use of org.hl7.fhir.r4b.model.Quantity 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.r4b.model.Quantity in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method renderQuantity.
private void renderQuantity(Quantity q, XhtmlNode x, boolean showCodeDetails) {
if (q.hasComparator())
x.addText(q.getComparator().toCode());
x.addText(q.getValue().toString());
if (q.hasUnit())
x.addText(" " + q.getUnit());
else if (q.hasCode())
x.addText(" " + q.getCode());
if (showCodeDetails && q.hasCode()) {
XhtmlNode sp = x.addTag("span");
sp.setAttribute("style", "background: LightGoldenRodYellow ");
sp.addText(" (Details: " + describeSystem(q.getSystem()) + " code " + q.getCode() + " = '" + lookupCode(q.getSystem(), q.getCode()) + "')");
}
}
use of org.hl7.fhir.r4b.model.Quantity in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method renderLeaf.
private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints) throws FHIRException, UnsupportedEncodingException, IOException {
if (ew == null)
return;
Base e = ew.getBase();
if (e instanceof StringType)
x.addText(((StringType) e).getValue());
else if (e instanceof CodeType)
x.addText(((CodeType) e).getValue());
else if (e instanceof IdType)
x.addText(((IdType) e).getValue());
else if (e instanceof Extension)
x.addText("Extensions: Todo");
else if (e instanceof InstantType)
x.addText(((InstantType) e).toHumanDisplay());
else if (e instanceof DateTimeType)
x.addText(((DateTimeType) e).toHumanDisplay());
else if (e instanceof Base64BinaryType)
x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
else if (e instanceof org.hl7.fhir.dstu2.model.DateType)
x.addText(((org.hl7.fhir.dstu2.model.DateType) e).toHumanDisplay());
else if (e instanceof Enumeration) {
Object ev = ((Enumeration<?>) e).getValue();
// todo: look up a display name if there is one
x.addText(ev == null ? "" : ev.toString());
} else if (e instanceof BooleanType)
x.addText(((BooleanType) e).getValue().toString());
else if (e instanceof CodeableConcept) {
renderCodeableConcept((CodeableConcept) e, x, showCodeDetails);
} else if (e instanceof Coding) {
renderCoding((Coding) e, x, showCodeDetails);
} else if (e instanceof Annotation) {
renderAnnotation((Annotation) e, x);
} else if (e instanceof Identifier) {
renderIdentifier((Identifier) e, x);
} else if (e instanceof org.hl7.fhir.dstu2.model.IntegerType) {
x.addText(Integer.toString(((org.hl7.fhir.dstu2.model.IntegerType) e).getValue()));
} else if (e instanceof org.hl7.fhir.dstu2.model.DecimalType) {
x.addText(((org.hl7.fhir.dstu2.model.DecimalType) e).getValue().toString());
} else if (e instanceof HumanName) {
renderHumanName((HumanName) e, x);
} else if (e instanceof SampledData) {
renderSampledData((SampledData) e, x);
} else if (e instanceof Address) {
renderAddress((Address) e, x);
} else if (e instanceof ContactPoint) {
renderContactPoint((ContactPoint) e, x);
} else if (e instanceof UriType) {
renderUri((UriType) e, x);
} else if (e instanceof Timing) {
renderTiming((Timing) e, x);
} else if (e instanceof Range) {
renderRange((Range) e, x);
} else if (e instanceof Quantity) {
renderQuantity((Quantity) e, x, showCodeDetails);
} else if (e instanceof Ratio) {
renderQuantity(((Ratio) e).getNumerator(), x, showCodeDetails);
x.addText("/");
renderQuantity(((Ratio) e).getDenominator(), x, showCodeDetails);
} else if (e instanceof Period) {
Period p = (Period) e;
x.addText(!p.hasStart() ? "??" : p.getStartElement().toHumanDisplay());
x.addText(" --> ");
x.addText(!p.hasEnd() ? "(ongoing)" : p.getEndElement().toHumanDisplay());
} else if (e instanceof Reference) {
Reference r = (Reference) e;
XhtmlNode c = x;
ResourceWithReference tr = null;
if (r.hasReferenceElement()) {
tr = resolveReference(res, r.getReference());
if (!r.getReference().startsWith("#")) {
if (tr != null && tr.getReference() != null)
c = x.addTag("a").attribute("href", tr.getReference());
else
c = x.addTag("a").attribute("href", r.getReference());
}
}
// what to display: if text is provided, then that. if the reference was resolved, then show the generated narrative
if (r.hasDisplayElement()) {
c.addText(r.getDisplay());
if (tr != null) {
c.addText(". Generated Summary: ");
generateResourceSummary(c, tr.getResource(), true, r.getReference().startsWith("#"));
}
} else if (tr != null) {
generateResourceSummary(c, tr.getResource(), r.getReference().startsWith("#"), r.getReference().startsWith("#"));
} else {
c.addText(r.getReference());
}
} else if (e instanceof Resource) {
return;
} else if (e instanceof ElementDefinition) {
x.addText("todo-bundle");
} else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta))
throw new NotImplementedException("type " + e.getClass().getName() + " not handled yet");
}
use of org.hl7.fhir.r4b.model.Quantity in project org.hl7.fhir.core by hapifhir.
the class FHIRPathEngine method opLessOrEqual.
private List<Base> opLessOrEqual(List<Base> left, List<Base> right) throws PathEngineException {
if (left.size() == 1 && right.size() == 1 && left.get(0).isPrimitive() && right.get(0).isPrimitive()) {
Base l = left.get(0);
Base r = right.get(0);
if (l.hasType("string") && r.hasType("string"))
return makeBoolean(l.primitiveValue().compareTo(r.primitiveValue()) <= 0);
else if ((l.hasType("integer", "decimal")) && (r.hasType("integer", "decimal")))
return makeBoolean(new Double(l.primitiveValue()) <= new Double(r.primitiveValue()));
else if ((l.hasType("date", "dateTime", "instant")) && (r.hasType("date", "dateTime", "instant")))
return makeBoolean(l.primitiveValue().compareTo(r.primitiveValue()) <= 0);
else if ((l.hasType("time")) && (r.hasType("time")))
return makeBoolean(l.primitiveValue().compareTo(r.primitiveValue()) <= 0);
} else if (left.size() == 1 && right.size() == 1 && left.get(0).fhirType().equals("Quantity") && right.get(0).fhirType().equals("Quantity")) {
List<Base> lUnits = left.get(0).listChildrenByName("unit");
String lunit = lUnits.size() == 1 ? lUnits.get(0).primitiveValue() : null;
List<Base> rUnits = right.get(0).listChildrenByName("unit");
String runit = rUnits.size() == 1 ? rUnits.get(0).primitiveValue() : null;
if ((lunit == null && runit == null) || lunit.equals(runit)) {
return opLessOrEqual(left.get(0).listChildrenByName("value"), right.get(0).listChildrenByName("value"));
} else {
throw new PathEngineException("Canonical Comparison isn't done yet");
}
}
return new ArrayList<Base>();
}
use of org.hl7.fhir.r4b.model.Quantity in project org.hl7.fhir.core by hapifhir.
the class FHIRPathEngine method opGreater.
private List<Base> opGreater(List<Base> left, List<Base> right) throws PathEngineException {
if (left.size() == 1 && right.size() == 1 && left.get(0).isPrimitive() && right.get(0).isPrimitive()) {
Base l = left.get(0);
Base r = right.get(0);
if (l.hasType("string") && r.hasType("string"))
return makeBoolean(l.primitiveValue().compareTo(r.primitiveValue()) > 0);
else if ((l.hasType("integer", "decimal")) && (r.hasType("integer", "decimal")))
return makeBoolean(new Double(l.primitiveValue()) > new Double(r.primitiveValue()));
else if ((l.hasType("date", "dateTime", "instant")) && (r.hasType("date", "dateTime", "instant")))
return makeBoolean(l.primitiveValue().compareTo(r.primitiveValue()) > 0);
else if ((l.hasType("time")) && (r.hasType("time")))
return makeBoolean(l.primitiveValue().compareTo(r.primitiveValue()) > 0);
} else if (left.size() == 1 && right.size() == 1 && left.get(0).fhirType().equals("Quantity") && right.get(0).fhirType().equals("Quantity")) {
List<Base> lUnit = left.get(0).listChildrenByName("unit");
List<Base> rUnit = right.get(0).listChildrenByName("unit");
if (Base.compareDeep(lUnit, rUnit, true)) {
return opGreater(left.get(0).listChildrenByName("value"), right.get(0).listChildrenByName("value"));
} else {
throw new PathEngineException("Canonical Comparison isn't done yet");
}
}
return new ArrayList<Base>();
}
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