use of org.hl7.fhir.dstu2.model.ContactPoint 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.dstu2.model.ContactPoint 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.dstu2.model.ContactPoint in project org.hl7.fhir.core by hapifhir.
the class NarrativeGenerator method displayContactPoint.
public static String displayContactPoint(ContactPoint contact) {
StringBuilder s = new StringBuilder();
s.append(describeSystem(contact.getSystem()));
if (Utilities.noString(contact.getValue()))
s.append("-unknown-");
else
s.append(contact.getValue());
if (contact.hasUse())
s.append("(" + contact.getUse().toString() + ")");
return s.toString();
}
use of org.hl7.fhir.dstu2.model.ContactPoint in project org.hl7.fhir.core by hapifhir.
the class JsonParser method composeType.
protected void composeType(String prefix, Type type) throws IOException {
if (type == null)
;
else if (type instanceof Age)
composeAge(prefix + "Age", (Age) type);
else if (type instanceof Count)
composeCount(prefix + "Count", (Count) type);
else if (type instanceof Money)
composeMoney(prefix + "Money", (Money) type);
else if (type instanceof Distance)
composeDistance(prefix + "Distance", (Distance) type);
else if (type instanceof Duration)
composeDuration(prefix + "Duration", (Duration) type);
else if (type instanceof SimpleQuantity)
composeSimpleQuantity(prefix + "SimpleQuantity", (SimpleQuantity) type);
else if (type instanceof Period)
composePeriod(prefix + "Period", (Period) type);
else if (type instanceof Coding)
composeCoding(prefix + "Coding", (Coding) type);
else if (type instanceof Range)
composeRange(prefix + "Range", (Range) type);
else if (type instanceof Quantity)
composeQuantity(prefix + "Quantity", (Quantity) type);
else if (type instanceof Attachment)
composeAttachment(prefix + "Attachment", (Attachment) type);
else if (type instanceof Ratio)
composeRatio(prefix + "Ratio", (Ratio) type);
else if (type instanceof Annotation)
composeAnnotation(prefix + "Annotation", (Annotation) type);
else if (type instanceof SampledData)
composeSampledData(prefix + "SampledData", (SampledData) type);
else if (type instanceof Reference)
composeReference(prefix + "Reference", (Reference) type);
else if (type instanceof CodeableConcept)
composeCodeableConcept(prefix + "CodeableConcept", (CodeableConcept) type);
else if (type instanceof Identifier)
composeIdentifier(prefix + "Identifier", (Identifier) type);
else if (type instanceof Signature)
composeSignature(prefix + "Signature", (Signature) type);
else if (type instanceof TriggerDefinition)
composeTriggerDefinition(prefix + "TriggerDefinition", (TriggerDefinition) type);
else if (type instanceof ElementDefinition)
composeElementDefinition(prefix + "ElementDefinition", (ElementDefinition) type);
else if (type instanceof Timing)
composeTiming(prefix + "Timing", (Timing) type);
else if (type instanceof ModuleMetadata)
composeModuleMetadata(prefix + "ModuleMetadata", (ModuleMetadata) type);
else if (type instanceof ActionDefinition)
composeActionDefinition(prefix + "ActionDefinition", (ActionDefinition) type);
else if (type instanceof Address)
composeAddress(prefix + "Address", (Address) type);
else if (type instanceof HumanName)
composeHumanName(prefix + "HumanName", (HumanName) type);
else if (type instanceof DataRequirement)
composeDataRequirement(prefix + "DataRequirement", (DataRequirement) type);
else if (type instanceof Meta)
composeMeta(prefix + "Meta", (Meta) type);
else if (type instanceof ParameterDefinition)
composeParameterDefinition(prefix + "ParameterDefinition", (ParameterDefinition) type);
else if (type instanceof ContactPoint)
composeContactPoint(prefix + "ContactPoint", (ContactPoint) type);
else if (type instanceof MarkdownType) {
composeMarkdownCore(prefix + "Markdown", (MarkdownType) type, false);
composeMarkdownExtras(prefix + "Markdown", (MarkdownType) type, false);
} else if (type instanceof UnsignedIntType) {
composeUnsignedIntCore(prefix + "UnsignedInt", (UnsignedIntType) type, false);
composeUnsignedIntExtras(prefix + "UnsignedInt", (UnsignedIntType) type, false);
} else if (type instanceof CodeType) {
composeCodeCore(prefix + "Code", (CodeType) type, false);
composeCodeExtras(prefix + "Code", (CodeType) type, false);
} else if (type instanceof IdType) {
composeIdCore(prefix + "Id", (IdType) type, false);
composeIdExtras(prefix + "Id", (IdType) type, false);
} else if (type instanceof OidType) {
composeOidCore(prefix + "Oid", (OidType) type, false);
composeOidExtras(prefix + "Oid", (OidType) type, false);
} else if (type instanceof PositiveIntType) {
composePositiveIntCore(prefix + "PositiveInt", (PositiveIntType) type, false);
composePositiveIntExtras(prefix + "PositiveInt", (PositiveIntType) type, false);
} else if (type instanceof UuidType) {
composeUuidCore(prefix + "Uuid", (UuidType) type, false);
composeUuidExtras(prefix + "Uuid", (UuidType) type, false);
} else if (type instanceof IntegerType) {
composeIntegerCore(prefix + "Integer", (IntegerType) type, false);
composeIntegerExtras(prefix + "Integer", (IntegerType) type, false);
} else if (type instanceof DateTimeType) {
composeDateTimeCore(prefix + "DateTime", (DateTimeType) type, false);
composeDateTimeExtras(prefix + "DateTime", (DateTimeType) type, false);
} else if (type instanceof DateType) {
composeDateCore(prefix + "Date", (DateType) type, false);
composeDateExtras(prefix + "Date", (DateType) type, false);
} else if (type instanceof DecimalType) {
composeDecimalCore(prefix + "Decimal", (DecimalType) type, false);
composeDecimalExtras(prefix + "Decimal", (DecimalType) type, false);
} else if (type instanceof UriType) {
composeUriCore(prefix + "Uri", (UriType) type, false);
composeUriExtras(prefix + "Uri", (UriType) type, false);
} else if (type instanceof Base64BinaryType) {
composeBase64BinaryCore(prefix + "Base64Binary", (Base64BinaryType) type, false);
composeBase64BinaryExtras(prefix + "Base64Binary", (Base64BinaryType) type, false);
} else if (type instanceof TimeType) {
composeTimeCore(prefix + "Time", (TimeType) type, false);
composeTimeExtras(prefix + "Time", (TimeType) type, false);
} else if (type instanceof StringType) {
composeStringCore(prefix + "String", (StringType) type, false);
composeStringExtras(prefix + "String", (StringType) type, false);
} else if (type instanceof BooleanType) {
composeBooleanCore(prefix + "Boolean", (BooleanType) type, false);
composeBooleanExtras(prefix + "Boolean", (BooleanType) type, false);
} else if (type instanceof InstantType) {
composeInstantCore(prefix + "Instant", (InstantType) type, false);
composeInstantExtras(prefix + "Instant", (InstantType) type, false);
} else
throw new Error("Unhandled type");
}
use of org.hl7.fhir.dstu2.model.ContactPoint in project org.hl7.fhir.core by hapifhir.
the class ResourceUtilities method showDECHeader.
private static DataElement showDECHeader(StringBuilder b, Bundle bundle) {
DataElement meta = new DataElement();
DataElement prototype = (DataElement) bundle.getEntry().get(0).getResource();
meta.setPublisher(prototype.getPublisher());
meta.getContact().addAll(prototype.getContact());
meta.setStatus(prototype.getStatus());
meta.setDate(prototype.getDate());
meta.addElement().getType().addAll(prototype.getElement().get(0).getType());
for (BundleEntryComponent e : bundle.getEntry()) {
DataElement de = (DataElement) e.getResource();
if (!Base.compareDeep(de.getPublisherElement(), meta.getPublisherElement(), false))
meta.setPublisherElement(null);
if (!Base.compareDeep(de.getContact(), meta.getContact(), false))
meta.getContact().clear();
if (!Base.compareDeep(de.getStatusElement(), meta.getStatusElement(), false))
meta.setStatusElement(null);
if (!Base.compareDeep(de.getDateElement(), meta.getDateElement(), false))
meta.setDateElement(null);
if (!Base.compareDeep(de.getElement().get(0).getType(), meta.getElement().get(0).getType(), false))
meta.getElement().get(0).getType().clear();
}
if (meta.hasPublisher() || meta.hasContact() || meta.hasStatus() || meta.hasDate()) /* || meta.hasType() */
{
b.append("<table class=\"grid\">\r\n");
if (meta.hasPublisher())
b.append("<tr><td>Publisher:</td><td>" + meta.getPublisher() + "</td></tr>\r\n");
if (meta.hasContact()) {
b.append("<tr><td>Contacts:</td><td>");
boolean firsti = true;
for (DataElementContactComponent c : meta.getContact()) {
if (firsti)
firsti = false;
else
b.append("<br/>");
if (c.hasName())
b.append(Utilities.escapeXml(c.getName()) + ": ");
boolean first = true;
for (ContactPoint cp : c.getTelecom()) {
if (first)
first = false;
else
b.append(", ");
renderContactPoint(b, cp);
}
}
b.append("</td></tr>\r\n");
}
if (meta.hasStatus())
b.append("<tr><td>Status:</td><td>" + meta.getStatus().toString() + "</td></tr>\r\n");
if (meta.hasDate())
b.append("<tr><td>Date:</td><td>" + meta.getDateElement().asStringValue() + "</td></tr>\r\n");
if (meta.getElement().get(0).hasType())
b.append("<tr><td>Type:</td><td>" + renderType(meta.getElement().get(0).getType()) + "</td></tr>\r\n");
b.append("</table>\r\n");
}
return meta;
}
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