected.extension(%`rsext-hl7v2-date-time`).value' ]
+    hl7Spec: [ '%{obrFieldPath}-7' ]
+
+  - name: observation-collected-datetime-start
+    condition: '%resource.collection.collected.is(Period)'
+    value: [ '%resource.collection.collected.start.extension(%`rsext-hl7v2-date-time`).value' ]
+    hl7Spec: [ '%{obrFieldPath}-7' ]
+
+  - name: observation-collected-end-datetime
+    condition: '%resource.collection.collected.is(Period)'
+    value: [ '%resource.collection.collected.end.extension(%`rsext-hl7v2-date-time`).value' ]
+    hl7Spec: [ '%{obrFieldPath}-8' ]
+
+  - name: specimen-collection-volume
+    resource: '%resource.collection.quantity'
+    constants:
+      cqFieldPath: '%{obrFieldPath}-9'
+    schema: classpath:/metadata/hl7_mapping/datatypes/Quantity/CQ.yml
+
+  - name: specimen-received-datetime
+    value: [ '%resource.receivedTime.extension(%`rsext-hl7v2-date-time`).value' ]
+    hl7Spec: [ '%{obrFieldPath}-14' ]
+
+  - name: specimen-source-name
+    resource: '%resource.type'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-1'
+
+  - name: specimen-source-additives
+    resource: '%resource.container.additive'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-2'
+
+  - name: specimen-source-collection-method-freetext
+    value: [ '%resource.note.where(extension(%`rsext-hl7v2Component`).value = "OBR.15.3").text' ]
+    hl7Spec: [ '%{obrFieldPath}-15-3' ]
+
+  - name: specimen-source-body-site
+    resource: '%resource.collection.bodySite'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-4'
+
+  - name: specimen-source-collection-method-code
+    resource: '%resource.condition'
+    schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
+    constants:
+      cweField: '%{obrFieldPath}-15-6'