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Remove SHR extensions from FHIR exporters
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@dehall
dehall committed Jun 10, 2024
1 parent e6534b6 commit bdaac16
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Showing 5 changed files with 9 additions and 363 deletions.
135 changes: 5 additions & 130 deletions src/main/java/org/mitre/synthea/export/FhirR4.java
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Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,6 @@ public class FhirR4 {
private static final String RXNORM_URI = "http://www.nlm.nih.gov/research/umls/rxnorm";
private static final String CVX_URI = "http://hl7.org/fhir/sid/cvx";
private static final String DISCHARGE_URI = "http://www.nubc.org/patient-discharge";
private static final String SHR_EXT = "http://standardhealthrecord.org/fhir/StructureDefinition/";
private static final String SYNTHEA_EXT = "http://synthetichealth.github.io/synthea/";
private static final String UNITSOFMEASURE_URI = "http://unitsofmeasure.org";
private static final String DICOM_DCM_URI = "http://dicom.nema.org/resources/ontology/DCM";
Expand All @@ -184,8 +183,6 @@ public class FhirR4 {
@SuppressWarnings("rawtypes")
private static final Map languageLookup = loadLanguageLookup();

protected static boolean USE_SHR_EXTENSIONS =
Config.getAsBoolean("exporter.fhir.use_shr_extensions");
protected static boolean TRANSACTION_BUNDLE =
Config.getAsBoolean("exporter.fhir.transaction_bundle");

Expand Down Expand Up @@ -237,9 +234,7 @@ protected static boolean useUSCore6() {
}

private static final String COUNTRY_CODE = Config.get("generate.geography.country_code");

private static final Table<String, String, String> SHR_MAPPING =
loadMapping("shr_mapping.csv");
private static final String PASSPORT_URI = Config.get("generate.geography.passport_uri", "http://hl7.org/fhir/sid/passport-USA");

private static final HashSet<Class<? extends Resource>> includedResources = new HashSet<>();
private static final HashSet<Class<? extends Resource>> excludedResources = new HashSet<>();
Expand Down Expand Up @@ -345,28 +340,6 @@ private static Map loadLanguageLookup() {
}


private static Table<String, String, String> loadMapping(String filename) {
Table<String, String, String> mappingTable = HashBasedTable.create();

List<LinkedHashMap<String, String>> csvData;
try {
csvData = SimpleCSV.parse(Utilities.readResource(filename));
} catch (IOException e) {
e.printStackTrace();
return null;
}

for (LinkedHashMap<String, String> line : csvData) {
String system = line.get("SYSTEM");
String code = line.get("CODE");
String url = line.get("URL");

mappingTable.put(system, code, url);
}

return mappingTable;
}

private static Map<String, Table<String, String, String>>
loadMappingWithVersions(String filename, String... supportedVersions) {
Map<String, Table<String,String,String>> versions = new HashMap<>();
Expand Down Expand Up @@ -601,7 +574,7 @@ private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long
Code passportCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "PPN", "Passport Number");
patientResource.addIdentifier()
.setType(mapCodeToCodeableConcept(passportCode, "http://terminology.hl7.org/CodeSystem/v2-0203"))
.setSystem(SHR_EXT + "passportNumber")
.setSystem(PASSPORT_URI)
.setValue((String) person.attributes.get(Person.IDENTIFIER_PASSPORT));
}

Expand Down Expand Up @@ -857,29 +830,6 @@ private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long
patientResource.setText(new Narrative().setStatus(NarrativeStatus.GENERATED)
.setDiv(new XhtmlNode(NodeType.Element).setValue(generatedBySynthea)));

if (USE_SHR_EXTENSIONS) {

patientResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Patient"));

// Patient profile requires race, ethnicity, birthsex,
// MothersMaidenName, FathersName, Person-extension

patientResource.addExtension()
.setUrl(SHR_EXT + "shr-actor-FictionalPerson-extension")
.setValue(new BooleanType(true));

String fathersName = (String) person.attributes.get(Person.NAME_FATHER);
Extension fathersNameExtension = new Extension(
SHR_EXT + "shr-entity-FathersName-extension", new HumanName().setText(fathersName));
patientResource.addExtension(fathersNameExtension);

String ssn = (String) person.attributes.get(Person.IDENTIFIER_SSN);
Extension ssnExtension = new Extension(
SHR_EXT + "shr-demographics-SocialSecurityNumber-extension",
new StringType(ssn));
patientResource.addExtension(ssnExtension);
}

// DALY and QALY values
// we only write the last(current) one to the patient record
Double dalyValue = (Double) person.attributes.get("most-recent-daly");
Expand Down Expand Up @@ -915,15 +865,6 @@ private static BundleEntryComponent encounter(Person person, BundleEntryComponen
meta.addProfile(
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter");
encounterResource.setMeta(meta);
} else if (USE_SHR_EXTENSIONS) {
encounterResource.setMeta(
new Meta().addProfile(SHR_EXT + "shr-encounter-EncounterPerformed"));
Extension performedContext = new Extension();
performedContext.setUrl(SHR_EXT + "shr-action-PerformedContext-extension");
performedContext.addExtension(
SHR_EXT + "shr-action-Status-extension",
new CodeType("finished"));
encounterResource.addExtension(performedContext);
}

Patient patient = (Patient) personEntry.getResource();
Expand Down Expand Up @@ -1683,11 +1624,6 @@ private static BundleEntryComponent condition(
conditionResource.addCategory(new CodeableConcept().addCoding(new Coding(
"http://terminology.hl7.org/CodeSystem/condition-category", "encounter-diagnosis",
"Encounter Diagnosis")));
} else if (USE_SHR_EXTENSIONS) {
conditionResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-condition-Condition"));
conditionResource.addCategory(new CodeableConcept().addCoding(new Coding(
"http://standardhealthrecord.org/shr/condition/vs/ConditionCategoryVS", "disease",
"Disease")));
}

conditionResource.setSubject(new Reference(personEntry.getFullUrl()));
Expand Down Expand Up @@ -1955,19 +1891,6 @@ private static BundleEntryComponent observation(
observationResource.setMeta(meta);
}
}
if (USE_SHR_EXTENSIONS) {
Meta meta = new Meta();
meta.addProfile(SHR_EXT + "shr-finding-Observation"); // all Observations are Observations
if ("vital-signs".equals(observation.category)) {
meta.addProfile(SHR_EXT + "shr-vital-VitalSign");
}
// add the specific profile based on code
String codeMappingUri = SHR_MAPPING.get(LOINC_URI, code.code);
if (codeMappingUri != null) {
meta.addProfile(codeMappingUri);
}
observationResource.setMeta(meta);
}

BundleEntryComponent entry = newEntry(bundle, observationResource, observation.uuid.toString());
observation.fullUrl = entry.getFullUrl();
Expand Down Expand Up @@ -2093,21 +2016,6 @@ private static BundleEntryComponent procedure(
}
}

if (USE_SHR_EXTENSIONS) {
procedureResource.setMeta(
new Meta().addProfile(SHR_EXT + "shr-procedure-ProcedurePerformed"));
// required fields for this profile are action-PerformedContext-extension,
// status, code, subject, performed[x]

Extension performedContext = new Extension();
performedContext.setUrl(SHR_EXT + "shr-action-PerformedContext-extension");
performedContext.addExtension(
SHR_EXT + "shr-action-Status-extension",
new CodeType("completed"));

procedureResource.addExtension(performedContext);
}

BundleEntryComponent procedureEntry =
newEntry(bundle, procedureResource, procedure.uuid.toString());
procedure.fullUrl = procedureEntry.getFullUrl();
Expand Down Expand Up @@ -2296,15 +2204,8 @@ private static BundleEntryComponent immunization(
meta.addProfile(
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-immunization");
immResource.setMeta(meta);
} else if (USE_SHR_EXTENSIONS) {
immResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-immunization-ImmunizationGiven"));
Extension performedContext = new Extension();
performedContext.setUrl(SHR_EXT + "shr-action-PerformedContext-extension");
performedContext.addExtension(
SHR_EXT + "shr-action-Status-extension",
new CodeType("completed"));
immResource.addExtension(performedContext);
}

immResource.setStatus(ImmunizationStatus.COMPLETED);
immResource.setOccurrence(convertFhirDateTime(immunization.start, true));
immResource.setVaccineCode(mapCodeToCodeableConcept(immunization.codes.get(0), CVX_URI));
Expand Down Expand Up @@ -2348,24 +2249,8 @@ private static BundleEntryComponent medicationRequest(
Code category = new Code("http://terminology.hl7.org/CodeSystem/medicationrequest-category",
"community", "Community");
medicationResource.addCategory(mapCodeToCodeableConcept(category, null));
} else if (USE_SHR_EXTENSIONS) {
medicationResource.addExtension()
.setUrl(SHR_EXT + "shr-base-ActionCode-extension")
.setValue(PRESCRIPTION_OF_DRUG_CC);

medicationResource.setMeta(new Meta()
.addProfile(SHR_EXT + "shr-medication-MedicationRequested"));

Extension requestedContext = new Extension();
requestedContext.setUrl(SHR_EXT + "shr-action-RequestedContext-extension");
requestedContext.addExtension(
SHR_EXT + "shr-action-Status-extension",
new CodeType("completed"));
requestedContext.addExtension(
SHR_EXT + "shr-action-RequestIntent-extension",
new CodeType("original-order"));
medicationResource.addExtension(requestedContext);
}

medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
medicationResource.setEncounter(new Reference(encounterEntry.getFullUrl()));

Expand Down Expand Up @@ -2597,11 +2482,6 @@ private static BundleEntryComponent medicationAdministration(
return medicationAdminEntry;
}

private static final Code PRESCRIPTION_OF_DRUG_CODE =
new Code("SNOMED-CT", "33633005", "Prescription of drug (procedure)");
private static final CodeableConcept PRESCRIPTION_OF_DRUG_CC =
mapCodeToCodeableConcept(PRESCRIPTION_OF_DRUG_CODE, SNOMED_URI);

/**
* Map the given Report to a FHIR DiagnosticReport resource, and add it to the given Bundle.
*
Expand Down Expand Up @@ -3195,13 +3075,8 @@ protected static BundleEntryComponent provider(Bundle bundle,
meta.addProfile(
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization");
organizationResource.setMeta(meta);
} else if (USE_SHR_EXTENSIONS) {
organizationResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Organization"));
organizationResource.addIdentifier()
.setSystem("urn:ietf:rfc:3986")
.setValue("urn:uuid" + provider.getResourceID());
organizationResource.addContact().setName(new HumanName().setText("Synthetic Provider"));
}

List<CodeableConcept> organizationType = new ArrayList<CodeableConcept>();
organizationType.add(
mapCodeToCodeableConcept(
Expand Down
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