use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class Provenance30_40 method convertProvenanceAgentComponent.
public static org.hl7.fhir.r4.model.Provenance.ProvenanceAgentComponent convertProvenanceAgentComponent(org.hl7.fhir.dstu3.model.Provenance.ProvenanceAgentComponent src) throws FHIRException {
if (src == null)
return null;
org.hl7.fhir.r4.model.Provenance.ProvenanceAgentComponent tgt = new org.hl7.fhir.r4.model.Provenance.ProvenanceAgentComponent();
ConversionContext30_40.INSTANCE.getVersionConvertor_30_40().copyElement(src, tgt);
for (org.hl7.fhir.dstu3.model.CodeableConcept t : src.getRole()) tgt.addRole(CodeableConcept30_40.convertCodeableConcept(t));
if (src.hasWho()) {
Type t = ConversionContext30_40.INSTANCE.getVersionConvertor_30_40().convertType(src.getWho());
if (t instanceof Reference)
tgt.setWho((Reference) t);
if (t instanceof UriType)
tgt.getWho().setReference(t.primitiveValue());
}
if (src.hasOnBehalfOf()) {
Type t = ConversionContext30_40.INSTANCE.getVersionConvertor_30_40().convertType(src.getOnBehalfOf());
if (t instanceof Reference)
tgt.setOnBehalfOf((Reference) t);
if (t instanceof UriType)
tgt.getOnBehalfOf().setReference(t.primitiveValue());
}
return tgt;
}
use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class IEEE11073Convertor method generateLoincMdcMap.
private static ConceptMap generateLoincMdcMap(CodeSystem mdc, String dst, String src) throws IOException, FHIRException {
ConceptMap cm = new ConceptMap();
cm.setId("loinc-mdc");
cm.setUrl("http:/???/fhir/ConceptMap/loinc-mdc");
cm.setVersion("[todo]");
cm.setName("LoincMdcCrossMap");
cm.setTitle("Cross Map between LOINC and MDC");
cm.setStatus(PublicationStatus.DRAFT);
cm.setExperimental(true);
cm.setDateElement(new DateTimeType());
cm.setPublisher("HL7, Inc");
ContactDetail cd = cm.addContact();
cd.setName("LOINC + IEEE");
ContactPoint cp = cd.addTelecom();
cp.setSystem(ContactPointSystem.URL);
cp.setValue("http://loinc.org");
cm.setDescription("A Cross Map between the LOINC and MDC Code systems");
cm.setPurpose("To implementers map between medical device codes and LOINC codes");
cm.setCopyright("This content LOINC \u00ae is copyright \u00a9 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use");
cm.setSource(new UriType("http://loinc.org/vs"));
cm.setTarget(new UriType(MDC_ALL_VALUES));
ConceptMapGroupComponent g = cm.addGroup();
g.setSource("urn:iso:std:iso:11073:10101");
g.setTarget("http://loinc.org");
CSVReader csv = new CSVReader(new FileInputStream(src));
csv.readHeaders();
while (csv.line()) {
SourceElementComponent e = g.addElement();
e.setCode(csv.cell("IEEE_CF_CODE10"));
e.setDisplay(csv.cell("IEEE_DESCRIPTION"));
TargetElementComponent t = e.addTarget();
t.setEquivalence(ConceptMapEquivalence.EQUIVALENT);
t.setCode(csv.cell("LOINC_NUM"));
t.setDisplay(csv.cell("LOINC_LONG_COMMON_NAME"));
}
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "conceptmap-" + cm.getId() + ".xml")), cm);
System.out.println("Done");
return cm;
}
use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class ISO21090Importer method produceProperties.
private void produceProperties(List<ElementDefinition> elements, String name, List<Property> properties, boolean attrMode, boolean snapshot) throws FHIRFormatError {
for (Property p : properties) {
if (p.isIsattr() == attrMode) {
ElementDefinition ed = new ElementDefinition();
elements.add(ed);
ed.setPath(name + "." + p.getName());
if (p.getType().startsWith("xsd:"))
ToolingExtensions.addStringExtension(ed.addType(), ToolingExtensions.EXT_XML_TYPE, p.getType());
else
ed.addType().setCode(p.getType());
ed.setMin(p.getMin());
ed.setMax(p.getMax() == Integer.MAX_VALUE ? "*" : Integer.toString(p.getMax()));
ed.setDefinition(p.getDoco());
if (p.isIsattr())
ed.addRepresentation(PropertyRepresentation.XMLATTR);
if (p.getBinding() != null)
ed.getBinding().setStrength(BindingStrength.REQUIRED).setValueSet(new UriType("http://hl7.org/fhir/iso21090/ValueSet/" + p.getBinding()));
if (snapshot)
ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
}
}
}
use of org.hl7.fhir.r4b.model.UriType in project org.hl7.fhir.core by hapifhir.
the class R5ToR5Loader method loadBundle.
@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
Resource r5 = null;
if (isJson)
r5 = new JsonParser().parse(stream);
else
r5 = new XmlParser().parse(stream);
Bundle b;
if (r5 instanceof Bundle)
b = (Bundle) r5;
else {
b = new Bundle();
b.setId(UUID.randomUUID().toString().toLowerCase());
b.setType(BundleType.COLLECTION);
b.addEntry().setResource(r5).setFullUrl(r5 instanceof CanonicalResource ? ((CanonicalResource) r5).getUrl() : null);
}
for (CodeSystem cs : cslist) {
BundleEntryComponent be = b.addEntry();
be.setFullUrl(cs.getUrl());
be.setResource(cs);
}
if (killPrimitives) {
List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
remove.add(be);
}
}
b.getEntry().removeAll(remove);
}
if (patchUrls) {
for (BundleEntryComponent be : b.getEntry()) {
if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
for (ElementDefinition ed : sd.getSnapshot().getElement()) patchUrl(ed);
for (ElementDefinition ed : sd.getDifferential().getElement()) patchUrl(ed);
}
}
}
return b;
}
use of org.hl7.fhir.r4b.model.UriType 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");
}
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