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• Observation.yml

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hl7.resource.Observation.yml Maven / Gradle / Ivy

#
# (C) Copyright IBM Corp. 2020, 2021
#
# SPDX-License-Identifier: Apache-2.0
#
#Observation resource
---

resourceType: Observation
id:
  type: STRING
  valueOf: 'UUID.randomUUID()'
  expressionType: JEXL

identifier_1: #joins filler | placer | MSH.7 with whatever gets returned from BUILD_FROM_CWE. that magic happens in identifier_Observation
  valueOf: datatype/Identifier_Observation
  generateList: true
  expressionType: resource
  vars:
    obx3: BUILD_IDENTIFIER_FROM_CWE, OBX.3
    fillpla: STRING, ORC.3.1 | OBR.3.1 | ORC.2.1 | OBR.2.1 | MSH.7
  constants:
      sys: "urn:id:extID"
      joinChar: '-'
identifier_2:
   condition: $valueIn NOT_NULL
   valueOf: datatype/Identifier_var
   generateList: true
   expressionType: resource
   vars:
      valueIn: OBX.21.1
      systemCX: OBX.21.2
identifier_3:
  condition: $id NOT_NULL
  valueOf: datatype/Identifier_Observation
  generateList: true
  expressionType: resource
  vars:
    obx3: BUILD_IDENTIFIER_FROM_CWE, OBX.5
    fillpla: STRING, ORC.3.1 | OBR.3.1 | ORC.2.1 | OBR.2.1 | MSH.7
  constants:
    sys: "urn:id:extID"
    joinChar: '-'
status:
   type: OBSERVATION_STATUS
   default: unknown
   valueOf: OBX.11
   expressionType: HL7Spec

# When OBX's are missing or TX based, we don't want to create an Observation.
# When TX, because content is already appended to an associated DiagnosticReport or DocumentReference
# Logic: if OBX exists AND ( (OBX.2 exists AND OBX.2 is NOT TX) OR (OBX.2 is null/empty) ) AND OBX.3 NOT NULL CREATE the Observation.
# 'code' is set 'required: true' to cause all or nothing creation logic
# The expression is nested and values are passed to the nested so that BOTH values control the 'all or nothing'
code:
   expressionType: nested
   required: true
   vars:
     obx3: OBX.3
     obx2: STRING, OBX.2
   expressions:
   -  condition: $obx3 NOT_NULL && $obx2 NOT_EQUALS_STRING TX
      valueOf: datatype/CodeableConcept
      expressionType: resource
      specs: $obx3

subject:
    valueOf: datatype/Reference
    expressionType: resource
    specs: $Patient

encounter:
    valueOf: datatype/Reference
    expressionType: resource
    specs: $Encounter

effectiveDateTime:
     type: DATE_TIME
     valueOf: OBX.14 | OBX.19
     expressionType: HL7Spec

issued:
     type: DATE_TIME
     valueOf: OBR.22 | OBX.19
     expressionType: HL7Spec

valueString:
    condition: $obx2 EQUALS ST
    type: STRING_ALL
    valueOf: OBX.5
    expressionType: HL7Spec
    vars:
      obx2: STRING, OBX.2

valueQuantity_1:
    valueOf: datatype/Quantity
    expressionType: resource
    condition: $obx2 EQUALS NM
    vars:
      value: OBX.5
      unit: OBX.6.1
      code: OBX.6.1
      obx2: STRING, OBX.2
      resolvedSystem: SYSTEM_URL, OBX.6.3

valueQuantity_2:
    valueOf: datatype/Quantity
    expressionType: resource
    condition: $obx2 EQUALS SN && $separator NULL
    vars:
      value: OBX.5.2
      unit: OBX.6.1
      code: OBX.6.1
      comparator: OBX.5.1
      obx2: STRING, OBX.2
      separator: STRING, OBX.5.3
      resolvedSystem: SYSTEM_URL, OBX.6.3

valueQuantity_3:
    valueOf: datatype/Quantity
    expressionType: resource
    condition: $obx2 EQUALS SN && $separator NOT_NULL && $separator NOT_EQUALS ':' && $separator NOT_EQUALS '/'
    vars:
      value: OBX.5.2
      unit: OBX.6.1
      code: OBX.6.1
      comparator: OBX.5.1
      obx2: STRING, OBX.2
      separator: STRING, OBX.5.3
      resolvedSystem: SYSTEM_URL, OBX.6.3

valueCodeableConcept:
     condition:  $obx2 EQUALS  CF || $obx2 EQUALS CNE || $obx2 EQUALS CWE || $obx2 EQUALS CE
     valueOf: datatype/CodeableConcept
     generateList: true
     expressionType: resource
     specs: OBX.5
     vars:
       obx2: STRING, OBX.2

valuePeriod:
   condition: $obx2 EQUALS DR
   valueOf: datatype/Period
   expressionType: resource
   vars:
     code: OBX.5
     obx2: STRING, OBX.2

valueDateTime:
   condition: $obx2 EQUALS DT || $obx2 EQUALS DTM
   type: DATE_TIME
   valueOf: OBX.5
   expressionType: HL7Spec
   vars:
     obx2: STRING, OBX.2

valueTime:
   condition: $obx2 EQUALS TM
   type: TIME
   valueOf: OBX.5
   expressionType: HL7Spec
   vars:
     obx2: STRING, OBX.2

valueRatio_1:
   condition: $obx2 EQUALS SN && $separator NOT_NULL && $separator EQUALS ':'
   valueOf: datatype/Ratio
   expressionType: resource
   specs: OBX.5
   vars:
     numerator: SN.2
     denominator: SN.4
     obx2: STRING, OBX.2
     separator: STRING, SN.3

valueRatio_2:
   condition: $obx2 EQUALS SN && $separator NOT_NULL && $separator EQUALS '/'
   valueOf: datatype/Ratio
   expressionType: resource
   specs: OBX.5
   vars:
     numerator: SN.2
     denominator: SN.4
     obx2: STRING, OBX.2
     separator: STRING, SN.3

interpretation:
   valueOf: datatype/CodeableConcept
   expressionType: resource
   specs: OBX.8

note_1:
   valueOf: datatype/Annotation
   expressionType: resource
   condition: $obx3 EQUALS 48767-8
   specs: OBX
   vars:
      obx3: STRING, OBX.3.1
      annotationText: STRING, OBX.5

note_2:
   valueOf: datatype/Annotation
   condition: $annotationText NOT_NULL
   expressionType: resource
   vars:
      annotationText: NTE.3 *&, GeneralUtils.concatenateWithChar(annotationText, '  \n')

bodySite:
   valueOf: datatype/CodeableConcept
   expressionType: resource
   specs: OBX.20

method:
   valueOf: datatype/CodeableConcept
   expressionType: resource
   specs: OBX.17

referenceRange:
   valueOf: secondary/ReferenceRange
   condition: $textValue NOT_NULL
   generateList: true
   expressionType: resource
   specs: OBX.7
   vars:
     low:  OBX.7, GeneralUtils.extractLow(low)
     high: OBX.7, GeneralUtils.extractHigh(high)
     appliestoValue: OBX.10
     textValue: OBX.7
     typeValue: OBX.10
     unit: OBX.6

performer_1:
   condition: $performerValue NOT_NULL
   valueOf: resource/Practitioner
   generateList: true
   expressionType: reference
   specs: OBX.16
   vars:
     performerValue: OBX.16

performer_2:
   condition: $performerValue2 NOT_NULL
   valueOf: resource/Organization
   generateList: true
   expressionType: reference
   specs: OBX.23
   vars:
     performerValue2: OBX.23
     orgAddressXAD: OBX.24
     orgContactXCN: OBX.25
   constants:  
     # Observation Organization needs an ADMIN purpose
     orgContactPurposeCode: 'ADMIN'
     orgContactPurposeSystemCode: 'contactentity-type'
     orgContactPurposeDisplay: 'Administrative'
     orgContactPurposeText: 'Organization Medical Director'

device:
   condition: $deviceValue NOT_NULL
   valueOf: resource/Device
   generateList: true
   expressionType: reference
   specs: OBX.18
   vars:
     deviceValue: OBX.18

category:
   condition: $specimen NOT_NULL
   valueOf: datatype/CodeableConcept_var
   generateList: true
   expressionType: resource
   vars:
      system: SYSTEM_URL, $system_code
      specimen: SPM.4
   constants:
      code: 'laboratory'
      system_code: 'observation-category'
      display: 'Laboratory'