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feat: convert admission medications (#66)
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9 files changed

+171
-3
lines changed

9 files changed

+171
-3
lines changed

‎data/Templates/eCR/DataType/_CodeableConcept.liquid‎

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{%- endif -%}
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{% endfor -%}
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{%- if minCardinality > 0 and bindingStrength != "required" and num_concepts == 0 -%}
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{%- if org_text == empty or org_test == nil -%}
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{%- if org_text == empty or org_text == nil -%}
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{% comment %} We only need to use a data-absent-reason coding if there is no coding, it has to exist (has a minimum cardinality > 0), and it has a binding strenght that allows use to use the data absent coding (anything but "required") {% endcomment %}
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{%- assign num_concepts = num_concepts | plus: 1 -%}
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{

‎data/Templates/eCR/EICR.liquid‎

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{% include 'Section/SocialHistory' -%}
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{% include 'Section/VitalSign' -%}
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{% include 'Section/PlanOfTreatment' -%}
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{% include 'Section/AdmissionMedication' -%}
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{% include 'Section/Procedure' -%}
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{% include 'Section/Immunization' -%}
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{% include 'Section/FunctionalStatus' -%}

‎data/Templates/eCR/Entry/AdmissionMedication/_entry.liquid‎

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{{ entry.act.entryRelationship | to_array | batch_render: 'Entry/AdmissionMedication/entry_act_entryRelationship', 'relationship' }}

‎data/Templates/eCR/Entry/AdmissionMedication/_entry_act_entryRelationship.liquid‎

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{% assign substanceAdministrationId = relationship.substanceAdministration | to_json_string | generate_uuid -%}
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{% include 'Resource/MedicationAdministration' medicationAdministration: relationship.substanceAdministration, ID: substanceAdministrationId -%}
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{% assign manufacturedMaterialId = relationship.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial | to_json_string | generate_uuid -%}
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{% include 'Resource/Medication' medication: relationship.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial, ID: manufacturedMaterialId -%}
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{% if relationship.substanceAdministration.author -%}
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{% evaluate practitionerAuthorId using 'Utils/GenerateId' obj: relationship.substanceAdministration.author.assignedAuthor -%}
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{% include 'Resource/Practitioner', practitioner: relationship.substanceAdministration.author.assignedAuthor, ID: practitionerAuthorId -%}
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{% assign fullPractitionerAuthorId = practitionerAuthorId | prepend: 'Practitioner/' -%}
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{% include 'Reference/MedicationAdministration/Performer_Actor' ID: substanceAdministrationId, REF: fullPractitionerAuthorId -%}
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{% endif -%}
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{% if relationship.substanceAdministration.author -%}
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{% evaluate practitionerAuthorId using 'Utils/GenerateId' obj: relationship.substanceAdministration.author.assignedAuthor -%}
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{% include 'Resource/Practitioner', practitioner: relationship.substanceAdministration.author.assignedAuthor, ID: practitionerAuthorId -%}
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{% assign fullPractitionerAuthorId = practitionerAuthorId | prepend: 'Practitioner/' -%}
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{% include 'Reference/MedicationAdministration/Performer_Actor' ID: substanceAdministrationId, REF: fullPractitionerAuthorId -%}
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{% endif -%}
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{% include 'Reference/MedicationAdministration/Subject' ID: substanceAdministrationId, REF: fullPatientId -%}
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{% assign fullManufacturedMaterialId = manufacturedMaterialId | prepend: 'Medication/' -%}
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{% include 'Reference/MedicationAdministration/MedicationReference' ID: substanceAdministrationId, REF: fullManufacturedMaterialId -%}
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{{ relationship.substanceAdministration.entryRelationship | to_array | batch_render: 'Entry/AdmissionMedication/entry_act_entryRelationship_substanceAdministration_entryRelationship', 'entryRelationship' }}

‎data/Templates/eCR/Entry/AdmissionMedication/_entry_act_entryRelationship_substanceAdministration_entryRelationship.liquid‎

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{% assign observationId = entryRelationship.observation | to_json_string | generate_uuid -%}
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{% assign templateIdString = entryRelationship.observation.templateId | to_json_string -%}
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{% if templateIdString contains '"2.16.840.1.113883.10.20.22.4.19"' -%}
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{% include 'Resource/Condition' conditionEntry: entryRelationship.observation, ID: observationId -%}
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{% assign fullObservationId = observationId | prepend: 'Condition/' -%}
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{% include 'Reference/MedicationAdministration/ReasonReference' ID: substanceAdministrationId, REF: fullObservationId-%}
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{% endif -%}
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{% if templateIdString contains '"2.16.840.1.113883.10.20.22.4.9"' -%}
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{% include 'Resource/AdverseEvent' adverseEventEntry: entryRelationship.observation, ID: observationId, REF: fullMedicationAdministrationId -%}
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{% include 'Reference/AdverseEvent/Subject' ID: observationId, REF: fullPatientId -%}
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{% assign fullAdverseEventId = observationId | prepend: 'AdverseEvent/' -%}
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{% include 'Reference/MedicationAdministration/SupportingInformation' ID: substanceAdministrationId, REF: fullAdverseEventId -%}
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{% endif -%}
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{% assign templateIdString = entryRelationship.supply.templateId | to_json_string -%}
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{% if templateIdString contains '"2.16.840.1.113883.10.20.22.4.17"' -%}
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{% if entryRelationship.supply.author.assignedAuthor -%}
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{% evaluate practitionerSupAuthId using 'Utils/GenerateId' obj: entryRelationship.supply.author.assignedAuthor -%}
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{% include 'Resource/Practitioner', practitioner: entryRelationship.supply.author.assignedAuthor, ID: practitionerSupAuthId -%}
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{% assign fullPractitionerSupAuthId = practitionerSupAuthId | prepend: 'Practitioner/' -%}
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{% include 'Reference/MedicationAdministration/Performer_Actor' ID: substanceAdministrationId, REF: fullPractitionerSupAuthId -%}
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{% endif -%}
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{% endif -%}
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{% if templateIdString contains '"2.16.840.1.113883.10.20.22.4.18"' -%}
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{% assign supplyId = entryRelationship.supply | to_json_string | generate_uuid -%}
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{% include 'Resource/MedicationDispense' medicationDispense: entryRelationship.supply, ID: supplyId -%}
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{% evaluate practitionerSupPerfId using 'Utils/GenerateId' obj: entryRelationship.supply.performer.assignedEntity -%}
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{% include 'Resource/Practitioner' practitioner: entryRelationship.supply.performer.assignedEntity, ID: practitionerSupPerfId -%}
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{% assign fullPractitionerSupPerfId = practitionerSupPerfId | prepend: 'Practitioner/' -%}
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{% include 'Reference/MedicationDispense/Performer_Actor' ID: supplyId, REF: fullPractitionerSupPerfId -%}
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{% include 'Reference/MedicationDispense/MedicationReference' ID: supplyId, REF: fullManufacturedMaterialId -%}
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{% include 'Reference/MedicationDispense/Subject' ID: supplyId, REF: fullPatientId -%}
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{% assign fullMedicationDispenseId = supplyId | prepend: 'MedicationDispense/' -%}
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{% include 'Reference/MedicationAdministration/PartOf' ID: substanceAdministrationId, REF: fullMedicationDispenseId -%}
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{% endif -%}

‎data/Templates/eCR/Resource/_AdverseEvent.liquid‎

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{
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"fullUrl":"urn:uuid:{{ID}}",
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"resource":{
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"resourceType": "AdverseEvent",
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"id":"{{ID}}",
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"identifier":
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[
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{% assign ids = adverseEventEntry.id | to_array -%}
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{% for i in ids -%}
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{% include 'DataType/Identifier' Identifier: i -%}
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{% endfor -%}
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],
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"status": "{{ adverseEventEntry.statusCode.code }}",
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"actuality": "actual",
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{% if adverseEventEntry.effectiveTime.low.value -%}
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"date": "{{ adverseEventEntry.effectiveTime.low.value | format_as_date_time }}",
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{% endif -%}
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{% if adverseEventEntry.effectiveTime.high.value -%}
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"extension": [
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{
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"url": "http://hl7.org/fhir/uv/ae-research-backport-ig/StructureDefinition/resolve-date",
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"valueDateTime": "{{ adverseEventEntry.effectiveTime.high.value | format_as_date_time }}"
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}
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],
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{% endif -%}
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"event": { {% include 'DataType/CodeableConcept' CodeableConcept: adverseEventEntry.value -%} },
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"suspectEntity": [
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{ "instance": { "reference": "{{ REF }}" } }
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]
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},
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},

‎data/Templates/eCR/Resource/_Composition.liquid‎

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{% endif -%}
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"entry":
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[
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{% if component.section.templateId.root == "2.16.840.1.113883.10.20.22.2.38" or component.section.templateId[0].root == "2.16.840.1.113883.10.20.22.2.38" %}
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{% if component.section.templateId.root == "2.16.840.1.113883.10.20.22.2.38" or component.section.templateId[0].root == "2.16.840.1.113883.10.20.22.2.38" or component.section.templateId[0].root == "2.16.840.1.113883.10.20.22.2.44" %}
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{% assign entries = component.section.entry | to_array -%}
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{% for entry in entries -%}
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{% assign medicationAdministrationId = entry.substanceAdministration | to_json_string | generate_uuid -%}
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},
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{% endfor %}
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{% endif %}
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{% if component.section.templateId.root == "2.16.840.1.113883.10.20.22.2.44" or component.section.templateId[0].root == "2.16.840.1.113883.10.20.22.2.44" %}
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{% assign entries = component.section.entry | to_array -%}
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{% for entry in entries -%}
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{% assign medicationAdministrationId = entry.act.entryRelationship.substanceAdministration | to_json_string | generate_uuid -%}
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{% assign fullMedicationAdministrationId = medicationAdministrationId | prepend: 'MedicationAdministration/' -%}
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{
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"reference": "{{ fullMedicationAdministrationId }}",
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},
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{% endfor %}
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{% endif %}
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{% if component.section.templateId.root == "2.16.840.1.113883.10.20.22.2.2.1" %}
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{% assign entries = component.section.entry | to_array -%}
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{% for entry in entries -%}

‎data/Templates/eCR/Section/_AdmissionMedication.liquid‎

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{% assign firstSections = msg | get_first_ccda_sections_by_template_id: '2.16.840.1.113883.10.20.22.2.44' -%}
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{{ firstSections.2_16_840_1_113883_10_20_22_2_44.entry | to_array | batch_render: 'Entry/AdmissionMedication/entry', 'entry' }}

‎src/Microsoft.Health.Fhir.Liquid.Converter.UnitTests/Templates/eCR/Resource/AdverseEventTests.cs‎

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using System;
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using System.Collections.Generic;
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using System.IO;
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using System.Text;
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using System.Linq;
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using DotLiquid;
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using Hl7.Fhir.Model;
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using Xunit;
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using Xunit.Abstractions;
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using Microsoft.Health.Fhir.Liquid.Converter.Parsers;
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namespace Microsoft.Health.Fhir.Liquid.Converter.UnitTests
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{
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public class AdverseEventTests : BaseECRLiquidTests
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{
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private static readonly string ECRPath = Path.Join(
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TestConstants.ECRTemplateDirectory,
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"Resource",
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"_AdverseEvent.liquid"
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);
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[Fact]
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public void AdverseEvent_AllFields()
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{
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// from 3.1 spec
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var xmlStr = @"
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<observation classCode=""OBS"" moodCode=""EVN"">
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<templateId root=""2.16.840.1.113883.10.20.22.4.9"" extension=""2014-06-09"" />
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<id root=""4adc1020-7b14-11db-9fe1-0800200c9a64"" />
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<code code=""ASSERTION"" codeSystem=""2.16.840.1.113883.5.4"" />
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<text>
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<reference value=""#reaction1"" />
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</text>
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<statusCode code=""completed"" />
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<effectiveTime>
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<low value=""200802260805-0800"" />
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<high value=""200802281205-0800"" />
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</effectiveTime>
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<value type=""CD"" code=""422587007"" codeSystem=""2.16.840.1.113883.6.96"" displayName=""Nausea"" />
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</observation>
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";
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var parsed = new CcdaDataParser().Parse(xmlStr) as Dictionary<string, object>;
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var attributes = new Dictionary<string, object>
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{
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{ "ID", "1234" },
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{ "adverseEventEntry", parsed["observation"]},
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};
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var actualFhir = GetFhirObjectFromTemplate<AdverseEvent>(ECRPath, attributes);
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Assert.Equal("AdverseEvent", actualFhir.TypeName);
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Assert.Equal("1234" ,actualFhir.Id);
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Assert.Equal("2008-02-26T08:05:00-08:00", actualFhir.Date);
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Assert.NotNull(actualFhir.Event);
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Assert.NotEmpty(actualFhir.Event.Coding);
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var coding = actualFhir.Event.Coding.First();
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Assert.Equal("Nausea", coding.Display);
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}
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}
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}

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