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

/**
 * Generate a definition for a referenced element
 * @param sd Containing structure definition
 * @param ed Inner element
 * @return ShEx representation of element reference
 */
private String genInnerTypeDef(StructureDefinition sd, ElementDefinition ed) {
  String path = ed.hasBase() ? ed.getBase().getPath() : ed.getPath();;
  ST element_reference = tmplt(SHAPE_DEFINITION_TEMPLATE);
  element_reference.add("resourceDecl", "");  // Not a resource
  element_reference.add("id", path);
  String comment = ed.getShort();
  element_reference.add("comment", comment == null? " " : "# " + comment);

  List<String> elements = new ArrayList<String>();
  for (ElementDefinition child: ProfileUtilities.getChildList(sd, path, null))
    elements.add(genElementDefinition(sd, child));

  element_reference.add("elements", StringUtils.join(elements, "\n"));
  return element_reference.render();
}
 

private String sliceSummary(ElementDefinition ed) {
  if (!ed.hasSlicing() && !ed.hasSliceName())
    return "";
  if (ed.hasSliceName())
    return " (slicename = "+ed.getSliceName()+")";
  
  StringBuilder b = new StringBuilder();
  boolean first = true;
  for (ElementDefinitionSlicingDiscriminatorComponent d : ed.getSlicing().getDiscriminator()) {
    if (first) 
      first = false;
    else
      b.append("|");
    b.append(d.getPath());
  }
  return " (slicing by "+b.toString()+")";
}
 

private void addChildMappings(StringBuilder b, String id, String indent, StructureDefinition sd, ElementDefinition ed, boolean inner) throws DefinitionException {
  boolean first = true;
  List<ElementDefinition> children = ProfileUtilities.getChildMap(sd, ed);
  for (ElementDefinition child : children) {
    if (first && inner) {
      b.append(" then {\r\n");
      first = false;
    }
    String map = getMapping(child, id);
    if (map != null) {
      b.append(indent+"  "+child.getPath()+": "+map);
      addChildMappings(b, id, indent+"  ", sd, child, true);
      b.append("\r\n");
    }
  }
  if (!first && inner)
    b.append(indent+"}");
  
}
 

public static List<ElementDefinition> getSliceList(StructureDefinition profile, ElementDefinition element) throws DefinitionException {
  if (!element.hasSlicing())
    throw new Error("getSliceList should only be called when the element has slicing");

  List<ElementDefinition> res = new ArrayList<ElementDefinition>();
  List<ElementDefinition> elements = profile.getSnapshot().getElement();
  String path = element.getPath();
  for (int index = elements.indexOf(element) + 1; index < elements.size(); index++) {
    ElementDefinition e = elements.get(index);
    if (e.getPath().startsWith(path + ".") || e.getPath().equals(path)) {
      // We want elements with the same path (until we hit an element that doesn't start with the same path)
      if (e.getPath().equals(element.getPath()))
        res.add(e);
    } else
      break;
  }
  return res;
}
 

private Element convertElement(Property property, Base base) throws FHIRException {
  if (base == null)
    return null;
  String tn = base.fhirType();
  StructureDefinition sd = context.fetchTypeDefinition(tn);
  if (sd == null)
    throw new FHIRException("Unable to find definition for type "+tn);
  Element res = new Element(property.getName(), property);
  if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE) 
    res.setValue(((PrimitiveType) base).asStringValue());

  List<ElementDefinition> children = ProfileUtilities.getChildMap(sd, sd.getSnapshot().getElementFirstRep()); 
  for (ElementDefinition child : children) {
    String n = tail(child.getPath());
    if (sd.getKind() != StructureDefinitionKind.PRIMITIVETYPE || !"value".equals(n)) {
      Base[] values = base.getProperty(n.hashCode(), n, false);
      if (values != null)
        for (Base value : values) {
          res.getChildren().add(convertElement(new Property(context, child, sd), value));
        }
    }
  }
  return res;
}
 

private void addComment(ST tmplt, ElementDefinition ed) {
  if(withComments && ed.hasShort() && !ed.getId().startsWith("Extension.")) {
    int nspaces;
    char[] sep;
    nspaces = Integer.max(COMMENT_COL - tmplt.add("comment", "#").render().indexOf('#'), MIN_COMMENT_SEP);
    tmplt.remove("comment");
    sep = new char[nspaces];
    Arrays.fill(sep, ' ');
    ArrayList<String> comment_lines = split_text(ed.getShort().replace("\n", " "), MAX_CHARS);
    StringBuilder comment = new StringBuilder("# ");
    char[] indent = new char[COMMENT_COL];
    Arrays.fill(indent, ' ');
    for(int i = 0; i < comment_lines.size();) {
      comment.append(comment_lines.get(i++));
      if(i < comment_lines.size())
        comment.append("\n" + new String(indent) + "# ");
    }
    tmplt.add("comment", new String(sep) + comment.toString());
  } else {
    tmplt.add("comment", " ");
  }
}
 

public boolean IsLogicalAndHasPrimitiveValue(String name) {
//		if (canBePrimitive!= null)
//			return canBePrimitive;
		
		canBePrimitive = false;
  	if (structure.getKind() != StructureDefinitionKind.LOGICAL)
  		return false;
  	if (!hasType(name))
  		return false;
  	StructureDefinition sd = context.fetchResource(StructureDefinition.class, structure.getUrl().substring(0, structure.getUrl().lastIndexOf("/")+1)+getType(name));
  	if (sd == null)
  	  sd = context.fetchTypeDefinition(getType(name));
    if (sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
      return true;
  	if (sd == null || sd.getKind() != StructureDefinitionKind.LOGICAL)
  		return false;
  	for (ElementDefinition ed : sd.getSnapshot().getElement()) {
  		if (ed.getPath().equals(sd.getId()+".value") && ed.getType().size() == 1 && isPrimitive(ed.getType().get(0).getCode())) {
  			canBePrimitive = true;
  			return true;
  		}
  	}
  	return false;
	}
 

private org.hl7.fhir.dstu3.elementmodel.Element createExampleElement(StructureDefinition profile, ElementDefinition ed, ExampleValueAccessor accessor) throws FHIRException {
  Type v = accessor.getExampleValue(ed);
  if (v != null) {
    return new ObjectConverter(context).convert(new Property(context, ed, profile), v);
  } else {
    org.hl7.fhir.dstu3.elementmodel.Element res = new org.hl7.fhir.dstu3.elementmodel.Element(tail(ed.getPath()), new Property(context, ed, profile));
    boolean hasValue = false;
    List<ElementDefinition> children = getChildMap(profile, ed);
    for (ElementDefinition child : children) {
      if (!child.hasContentReference()) {
      org.hl7.fhir.dstu3.elementmodel.Element e = createExampleElement(profile, child, accessor);
      if (e != null) {
        hasValue = true;
        res.getChildren().add(e);
      }
    }
    }
    if (hasValue)
      return res;
    else
      return null;
  }
}
 

private boolean isExempt(ElementDefinition element, ElementDefinition child) {
  String n = tail(child.getPath());
  String t = "";
  if (!element.getType().isEmpty())
    t =  element.getType().get(0).getCode();

  // we don't generate questions for the base stuff in every element
  if (t.equals("Resource")  && (n.equals("text") || n.equals("language") || n.equals("contained")))
    return true;
    // we don't generate questions for extensions
  else if (n.equals("extension") || n.equals("modifierExtension")) {
    if (child.getType().size() > 0 && !child.getType().get(0).hasProfile()) 
    return false;
    else
      return true;
  } else
    return false;
}
 

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());
    }
  }
}
 

@Override
public Type getExampleValue(ElementDefinition ed) {
  if (ed.hasFixed())
    return ed.getFixed();
  for (Extension ex : ed.getExtension()) {
   String ndx = ToolingExtensions.readStringExtension(ex, "index");
   Type value = ToolingExtensions.getExtension(ex, "exValue").getValue();
   if (index.equals(ndx) && value != null)
     return value;
  }
  return null;
}
 

private boolean hasMissingIds(List<ElementDefinition> list) {
  for (ElementDefinition ed : list) {
    if (!ed.hasId())
      return true;
  }    
  return false;
}
 

public static ElementDefinition fixElement(ElementDefinition element) {

        if (element.hasBinding() && element.getBinding().hasValueSetReference()) {
            // Remove invalid SNOMED reference
            if (element.getBinding().getValueSetReference().getReference().equals("http://snomed.info/sct")) {
                log.info("Removing invalid SNOMED valueSet reference");
                element.setBinding(null);
            } else
            if (removeTooCostlyECL(element.getBinding().getValueSetReference().getReference())) {
                log.info("Removing costly valueSet reference");
                element.setBinding(null);
            }
        }
        if (element.hasBinding() && element.getBinding().hasValueSetUriType()) {
            if (element.getBinding().getValueSetUriType().equals("http://snomed.info/sct")) {
                log.info("Removing invalid SNOMED valueSet reference");
                element.setBinding(null);
            } else
            if (removeTooCostlyECL(element.getBinding().getValueSetUriType().getValue())) {
                log.info("Removing costly valueSet reference");
                element.setBinding(null);
            }
        }

        if (element.hasBinding() && element.getBinding().hasValueSetReference()) {
            // Remove invalid SNOMED reference

        }
        if (element.hasBinding() && element.getBinding().hasValueSetUriType() &&
                element.getBinding().getValueSetUriType().equals("http://snomed.info/sct")) {
                log.info("Removing invalid SNOMED valueSet reference");
                element.setBinding(null);

        }

        return element;
    }
 

private void addCodeQuestions(QuestionnaireItemComponent group, ElementDefinition element, String path, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups) throws FHIRException {
  ToolingExtensions.addFhirType(group, "code");
  ValueSet vs = resolveValueSet(null, element.hasBinding() ? element.getBinding() : null);
  addQuestion(group, QuestionnaireItemType.CHOICE, path, "value", unCamelCase(tail(element.getPath())), answerGroups, vs);
  group.setText(null);
  for (QuestionnaireResponse.QuestionnaireResponseItemComponent ag : answerGroups)
    ag.setText(null);
}
 

/**
 * This is simple: we just create an empty differential, generate the snapshot, and then insist it must match the base 
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testSimple() 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("Patient");
  focus.setDerivation(TypeDerivationRule.CONSTRAINT);
  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);
        ok = Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation simple test failed");
  } else 
    System.out.println("Snap shot generation simple test passed");
}
 

private static void renderDE(DataElement de, List<String> cols, StringBuilder b, boolean profileLink, String linkBase) {
  b.append("<tr>");
  for (String col : cols) {
    String v;
    ElementDefinition dee = de.getElement().get(0);
    if (col.equals("DataElement.name")) {
      v = de.hasName() ? Utilities.escapeXml(de.getName()) : "";
    } else if (col.equals("DataElement.status")) {
      v = de.hasStatusElement() ? de.getStatusElement().asStringValue() : "";
    } else if (col.equals("DataElement.code")) {
      v = renderCoding(dee.getCode());
    } else if (col.equals("DataElement.type")) {
      v = dee.hasType() ? Utilities.escapeXml(dee.getType().get(0).getCode()) : "";
    } else if (col.equals("DataElement.units")) {
      v = renderDEUnits(ToolingExtensions.getAllowedUnits(dee));
    } else if (col.equals("DataElement.binding")) {
      v = renderBinding(dee.getBinding());
    } else if (col.equals("DataElement.minValue")) {
      v = ToolingExtensions.hasExtension(de, "http://hl7.org/fhir/StructureDefinition/minValue") ? Utilities.escapeXml(ToolingExtensions.readPrimitiveExtension(de, "http://hl7.org/fhir/StructureDefinition/minValue").asStringValue()) : "";
    } else if (col.equals("DataElement.maxValue")) {
      v = ToolingExtensions.hasExtension(de, "http://hl7.org/fhir/StructureDefinition/maxValue") ? Utilities.escapeXml(ToolingExtensions.readPrimitiveExtension(de, "http://hl7.org/fhir/StructureDefinition/maxValue").asStringValue()) : "";
    } else if (col.equals("DataElement.maxLength")) {
      v = ToolingExtensions.hasExtension(de, "http://hl7.org/fhir/StructureDefinition/maxLength") ? Utilities.escapeXml(ToolingExtensions.readPrimitiveExtension(de, "http://hl7.org/fhir/StructureDefinition/maxLength").asStringValue()) : "";
    } else if (col.equals("DataElement.mask")) {
      v = ToolingExtensions.hasExtension(de, "http://hl7.org/fhir/StructureDefinition/mask") ? Utilities.escapeXml(ToolingExtensions.readPrimitiveExtension(de, "http://hl7.org/fhir/StructureDefinition/mask").asStringValue()) : "";
    } else 
      throw new Error("Unknown column name: "+col);

    b.append("<td>"+v+"</td>");
  }
  if (profileLink) {
    b.append("<td><a href=\""+linkBase+"-"+de.getId()+".html\">Profile</a>, <a href=\"http://www.opencem.org/#/20140917/Intermountain/"+de.getId()+"\">CEM</a>");
    if (ToolingExtensions.hasExtension(de, ToolingExtensions.EXT_CIMI_REFERENCE)) 
      b.append(", <a href=\""+ToolingExtensions.readStringExtension(de, ToolingExtensions.EXT_CIMI_REFERENCE)+"\">CIMI</a>");
    b.append("</td>");
  }
  b.append("</tr>\r\n");
}
 

private void copyElements(StructureDefinition sd, List<ElementDefinition> list) {
  for (ElementDefinition ed : list) {
    if (ed.getPath().contains(".")) {
      ElementDefinition n = ed.copy();
      n.setPath(sd.getSnapshot().getElementFirstRep().getPath()+"."+ed.getPath().substring(ed.getPath().indexOf(".")+1));
      sd.getSnapshot().addElement(n);
    }
  }
}
 

private ElementDefinition getByPath(StructureDefinition base, String path) {
for (ElementDefinition ed : base.getSnapshot().getElement()) {
	if (ed.getPath().equals(path))
		return ed;
	if (ed.getPath().endsWith("[x]") && ed.getPath().length() <= path.length()-3 &&  ed.getPath().substring(0, ed.getPath().length()-3).equals(path.substring(0, ed.getPath().length()-3)))
		return ed;
  }
 return null;
}
 

private List<ElementDefinition> getChildren(List<ElementDefinition> all, ElementDefinition element) {
  List<ElementDefinition> result = new ArrayList<ElementDefinition>();
  int i = all.indexOf(element)+1;
  while (i < all.size() && all.get(i).getPath().length() > element.getPath().length()) {
    if ((all.get(i).getPath().substring(0, element.getPath().length()+1).equals(element.getPath()+".")) && !all.get(i).getPath().substring(element.getPath().length()+1).contains("."))
      result.add(all.get(i));
    i++;
  }
  return result;
}
 

private boolean ruleEqual(String path, ElementDefinition ed, String vLeft, String vRight, String description, boolean nullOK) {
  if (vLeft == null && vRight == null && nullOK)
    return true;
  if (vLeft == null && vRight == null) {
    messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, description+" and not null (null/null)", ValidationMessage.IssueSeverity.ERROR));
    if (ed != null)
      status(ed, ProfileUtilities.STATUS_ERROR);
  }
  if (vLeft == null || !vLeft.equals(vRight)) {
    messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, description+" ("+vLeft+"/"+vRight+")", ValidationMessage.IssueSeverity.ERROR));
    if (ed != null)
      status(ed, ProfileUtilities.STATUS_ERROR);
  }
  return true;
}
 

private boolean onlyInformationIsMapping(ElementDefinition d) {
  return !d.hasShort() && !d.hasDefinition() &&
      !d.hasRequirements() && !d.getAlias().isEmpty() && !d.hasMinElement() &&
      !d.hasMax() && !d.getType().isEmpty() && !d.hasContentReference() &&
      !d.hasExample() && !d.hasFixed() && !d.hasMaxLengthElement() &&
      !d.getCondition().isEmpty() && !d.getConstraint().isEmpty() && !d.hasMustSupportElement() &&
      !d.hasBinding();
}
 

@Override
public List<PropertyWrapper> children() {
  if (list == null) {
    children = ProfileUtilities.getChildList(structure, definition);
    list = new ArrayList<NarrativeGenerator.PropertyWrapper>();
    for (ElementDefinition child : children) {
      List<Element> elements = new ArrayList<Element>();
      XMLUtil.getNamedChildrenWithWildcard(element, tail(child.getPath()), elements);
      list.add(new PropertyWrapperElement(structure, child, elements));
    }
  }
  return list;
}
 

private void addQuantityQuestions(QuestionnaireItemComponent group, ElementDefinition element, String path, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups) throws FHIRException {
  ToolingExtensions.addFhirType(group, "Quantity");
  addQuestion(group, QuestionnaireItemType.CHOICE, path, "comparator", "comp:", answerGroups, resolveValueSet("http://hl7.org/fhir/vs/quantity-comparator"));
  addQuestion(group, QuestionnaireItemType.DECIMAL, path, "value", "value:", answerGroups);
  addQuestion(group, QuestionnaireItemType.STRING, path, "units", "units:", answerGroups);
  addQuestion(group, QuestionnaireItemType.STRING, path, "code", "coded units:", answerGroups);
  addQuestion(group, QuestionnaireItemType.STRING, path, "system", "units system:", answerGroups);
}
 

private String describeCardinality(ElementDefinition definition, ElementDefinition fallback, UnusedTracker tracker) {
  IntegerType min = definition.hasMinElement() ? definition.getMinElement() : new IntegerType();
  StringType max = definition.hasMaxElement() ? definition.getMaxElement() : new StringType();
  if (min.isEmpty() && fallback != null)
    min = fallback.getMinElement();
  if (max.isEmpty() && fallback != null)
    max = fallback.getMaxElement();

  tracker.used = !max.isEmpty() && !max.getValue().equals("0");

  if (min.isEmpty() && max.isEmpty())
    return null;
  else
    return (!min.hasValue() ? "" : Integer.toString(min.getValue())) + ".." + (!max.hasValue() ? "" : max.getValue());
}
 

private boolean exemptFromRendering(ElementDefinition child) {
  if (child == null)
    return false;
  if ("Composition.subject".equals(child.getPath()))
    return true;
  if ("Composition.section".equals(child.getPath()))
    return true;
  return false;
}
 

private boolean includeInSummary(ElementDefinition child) {
  if (child.getIsModifier())
    return true;
  if (child.getMustSupport())
    return true;
  if (child.getType().size() == 1) {
    String t = child.getType().get(0).getCode();
    if (t.equals("Address") || t.equals("Contact") || t.equals("Reference") || t.equals("Uri"))
      return false;
  }
  return true;
}
 

private ElementDefinition getUrlFor(StructureDefinition ed, ElementDefinition c) {
  int i = ed.getSnapshot().getElement().indexOf(c) + 1;
  while (i < ed.getSnapshot().getElement().size() && ed.getSnapshot().getElement().get(i).getPath().startsWith(c.getPath()+".")) {
    if (ed.getSnapshot().getElement().get(i).getPath().equals(c.getPath()+".url"))
      return ed.getSnapshot().getElement().get(i);
    i++;
  }
  return null;
}
 

private List<String> listReferenceProfiles(ElementDefinition ed) {
  List<String> res = new ArrayList<String>();
  for (TypeRefComponent tr : ed.getType()) {
    // code is null if we're dealing with "value" and profile is null if we just have Reference()
    if (tr.getCode()!= null && "Reference".equals(tr.getCode()) && tr.getTargetProfile() != null)
      res.add(tr.getTargetProfile());
  }
  return res ;
}
 

private void addDecimalQuestions(QuestionnaireItemComponent group, ElementDefinition element, String path, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups) throws FHIRException {
  ToolingExtensions.addFhirType(group, "decimal");
  addQuestion(group, QuestionnaireItemType.DECIMAL, path, "value", group.getText(), answerGroups);
 group.setText(null);
  for (QuestionnaireResponse.QuestionnaireResponseItemComponent ag : answerGroups)
    ag.setText(null);
}
 

private void addCodingQuestions(QuestionnaireItemComponent group, ElementDefinition element, String path, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups) throws FHIRException {
  ToolingExtensions.addFhirType(group, "Coding");
  addQuestion(group, answerTypeForBinding(element.hasBinding() ? element.getBinding() : null), path, "value", group.getText(), answerGroups, resolveValueSet(null, element.hasBinding() ? element.getBinding() : null));
  group.setText(null);
  for (QuestionnaireResponse.QuestionnaireResponseItemComponent ag : answerGroups)
    ag.setText(null);
}