Move phdi customizations into fork

.github/workflows/test.yml

@@ -0,0 +1,32 @@
+name: Test fhir-converter
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  unit-test-dotnet-fhir-converter:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Setup dotnet
+        uses: actions/setup-dotnet@v3
+        with:
+          dotnet-version: "6.0.x"
+      - name: Run tests
+        run: dotnet test --filter FullyQualifiedName~Converter.UnitTests
+
+  functional-test-dotnet-fhir-converter:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Setup dotnet
+        uses: actions/setup-dotnet@v3
+        with:
+          dotnet-version: "6.0.x"
+      - name: Run tests
+        run: dotnet test --filter FullyQualifiedName~Converter.FunctionalTests

.gitignore

@@ -38,6 +38,7 @@ bld/
 
 # Visual Studio 2015/2017 cache/options directory
 .vs/
+.vscode/
 # Uncomment if you have tasks that create the project's static files in wwwroot
 #wwwroot/
 
@@ -363,4 +364,12 @@ MigrationBackup/
 .ionide/
 
 # Fody - auto-generated XML schema
-FodyWeavers.xsd
+FodyWeavers.xsd
+
+# ASDF
+.tool-versions
+
+# Common test files
+/input.txt
+/output.json
+output/

CustomAnalysisRules.ruleset

@@ -12,5 +12,6 @@
     <Rule Id="SA1623" Action="None" />
     <Rule Id="SA1629" Action="None" />
     <Rule Id="SA1652" Action="None" />
+    <Rule Id="SA1633" Action="None" />
   </Rules>
-</RuleSet>
+</RuleSet>

LICENSE

@@ -1,6 +1,7 @@
     MIT License
 
     Copyright (c) Microsoft Corporation. All rights reserved.
+    Copyright (c) 2024 Skylight. All rights reserved.
 
     Permission is hereby granted, free of charge, to any person obtaining a copy
     of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,8 +1,10 @@
-# FHIR Converter
+# Skylight fork of microsoft/FHIR Converter
 
 FHIR converter is an open source project that enables conversion of health data from legacy formats to and from FHIR.  The FHIR converter uses the [Liquid template language](https://shopify.github.io/liquid/) and the .NET runtime.
 
-The FHIR converter supports the following conversions: **HL7v2 to FHIR**, **C-CDA to FHIR**, **JSON to FHIR**, **FHIR STU3 to R4**, and **FHIR to HL7v2** (*Preview*).
+The Microsoft FHIR converter supports the following conversions: **HL7v2 to FHIR**, **C-CDA to FHIR**, **JSON to FHIR**, **FHIR STU3 to R4**, and **FHIR to HL7v2** (*Preview*).
+
+The Skylight fork has added support for **eCR to FHIR** and **ELR to FHIR**. Some other changes to the code were needed to support these conversions in addition to the new functionality. These converters are still under active development and are not yet fully validated.
 
 The converter uses templates that define mappings between these different data formats. The templates are written in [Liquid](https://shopify.github.io/liquid/) templating language and make use of custom [filters](docs/Filters-and-Tags.md).  
 

data/Templates/eCR/ConsultationNote.liquid

@@ -0,0 +1,27 @@
+{
+    "resourceType": "Bundle",
+    "type": "batch",
+    "entry": [
+        {% evaluate patientId using 'Utils/GenerateId' obj: msg.ClinicalDocument.recordTarget.patientRole -%}
+        {% assign fullPatientId = patientId | prepend: 'Patient/' -%}
+        {% include 'Header' -%}
+        {% include 'Section/AllergiesAndAdverseReaction' -%}
+        {% include 'Section/Problem' -%}
+
+        {% include 'Section/FamilyHistory' -%}
+        {% include 'Section/Immunization' -%}
+        {% include 'Section/Medication' -%}
+        {% include 'Section/Procedure' -%}
+        {% include 'Section/Result' -%}
+        {% include 'Section/SocialHistory' -%}
+        {% include 'Section/VitalSign' -%}
+        {% include 'Section/FunctionalStatus' -%}
+        {% include 'Section/MedicalEquipment' -%}
+        {% include 'Section/AdvanceDirective' -%}
+        {% include 'Section/MentalStatus' -%}
+        {% include 'Section/Nutrition' -%}
+
+        {% assign documentId = msg | to_json_string | generate_uuid -%}
+        {% include 'Resource/DocumentReference' documentReference: msg ID: documentId -%}
+    ]
+}

data/Templates/eCR/DataType/_Address.liquid

@@ -0,0 +1,16 @@
+{% assign lines = Address.streetAddressLine | to_array -%}
+{% if lines.first._ or Address.city._ or Address.state._ or Address.country._ or Address.postalCode._ or Address.county._ -%}
+    "use": "{{ Address.use | get_property: 'ValueSet/AddressUse' }}",
+
+    "line": [
+        {% assign lines = Address.streetAddressLine | to_array -%}
+        {% for l in lines -%}
+            "{{l._}}",
+        {% endfor -%}
+    ],
+    "city": "{{Address.city._}}",
+    "state": "{{Address.state._}}",
+    "country": "{{Address.country._}}",
+    "postalCode": "{{Address.postalCode._}}",
+    "district": "{{Address.county._}}",
+{% endif -%}

data/Templates/eCR/DataType/_CodeableConcept.liquid

@@ -0,0 +1,7 @@
+"coding": 
+[
+	{% assign concepts = CodeableConcept | to_array -%}
+	{% for concept in concepts -%}
+	{ {% include 'DataType/Coding' Coding: concept -%} },
+	{% endfor -%}
+],

data/Templates/eCR/DataType/_Coding.liquid

@@ -0,0 +1,16 @@
+"code": "{{ Coding.code }}",
+{%- capture codeSystemName -%}
+  {% include 'ValueSet/SystemReference' code: Coding.codeSystem %}
+{%- endcapture -%}
+"system": {{ codeSystemName }},
+{% if Coding.displayName -%}
+  "display": "{{ Coding.displayName | strip }}",
+{% elsif Coding.originalText._ -%}
+  "display": "{{ Coding.originalText._ | strip }}",
+{% elsif Coding.originalText.reference._ -%}
+  "display": "{{ Coding.originalText.reference._ }}",
+{% elsif codeSystemName contains "loinc" -%}
+  "display": "{{ Coding.code | get_loinc_name }}",
+{% elsif codeSystemName contains "rxnorm" -%}
+  "display": "{{ Coding.code | get_rxnorm_name }}",
+{% endif -%}

data/Templates/eCR/DataType/_ContactPoint.liquid

@@ -0,0 +1,11 @@
+{% if ContactPoint.value -%}
+	{% if ContactPoint.value contains 'tel:' -%}
+		"system":"phone",
+		"value": "{{ContactPoint.value | replace: 'tel:\s*', ''}}",
+		"use": "{{ ContactPoint.use | get_property: 'ValueSet/TelecomUse' }}",
+	{% elsif ContactPoint.value contains 'mailto:' or ContactPoint.value contains '@' -%}
+		"system":"email",
+		"value": "{{ContactPoint.value | replace: 'mailto:\s*', ''}}",
+		"use": "{{ ContactPoint.use | get_property: 'ValueSet/TelecomUse' }}",
+	{% endif -%}
+{% endif -%}

data/Templates/eCR/DataType/_HumanName.liquid

@@ -0,0 +1,16 @@
+"use":"{{ HumanName.use | get_property: 'ValueSet/NameUse' }}",
+"family":"{{HumanName.family._}}",
+"given":[
+	{% assign givens = HumanName.given | to_array -%}
+	{% for g in givens -%}
+		"{{g._}}",
+	{% endfor -%}
+],
+"prefix":
+[
+	"{{HumanName.prefix._}}",
+],
+"suffix":
+[
+	"{{HumanName.suffix._}}",
+]

data/Templates/eCR/DataType/_Identifier.liquid

@@ -0,0 +1,13 @@
+{% if Identifier.nullFlavor == null -%}
+    {% if Identifier.extension -%}
+        "system":{% include 'ValueSet/SystemReference' code: Identifier.root -%},
+        "value":"{{Identifier.extension}}",
+        "assigner":
+        {
+            "display":"{{Identifier.assigningAuthorityName}}"
+        }
+    {% else -%}
+        "system":"urn:ietf:rfc:3986",
+        "value":"urn:uuid:{{Identifier.root}}",
+    {% endif -%}
+{% endif -%}

data/Templates/eCR/DataType/_IdentifierRoot.liquid

@@ -0,0 +1,9 @@
+{% if Identifier.nullFlavor == null -%}
+        "value":"{{Identifier.root}}",
+        {% if Identifier.assigningAuthorityName -%}
+            "assigner":
+            {
+                "display":"{{Identifier.assigningAuthorityName}}"
+            }
+        {% endif -%}
+{% endif -%}

data/Templates/eCR/DataType/_Period.liquid

@@ -0,0 +1,2 @@
+"start":"{{ Period.low.value | format_as_date_time }}",
+"end":"{{ Period.high.value | format_as_date_time }}",

data/Templates/eCR/DataType/_Reason.liquid

@@ -0,0 +1,11 @@
+{% assign key = "2_16_840_1_113883_10_20_22_2_12" -%}
+{% assign reas_n = Reason[key] -%}
+{% if reason and reas_n.entry and reas_n.entry.observation and reas_n.entry.observation.value and reas_n.entry.observation.value.originalText and reas_n.entry.observation.value.originalText._ %}
+  "reason": [{
+    "value": [{
+      "concept": {
+        "text": "{{ reas_n.entry.observation.value.originalText._ }}",
+      }
+    }]
+  }],
+{% endif -%}

data/Templates/eCR/DischargeSummary.liquid

@@ -0,0 +1,24 @@
+{
+    "resourceType": "Bundle",
+    "type": "batch",
+    "entry": [
+        {% evaluate patientId using 'Utils/GenerateId' obj: msg.ClinicalDocument.recordTarget.patientRole -%}
+        {% assign fullPatientId = patientId | prepend: 'Patient/' -%}
+        {% include 'Header' -%}
+        {% include 'Section/AllergiesAndAdverseReaction' -%}
+        {% include 'Section/HospitalDischargeDiagnosis' -%}
+
+        {% include 'Section/FunctionalStatus' -%}
+        {% include 'Section/HospitalAdmissionDiagnosis' -%}
+        {% include 'Section/Problem' -%}
+        {% include 'Section/Procedure' -%}
+        {% include 'Section/VitalSign' -%}
+        {% include 'Section/SocialHistory' -%}
+        {% include 'Section/Immunization' -%}
+        {% include 'Section/FamilyHistory' -%}
+        {% include 'Section/HospitalDischargeMedication' -%}
+
+        {% assign documentId = msg | to_json_string | generate_uuid -%}
+        {% include 'Resource/DocumentReference' documentReference: msg ID: documentId -%}
+    ]
+}

data/Templates/eCR/EICR.liquid

@@ -0,0 +1,26 @@
+{
+"resourceType": "Bundle",
+    "type": "batch",
+    "entry": [{% evaluate patientId using 'Utils/GenerateId' obj: msg.ClinicalDocument.recordTarget.patientRole -%}
+{% assign fullPatientId = patientId | prepend: 'Patient/' -%}
+
+{% include 'Header' -%}
+{% include 'Section/AllergiesAndAdverseReaction' -%}
+{% include 'Section/Medication' -%}
+{% include 'Section/Problem' -%}
+{% include 'Section/Pregnancy' -%}
+{% include 'Section/Result' -%}
+{% include 'Section/SocialHistory' -%}
+{% include 'Section/VitalSign' -%}
+
+{% include 'Section/Procedure' -%}
+{% include 'Section/Immunization' -%}
+{% include 'Section/FunctionalStatus' -%}
+{% include 'Section/FamilyHistory' -%}
+{% include 'Section/AdvanceDirective' -%}
+{% include 'Section/MedicalEquipment' -%}
+{% include 'Section/MentalStatus' -%}
+{% include 'Section/Nutrition' -%}
+{% include 'Section/Payer' -%}
+]
+}

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

@@ -0,0 +1,19 @@
+{% if entry.organizer -%}
+    {% assign organizationId = entry.organizer | to_json_string | generate_uuid -%}
+    {% include 'Resource/Consent' consentScope: 'adr', consentEntry: entry.organizer, ID: organizationId -%}
+    {% include 'Reference/Consent/Patient' ID: organizationId, REF: fullPatientId -%}
+
+    {% if entry.organizer.component.observation.reference -%}
+        {% assign referenceId = entry.organizer.component.observation.reference | to_json_string | generate_uuid -%}
+        {% include 'Resource/DocumentReference2' docref: entry.organizer.component.observation.reference, ID: referenceId -%}
+        {% assign fullReferenceId = referenceId | prepend: 'DocumentReference/' -%}
+        {% include 'Reference/Consent/SourceReference' ID: organizationId, REF: fullReferenceId -%}
+    {% endif -%}
+
+    {% if entry.organizer.component.observation.author.assignedAuthor -%}
+        {% evaluate practitionerADId using 'Utils/GenerateId' obj: entry.organizer.component.observation.author.assignedAuthor -%}
+        {% include 'Resource/Practitioner' practitioner: entry.organizer.component.observation.author.assignedAuthor, ID: practitionerADId -%}
+        {% assign fullPractitionerADId = practitionerADId | prepend: 'Practitioner/' -%}
+        {% include 'Reference/Consent/Performer' ID: organizationId, REF: fullPractitionerADId -%}
+    {% endif -%}
+{% endif -%}

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

@@ -0,0 +1,3 @@
+{% assign statusCode = entry.act.statusCode -%}
+{{ entry.act.entryRelationship | to_array | batch_render: 'Entry/AllergiesAndAdverseReaction/entry_act_entryRelationship', 'relationship' }}
+

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

@@ -0,0 +1,6 @@
+{% assign templateIdString = relationship.observation.templateId | to_json_string -%}
+{% if templateIdString contains '"2.16.840.1.113883.10.20.22.4.7"' -%}
+    {% assign allergyId = relationship.observation | to_json_string | generate_uuid -%}
+    {% include 'Resource/AllergyIntolerance' allergyStatus: statusCode, allergyEntry: relationship.observation, ID: allergyId -%}
+    {% include 'Reference/AllergyIntolerance/Patient' ID: allergyId, REF: fullPatientId -%}
+{% endif -%}

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

@@ -0,0 +1,3 @@
+{% assign observationId = entry.observation | to_json_string | generate_uuid -%}
+{% include 'Resource/Condition' conditionEntry: entry.observation, ID: observationId -%}
+{% include 'Reference/Condition/Subject' ID: observationId, REF: fullPatientId -%}

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

@@ -0,0 +1,14 @@
+{% assign encounterId = entry | to_json_string | generate_uuid -%}
+{% include 'Resource/Encounter' encounter: entry.encounter, ID: encounterId -%}
+{% include 'Reference/Encounter/Subject' ID: encounterId, REF: fullPatientId -%}
+
+{% if entry.encounter.performer.assignedEntity -%}
+    {% assign practitionerEncPerfId = entry.encounter.performer.assignedEntity | to_json_string | generate_uuid -%}
+    {% include 'Resource/Practitioner' practitioner: entry.encounter.performer.assignedEntity, ID: practitionerEncPerfId -%}
+    {% assign fullPractitionerEncPerfId = practitionerEncPerfId | prepend: 'Practitioner/' -%}
+    {% include 'Reference/Encounter/Participant_Individual' ID: encounterId, REF: fullPractitionerEncPerfId -%}
+{% endif -%}
+
+{{ entry.encounter.participant | to_array | batch_render: 'Entry/Encounter/entry_encounter_participant', 'participant' }}
+{{ entry.encounter.entryRelationship | to_array | batch_render: 'Entry/Encounter/entry_encounter_entryRelationship', 'relationship' }}
+

data/Templates/eCR/Entry/Encounter/_entry_encounter_entryRelationship.liquid

@@ -0,0 +1 @@
+{{ relationship.act.entryRelationship | to_array | batch_render: 'Entry/Encounter/entry_encounter_entryRelationship_act_entryRelationship', 'entryRelationship' }}

data/Templates/eCR/Entry/Encounter/_entry_encounter_entryRelationship_act_entryRelationship.liquid

@@ -0,0 +1,7 @@
+{% if entryRelationship.observation -%}
+    {% assign observationId = entryRelationship.observation | to_json_string | generate_uuid -%}
+    {% include 'Resource/Condition' conditionEntry: entryRelationship.observation, ID: observationId -%}
+    {% include 'Reference/Condition/Subject' ID: observationId, REF: fullPatientId -%}
+    {% assign fullObservationId = observationId | prepend: 'Condition/' -%}
+    {% include 'Reference/Encounter/Diagnosis_Condition' ID: encounterId, -%}
+{% endif -%}

data/Templates/eCR/Entry/Encounter/_entry_encounter_participant.liquid

@@ -0,0 +1,9 @@
+{% if participant.typeCode == 'LOC' -%}
+    {% assign templateIdString = participant.participantRole.templateId | to_json_string -%}
+    {% if templateIdString contains '"2.16.840.1.113883.10.20.22.4.32"'-%}
+        {% assign locationId = participant.participantRole | to_json_string | generate_uuid -%}
+        {% include 'Resource/Location' location: participant.participantRole, ID: locationId -%}
+        {% assign fullLocationId = locationId | prepend: 'Location/' -%}
+        {% include 'Reference/Encounter/Location_Location' ID: encounterId, REF: fullLocationId -%}
+    {% endif -%}
+{% endif -%}

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

@@ -0,0 +1,3 @@
+{% assign organizationId = entry.organizer | to_json_string | generate_uuid -%}
+{% include 'Resource/FamilyMemberHistory' familyEntry: entry.organizer ID: organizationId -%}
+{% include 'Reference/FamilyMemberHistory/Patient' ID: organizationId, REF:fullPatientId -%}

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

@@ -0,0 +1,12 @@
+{% assign observationId = entry.observation | to_json_string | generate_uuid -%}
+{{ entry.observation.templateId | to_array | batch_render: 'Entry/HospitalDischargeDiagnosis/entry_act_entryRelationship', 'relationship' }}
+{% for templateId in entry.observation.templateId -%}
+    {% if templateId.root == "2.16.840.1.113883.10.20.22.4.4" -%}
+        {% include 'Resource/Condition' conditionEntry: entry.observation, ID: observationId -%}
+        {% include 'Reference/Condition/Subject' ID: observationId, REF: fullPatientId -%}
+    {% endif -%}
+    {% if templateId.root == "2.16.840.1.113883.10.20.22.4.2" -%}
+        {% include 'Resource/Observation' observationEntry: entry.observation, ID: observationId -%}
+        {% include 'Reference/Observation/Subject' ID: observationId, REF: fullPatientId -%}
+    {% endif -%}
+{% endfor -%}

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

@@ -0,0 +1,3 @@
+    {% assign observationId = entry.observation | to_json_string | generate_uuid -%}
+    {% include 'Resource/Goal' goalEntry: entry.observation, ID: observationId -%}
+    {$ include 'Reference/Goal/Subject' ID: observationId, REF: fullPatientId -$}

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

@@ -0,0 +1 @@
+{{ entry.act.entryRelationship | to_array | batch_render: 'Entry/HealthConcern/entry_act_entryRelationship', 'relationship' }}

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

@@ -0,0 +1,5 @@
+{% if relationship.observation -%}
+    {% assign observationId = relationship.observation | to_json_string | generate_uuid -%}
+    {% include 'Resource/Condition' conditionEntry: relationship.observation, ID: observationId -%}
+    {% include 'Reference/Condition/Subject' ID: observationId, REF: fullPatientId -%}
+{% endif -%}

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

@@ -0,0 +1 @@
+{{ entry.act.entryRelationship | to_array | batch_render: 'Entry/HospitalAdmissionDiagnosis/entry_act_entryRelationship', 'relationship' }}