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Merge pull request #1450 from synthetichealth/uscore6
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Add support for US Core 3.1.1 and 6.1.0
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@jawalonoski
jawalonoski authored May 3, 2024
2 parents c86a5c1 + afb1951 commit 637fe9f
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Showing 182 changed files with 640 additions and 139 deletions.
127 changes: 86 additions & 41 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 @@ -20,6 +20,7 @@
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.UUID;
import java.util.stream.Collectors;

Expand Down Expand Up @@ -188,18 +189,28 @@ public class FhirR4 {
protected static boolean TRANSACTION_BUNDLE =
Config.getAsBoolean("exporter.fhir.transaction_bundle");

/* For the most part the US Core changes from v4 -> v5 are backwards compatible,
* so for those cases just check USE_US_CORE_IG.
* If there are version differences then use USE_US_CORE_(#) to separate them out.
*/
protected static boolean USE_US_CORE_IG =
Config.getAsBoolean("exporter.fhir.use_us_core_ig");
protected static String US_CORE_VERSION =
Config.get("exporter.fhir.us_core_version", "5.0.1");
Config.get("exporter.fhir.us_core_version", "6.1.0");

private static Table<String, String, String> US_CORE_MAPPING;
private static final Table<String, String, String> US_CORE_3_MAPPING;
private static final Table<String, String, String> US_CORE_4_MAPPING;
private static final Table<String, String, String> US_CORE_5_MAPPING;
private static final Table<String, String, String> US_CORE_6_MAPPING;

public static enum USCoreVersion {
v311, v400, v501, v610
}

protected static boolean useUSCore3() {
boolean useUSCore3 = USE_US_CORE_IG && US_CORE_VERSION.startsWith("3");
if (useUSCore3) {
US_CORE_MAPPING = US_CORE_3_MAPPING;
}
return useUSCore3;
}

protected static boolean useUSCore4() {
boolean useUSCore4 = USE_US_CORE_IG && US_CORE_VERSION.startsWith("4");
Expand All @@ -217,6 +228,14 @@ protected static boolean useUSCore5() {
return useUSCore5;
}

protected static boolean useUSCore6() {
boolean useUSCore6 = USE_US_CORE_IG && US_CORE_VERSION.startsWith("6");
if (useUSCore6) {
US_CORE_MAPPING = US_CORE_6_MAPPING;
}
return useUSCore6;
}

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

private static final Table<String, String, String> SHR_MAPPING =
Expand All @@ -229,15 +248,21 @@ protected static boolean useUSCore5() {
reloadIncludeExclude();

Map<String, Table<String, String, String>> usCoreMappings =
loadMappingWithVersions("us_core_mapping.csv", "4", "5");
loadMappingWithVersions("us_core_mapping.csv", "3", "4", "5", "6");

US_CORE_3_MAPPING = usCoreMappings.get("3");
US_CORE_4_MAPPING = usCoreMappings.get("4");
US_CORE_5_MAPPING = usCoreMappings.get("5");
US_CORE_6_MAPPING = usCoreMappings.get("6");

if (US_CORE_VERSION.startsWith("4")) {
if (US_CORE_VERSION.startsWith("3")) {
US_CORE_MAPPING = US_CORE_3_MAPPING;
} else if (US_CORE_VERSION.startsWith("4")) {
US_CORE_MAPPING = US_CORE_4_MAPPING;
} else if (US_CORE_VERSION.startsWith("5")) {
US_CORE_MAPPING = US_CORE_5_MAPPING;
} else if (US_CORE_VERSION.startsWith("6")) {
US_CORE_MAPPING = US_CORE_6_MAPPING;
}
}

Expand Down Expand Up @@ -364,17 +389,15 @@ private static Table<String, String, String> loadMapping(String filename) {
String url = line.get("URL");
String version = line.get("VERSION");

if (StringUtils.isBlank(version)) {
// blank means applies to ALL versions
versions.values().forEach(table -> table.put(system, code, url));
} else {
Table<String, String, String> mappingTable = versions.get(version);
if (mappingTable == null) {
throw new IllegalArgumentException("Error in loading mapping from file " + filename
+ ". File contains row with version '" + version
+ "' but supported version numbers are: " + String.join(",", supportedVersions));
for (Entry<String, Table<String, String, String>> e : versions.entrySet()) {
String versionKey = e.getKey();
Table<String, String, String> mappingTable = e.getValue();

if (StringUtils.isBlank(version) || version.contains(versionKey)) {
// blank means applies to ALL versions
// version.contains allows for things like "4,5,6"
mappingTable.put(system, code, url);
}
mappingTable.put(system, code, url);
}
}

Expand Down Expand Up @@ -1649,7 +1672,7 @@ private static BundleEntryComponent condition(

if (USE_US_CORE_IG) {
Meta meta = new Meta();
if (useUSCore5()) {
if (useUSCore5() || useUSCore6()) {
meta.addProfile(
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis");
} else {
Expand Down Expand Up @@ -1880,29 +1903,51 @@ private static BundleEntryComponent observation(
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab");
}

if (useUSCore5() && observation.category != null) {
switch (observation.category) {
case "imaging":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging");
break;
case "social-history":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-social-history");
break;
case "survey":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey");
// note that the -sdoh-assessment profile is a subset of -survey,
// those are handled by code in US_CORE_MAPPING above
break;
case "exam":
// this one is a little nebulous -- are all exams also clinical tests?
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test");

observationResource.addCategory().addCoding().setCode("clinical-test")
.setSystem("http://hl7.org/fhir/us/core/CodeSystem/us-core-observation-category")
.setDisplay("Clinical Test");
break;
default:
// do nothing
if (observation.category != null) {
if (useUSCore6()) {
switch (observation.category) {
case "imaging":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-result");
break;
case "social-history":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation");
break;
case "survey":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-screening-assessment");
break;
case "exam":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-result");
break;
case "laboratory":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab");
break;
default:
// do nothing
}
} else if (useUSCore5()) {
switch (observation.category) {
case "imaging":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging");
break;
case "social-history":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-social-history");
break;
case "survey":
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey");
// note that the -sdoh-assessment profile is a subset of -survey,
// those are handled by code in US_CORE_MAPPING above
break;
case "exam":
// this one is a little nebulous -- are all exams also clinical tests?
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test");

observationResource.addCategory().addCoding().setCode("clinical-test")
.setSystem("http://hl7.org/fhir/us/core/CodeSystem/us-core-observation-category")
.setDisplay("Clinical Test");
break;
default:
// do nothing
}
}
}

Expand Down
5 changes: 5 additions & 0 deletions src/main/resources/modules/sepsis.json
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Original file line number Diff line number Diff line change
Expand Up @@ -293,6 +293,11 @@
"system": "LOINC",
"code": "2713-6",
"display": "Oxygen saturation Calculated from oxygen partial pressure in Blood"
},
{
"system": "LOINC",
"code": "2708-6",
"display": "Oxygen saturation in Arterial blood"
}
],
"direct_transition": "Lactate_Level1",
Expand Down
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