Java Code Examples for org.hl7.fhir.dstu3.model.ElementDefinition#setDefinition()

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());
    }
  }
}
 

private void genElements(StructureDefinition sd, String path, NodeTreeEntry item) throws Exception {
  ElementDefinition ed = sd.getSnapshot().addElement();
  ed.setPath(path);
  ed.setMax(item.cardinality.max);
  ed.setMin(Integer.parseInt(item.cardinality.min));
  ed.setShort(texts.get(item.atCode).text);
  ed.setDefinition(texts.get(item.atCode).description);
  ed.setComment(texts.get(item.atCode).comment);
  Element te = findTypeElement(item.typeName);
  if (te.hasAttribute("profile"))
    ed.addType().setCode(te.getAttribute("fhir")).setProfile(te.getAttribute("profile"));
  else
  	ed.addType().setCode(te.getAttribute("fhir"));
   ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());

 	for (NodeTreeEntry child : item.children) {
 		genElements(sd, path+"."+child.name, child);
 	}
}
 

private boolean checkExtensionDoco(ElementDefinition base) {
  // see task 3970. For an extension, there's no point copying across all the underlying definitional stuff
  boolean isExtension = base.getPath().equals("Extension") || base.getPath().endsWith(".extension") || base.getPath().endsWith(".modifierExtension");
  if (isExtension) {
    base.setDefinition("An Extension");
    base.setShort("Extension");
    base.setCommentElement(null);
    base.setRequirementsElement(null);
    base.getAlias().clear();
    base.getMapping().clear();
  }
  return isExtension;
}
 

private void testSlicingTask8742() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Organization").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Organization.address");
  id.setMin(1);
  id.setMax("1");
  id.setMustSupport(true);
      
  id = focus.getDifferential().addElement();
  id.setPath("Organization.address.extension");
  id.setSliceName("USLabCountycodes");
  id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator().setPath("url").setType(DiscriminatorType.VALUE);
  id.setShort("County/Parish FIPS codes");
  id.setDefinition("County/Parish FIPS codes.");
  id.setRequirements("County/Parish Code SHALL use FIPS 6-4  ( INCITS 31:2009).");
  id.setMin(0);
  id.setMax("1");
  id.addType().setCode("Extension").setProfile("http://hl7.org/fhir/StructureDefinition/us-core-county");
  id.setMustSupport(true);
  id.getBinding().setStrength(BindingStrength.REQUIRED).setDescription("FIPS codes for US counties and county equivalent entities.").setValueSet(new Reference().setReference("http://hl7.org/fhir/ValueSet/fips-county"));
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // 14 for address with one sliced extension
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 13;
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation test 8742 failed");
  } else 
    System.out.println("Snap shot generation test 8742 passed");
}
 

private void processLoincCodes() {
	Element row = XMLUtil.getFirstChild(xml.getDocumentElement());
	int i = 0;
	while (row != null) {
		i++;
		if (i % 1000 == 0)
			System.out.print(".");
			String code = col(row, "LOINC_NUM");
			String comp = col(row, "COMPONENT");
			DataElement de = new DataElement();
			de.setId("loinc-"+code);
	    de.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
			bundle.getEntry().add(new BundleEntryComponent().setResource(de));
			Identifier id = new Identifier();
			id.setSystem("http://hl7.org/fhir/commondataelement/loinc");
			id.setValue(code);
			de.addIdentifier(id);
			de.setPublisher("Regenstrief + FHIR Project Team");
			if (!col(row, "STATUS").equals("ACTIVE"))
 				de.setStatus(PublicationStatus.DRAFT); // till we get good at this
			else
				de.setStatus(PublicationStatus.RETIRED);
			de.setDateElement(DateTimeType.now());
			de.setName(comp);
			ElementDefinition dee = de.addElement();

			// PROPERTY	ignore
			// TIME_ASPCT	
			// SYSTEM	
			// SCALE_TYP	
			// METHOD_TYP	
			// dee.getCategory().add(new CodeableConcept().setText(col(row, "CLASS")));
			// SOURCE	
			// DATE_LAST_CHANGED - should be in ?	
			// CHNG_TYPE	
			dee.setComment(col(row , "COMMENTS"));
			if (hasCol(row, "CONSUMER_NAME"))
				dee.addAlias(col(row, "CONSUMER_NAME"));	
			// MOLAR_MASS	
			// CLASSTYPE	
			// FORMULA	
			// SPECIES	
			// EXMPL_ANSWERS	
			// ACSSYM	
			// BASE_NAME - ? this is a relationship	
			// NAACCR_ID	
			// ---------- CODE_TABLE todo	
			// SURVEY_QUEST_TEXT	
			// SURVEY_QUEST_SRC	
			if (hasCol(row, "RELATEDNAMES2")) {
        String n = col(row, "RELATEDNAMES2");
        for (String s : n.split("\\;")) {
					if (!Utilities.noString(s))
						dee.addAlias(s);	
        }
			}
			dee.addAlias(col(row, "SHORTNAME"));	
			// ORDER_OBS	
			// CDISC Code	
			// HL7_FIELD_SUBFIELD_ID	
			//  ------------------ EXTERNAL_COPYRIGHT_NOTICE todo	
			dee.setDefinition(col(row, "LONG_COMMON_NAME"));	
			// HL7_V2_DATATYPE	
			String cc = makeType(col(row, "HL7_V3_DATATYPE"), code);
			if (cc != null)
			  dee.addType().setCode(cc);	
			// todo... CURATED_RANGE_AND_UNITS	
			// todo: DOCUMENT_SECTION	
			// STATUS_REASON	
			// STATUS_TEXT	
			// CHANGE_REASON_PUBLIC	
			// COMMON_TEST_RANK	
			// COMMON_ORDER_RANK	
			// COMMON_SI_TEST_RANK	
			// HL7_ATTACHMENT_STRUCTURE

			// units:
			// UNITSREQUIRED	
			// SUBMITTED_UNITS
			ToolingExtensions.setAllowableUnits(dee, makeUnits(col(row, "EXAMPLE_UNITS"), col(row, "EXAMPLE_UCUM_UNITS")));
			// EXAMPLE_SI_UCUM_UNITS	
		
		row = XMLUtil.getNextSibling(row);
	}
	System.out.println("done");
}
 

/**
   * left and right refer to the same element. Are they compatible?   
   * @param outcome 
   * @param outcome
   * @param path
   * @param left
   * @param right
   * @- if there's a problem that needs fixing in this code
   * @throws DefinitionException 
   * @throws IOException 
   * @throws FHIRFormatError 
   */
  private boolean compareElements(ProfileComparison outcome, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
//    preconditions:
    assert(path != null);
    assert(left != null);
    assert(right != null);
    assert(left.path().equals(right.path()));
    
    // we ignore slicing right now - we're going to clone the root one anyway, and then think about clones 
    // simple stuff
    ElementDefinition subset = new ElementDefinition();
    subset.setPath(left.path());
    
    // not allowed to be different: 
    subset.getRepresentation().addAll(left.current().getRepresentation()); // can't be bothered even testing this one
    if (!outcome.ruleCompares(subset, left.current().getDefaultValue(), right.current().getDefaultValue(), path+".defaultValue[x]", BOTH_NULL))
      return false;
    subset.setDefaultValue(left.current().getDefaultValue());
    if (!outcome.ruleEqual(path, subset, left.current().getMeaningWhenMissing(), right.current().getMeaningWhenMissing(), "meaningWhenMissing Must be the same", true))
      return false;
    subset.setMeaningWhenMissing(left.current().getMeaningWhenMissing());
    if (!outcome.ruleEqual(subset, left.current().getIsModifier(), right.current().getIsModifier(), path, "isModifier"))
      return false;
    subset.setIsModifier(left.current().getIsModifier());
    if (!outcome.ruleEqual(subset, left.current().getIsSummary(), right.current().getIsSummary(), path, "isSummary"))
      return false;
    subset.setIsSummary(left.current().getIsSummary());
    
    // descriptive properties from ElementDefinition - merge them:
    subset.setLabel(mergeText(subset, outcome, path, "label", left.current().getLabel(), right.current().getLabel()));
    subset.setShort(mergeText(subset, outcome, path, "short", left.current().getShort(), right.current().getShort()));
    subset.setDefinition(mergeText(subset, outcome, path, "definition", left.current().getDefinition(), right.current().getDefinition()));
    subset.setComment(mergeText(subset, outcome, path, "comments", left.current().getComment(), right.current().getComment()));
    subset.setRequirements(mergeText(subset, outcome, path, "requirements", left.current().getRequirements(), right.current().getRequirements()));
    subset.getCode().addAll(mergeCodings(left.current().getCode(), right.current().getCode()));
    subset.getAlias().addAll(mergeStrings(left.current().getAlias(), right.current().getAlias()));
    subset.getMapping().addAll(mergeMappings(left.current().getMapping(), right.current().getMapping()));
    // left will win for example
    subset.setExample(left.current().hasExample() ? left.current().getExample() : right.current().getExample());

    subset.setMustSupport(left.current().getMustSupport() || right.current().getMustSupport());
    ElementDefinition superset = subset.copy();


    // compare and intersect
    superset.setMin(unionMin(left.current().getMin(), right.current().getMin()));
    superset.setMax(unionMax(left.current().getMax(), right.current().getMax()));
    subset.setMin(intersectMin(left.current().getMin(), right.current().getMin()));
    subset.setMax(intersectMax(left.current().getMax(), right.current().getMax()));
    outcome.rule(subset, subset.getMax().equals("*") || Integer.parseInt(subset.getMax()) >= subset.getMin(), path, "Cardinality Mismatch: "+card(left)+"/"+card(right));
    
    superset.getType().addAll(unionTypes(path, left.current().getType(), right.current().getType()));
    subset.getType().addAll(intersectTypes(subset, outcome, path, left.current().getType(), right.current().getType()));
    outcome.rule(subset, !subset.getType().isEmpty() || (!left.current().hasType() && !right.current().hasType()), path, "Type Mismatch:\r\n  "+typeCode(left)+"\r\n  "+typeCode(right));
//    <fixed[x]><!-- ?? 0..1 * Value must be exactly this --></fixed[x]>
//    <pattern[x]><!-- ?? 0..1 * Value must have at least these property values --></pattern[x]>
    superset.setMaxLengthElement(unionMaxLength(left.current().getMaxLength(), right.current().getMaxLength()));
    subset.setMaxLengthElement(intersectMaxLength(left.current().getMaxLength(), right.current().getMaxLength()));
    if (left.current().hasBinding() || right.current().hasBinding()) {
      compareBindings(outcome, subset, superset, path, left.current(), right.current());
    }

    // note these are backwards
    superset.getConstraint().addAll(intersectConstraints(path, left.current().getConstraint(), right.current().getConstraint()));
    subset.getConstraint().addAll(unionConstraints(subset, outcome, path, left.current().getConstraint(), right.current().getConstraint()));

    // now process the slices
    if (left.current().hasSlicing() || right.current().hasSlicing()) {
      if (isExtension(left.path()))
        return compareExtensions(outcome, path, superset, subset, left, right);
//      return true;
      else
        throw new DefinitionException("Slicing is not handled yet");
    // todo: name 
    }

    // add the children
    outcome.subset.getSnapshot().getElement().add(subset);
    outcome.superset.getSnapshot().getElement().add(superset);
    return compareChildren(subset, outcome, path, left, right);
  }
 

/**
 * check that documentation appending is working
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testDocumentationAppend() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  ElementDefinition id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setDefinition("... some more doco");
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
  for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
    if (ok) {
      ElementDefinition b = base.getSnapshot().getElement().get(i);
      ElementDefinition f = focus.getSnapshot().getElement().get(i);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getDefinition().length() > b.getDefinition().length();
          if (ok) {
            f.setDefinition(null);
            b.setDefinition(null);
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation documentation append failed");
  } else 
    System.out.println("Snap shot generation documentation append test passed");
}