use of org.hl7.fhir.r4b.model.CodeType in project org.hl7.fhir.core by hapifhir.
the class SearchParameter10_50 method convertSearchParameter.
public static org.hl7.fhir.dstu2.model.SearchParameter convertSearchParameter(org.hl7.fhir.r5.model.SearchParameter src) throws FHIRException {
if (src == null || src.isEmpty())
return null;
org.hl7.fhir.dstu2.model.SearchParameter tgt = new org.hl7.fhir.dstu2.model.SearchParameter();
ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().copyDomainResource(src, tgt);
if (src.hasUrlElement())
tgt.setUrlElement(Uri10_50.convertUri(src.getUrlElement()));
if (src.hasNameElement())
tgt.setNameElement(String10_50.convertString(src.getNameElement()));
if (src.hasStatus())
tgt.setStatusElement(Enumerations10_50.convertConformanceResourceStatus(src.getStatusElement()));
if (src.hasExperimental())
tgt.setExperimentalElement(Boolean10_50.convertBoolean(src.getExperimentalElement()));
if (src.hasDate())
tgt.setDateElement(DateTime10_50.convertDateTime(src.getDateElement()));
if (src.hasPublisherElement())
tgt.setPublisherElement(String10_50.convertString(src.getPublisherElement()));
for (org.hl7.fhir.r5.model.ContactDetail t : src.getContact()) tgt.addContact(convertSearchParameterContactComponent(t));
if (src.hasPurpose())
tgt.setRequirements(src.getPurpose());
if (src.hasCodeElement())
tgt.setCodeElement(Code10_50.convertCode(src.getCodeElement()));
for (CodeType t : src.getBase()) tgt.setBase(t.asStringValue());
if (src.hasType())
tgt.setTypeElement(Enumerations10_50.convertSearchParamType(src.getTypeElement()));
if (src.hasDescription())
tgt.setDescription(src.getDescription());
org.hl7.fhir.dstu2.utils.ToolingExtensions.setStringExtension(tgt, ToolingExtensions.EXT_EXPRESSION, src.getExpression());
if (src.hasXpathElement())
tgt.setXpathElement(String10_50.convertString(src.getXpathElement()));
if (src.hasXpathUsage())
tgt.setXpathUsageElement(convertXPathUsageType(src.getXpathUsageElement()));
for (CodeType t : src.getTarget()) tgt.addTarget(t.getValue());
return tgt;
}
use of org.hl7.fhir.r4b.model.CodeType in project org.hl7.fhir.core by hapifhir.
the class IEEE11073Convertor method generateMDC.
public static CodeSystem generateMDC(String src, String dst, UcumService ucum) throws IOException, FHIRException {
CSVReader csv = new CSVReader(new FileInputStream(src));
csv.readHeaders();
CodeSystem cs = new CodeSystem();
Map<String, String> ucumIssues = new HashMap<String, String>();
int errorCount = 0;
cs.setId("MDC");
cs.setUrl("urn:iso:std:iso:11073:10101");
cs.setVersion("[todo]");
cs.setName("11073:10101 codes for the FHIR community");
cs.setStatus(PublicationStatus.ACTIVE);
cs.setExperimental(false);
cs.setDateElement(new DateTimeType());
cs.setPublisher("HL7 (FHIR Project)");
ContactDetail cd = cs.addContact();
ContactPoint cp = cd.addTelecom();
cp.setSystem(ContactPointSystem.URL);
cp.setValue("http://ieee?");
cs.setDescription("1073 Codes for the FHIR community (generated from the Rosetta data");
Identifier i = new Identifier();
cs.setIdentifier(i);
i.setSystem("urn:ietf:rfc:3986");
i.setValue("urn:oid:2.16.840.1.113883.6.24");
cs.setCaseSensitive(false);
cs.setContent(CodeSystemContentMode.COMPLETE);
cs.addProperty().setCode("ucum").setDescription("UCUM units associated with Concept").setType(PropertyType.STRING);
cs.addProperty().setCode("unit").setDescription("MDC units associated with Concept").setType(PropertyType.STRING);
cs.addProperty().setCode("refid").setDescription("MDC Reference Id for Concept").setType(PropertyType.CODE);
Set<String> codes = new HashSet<String>();
while (csv.line()) {
if (csv.has("CF_CODE10")) {
String code = csv.cell("CF_CODE10");
if (codes.contains(code))
System.out.println("Duplicate Code " + code);
else {
codes.add(code);
ConceptDefinitionComponent c = cs.addConcept();
c.setCode(code);
c.setDisplay(csv.cell("Common Term"));
c.setDefinition(csv.cell("Term Description"));
String vd = csv.cell("Vendor_Description");
if (!c.hasDefinition())
c.setDefinition(vd);
if (!c.hasDisplay())
c.setDisplay(vd);
String refid = csv.cell("REFID");
c.addProperty().setCode("refid").setValue(new CodeType().setValue(refid));
if (csv.has("Synonym"))
c.addDesignation().setValue(csv.cell("Synonym")).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setCode("synonym"));
if (csv.has("Acronym"))
c.addDesignation().setValue(csv.cell("Acronym")).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setDisplay("acronym"));
if (csv.has("Systematic Name")) {
String sysName = csv.cell("Systematic Name");
if (!c.hasDefinition())
c.setDefinition(sysName);
c.addDesignation().setValue(sysName).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setCode("structured-name"));
}
if (csv.has("UOM_MDC"))
c.addProperty().setCode("unit").setValue(new StringType().setValue(csv.cell("UOM_MDC")));
if (csv.has("UOM_UCUM")) {
CommaSeparatedStringBuilder ul = new CommaSeparatedStringBuilder();
for (String u : csv.cell("UOM_UCUM").split(" ")) {
String msg = ucum.validate(u);
if (msg != null) {
errorCount++;
ucumIssues.put(u, msg);
} else
ul.append(u);
}
if (ul.length() > 0)
c.addProperty().setCode("ucum").setValue(new StringType().setValue(ul.toString()));
}
}
}
}
csv.close();
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "codesystem-" + cs.getId() + ".xml")), cs);
System.out.println(errorCount + "UCUM errors");
for (String u : sorted(ucumIssues.keySet())) System.out.println("Invalid UCUM code: " + u + " because " + ucumIssues.get(u));
return cs;
}
use of org.hl7.fhir.r4b.model.CodeType in project org.hl7.fhir.core by hapifhir.
the class CountryCodesConverter method execute.
private void execute() throws ParserConfigurationException, SAXException, IOException {
Document src = load();
CodeSystem cs1 = new CodeSystem();
CodeSystem cs2 = new CodeSystem();
CodeSystem cs3 = new CodeSystem();
setMetadata(src, cs1, "iso3166", "urn:iso:std:iso:3166", "", "");
setMetadata(src, cs2, "iso3166-2", "urn:iso:std:iso:3166:-2", "Part2", " Part 2");
cs1.addProperty().setCode("canonical").setDescription("The 2 letter code that identifies the same country (so 2/3/numeric codes can be aligned)").setType(PropertyType.CODE);
cs2.addProperty().setCode("country").setDescription("The 2 letter code that identifies the country for the subdivision").setType(PropertyType.CODE);
for (Element e : XMLUtil.getNamedChildren(src.getDocumentElement(), "country")) {
System.out.println(e.getAttribute("id"));
String c2 = XMLUtil.getNamedChildText(e, "alpha-2-code");
String c3 = XMLUtil.getNamedChildText(e, "alpha-3-code");
String cN = XMLUtil.getNamedChildText(e, "numeric-code");
Element n = XMLUtil.getNamedChildByAttribute(e, "short-name", "lang3code", "eng");
if (n == null)
n = XMLUtil.getNamedChildByAttribute(e, "short-name-upper-case", "lang3code", "eng");
if (n == null)
continue;
String name = n.getTextContent();
n = XMLUtil.getNamedChildByAttribute(e, "full-name", "lang3code", "eng");
if (n == null)
n = XMLUtil.getNamedChildByAttribute(e, "full-name-upper-case", "lang3code", "eng");
if (n == null)
n = XMLUtil.getNamedChildByAttribute(e, "short-name", "lang3code", "eng");
if (n == null)
n = XMLUtil.getNamedChildByAttribute(e, "short-name-upper-case", "lang3code", "eng");
String desc = n.getTextContent();
ConceptDefinitionComponent cc = cs1.addConcept();
cc.setCode(c2);
cc.setDisplay(name);
cc.setDefinition(desc);
poplang(e, cc);
if (c3 != null) {
cc = cs1.addConcept();
cc.setCode(c3);
cc.setDisplay(name);
cc.setDefinition(desc);
cc.addProperty().setCode("canonical").setValue(new CodeType(c2));
poplang(e, cc);
}
if (cN != null) {
cc = cs1.addConcept();
cc.setCode(cN);
cc.setDisplay(name);
cc.setDefinition(desc);
cc.addProperty().setCode("canonical").setValue(new CodeType(c2));
poplang(e, cc);
}
for (Element sd : XMLUtil.getNamedChildren(e, "subdivision")) {
cc = cs2.addConcept();
cc.setCode(XMLUtil.getNamedChildText(sd, "subdivision-code"));
Element l = XMLUtil.getNamedChild(sd, "subdivision-locale");
cc.setDisplay(XMLUtil.getNamedChildText(l, "subdivision-locale-name"));
cc.addProperty().setCode("country").setValue(new CodeType(c2));
}
}
cs1.setCount(cs1.getConcept().size());
cs2.setCount(cs2.getConcept().size());
throw new Error("Needs revisiting");
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166.json")), cs1);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166.json")), cs1); // format hasn't changed
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166-2.json")), cs2);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166-2.json")), cs2); // format hasn't changed
}
use of org.hl7.fhir.r4b.model.CodeType in project org.hl7.fhir.core by hapifhir.
the class ICD11Generator method processMMSEntity.
private void processMMSEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
System.out.print(".");
JsonObject entity = fetchJson(url(base, ref));
cc.setId(tail(ref));
if (entity.has("code") && !Utilities.noString(entity.get("code").getAsString())) {
cc.setCode(entity.get("code").getAsString());
} else if (entity.has("blockId") && !Utilities.noString(entity.get("blockId").getAsString())) {
cc.setCode(entity.get("blockId").getAsString());
} else {
cc.setCode(cc.getId());
cc.addProperty().setCode("abstract").setValue(new BooleanType(true));
}
if (entity.has("classKind") && !Utilities.noString(entity.get("classKind").getAsString()) && !"category".equals(entity.get("classKind").getAsString())) {
cc.addProperty().setCode("kind").setValue(new CodeType(entity.get("classKind").getAsString()));
}
cc.setDisplay(readString(entity, "title"));
StringBuilder defn = new StringBuilder();
String d = readString(entity, "definition");
if (d != null) {
defn.append(d);
}
if (d == null && (entity.has("inclusion") || entity.has("exclusion"))) {
defn.append(cc.getDisplay());
}
if (entity.has("inclusion")) {
defn.append(". Includes: ");
boolean first = true;
for (JsonElement child : entity.getAsJsonArray("inclusion")) {
if (first)
first = false;
else
defn.append(", ");
defn.append(readString((JsonObject) child, "label"));
}
}
if (entity.has("exclusion")) {
defn.append(". Excludes: ");
boolean first = true;
for (JsonElement child : entity.getAsJsonArray("exclusion")) {
if (first)
first = false;
else
defn.append(", ");
JsonObject co = (JsonObject) child;
String v = readString(co, "label");
if (v != null) {
defn.append(v);
if (co.has("linearizationReference")) {
cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/mms").setCode(tail(co.get("linearizationReference").getAsString())).setDisplay(v)).setCode("exclusion");
}
}
}
}
cc.setDefinition(defn.toString());
addDesignation(readString(entity, "longDefinition"), cc, "http://id.who.int/icd11/mms/designation", "longDefinition");
addDesignation(readString(entity, "fullySpecifiedName"), cc, "http://snomed.info/sct", "900000000000003001");
addProperty(readString(entity, "codingNote"), cc, "codingNote");
if (entity.has("indexTerm")) {
// }
for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
processIndexTerm(cc, (JsonObject) child);
}
}
if (entity.has("postcoordinationScale")) {
for (JsonElement child : entity.getAsJsonArray("postcoordinationScale")) {
JsonObject o = (JsonObject) child;
String name = tail(o.get("axisName").getAsString());
ConceptPropertyComponent prop = cc.addProperty();
prop.setCode("postcoordinationScale");
prop.setValue(new CodeType(name));
ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/required", o.get("requiredPostcoordination").getAsBoolean());
ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/repeats", o.get("allowMultipleValues").getAsBoolean());
if (o.has("scaleEntity")) {
ToolingExtensions.addUriExtension(prop, "http://id.who.int/icd11/extensions/valueSet", buildValueSet(cs, cc.getCode(), name, o, dest));
}
}
}
if (entity.has("child")) {
for (JsonElement child : entity.getAsJsonArray("child")) {
processMMSEntity(cs, base, child.getAsString(), cc.addConcept(), dest);
}
}
}
use of org.hl7.fhir.r4b.model.CodeType 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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