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gasperr merged 3 commits into from
Jan 26, 2026
Merged

#168 openehrcondition in manuals #170

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5784812
#168: fixed openehrcondition in manual mappings
gasperr Jan 24, 2026
71b37c1
#168: fixed openehrcondition in manual mappings
gasperr Jan 24, 2026
88aa43f
#168: fixed openehrcondition in manual mappings
gasperr Jan 24, 2026
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12 changes: 6 additions & 6 deletions src/main/java/com/medblocks/openfhir/tofhir/IntermediateCacheProcessing.java
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Original file line number Diff line number Diff line change
Expand Up @@ -222,23 +222,23 @@ private void handlePopulationNoParent(final FhirInstanceCreator.InstantiateAndSe
final String fullOpenEhrPath,
final String followedByParentOpenEhr,
final boolean lastOpenEhrIsDigit) {
final String fhirPath = path + (StringUtils.isEmpty(hardcodedReturn.getPath()) ? "" : ("." + hardcodedReturn.getPath()));
if (hardcodedReturn.isList()) {
final String openEhrPath = lastOpenEhrIsDigit ? fullOpenEhrPath.substring(0, fullOpenEhrPath.lastIndexOf(":")) : fullOpenEhrPath;

// puts in the list
instantiatedIntermediateElements.put(createKeyForIntermediateElements(objectRef, path + "." + hardcodedReturn.getPath(), openEhrPath),
instantiatedIntermediateElements.put(createKeyForIntermediateElements(objectRef, fhirPath, openEhrPath),
hardcodedReturn.getReturning());

final Integer lastIndex = openFhirStringUtils.getLastIndex(fullOpenEhrPath);
final List returningList = (List) hardcodedReturn.getReturning();
if (lastOpenEhrIsDigit) {
final Object toAddToCache = returningList.get(returningList.size() - 1); // todo: always takes the last one, is this ok?
instantiatedIntermediateElements.put(createKeyForIntermediateElements(objectRef, path + "." + hardcodedReturn.getPath(),
fullOpenEhrPath),
instantiatedIntermediateElements.put(createKeyForIntermediateElements(objectRef, fhirPath,
fullOpenEhrPath),
toAddToCache);
}
} else {
instantiatedIntermediateElements.put(createKeyForIntermediateElements(objectRef, path + "." + hardcodedReturn.getPath(), fullOpenEhrPath),
instantiatedIntermediateElements.put(createKeyForIntermediateElements(objectRef, fhirPath, fullOpenEhrPath),
hardcodedReturn.getReturning());
}

Expand All @@ -247,7 +247,7 @@ private void handlePopulationNoParent(final FhirInstanceCreator.InstantiateAndSe
populateIntermediateCache(hardcodedReturn.getInner(),
objectRef,
instantiatedIntermediateElements,
path + "." + hardcodedReturn.getPath(),
fhirPath,
fullOpenEhrPath,
null,
followedByParentOpenEhr);
Expand Down
96 changes: 63 additions & 33 deletions src/main/java/com/medblocks/openfhir/tofhir/OpenEhrToFhir.java
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Expand Up @@ -1053,11 +1053,16 @@ void prepareOpenEhrToFhirHelpers(final OpenFhirFhirConnectModelMapper theMapper,
}

String fixedOpenEhr = definedMappingWithOpenEhr
.replace(FhirConnectConst.REFERENCE, "")
.replace(FhirConnectConst.REFERENCE + "/", "")
.replace(FhirConnectConst.REFERENCE, "")
.replace(OPENEHR_ARCHETYPE_FC, firstFlatPath)
.replace(OPENEHR_COMPOSITION_FC, webTemplate.getTree().getId());
String openehrAqlPath = mappingRootElement && !definedMappingWithOpenEhr.startsWith(OPENEHR_COMPOSITION_FC) ? firstFlatPath : getOpenEhrKey(fixedOpenEhr, parentFollowedByOpenEhr, firstFlatPath);
if (mapping.getReference() != null) {
mapping.getWith().setType(OPENEHR_TYPE_NONE);
}
String openehrAqlPath =
mappingRootElement && !definedMappingWithOpenEhr.startsWith(OPENEHR_COMPOSITION_FC) ? firstFlatPath
: getOpenEhrKey(fixedOpenEhr, parentFollowedByOpenEhr, firstFlatPath);
String openehr = getPathFromAqlPath(openehrAqlPath, webTemplate, mapping.getWith().getType());
String parentFollowedByOpenEhrWithOutAqlPath = null;
if (parentFollowedByOpenEhr != null) {
Expand Down Expand Up @@ -1170,8 +1175,10 @@ private void prepareOpenEhrCondition(final Condition openEhrCondition,
final String newAttribute =
formattedOpenEhrConditionAttribute + openFhirMapperUtils.replaceAqlSuffixWithFlatSuffix(
openEhrConditionTargetAttributeWithAqlPath);
if (newAttribute.startsWith(openEhrCondition.getTargetRoot())) {
if (newAttribute.startsWith(openEhrCondition.getTargetRoot() + "/")) {
newAttributes.add(newAttribute.replace(openEhrCondition.getTargetRoot() + "/", ""));
} else if (newAttribute.startsWith(openEhrCondition.getTargetRoot())) {
newAttributes.add(newAttribute.replace(openEhrCondition.getTargetRoot(), ""));
} else {
newAttributes.add(newAttribute);
}
Expand Down Expand Up @@ -1356,6 +1363,19 @@ private void handleReferenceMapping(final Mapping mapping, final String resource
final String wConditions = openFhirStringUtils.getFhirPathWithConditions(mapping.getWith().getFhir(),
mapping.getFhirCondition(),
resourceType, parentFollowedByFhir);

// if it's a referenced mapping, we need to add this so it adds reference to the intermediateCache under the right cache key
final Mapping staticMapping = new Mapping();
staticMapping.setName("staticMapping");
final With with = new With();
with.setFhir("$fhirRoot");
with.setOpenehr(referencedMapping.get(0).getWith().getOpenehr());
with.setValue("openFhirDontPopulate");
staticMapping.setWith(with);
staticMapping.setFhirCondition(mapping.getFhirCondition());
referencedMapping.add(0, staticMapping);


openFhirMapperUtils.prepareReferencedMappings(wConditions, openehr, referencedMapping, firstFlatPath);

// now conditions
Expand Down Expand Up @@ -1450,36 +1470,8 @@ private List<OpenEhrToFhirHelper.DataWithIndex> extractValues(final Mapping mapp
List<OpenEhrToFhirHelper.DataWithIndex> values = new ArrayList<>();
if (!OPENEHR_TYPE_NONE.equals(mapping.getWith().getType())) {
if (StringUtils.isNotEmpty(hardcodedValue) && !joinedEntries.isEmpty()) {
values = new ArrayList<>();
final Condition openehrCondition = mapping.getOpenehrCondition();
final String fullOpenEhrPath;
if (openehrCondition == null) {
fullOpenEhrPath = OPENEHR_ARCHETYPE_FC;
} else {
final List<String> targetAttributes = mapping.getOpenehrCondition().getTargetAttributes();
final String targetRoot = mapping.getOpenehrCondition().getTargetRoot();
// final String rootWithAttrs = targetRoot + ((targetAttributes != null && !targetAttributes.isEmpty()) ? "" : ("/" + targetAttributes.get(0)));
final String piped = openFhirStringUtils.addRegexPatternToSimplifiedFlatFormat(targetRoot);
final List<String> allEntriesThatMatch = openFhirStringUtils.getAllEntriesThatMatch(piped,
flatJsonObject);
fullOpenEhrPath = allEntriesThatMatch.get(0);
}
int index = getHardcodedIndex(mapping, flatJsonObject);
if (index == -1) {
// get outer most index of all indexes in flatJsonObject that is the same for all entries, because
// while -1 means it has to be for all entries, it more than that means it has to be for all entries
// on the currently evaluated items!
index = openFhirStringUtils.getLastMostCommonIndex(new ArrayList<>(flatJsonObject.keySet()));
}
values.add(new OpenEhrToFhirHelper.DataWithIndex(new StringType(hardcodedValue), index,
fullOpenEhrPath));
}
// TO DO : Program mapping from openEHR to FHIR
// else if(mapping.getMappingCode()!=null){

// }

else {
handleHardcodedMappings(values, mapping, flatJsonObject, joinedEntries, hardcodedValue);
} else {
values = joinedEntries.values().stream()
.map(strings -> valueToDataPoint(strings, rmType, flatJsonObject, true))
.filter(Objects::nonNull)
Expand All @@ -1500,6 +1492,44 @@ private List<OpenEhrToFhirHelper.DataWithIndex> extractValues(final Mapping mapp
return values;
}

private void handleHardcodedMappings(final List<OpenEhrToFhirHelper.DataWithIndex> values,
final Mapping mapping, final JsonObject flatJsonObject,
final Map<String, List<String>> joinedEntries,
final String hardcodedValue) {

final Condition openehrCondition = mapping.getOpenehrCondition();
final String fullOpenEhrPath;
if (openehrCondition == null) {
fullOpenEhrPath = OPENEHR_ARCHETYPE_FC;
} else {
final String targetRoot = mapping.getOpenehrCondition().getTargetRoot();
final String piped = openFhirStringUtils.addRegexPatternToSimplifiedFlatFormat(targetRoot);
final List<String> allEntriesThatMatch = openFhirStringUtils.getAllEntriesThatMatch(piped,
flatJsonObject);
fullOpenEhrPath = allEntriesThatMatch.get(0);
}
int index = getHardcodedIndex(mapping, flatJsonObject);

if (index == -1) {
// get outer most index of all indexes in flatJsonObject that is the same for all entries, because
// while -1 means it has to be for all entries, it more than that means it has to be for all entries
// on the currently evaluated items!
index = openFhirStringUtils.getLastMostCommonIndex(new ArrayList<>(flatJsonObject.keySet()));
}

if (openehrCondition == null) {
joinedEntries.keySet().forEach(key -> {
final Integer lastIndex = openFhirStringUtils.getLastIndex(key);
values.add(new OpenEhrToFhirHelper.DataWithIndex(new StringType(hardcodedValue),
lastIndex,
key));
});
} else {
values.add(new OpenEhrToFhirHelper.DataWithIndex(new StringType(hardcodedValue), index,
fullOpenEhrPath));
}
}

private int getHardcodedIndex(final Mapping mapping, final JsonObject flatJsonObject) {
if (mapping.getOpenehrCondition() == null) {
return -1; // goes for all anyway
Expand Down
6 changes: 6 additions & 0 deletions src/main/java/com/medblocks/openfhir/util/FhirInstancePopulator.java
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Expand Up @@ -77,11 +77,17 @@ private void populateListElement(List<?> toPopulate, Base data) {
if (lastElement.toString() == null || objectIsEmpty(lastElement)) {
populateElement(lastElement, data); // Populate last element if empty
} else {
if (data instanceof StringType && "openFhirDontPopulate".equals(((StringType) data).getValueAsString())) {
return;
}
((List<Object>) toPopulate).add(data); // Otherwise, add new entry
}
}

private void handleSpecificTypePopulation(final Object toPopulate, final Base data) {
if (data instanceof StringType && "openFhirDontPopulate".equals(((StringType) data).getValueAsString())) {
return;
}
if (data instanceof Quantity) {
populateQuantity(toPopulate, (Quantity) data);
} else if (data instanceof IntegerType) {
Expand Down
18 changes: 11 additions & 7 deletions src/main/java/com/medblocks/openfhir/util/OpenEhrConditionEvaluator.java
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Expand Up @@ -10,6 +10,7 @@
import java.util.Set;
import java.util.stream.Collectors;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

Expand Down Expand Up @@ -73,14 +74,17 @@ private JsonObject handleOneOfOperatorSplit(final Condition openEhrCondition,
final JsonObject modifiedJsonObject = new JsonObject();
final Set<String> notAddingForThisCondition = new HashSet<>();
for (final String extractedValueKey : extractedValueKeys) {
final String preparedTargetAttribute = openFhirStringUtils.prepareOpenEhrSyntax(
targetAttribute,
"");
final String openEhrKey = preparedTargetAttribute == null ? extractedValueKey : String.format("%s/%s", extractedValueKey, preparedTargetAttribute);
final JsonPrimitive extractedValueJson = fullFlatPath.getAsJsonPrimitive(openEhrKey);

final boolean subPath = targetAttribute.startsWith("|");
if(subPath && !extractedValueKey.endsWith(targetAttribute)){
// wrong subpath to check for
continue;
}
final String keyToCheckFor = subPath ? extractedValueKey : extractedValueKey + "/" + targetAttribute;
final JsonPrimitive extractedValueJson = fullFlatPath.getAsJsonPrimitive(keyToCheckFor);
final String extractedValue = extractedValueJson == null ? "" : extractedValueJson.getAsString();

if (openEhrCondition.getCriteria().contains(extractedValue)) {
if (StringUtils.isNotEmpty(extractedValue) && openEhrCondition.getCriteria().contains(extractedValue)) {
fullFlatPath.entrySet().forEach((entry) -> {
if (entry.getKey().startsWith(extractedValueKey)) {
modifiedJsonObject.add(entry.getKey(), entry.getValue());
Expand All @@ -91,7 +95,7 @@ private JsonObject handleOneOfOperatorSplit(final Condition openEhrCondition,

log.info(
"Flat path {} evaluated to {}, condition.criteria requires it to be {}, therefore excluding all {} from mapping.",
openEhrKey, extractedValue, openEhrCondition.getCriteria(), extractedValueKey);
extractedValueKey, extractedValue, openEhrCondition.getCriteria(), extractedValueKey);
notAddingForThisCondition.add(extractedValueKey);

fullFlatPath.entrySet().forEach((entry) -> {
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/com/medblocks/openfhir/util/OpenFhirMapperUtils.java
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Expand Up @@ -318,7 +318,7 @@ public void prepareFollowedByMappings(final List<Mapping> followedByMappings,
.replace(FhirConnectConst.OPENEHR_ARCHETYPE_FC + ".", "")
.replace(FhirConnectConst.OPENEHR_ARCHETYPE_FC, ""));
} else if (conditionRoot.equals(FhirConnectConst.OPENEHR_ARCHETYPE_FC)) {
openehrCondition.setTargetRoot(openehr);
openehrCondition.setTargetRoot(slotContext);
} else {
openehrCondition.setTargetRoot(
new OpenFhirStringUtils().prepareOpenEhrSyntax(conditionRoot,
Expand Down
23 changes: 11 additions & 12 deletions src/test/java/com/medblocks/openfhir/kds/DiagnoseTest.java
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Expand Up @@ -136,9 +136,17 @@ private void assertCondition(final Condition condition, final boolean second) {
// - name: "mehrfachcodierung"
final CodeableConcept mehrfachcodierung = (CodeableConcept) icd10code.getExtensionByUrl(
"http://fhir.de/StructureDefinition/icd-10-gm-mehrfachcodierungs-kennzeichen").getValue();
Assert.assertEquals("!", mehrfachcodierung.getCodingFirstRep().getCode());

if(second) {
Assert.assertEquals("*", mehrfachcodierung.getCodingFirstRep().getCode());
Assert.assertEquals("*", mehrfachcodierung.getCodingFirstRep().getDisplay());
} else {
Assert.assertEquals("†", mehrfachcodierung.getCodingFirstRep().getCode()); // because openEhr condition says if it's 'at0002' it needs to be † and flatpath of diagnose/diagnose:0/mehrfachkodierungskennzeichen_icd-10-gm/mehrfachkodierungkennzeichen|code is at0002
Assert.assertEquals("†", mehrfachcodierung.getCodingFirstRep().getDisplay());
}

Assert.assertEquals("http://fhir.de/ValueSet/icd-10-gm-mehrfachcodierungs-kennzeichen", mehrfachcodierung.getCodingFirstRep().getSystem());
Assert.assertEquals("!", mehrfachcodierung.getCodingFirstRep().getDisplay());


// - name: "seitenlokalisation"
final CodeableConcept seitenlokalisation = (CodeableConcept) icd10code.getExtensionByUrl(
Expand All @@ -165,16 +173,7 @@ public void toFhir() {
final Condition conditionSecond = (Condition) allConditions.get(1).getResource(); // second condition

assertCondition(condition, false);
// assertCondition(conditionSecond, true);

final Type referencedExtensionCondition = condition.getExtensionByUrl(
"http://hl7.org/fhir/StructureDefinition/condition-related")
.getValue();
Assert.assertNotNull(referencedExtensionCondition);
Assert.assertTrue(conditionSecond.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-related")
.getValue().isEmpty());

assertCondition((Condition) ((Reference) referencedExtensionCondition).getResource(), true);
assertCondition(conditionSecond, true);

}

Expand Down
2 changes: 1 addition & 1 deletion src/test/java/com/medblocks/openfhir/kds/StudienteilnahmeTest.java
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Expand Up @@ -47,7 +47,7 @@ public void toFhir() {

final Consent consent = (Consent) allConsents.get(0).getResource();

Assert.assertEquals("entered-in-error", consent.getStatusElement().getValueAsString());
Assert.assertEquals("stopped", consent.getStatusElement().getValueAsString());

// - name: "period"
final DateTimeType periodStart = consent.getProvision().getPeriod().getStartElement();
Expand Down
6 changes: 3 additions & 3 deletions src/test/resources/kds/diagnose/KDS_Diagnose_multiple_Composition.flat.json
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Expand Up @@ -84,9 +84,9 @@
"diagnose/diagnose:1/lebensphase/ende|code": "referenced_44",
"diagnose/diagnose:1/lebensphase/ende|value": "referenced_No example for termínology '//fhir.hl7.org//ValueSet/$expand?url=http://fhir.de/ValueSet/lebensphase-de' available",
"diagnose/diagnose:1/lebensphase/ende|terminology": "referenced_//fhir.hl7.org//ValueSet/$expand?url=http://fhir.de/ValueSet/lebensphase-de",
"diagnose/diagnose:1/mehrfachkodierungskennzeichen_icd-10-gm/mehrfachkodierungkennzeichen|value": "referenced_†",
"diagnose/diagnose:1/mehrfachkodierungskennzeichen_icd-10-gm/mehrfachkodierungkennzeichen|code": "referenced_at0002",
"diagnose/diagnose:1/mehrfachkodierungskennzeichen_icd-10-gm/mehrfachkodierungkennzeichen|terminology": "referenced_local",
"diagnose/diagnose:1/mehrfachkodierungskennzeichen_icd-10-gm/mehrfachkodierungkennzeichen|value": "*",
"diagnose/diagnose:1/mehrfachkodierungskennzeichen_icd-10-gm/mehrfachkodierungkennzeichen|code": "at0003",
"diagnose/diagnose:1/mehrfachkodierungskennzeichen_icd-10-gm/mehrfachkodierungkennzeichen|terminology": "local",
"diagnose/diagnose:1/klinisch_relevanter_zeitraum_zeitpunkt_der_genesung": "3022-02-03T04:05:06",
"diagnose/diagnose:1/klinischer_status/diagnosestatus|code": "at0088",
"diagnose/diagnose:1/klinischer_status/diagnosestatus|terminology": "local",
Expand Down
22 changes: 21 additions & 1 deletion src/test/resources/kds_new/model/action/org.openehr/informed_consent.v0.yml
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Expand Up @@ -166,7 +166,27 @@ mappings:
operator: "one of"
criteria: "528"


- name: "aborted"
fhir:
- path: "status"
value: "stopped"
openehrCondition:
targetRoot: "$openehrRoot"
targetAttribute: "defining_code/code_string"
operator: "one of"
criteria: "531"
openehr:
- path: "defining_code/terminology_id"
value: "openehr"
- path: "value"
value: "Aborted"
- path: "defining_code/code_string"
value: "531"
fhirCondition:
targetRoot: "$fhirRoot"
targetAttribute: "status"
operator: "one of"
criteria: "stopped"

- name: "study"
with:
Expand Down
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