org.hl7.fhir.dstu3.model.UriType Java Examples

private void produceProperties(List<ElementDefinition> elements, String name, List<Property> properties, boolean attrMode, boolean snapshot) throws FHIRFormatError {
  for (Property p : properties) {
    if (p.isattr == attrMode) {
      ElementDefinition ed = new ElementDefinition();
      elements.add(ed);
      ed.setPath(name+"."+p.name);
      if (p.type.startsWith("xsd:"))
        ToolingExtensions.addStringExtension(ed.addType(), ToolingExtensions.EXT_XML_TYPE, p.type);
      else
        ed.addType().setCode(p.type);
      ed.setMin(p.min);
      ed.setMax(p.max == Integer.MAX_VALUE ? "*" : Integer.toString(p.max));
      ed.setDefinition(p.doco);
      if (p.isattr)
        ed.addRepresentation(PropertyRepresentation.XMLATTR);
      if (p.binding != null)
        ed.getBinding().setStrength(BindingStrength.REQUIRED).setValueSet(new UriType("http://hl7.org/fhir/iso21090/ValueSet/"+p.binding));
      if (snapshot)
        ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
    }
  }
}
 

public static Stream<Arguments> dstu3PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(BooleanType.class.getSimpleName(), new BooleanType()),
    Arguments.arguments(CodeType.class.getSimpleName(), new CodeType()),
    Arguments.arguments(DateType.class.getSimpleName(), new DateType()),
    Arguments.arguments(DateTimeType.class.getSimpleName(), new DateTimeType()),
    Arguments.arguments(DecimalType.class.getSimpleName(), new DecimalType()),
    Arguments.arguments(InstantType.class.getSimpleName(), new InstantType()),
    Arguments.arguments(PositiveIntType.class.getSimpleName(), new PositiveIntType()),
    Arguments.arguments(UnsignedIntType.class.getSimpleName(), new UnsignedIntType()),
    Arguments.arguments(IntegerType.class.getSimpleName(), new IntegerType()),
    Arguments.arguments(MarkdownType.class.getSimpleName(), new MarkdownType()),
    Arguments.arguments(OidType.class.getSimpleName(), new OidType()),
    Arguments.arguments(StringType.class.getSimpleName(), new StringType()),
    Arguments.arguments(TimeType.class.getSimpleName(), new TimeType()),
    Arguments.arguments(UuidType.class.getSimpleName(), new UuidType()),
    Arguments.arguments(Base64BinaryType.class.getSimpleName(), new Base64BinaryType()),
    Arguments.arguments(UriType.class.getSimpleName(), new UriType()));
}
 

public static Stream<Arguments> r5PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(org.hl7.fhir.r5.model.BooleanType.class.getSimpleName(), new org.hl7.fhir.r5.model.BooleanType()),
    Arguments.arguments(org.hl7.fhir.r5.model.CodeType.class.getSimpleName(), new org.hl7.fhir.r5.model.CodeType()),
    Arguments.arguments(org.hl7.fhir.r5.model.DateType.class.getSimpleName(), new org.hl7.fhir.r5.model.DateType()),
    Arguments.arguments(org.hl7.fhir.r5.model.DateTimeType.class.getSimpleName(), new org.hl7.fhir.r5.model.DateTimeType()),
    Arguments.arguments(org.hl7.fhir.r5.model.DecimalType.class.getSimpleName(), new org.hl7.fhir.r5.model.DecimalType()),
    Arguments.arguments(org.hl7.fhir.r5.model.InstantType.class.getSimpleName(), new org.hl7.fhir.r5.model.InstantType()),
    Arguments.arguments(org.hl7.fhir.r5.model.PositiveIntType.class.getSimpleName(), new org.hl7.fhir.r5.model.PositiveIntType()),
    Arguments.arguments(org.hl7.fhir.r5.model.UnsignedIntType.class.getSimpleName(), new org.hl7.fhir.r5.model.UnsignedIntType()),
    Arguments.arguments(org.hl7.fhir.r5.model.IntegerType.class.getSimpleName(), new org.hl7.fhir.r5.model.IntegerType()),
    Arguments.arguments(org.hl7.fhir.r5.model.MarkdownType.class.getSimpleName(), new org.hl7.fhir.r5.model.MarkdownType()),
    Arguments.arguments(org.hl7.fhir.r5.model.OidType.class.getSimpleName(), new org.hl7.fhir.r5.model.OidType()),
    Arguments.arguments(org.hl7.fhir.r5.model.StringType.class.getSimpleName(), new org.hl7.fhir.r5.model.StringType()),
    Arguments.arguments(org.hl7.fhir.r5.model.TimeType.class.getSimpleName(), new org.hl7.fhir.r5.model.TimeType()),
    Arguments.arguments(org.hl7.fhir.r5.model.UuidType.class.getSimpleName(), new org.hl7.fhir.r5.model.UuidType()),
    Arguments.arguments(org.hl7.fhir.r5.model.Base64BinaryType.class.getSimpleName(), new org.hl7.fhir.r5.model.Base64BinaryType()),
    Arguments.arguments(org.hl7.fhir.r5.model.UriType.class.getSimpleName(), new org.hl7.fhir.r5.model.UriType()));
}
 

public static Stream<Arguments> dstu3PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(BooleanType.class.getSimpleName(), new BooleanType()),
    Arguments.arguments(CodeType.class.getSimpleName(), new CodeType()),
    Arguments.arguments(DateType.class.getSimpleName(), new DateType()),
    Arguments.arguments(DateTimeType.class.getSimpleName(), new DateTimeType()),
    Arguments.arguments(DecimalType.class.getSimpleName(), new DecimalType()),
    Arguments.arguments(InstantType.class.getSimpleName(), new InstantType()),
    Arguments.arguments(PositiveIntType.class.getSimpleName(), new PositiveIntType()),
    Arguments.arguments(UnsignedIntType.class.getSimpleName(), new UnsignedIntType()),
    Arguments.arguments(IntegerType.class.getSimpleName(), new IntegerType()),
    Arguments.arguments(MarkdownType.class.getSimpleName(), new MarkdownType()),
    Arguments.arguments(OidType.class.getSimpleName(), new OidType()),
    Arguments.arguments(StringType.class.getSimpleName(), new StringType()),
    Arguments.arguments(TimeType.class.getSimpleName(), new TimeType()),
    Arguments.arguments(UuidType.class.getSimpleName(), new UuidType()),
    Arguments.arguments(Base64BinaryType.class.getSimpleName(), new Base64BinaryType()),
    Arguments.arguments(UriType.class.getSimpleName(), new UriType()));
}
 

public static Stream<Arguments> r4PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(org.hl7.fhir.r4.model.BooleanType.class.getSimpleName(), new org.hl7.fhir.r4.model.BooleanType()),
    Arguments.arguments(org.hl7.fhir.r4.model.CodeType.class.getSimpleName(), new org.hl7.fhir.r4.model.CodeType()),
    Arguments.arguments(org.hl7.fhir.r4.model.DateType.class.getSimpleName(), new org.hl7.fhir.r4.model.DateType()),
    Arguments.arguments(org.hl7.fhir.r4.model.DateTimeType.class.getSimpleName(), new org.hl7.fhir.r4.model.DateTimeType()),
    Arguments.arguments(org.hl7.fhir.r4.model.DecimalType.class.getSimpleName(), new org.hl7.fhir.r4.model.DecimalType()),
    Arguments.arguments(org.hl7.fhir.r4.model.InstantType.class.getSimpleName(), new org.hl7.fhir.r4.model.InstantType()),
    Arguments.arguments(org.hl7.fhir.r4.model.PositiveIntType.class.getSimpleName(), new org.hl7.fhir.r4.model.PositiveIntType()),
    Arguments.arguments(org.hl7.fhir.r4.model.UnsignedIntType.class.getSimpleName(), new org.hl7.fhir.r4.model.UnsignedIntType()),
    Arguments.arguments(org.hl7.fhir.r4.model.IntegerType.class.getSimpleName(), new org.hl7.fhir.r4.model.IntegerType()),
    Arguments.arguments(org.hl7.fhir.r4.model.MarkdownType.class.getSimpleName(), new org.hl7.fhir.r4.model.MarkdownType()),
    Arguments.arguments(org.hl7.fhir.r4.model.OidType.class.getSimpleName(), new org.hl7.fhir.r4.model.OidType()),
    Arguments.arguments(org.hl7.fhir.r4.model.StringType.class.getSimpleName(), new org.hl7.fhir.r4.model.StringType()),
    Arguments.arguments(org.hl7.fhir.r4.model.TimeType.class.getSimpleName(), new org.hl7.fhir.r4.model.TimeType()),
    Arguments.arguments(org.hl7.fhir.r4.model.UuidType.class.getSimpleName(), new org.hl7.fhir.r4.model.UuidType()),
    Arguments.arguments(org.hl7.fhir.r4.model.Base64BinaryType.class.getSimpleName(), new org.hl7.fhir.r4.model.Base64BinaryType()),
    Arguments.arguments(org.hl7.fhir.r4.model.UriType.class.getSimpleName(), new org.hl7.fhir.r4.model.UriType()));
}
 

private String getIncSummary(ConceptSetComponent cc) {
  CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
  for (UriType vs : cc.getValueSet()) {
    b.append(vs.asStringValue());
  }
  String vsd =
    b.length() > 0 ? " where the codes are in the value sets (" + b.toString() + ")" : "";
  String system = cc.getSystem();
  if (cc.hasConcept()) {
    return Integer.toString(cc.getConcept().size()) + " codes from " + system + vsd;
  }
  if (cc.hasFilter()) {
    String s = "";
    for (ConceptSetFilterComponent f : cc.getFilter()) {
      if (!Utilities.noString(s)) {
        s = s + " & ";
      }
      s = s + f.getProperty() + " " + f.getOp().toCode() + " " + f.getValue();
    }
    return "from " + system + " where " + s + vsd;
  }
  return "All codes from " + system + vsd;
}
 

private Slicer generateSlicer(ElementDefinition child, ElementDefinitionSlicingComponent slicing, StructureDefinition structure) {
  // given a child in a structure, it's sliced. figure out the slicing xpath
  if (child.getPath().endsWith(".extension")) {
    ElementDefinition ued = getUrlFor(structure, child);
    if ((ued == null || !ued.hasFixed()) && !(child.hasType() && (child.getType().get(0).hasProfile())))
      return new Slicer(false);
    else {
    Slicer s = new Slicer(true);
    String url = (ued == null || !ued.hasFixed()) ? child.getType().get(0).getProfile() : ((UriType) ued.getFixed()).asStringValue();
    s.name = " with URL = '"+url+"'";
    s.criteria = "[@url = '"+url+"']";
    return s;
    }
  } else
    return new Slicer(false);
}
 

private ValueSet resolveBindingReference(DomainResource ctxt, Type reference) {
  if (reference instanceof UriType) {
    return context.fetchResource(ValueSet.class, ((UriType) reference).getValue().toString());
  }
  else if (reference instanceof Reference) {
    String s = ((Reference) reference).getReference();
    if (s.startsWith("#")) {
      for (Resource c : ctxt.getContained()) {
        if (c.getId().equals(s.substring(1)) && (c instanceof ValueSet))
          return (ValueSet) c;
      }
      return null;
    } else {
      return context.fetchResource(ValueSet.class, ((Reference) reference).getReference());
    }
  }
  else
    return null;
}
 

public static String readStringExtension(Element c, String uri) {
  Extension ex = ExtensionHelper.getExtension(c, uri);
  if (ex == null)
    return null;
  if (ex.getValue() instanceof UriType)
    return ((UriType) ex.getValue()).getValue();
  if (ex.getValue() instanceof CodeType)
    return ((CodeType) ex.getValue()).getValue();
  if (ex.getValue() instanceof IntegerType)
    return ((IntegerType) ex.getValue()).asStringValue();
  if ((ex.getValue() instanceof MarkdownType))
    return ((MarkdownType) ex.getValue()).getValue();
  if (!(ex.getValue() instanceof StringType))
    return null;
  return ((StringType) ex.getValue()).getValue();
}
 

public static String readStringExtension(DomainResource c, String uri) {
  Extension ex = getExtension(c, uri);
  if (ex == null)
    return null;
  if ((ex.getValue() instanceof StringType))
    return ((StringType) ex.getValue()).getValue();
  if ((ex.getValue() instanceof UriType))
    return ((UriType) ex.getValue()).getValue();
  if (ex.getValue() instanceof CodeType)
    return ((CodeType) ex.getValue()).getValue();
  if (ex.getValue() instanceof IntegerType)
    return ((IntegerType) ex.getValue()).asStringValue();
  if ((ex.getValue() instanceof MarkdownType))
    return ((MarkdownType) ex.getValue()).getValue();
  return null;
}
 

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;
}
 

public static void addDEReference(DataElement de, String value) {
  for (Extension e : de.getExtension()) 
    if (e.getUrl().equals(EXT_CIMI_REFERENCE)) {
      e.setValue(new UriType(value));
      return;
    }
  de.getExtension().add(new Extension().setUrl(EXT_CIMI_REFERENCE).setValue(new UriType(value)));
}
 

public static void setIntegerExtension(DomainResource resource, String uri, int value) {
  Extension ext = getExtension(resource, uri);
  if (ext != null)
    ext.setValue(new IntegerType(value));
  else
    resource.getExtension().add(new Extension(new UriType(uri)).setValue(new IntegerType(value)));
}
 

public static void setCodeExtension(DomainResource resource, String uri, String value) {
  Extension ext = getExtension(resource, uri);
  if (ext != null)
    ext.setValue(new CodeType(value));
  else
    resource.getExtension().add(new Extension(new UriType(uri)).setValue(new CodeType(value)));
}
 

public static void setStringExtension(Element element, String uri, String value) {
  Extension ext = getExtension(element, uri);
  if (ext != null)
    ext.setValue(new StringType(value));
  else
    element.getExtension().add(new Extension(new UriType(uri)).setValue(new StringType(value)));
}
 

public static void setStringExtension(DomainResource resource, String uri, String value) {
  Extension ext = getExtension(resource, uri);
  if (ext != null)
    ext.setValue(new StringType(value));
  else
    resource.getExtension().add(new Extension(new UriType(uri)).setValue(new StringType(value)));
}
 

private static void renderImports(StringBuilder b, StructureMap map) {
	for (UriType s : map.getImport()) {
		b.append("imports \"");
		b.append(s.getValue());
		b.append("\"\r\n");
	}
	if (map.hasImport())
		b.append("\r\n");
}
 

private ValueSet resolveVS(StructureDefinition ctxtLeft, Type vsRef) {
  if (vsRef == null)
    return null;
  if (vsRef instanceof UriType)
    return null;
  else {
    Reference ref = (Reference) vsRef;
    if (!ref.hasReference())
      return null;
    return context.fetchResource(ValueSet.class, ref.getReference());
  }
}
 

public static void checkShareable(ValueSet vs) {
  if (!vs.hasMeta())
    throw new Error("ValueSet "+vs.getUrl()+" is not shareable");
  for (UriType t : vs.getMeta().getProfile()) {
    if (t.getValue().equals("http://hl7.org/fhir/StructureDefinition/shareablevalueset"))
      return;
  }
  throw new Error("ValueSet "+vs.getUrl()+" is not shareable");    
}
 

public static ValueSet makeShareable(ValueSet vs) {
  if (!vs.hasMeta())
    vs.setMeta(new Meta());
  for (UriType t : vs.getMeta().getProfile()) 
    if (t.getValue().equals("http://hl7.org/fhir/StructureDefinition/shareablevalueset"))
      return vs;
  vs.getMeta().getProfile().add(new UriType("http://hl7.org/fhir/StructureDefinition/shareablevalueset"));
  return vs;
}
 

public static CodeSystem makeShareable(CodeSystem cs) {
  if (!cs.hasMeta())
    cs.setMeta(new Meta());
  for (UriType t : cs.getMeta().getProfile()) 
    if (t.getValue().equals("http://hl7.org/fhir/StructureDefinition/shareablecodesystem"))
      return cs;
  cs.getMeta().getProfile().add(new UriType("http://hl7.org/fhir/StructureDefinition/shareablecodesystem"));
  return cs;
}
 

public void setTargetSystem(UriType theTargetSystem) {
	myTargetSystem = theTargetSystem;
}
 

private Base runTransform(String ruleId, TransformContext context, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, Variables vars, Base dest, String element, String srcVar) throws FHIRException {
	  try {
	    switch (tgt.getTransform()) {
	    case CREATE :
	      String tn;
	      if (tgt.getParameter().isEmpty()) {
	        // we have to work out the type. First, we see if there is a single type for the target. If there is, we use that
	        String[] types = dest.getTypesForProperty(element.hashCode(), element);
	        if (types.length == 1 && !"*".equals(types[0]) && !types[0].equals("Resource"))
	          tn = types[0];
	        else if (srcVar != null) {
	          tn = determineTypeFromSourceType(map, group, vars.get(VariableMode.INPUT, srcVar), types);
	        } else
	          throw new Error("Cannot determine type implicitly because there is no single input variable");
	      } else
	        tn = getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString());
	      Base res = services != null ? services.createType(context.getAppInfo(), tn) : ResourceFactory.createResourceOrType(tn);
	      if (res.isResource() && !res.fhirType().equals("Parameters")) {
//	        res.setIdBase(tgt.getParameter().size() > 1 ? getParamString(vars, tgt.getParameter().get(0)) : UUID.randomUUID().toString().toLowerCase());
	        if (services != null) 
	          res = services.createResource(context.getAppInfo(), res);
	      }
	      if (tgt.hasUserData("profile"))
	        res.setUserData("profile", tgt.getUserData("profile"));
	      return res;
	    case COPY : 
	      return getParam(vars, tgt.getParameter().get(0));
	    case EVALUATE :
	      ExpressionNode expr = (ExpressionNode) tgt.getUserData(MAP_EXPRESSION);
	      if (expr == null) {
	        expr = fpe.parse(getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString()));
	        tgt.setUserData(MAP_WHERE_EXPRESSION, expr);
	      }
	      List<Base> v = fpe.evaluate(vars, null, tgt.getParameter().size() == 2 ? getParam(vars, tgt.getParameter().get(0)) : new BooleanType(false), expr);
	      if (v.size() == 0)
	        return null;
	      else if (v.size() != 1)
	        throw new FHIRException("Rule \""+ruleId+"\": Evaluation of "+expr.toString()+" returned "+Integer.toString(v.size())+" objects");
	      else
	        return v.get(0);

	    case TRUNCATE : 
	      String src = getParamString(vars, tgt.getParameter().get(0));
	      String len = getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString());
	      if (Utilities.isInteger(len)) {
	        int l = Integer.parseInt(len);
	        if (src.length() > l)
	          src = src.substring(0, l);
	      }
	      return new StringType(src);
	    case ESCAPE : 
	      throw new Error("Rule \""+ruleId+"\": Transform "+tgt.getTransform().toCode()+" not supported yet");
	    case CAST :
	      throw new Error("Rule \""+ruleId+"\": Transform "+tgt.getTransform().toCode()+" not supported yet");
	    case APPEND : 
	      throw new Error("Rule \""+ruleId+"\": Transform "+tgt.getTransform().toCode()+" not supported yet");
	    case TRANSLATE : 
	      return translate(context, map, vars, tgt.getParameter());
	    case REFERENCE :
	      Base b = getParam(vars, tgt.getParameter().get(0));
	      if (b == null)
	        throw new FHIRException("Rule \""+ruleId+"\": Unable to find parameter "+((IdType) tgt.getParameter().get(0).getValue()).asStringValue());
	      if (!b.isResource())
	        throw new FHIRException("Rule \""+ruleId+"\": Transform engine cannot point at an element of type "+b.fhirType());
	      else {
	        String id = b.getIdBase();
	        if (id == null) {
	          id = UUID.randomUUID().toString().toLowerCase();
	          b.setIdBase(id);
	        }
	        return new Reference().setReference(b.fhirType()+"/"+id);
	      }
	    case DATEOP :
	      throw new Error("Rule \""+ruleId+"\": Transform "+tgt.getTransform().toCode()+" not supported yet");
	    case UUID :
	      return new IdType(UUID.randomUUID().toString());
	    case POINTER :
	      b = getParam(vars, tgt.getParameter().get(0));
	      if (b instanceof Resource)
	        return new UriType("urn:uuid:"+((Resource) b).getId());
	      else
	        throw new FHIRException("Rule \""+ruleId+"\": Transform engine cannot point at an element of type "+b.fhirType());
	    case CC:
	      CodeableConcept cc = new CodeableConcept();
	      cc.addCoding(buildCoding(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString()), getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString())));
	      return cc;
	    case C: 
	      Coding c = buildCoding(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString()), getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString()));
	      return c;
	    default:
	      throw new Error("Rule \""+ruleId+"\": Transform Unknown: "+tgt.getTransform().toCode());
	    }
	  } catch (Exception e) {
	    throw new FHIRException("Exception executing transform "+tgt.toString()+" on Rule \""+ruleId+"\": "+e.getMessage(), e);
	  }
	}
 

public UriType getTargetSystem() {
	return myTargetSystem;
}
 

public void setTarget(UriType theTarget) {
	myTarget = theTarget;
}
 

public UriType getTarget() {
	return myTarget;
}
 

public void setSource(UriType theSource) {
	mySource = theSource;
}
 

public UriType getSource() {
	return mySource;
}
 

public TranslationRequests setTargetSystem(UriType theTargetSystem) {
	myTargetSystem = theTargetSystem;
	return this;
}
 

public UriType getTargetSystem() {
	return myTargetSystem;
}