use of org.hl7.fhir.r4.model.MedicationStatement in project org.hl7.fhir.core by hapifhir.
the class ArgonautConverter method processMedicationsSection.
private void processMedicationsSection(CDAUtilities cda, Convert convert, Element section, Context context) throws Exception {
scanSection("Medications", section);
ListResource list = new ListResource();
list.setId(context.getBaseId() + "-list-medications");
list.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/list-daf-dafmedicationlist");
list.setSubject(context.getSubjectRef());
list.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")), null));
list.setTitle(cda.getChild(section, "title").getTextContent());
list.setStatus(ListStatus.CURRENT);
list.setMode(ListMode.SNAPSHOT);
list.setDateElement(context.getNow());
list.setSource(context.getAuthorRef());
buildNarrative(list, cda.getChild(section, "text"));
int i = 0;
for (Element c : cda.getChildren(section, "entry")) {
// allergy problem act
Element sa = cda.getChild(c, "substanceAdministration");
MedicationStatement ms = new MedicationStatement();
ms.setId(context.getBaseId() + "-medication-" + i);
ms.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/medicationstatement-daf-dafmedicationstatement");
i++;
ms.setSubject(context.getSubjectRef());
boolean found = false;
for (Element e : cda.getChildren(sa, "id")) {
Identifier id = convert.makeIdentifierFromII(e);
ms.getIdentifier().add(id);
}
if (!found) {
ms.setStatus(MedicationStatementStatus.COMPLETED);
list.addEntry().setItem(new Reference().setReference("MedicationStatement/" + ms.getId()));
// allergy observation
Element mm = cda.getChild(cda.getChild(cda.getChild(sa, "consumable"), "manufacturedProduct"), "manufacturedMaterial");
ms.setMedication(new Reference().setReference("#med"));
Medication med = new Medication();
med.setId("med");
med.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(mm, "code")), null));
ms.getContained().add(med);
Dosage dosage = ms.addDosage();
// allergy observation
Element qty = cda.getChild(sa, "doseQuantity");
try {
if (cda.getChild(qty, "low") != null) {
// todo: this is not correct?
dosage.getExtension().add(new Extension().setUrl("http://healthintersections.com.au/fhir/extensions/medication-statement-range").setValue(convert.makeRangeFromIVLPQ(qty)));
} else {
dosage.setDose(convert.makeQuantityFromPQ(qty));
}
} catch (Exception e) {
System.out.println(" invalid dose quantity '" + qty.getAttribute("value") + " " + qty.getAttribute("unit") + "' (" + e.getClass().getName() + ") in " + context.getBaseId());
}
dosage.setRoute(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(sa, "routeCode")), null));
Type t = convert.makeSomethingFromGTS(cda.getChildren(sa, "effectiveTime"));
if (t instanceof Timing) {
dosage.setTiming((Timing) t);
if (dosage.getTiming().hasRepeat() && dosage.getTiming().getRepeat().hasBounds())
ms.setEffective(dosage.getTiming().getRepeat().getBounds());
} else if (t instanceof Period)
ms.setEffective(t);
else
throw new Exception("Undecided how to handle " + t.getClass().getName());
for (Element e : cda.getChildren(sa, "author")) {
if (ms.hasInformationSource())
throw new Error("additional author discovered");
Practitioner p = processPerformer(cda, convert, context, e, "assignedAuthor", "assignedPerson");
Reference ref = new Reference().setReference("Practitioner/" + p.getId()).setDisplay(p.getUserString("display"));
ms.setInformationSource(ref);
ms.setDateAssertedElement(convert.makeDateTimeFromTS(cda.getChild(e, "time")));
}
saveResource(ms);
}
}
saveResource(list);
}
use of org.hl7.fhir.r4.model.MedicationStatement in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilitiesTests method execute.
public void execute(String[] args) throws FileNotFoundException, IOException, FHIRException {
System.out.println("loading context");
context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation.zip"));
comp = new ProfileComparer(context);
compare("patient-daf-dafpatient.profile.xml", "patient-qicore-qicore-patient.profile.xml");
compare("encounter-daf-dafencounter.profile.xml", "encounter-qicore-qicore-encounter.profile.xml");
compare("substance-daf-dafsubstance.profile.xml", "substance-qicore-qicore-substance.profile.xml");
compare("medication-daf-dafmedication.profile.xml", "medication-qicore-qicore-medication.profile.xml");
compare("procedure-daf-dafprocedure.profile.xml", "procedure-qicore-qicore-procedure.profile.xml");
compare("familymemberhistory-daf-daffamilymemberhistory.profile.xml", "familymemberhistory-qicore-qicore-familymemberhistory.profile.xml");
compare("immunization-daf-dafimmunization.profile.xml", "immunization-qicore-qicore-immunization.profile.xml");
compare("condition-daf-dafcondition.profile.xml", "condition-qicore-qicore-condition.profile.xml");
compare("allergyintolerance-daf-dafallergyintolerance.profile.xml", "allergyintolerance-qicore-qicore-allergyintolerance.profile.xml");
compare("medicationadministration-daf-dafmedicationadministration.profile.xml", "medicationadministration-qicore-qicore-medicationadministration.profile.xml");
compare("medicationdispense-daf-dafmedicationdispense.profile.xml", "medicationdispense-qicore-qicore-medicationdispense.profile.xml");
compare("medicationprescription-daf-dafmedicationprescription.profile.xml", "medicationprescription-qicore-qicore-medicationprescription.profile.xml");
compare("medicationstatement-daf-dafmedicationstatement.profile.xml", "medicationstatement-qicore-qicore-medicationstatement.profile.xml");
compare("observation-daf-smokingstatus-dafsmokingstatus.profile.xml", "observation-qicore-qicore-observation.profile.xml");
compare("observation-daf-vitalsigns-dafvitalsigns.profile.xml", "observation-qicore-qicore-observation.profile.xml");
// compare("observation-daf-results-dafresultobs.profile.xml", "observation-qicore-qicore-observation.profile.xml");
// compare("diagnosticorder-daf-dafdiagnosticorder.profile.xml", "diagnosticorder-qicore-qicore-diagnosticorder.profile.xml");
// compare("diagnosticreport-daf-dafdiagnosticreport.profile.xml", "diagnosticreport-qicore-qicore-diagnosticreport.profile.xml");
System.out.println("processing output");
for (ProfileComparison outcome : comp.getComparisons()) {
if (outcome.getSubset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")), outcome.getSubset());
if (outcome.getSuperset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
System.out.println("\r\n" + outcome.getId() + ": Comparison of " + outcome.getLeft().getUrl() + " and " + outcome.getRight().getUrl());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.INFORMATION)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.WARNING)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.ERROR)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.FATAL)
System.out.println(vm.summary());
System.out.println("done. " + Integer.toString(outcome.getMessages().size()) + " messages");
System.out.println("=================================================================");
}
}
use of org.hl7.fhir.r4.model.MedicationStatement in project fhir-bridge by ehrbase.
the class AntikoagulanzienBeliebigesEreignisPointEventConverter method convertInternal.
@Override
protected AntikoagulanzienBeliebigesEreignisPointEvent convertInternal(MedicationStatement resource) {
AntikoagulanzienBeliebigesEreignisPointEvent antikoagulanzienBeliebigesEreignisPointEvent = new AntikoagulanzienBeliebigesEreignisPointEvent();
for (Coding coding : resource.getMedicationCodeableConcept().getCoding()) {
if (coding.getSystem().equals("http://fhir.de/CodeSystem/bfarm/atc")) {
DvCodedTextParser.getInstance().parseFHIRCoding(coding).ifPresent(antikoagulanzienBeliebigesEreignisPointEvent::setArzneimittelName);
}
}
getGrundDefiningCode(resource).ifPresent(antikoagulanzienBeliebigesEreignisPointEvent::setGrund);
return antikoagulanzienBeliebigesEreignisPointEvent;
}
use of org.hl7.fhir.r4.model.MedicationStatement in project fhir-bridge by ehrbase.
the class AntikoagulanzienObservationConverter method convertInternal.
@Override
protected AntikoagulanzienObservation convertInternal(MedicationStatement resource) {
AntikoagulanzienObservation antikoagulanzienObservation = new AntikoagulanzienObservation();
List<AntikoagulanzienBeliebigesEreignisChoice> ereignisList = new ArrayList<>();
for (Coding coding : resource.getMedicationCodeableConcept().getCoding()) {
if (coding.getSystem().equals("http://fhir.de/CodeSystem/bfarm/atc")) {
ereignisList.add(new AntikoagulanzienBeliebigesEreignisPointEventConverter().convert(resource));
}
}
antikoagulanzienObservation.setBeliebigesEreignis(ereignisList);
return antikoagulanzienObservation;
}
use of org.hl7.fhir.r4.model.MedicationStatement in project fhir-bridge by ehrbase.
the class Covid19TherapieObservationConverter method convertInternal.
@Override
protected Covid19TherapieObservation convertInternal(MedicationStatement resource) {
Covid19TherapieObservation covid19TherapieObservation = new Covid19TherapieObservation();
List<Covid19TherapieBeliebigesEreignisChoice> ereignisList = new ArrayList<>();
for (Coding coding : resource.getMedicationCodeableConcept().getCoding()) {
if (coding.getSystem().equals("http://fhir.de/CodeSystem/bfarm/atc")) {
ereignisList.add(new Covid19TherapieBeliebigesEreignisPointEventConverter().convert(resource));
}
}
covid19TherapieObservation.setBeliebigesEreignis(ereignisList);
return covid19TherapieObservation;
}
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