use of org.hl7.fhir.r4b.model.Enumeration in project org.hl7.fhir.core by hapifhir.
the class CSVWriter method itemList.
private String itemList(List l) {
StringBuilder s = new StringBuilder();
for (int i = 0; i < l.size(); i++) {
Object o = l.get(i);
String val = "";
if (o instanceof StringType) {
val = ((StringType) o).getValue();
} else if (o instanceof UriType) {
val = ((UriType) o).getValue();
} else if (o instanceof IdType) {
val = ((IdType) o).getValue();
} else if (o instanceof Enumeration<?>) {
val = o.toString();
} else if (o instanceof TypeRefComponent) {
TypeRefComponent t = (TypeRefComponent) o;
val = t.getWorkingCode() + (t.getProfile() == null ? "" : " {" + t.getProfile() + "}") + (t.getTargetProfile() == null ? "" : " {" + t.getTargetProfile() + "}") + (t.getAggregation() == null || t.getAggregation().isEmpty() ? "" : " (" + itemList(t.getAggregation()) + ")");
} else if (o instanceof Coding) {
Coding t = (Coding) o;
val = (t.getSystem() == null ? "" : t.getSystem()) + (t.getCode() == null ? "" : "#" + t.getCode()) + (t.getDisplay() == null ? "" : " (" + t.getDisplay() + ")");
} else if (o instanceof ElementDefinitionConstraintComponent) {
ElementDefinitionConstraintComponent c = (ElementDefinitionConstraintComponent) o;
val = c.getKey() + ":" + c.getHuman() + " {" + c.getExpression() + "}";
} else if (o instanceof ElementDefinitionSlicingDiscriminatorComponent) {
ElementDefinitionSlicingDiscriminatorComponent c = (ElementDefinitionSlicingDiscriminatorComponent) o;
val = c.getType().toCode() + ":" + c.getPath() + "}";
} else {
val = o.toString();
val = val.substring(val.indexOf("[") + 1);
val = val.substring(0, val.indexOf("]"));
}
s = s.append(val);
if (i == 0)
s.append("\n");
}
return s.toString();
}
use of org.hl7.fhir.r4b.model.Enumeration in project org.hl7.fhir.core by hapifhir.
the class ProfileDrivenRenderer method renderLeaf.
private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode parent, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
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)
return;
else if (e instanceof InstantType)
x.addText(((InstantType) e).toHumanDisplay());
else if (e instanceof DateTimeType) {
renderDateTime(x, e);
} else if (e instanceof Base64BinaryType)
x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
else if (e instanceof org.hl7.fhir.r5.model.DateType) {
org.hl7.fhir.r5.model.DateType dt = ((org.hl7.fhir.r5.model.DateType) e);
renderDate(x, dt);
} 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(x, (CodeableConcept) e, showCodeDetails);
} else if (e instanceof Coding) {
renderCoding(x, (Coding) e, showCodeDetails);
} else if (e instanceof CodeableReference) {
renderCodeableReference(x, (CodeableReference) e, showCodeDetails);
} else if (e instanceof Annotation) {
renderAnnotation(x, (Annotation) e);
} else if (e instanceof Identifier) {
renderIdentifier(x, (Identifier) e);
} else if (e instanceof org.hl7.fhir.r5.model.IntegerType) {
if (((org.hl7.fhir.r5.model.IntegerType) e).hasValue()) {
x.addText(Integer.toString(((org.hl7.fhir.r5.model.IntegerType) e).getValue()));
} else {
x.addText("??");
}
} else if (e instanceof org.hl7.fhir.r5.model.Integer64Type) {
if (((org.hl7.fhir.r5.model.Integer64Type) e).hasValue()) {
x.addText(Long.toString(((org.hl7.fhir.r5.model.Integer64Type) e).getValue()));
} else {
x.addText("??");
}
} else if (e instanceof org.hl7.fhir.r5.model.DecimalType) {
x.addText(((org.hl7.fhir.r5.model.DecimalType) e).getValue().toString());
} else if (e instanceof HumanName) {
renderHumanName(x, (HumanName) e);
} else if (e instanceof SampledData) {
renderSampledData(x, (SampledData) e);
} else if (e instanceof Address) {
renderAddress(x, (Address) e);
} else if (e instanceof ContactPoint) {
renderContactPoint(x, (ContactPoint) e);
} else if (e instanceof Expression) {
renderExpression(x, (Expression) e);
} else if (e instanceof Money) {
renderMoney(x, (Money) e);
} else if (e instanceof ContactDetail) {
ContactDetail cd = (ContactDetail) e;
if (cd.hasName()) {
x.tx(cd.getName() + ": ");
}
boolean first = true;
for (ContactPoint c : cd.getTelecom()) {
if (first)
first = false;
else
x.tx(",");
renderContactPoint(x, c);
}
} else if (e instanceof UriType) {
renderUri(x, (UriType) e, defn.getPath(), rcontext != null && rcontext.getResourceResource() != null ? rcontext.getResourceResource().getId() : null);
} else if (e instanceof Timing) {
renderTiming(x, (Timing) e);
} else if (e instanceof Range) {
renderRange(x, (Range) e);
} else if (e instanceof Quantity) {
renderQuantity(x, (Quantity) e, showCodeDetails);
} else if (e instanceof Ratio) {
renderQuantity(x, ((Ratio) e).getNumerator(), showCodeDetails);
x.tx("/");
renderQuantity(x, ((Ratio) e).getDenominator(), showCodeDetails);
} else if (e instanceof Period) {
Period p = (Period) e;
renderPeriod(x, p);
} else if (e instanceof Reference) {
Reference r = (Reference) e;
if (r.getReference() != null && r.getReference().contains("#")) {
if (containedIds.contains(r.getReference().substring(1))) {
x.ah(r.getReference()).tx("See " + r.getReference());
} else {
// in this case, we render the resource in line
ResourceWrapper rw = null;
for (ResourceWrapper t : res.getContained()) {
if (r.getReference().substring(1).equals(t.getId())) {
rw = t;
}
}
if (rw == null) {
renderReference(res, x, r);
} else {
x.an(rw.getId());
ResourceRenderer rr = RendererFactory.factory(rw, context.copy().setAddGeneratedNarrativeHeader(false));
rr.render(parent.blockquote(), rw);
}
}
} else {
renderReference(res, x, r);
}
} else if (e instanceof Resource) {
return;
} else if (e instanceof DataRequirement) {
DataRequirement p = (DataRequirement) e;
renderDataRequirement(x, p);
} else if (e instanceof PrimitiveType) {
x.tx(((PrimitiveType) e).primitiveValue());
} else if (e instanceof ElementDefinition) {
x.tx("todo-bundle");
} else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta)) {
throw new NotImplementedException("type " + e.getClass().getName() + " not handled - should not be here");
}
}
use of org.hl7.fhir.r4b.model.Enumeration in project org.hl7.fhir.core by hapifhir.
the class SearchParameterRenderer method render.
public boolean render(XhtmlNode x, SearchParameter spd) throws IOException, FHIRException, EOperationOutcome {
x.h2().addText(spd.getName());
XhtmlNode p = x.para();
p.tx("Parameter ");
p.code().tx(spd.getCode());
p.tx(":");
p.code().tx(spd.getType().toCode());
addMarkdown(x, spd.getDescription());
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
tr.td().tx(Utilities.pluralize("Resource", spd.getBase().size()));
XhtmlNode td = tr.td();
for (CodeType t : spd.getBase()) {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
if (sd != null && sd.hasUserData("path")) {
td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
} else {
td.sep(", ").tx(t.getCode());
}
}
tr = tbl.tr();
tr.td().tx("Expression");
if (spd.hasExpression()) {
tr.td().code().tx(spd.getExpression());
} else {
tr.td().tx("(none)");
}
if (spd.hasXpathUsage()) {
tr = tbl.tr();
tr.td().tx("Usage");
tr.td().tx(spd.getXpathUsage().getDisplay());
}
if (spd.hasXpath()) {
tr = tbl.tr();
tr.td().tx("XPath");
tr.td().code().tx(spd.getXpath());
}
if (spd.hasTarget()) {
tr = tbl.tr();
tr.td().tx(Utilities.pluralize("Target Resources", spd.getTarget().size()));
td = tr.td();
for (CodeType t : spd.getTarget()) {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
if (sd != null && sd.hasUserData("path")) {
td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
} else {
td.sep(", ").tx(t.getCode());
}
}
}
tr = tbl.tr();
tr.td().tx("Multiples");
if (spd.getMultipleAnd() && spd.getMultipleOr()) {
tr.td().tx("The parameter can repeat (and) and can have repeating values (or)");
} else if (spd.getMultipleOr()) {
tr.td().tx("The parameter can repeat (and) but each repeat can only have one value");
} else if (spd.getMultipleAnd()) {
tr.td().tx("The parameter cannot repeat (and) but the single parameter can have multiple values (or)");
} else {
tr.td().tx("The parameter cannot repeat or have multiple values");
}
if (spd.hasComparator()) {
tr = tbl.tr();
tr.td().tx("Comparators");
td = tr.td().tx("Allowed: ");
for (Enumeration<SearchComparator> t : spd.getComparator()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasModifier()) {
tr = tbl.tr();
tr.td().tx("Modifiers");
td = tr.td().tx("Allowed: ");
for (Enumeration<SearchModifierCode> t : spd.getModifier()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasChain()) {
tr = tbl.tr();
tr.td().tx("Chains");
td = tr.td().tx("Allowed: ");
for (StringType t : spd.getChain()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasComponent()) {
x.para().b().tx("Components");
tbl = x.table("grid");
for (SearchParameterComponentComponent t : spd.getComponent()) {
tr = tbl.tr();
SearchParameter tsp = context.getWorker().fetchResource(SearchParameter.class, t.getDefinition());
if (tsp != null && tsp.hasUserData("path")) {
tr.td().ah(tsp.getUserString("path")).tx(tsp.present());
} else {
tr.td().tx(t.getDefinition());
}
tr.td().code().tx(t.getExpression());
}
}
return false;
}
use of org.hl7.fhir.r4b.model.Enumeration in project org.hl7.fhir.core by hapifhir.
the class DataRenderer method displayTiming.
private String displayTiming(Timing s) throws FHIRException {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (s.hasCode())
b.append("Code: " + displayCodeableConcept(s.getCode()));
if (s.getEvent().size() > 0) {
CommaSeparatedStringBuilder c = new CommaSeparatedStringBuilder();
for (DateTimeType p : s.getEvent()) {
if (p.hasValue()) {
c.append(displayDateTime(p));
} else if (!renderExpression(c, p)) {
c.append("??");
}
}
b.append("Events: " + c.toString());
}
if (s.hasRepeat()) {
TimingRepeatComponent rep = s.getRepeat();
if (rep.hasBoundsPeriod() && rep.getBoundsPeriod().hasStart())
b.append("Starting " + displayDateTime(rep.getBoundsPeriod().getStartElement()));
if (rep.hasCount())
b.append("Count " + Integer.toString(rep.getCount()) + " times");
if (rep.hasDuration())
b.append("Duration " + rep.getDuration().toPlainString() + displayTimeUnits(rep.getPeriodUnit()));
if (rep.hasWhen()) {
String st = "";
if (rep.hasOffset()) {
st = Integer.toString(rep.getOffset()) + "min ";
}
b.append("Do " + st);
for (Enumeration<EventTiming> wh : rep.getWhen()) b.append(displayEventCode(wh.getValue()));
} else {
String st = "";
if (!rep.hasFrequency() || (!rep.hasFrequencyMax() && rep.getFrequency() == 1))
st = "Once";
else {
st = Integer.toString(rep.getFrequency());
if (rep.hasFrequencyMax())
st = st + "-" + Integer.toString(rep.getFrequency());
}
if (rep.hasPeriod()) {
st = st + " per " + rep.getPeriod().toPlainString();
if (rep.hasPeriodMax())
st = st + "-" + rep.getPeriodMax().toPlainString();
st = st + " " + displayTimeUnits(rep.getPeriodUnit());
}
b.append("Do " + st);
}
if (rep.hasBoundsPeriod() && rep.getBoundsPeriod().hasEnd())
b.append("Until " + displayDateTime(rep.getBoundsPeriod().getEndElement()));
}
return b.toString();
}
use of org.hl7.fhir.r4b.model.Enumeration in project redmatch by aehrc.
the class FhirExporter method getValue.
/**
* Resolves a value.
*
* @param value The value specified in the transformation rules.
* @param fhirType The type of the FHIR attribute where this value will be set.
* @param vertex A vertex with patient data.
* @param recordId The id of this record. Used to create the references to FHIR ids.
* @param enumFactory If the type is an enumeration, this is the factory to create an instance.
* @param fhirPackage The target FHIR package.
* @return The value or null if the value cannot be determined. This can also be a list.
*/
private Base getValue(Value value, Class<?> fhirType, JsonObject vertex, String recordId, Class<?> enumFactory, VersionedFhirPackage fhirPackage) throws IOException {
// If this is a field-based value then make sure that there is a value and if not return null
if (value instanceof FieldBasedValue) {
FieldBasedValue fbv = (FieldBasedValue) value;
// Account for field ids of the form xx___y
String fieldId = fbv.getFieldId();
String shortFieldId = null;
String regex = "(?<fieldId>.*)___\\d+$";
Pattern pattern = Pattern.compile(regex);
Matcher matcher = pattern.matcher(fieldId);
if (matcher.find()) {
shortFieldId = matcher.group("fieldId");
log.debug("Transformed fieldId into '" + fieldId + "'");
}
boolean hasValue = false;
JsonElement jsonElement = vertex.get(fieldId);
if (jsonElement != null) {
String rawValue = jsonElement.getAsString();
if (!rawValue.isEmpty()) {
hasValue = true;
}
}
if (!hasValue && shortFieldId != null) {
jsonElement = vertex.get(shortFieldId);
if (jsonElement != null) {
String rawValue = jsonElement.getAsString();
if (!rawValue.isEmpty()) {
hasValue = true;
}
}
}
if (!hasValue) {
return null;
}
}
if (value instanceof BooleanValue) {
return new BooleanType(((BooleanValue) value).getValue());
} else if (value instanceof CodeLiteralValue) {
String code = ((CodeLiteralValue) value).getCode();
return getCode(code, enumFactory);
} else if (value instanceof ConceptLiteralValue) {
ConceptLiteralValue clv = (ConceptLiteralValue) value;
String system = clv.getSystem();
String code = clv.getCode();
String display = clv.getDisplay() != null ? clv.getDisplay() : "";
return getConcept(system, code, display, fhirType);
} else if (value instanceof DoubleValue) {
return new DecimalType(((DoubleValue) value).getValue());
} else if (value instanceof IntegerValue) {
return new IntegerType(((IntegerValue) value).getValue());
} else if (value instanceof ReferenceValue) {
ReferenceValue rv = (ReferenceValue) value;
Reference ref = new Reference();
String resourceType = rv.getResourceType();
String resourceId = rv.getResourceId();
boolean unique = uniqueIds.contains(resourceType + "<" + resourceId + ">");
CodeInfo codeInfo = terminologyService.lookup(fhirPackage, resourceType);
if (codeInfo.isProfile()) {
resourceType = StringUtils.getLastPath(codeInfo.getBaseResource());
}
if (unique) {
// This is a reference to a unique resource - no need to append row id
if (fhirResourceMap.containsKey(resourceId)) {
ref.setReference("/" + resourceType + "/" + resourceId);
} else {
log.debug("Did not find resource " + resourceType + "/" + resourceId);
}
} else {
if (fhirResourceMap.containsKey(resourceId + "-" + recordId)) {
ref.setReference("/" + resourceType + "/" + resourceId + "-" + recordId);
} else {
log.debug("Did not find resource " + resourceType + "/" + resourceId + "-" + recordId);
}
}
return ref;
} else if (value instanceof StringValue) {
if (fhirType.equals(StringType.class)) {
return new StringType(((StringValue) value).getStringValue());
} else if (fhirType.equals(MarkdownType.class)) {
return new MarkdownType(((StringValue) value).getStringValue());
} else if (fhirType.equals(IdType.class)) {
return new IdType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UriType.class)) {
return new UriType(((StringValue) value).getStringValue());
} else if (fhirType.equals(OidType.class)) {
return new OidType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UuidType.class)) {
return new UuidType(((StringValue) value).getStringValue());
} else if (fhirType.equals(CanonicalType.class)) {
return new CanonicalType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UrlType.class)) {
return new UrlType(((StringValue) value).getStringValue());
} else {
throw new TransformationException("Got StringValue for FHIR type " + fhirType.getName() + ". This should not happen!");
}
} else if (value instanceof CodeSelectedValue) {
CodeSelectedValue csv = (CodeSelectedValue) value;
String fieldId = csv.getFieldId();
Mapping m = getSelectedMapping(fieldId, vertex);
if (m == null) {
throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
}
return getTarget(m).getCodeElement();
} else if (value instanceof ConceptSelectedValue) {
ConceptSelectedValue csv = (ConceptSelectedValue) value;
String fieldId = csv.getFieldId();
Mapping m = getSelectedMapping(fieldId, vertex);
if (m == null) {
throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
}
if (fhirType.isAssignableFrom(Coding.class)) {
return getTarget(m);
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(getTarget(m));
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT_SELECTED.");
}
} else if (value instanceof ConceptValue) {
// Ontoserver REDCap plugin format: 74400008|Appendicitis|http://snomed.info/sct
ConceptValue cv = (ConceptValue) value;
String fieldId = cv.getFieldId();
Mapping m = getMapping(fieldId);
if (m != null) {
if (fhirType.isAssignableFrom(Coding.class)) {
return getTarget(m);
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(getTarget(m));
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
}
} else {
au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
Coding c = field.getCoding(vertex);
if (c != null) {
if (fhirType.isAssignableFrom(Coding.class)) {
return c;
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(c);
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
}
}
}
throw new TransformationException("Could not get concept for field " + fieldId + ".");
} else if (value instanceof FieldValue) {
FieldValue fv = (FieldValue) value;
String fieldId = fv.getFieldId();
FieldValue.DatePrecision pr = fv.getDatePrecision();
au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
return field.getValue(vertex, fhirType, pr);
} else {
throw new TransformationException("Unable to get VALUE for " + value);
}
}
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