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

private String getCardinality(ElementDefinition ed, List<ElementDefinition> list) {
  int min = ed.getMin();
  int max = !ed.hasMax() || ed.getMax().equals("*") ? Integer.MAX_VALUE : Integer.parseInt(ed.getMax());
  while (ed != null && ed.getPath().contains(".")) {
    ed = findParent(ed, list);
    if (ed.getMax().equals("0"))
      max = 0;
    else if (!ed.getMax().equals("1") && !ed.hasSlicing())
      max = Integer.MAX_VALUE;
    if (ed.getMin() == 0)
      min = 0;
  }
  return Integer.toString(min)+".."+(max == Integer.MAX_VALUE ? "*" : Integer.toString(max));
}
 

private List<PropertyWrapper> splitExtensions(StructureDefinition profile, List<PropertyWrapper> children) throws UnsupportedEncodingException, IOException, FHIRException {
  List<PropertyWrapper> results = new ArrayList<PropertyWrapper>();
  Map<String, PropertyWrapper> map = new HashMap<String, PropertyWrapper>();
  for (PropertyWrapper p : children)
    if (p.getName().equals("extension") || p.getName().equals("modifierExtension")) {
      // we're going to split these up, and create a property for each url
      if (p.hasValues()) {
        for (BaseWrapper v : p.getValues()) {
          Extension ex  = (Extension) v.getBase();
          String url = ex.getUrl();
          StructureDefinition ed = context.fetchResource(StructureDefinition.class, url);
          if (p.getName().equals("modifierExtension") && ed == null)
            throw new DefinitionException("Unknown modifier extension "+url);
          PropertyWrapper pe = map.get(p.getName()+"["+url+"]");
          if (pe == null) {
            if (ed == null) {
              if (url.startsWith("http://hl7.org/fhir"))
                throw new DefinitionException("unknown extension "+url);
              // System.out.println("unknown extension "+url);
              pe = new PropertyWrapperDirect(new Property(p.getName()+"["+url+"]", p.getTypeCode(), p.getDefinition(), p.getMinCardinality(), p.getMaxCardinality(), ex));
            } else {
              ElementDefinition def = ed.getSnapshot().getElement().get(0);
              pe = new PropertyWrapperDirect(new Property(p.getName()+"["+url+"]", "Extension", def.getDefinition(), def.getMin(), def.getMax().equals("*") ? Integer.MAX_VALUE : Integer.parseInt(def.getMax()), ex));
              ((PropertyWrapperDirect) pe).wrapped.setStructure(ed);
            }
            results.add(pe);
          } else
            pe.getValues().add(v);
        }
      }
    } else
      results.add(p);
  return results;
}
 

/**
 * Change one cardinality.
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testCardinalityChange() 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.setMin(1);
  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.getMin() == 1;
          if (ok)
            f.setMin(0);
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation chenge cardinality test failed");
  } else 
    System.out.println("Snap shot generation chenge cardinality test passed");
}
 

/**
 * Generate a ShEx element definition
 * @param sd Containing structure definition
 * @param ed Containing element definition
 * @return ShEx definition
 */
private String genElementDefinition(StructureDefinition sd, ElementDefinition ed) {
  String id = ed.hasBase() ? ed.getBase().getPath() : ed.getPath();
  String shortId = id.substring(id.lastIndexOf(".") + 1);
  String defn;
  ST element_def;
  String card = ("*".equals(ed.getMax()) ? (ed.getMin() == 0 ? "*" : "+") : (ed.getMin() == 0 ? "?" : "")) + ";";

  if(id.endsWith("[x]")) {
    element_def = ed.getType().size() > 1? tmplt(INNER_SHAPE_TEMPLATE) : tmplt(ELEMENT_TEMPLATE);
    element_def.add("id", "");
  } else {
    element_def = tmplt(ELEMENT_TEMPLATE);
    element_def.add("id", "fhir:" + (id.charAt(0) == id.toLowerCase().charAt(0)? shortId : id) + " ");
  }

  List<ElementDefinition> children = ProfileUtilities.getChildList(sd, ed);
  if (children.size() > 0) {
    innerTypes.add(new ImmutablePair<StructureDefinition, ElementDefinition>(sd, ed));
    defn = simpleElement(sd, ed, id);
  } else if(id.endsWith("[x]")) {
    defn = genChoiceTypes(sd, ed, id);
  }
  else if (ed.getType().size() == 1) {
    // Single entry
    defn = genTypeRef(sd, ed, id, ed.getType().get(0));
  } else if (ed.getContentReference() != null) {
    // Reference to another element
    String ref = ed.getContentReference();
    if(!ref.startsWith("#"))
      throw new AssertionError("Not equipped to deal with absolute path references: " + ref);
    String refPath = null;
    for(ElementDefinition ed1: sd.getSnapshot().getElement()) {
      if(ed1.getId() != null && ed1.getId().equals(ref.substring(1))) {
        refPath = ed1.getPath();
        break;
      }
    }
    if(refPath == null)
      throw new AssertionError("Reference path not found: " + ref);
    // String typ = id.substring(0, id.indexOf(".") + 1) + ed.getContentReference().substring(1);
    defn = simpleElement(sd, ed, refPath);
  } else if(id.endsWith("[x]")) {
    defn = genChoiceTypes(sd, ed, id);
  } else {
    // TODO: Refactoring required here
    element_def = genAlternativeTypes(ed, id, shortId);
    element_def.add("id", id.charAt(0) == id.toLowerCase().charAt(0)? shortId : id);
    element_def.add("card", card);
    addComment(element_def, ed);
    return element_def.render();
  }
  element_def.add("defn", defn);
  element_def.add("card", card);
  addComment(element_def, ed);
  return element_def.render();
}
 

private void buildGroup(QuestionnaireItemComponent group, StructureDefinition profile, ElementDefinition element,
    List<ElementDefinition> parents, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups) throws FHIRException {
 group.setLinkId(element.getPath()); // todo: this will be wrong when we start slicing
 group.setText(element.getShort()); // todo - may need to prepend the name tail... 
 if (element.getComment() != null) {
 	Questionnaire.QuestionnaireItemComponent display = new Questionnaire.QuestionnaireItemComponent();
 	display.setType(QuestionnaireItemType.DISPLAY);
 	display.setText(element.getComment());
 	group.addItem(display);
 }
 group.setType(QuestionnaireItemType.GROUP);
 ToolingExtensions.addFlyOver(group, element.getDefinition());
  group.setRequired(element.getMin() > 0);
  if (element.getMin() > 0)
  	ToolingExtensions.addMin(group, element.getMin());
  group.setRepeats(!element.getMax().equals("1"));
  if (!element.getMax().equals("*"))
  	ToolingExtensions.addMax(group, Integer.parseInt(element.getMax()));

  for (org.hl7.fhir.dstu3.model.QuestionnaireResponse.QuestionnaireResponseItemComponent ag : answerGroups) {
    ag.setLinkId(group.getLinkId());
    ag.setText(group.getText());
  }

  // now, we iterate the children
  List<ElementDefinition> list = ProfileUtilities.getChildList(profile, element);
  for (ElementDefinition child : list) {

    if (!isExempt(element, child) && !parents.contains(child)) {
		List<ElementDefinition> nparents = new ArrayList<ElementDefinition>();
      nparents.addAll(parents);
      nparents.add(child);
      QuestionnaireItemComponent childGroup = group.addItem();
      childGroup.setType(QuestionnaireItemType.GROUP);

      List<QuestionnaireResponse.QuestionnaireResponseItemComponent> nResponse = new ArrayList<QuestionnaireResponse.QuestionnaireResponseItemComponent>();
      processExisting(child.getPath(), answerGroups, nResponse);
      // if the element has a type, we add a question. else we add a group on the basis that
      // it will have children of its own
      if (child.getType().isEmpty() || isAbstractType(child.getType())) 
        buildGroup(childGroup, profile, child, nparents, nResponse);
      else if (isInlineDataType(child.getType()))
        buildGroup(childGroup, profile, child, nparents, nResponse); // todo: get the right children for this one...
      else
        buildQuestion(childGroup, profile, child, child.getPath(), nResponse);
    }
  }
}
 

private void buildQuestion(QuestionnaireItemComponent group, StructureDefinition profile, ElementDefinition element, String path, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups) throws FHIRException {
    group.setLinkId(path);

    // in this context, we don't have any concepts to mark...
    group.setText(element.getShort()); // prefix with name?
    group.setRequired(element.getMin() > 0);
   if (element.getMin() > 0)
   	ToolingExtensions.addMin(group, element.getMin());
    group.setRepeats(!element.getMax().equals('1'));
   if (!element.getMax().equals("*"))
   	ToolingExtensions.addMax(group, Integer.parseInt(element.getMax()));

    for (QuestionnaireResponse.QuestionnaireResponseItemComponent ag : answerGroups) {
      ag.setLinkId(group.getLinkId());
      ag.setText(group.getText());
    }

    if (!Utilities.noString(element.getComment())) 
      ToolingExtensions.addFlyOver(group, element.getDefinition()+" "+element.getComment());
    else
      ToolingExtensions.addFlyOver(group, element.getDefinition());

    if (element.getType().size() > 1 || element.getType().get(0).getCode().equals("*")) {
      List<TypeRefComponent> types = expandTypeList(element.getType());
      Questionnaire.QuestionnaireItemComponent q = addQuestion(group, QuestionnaireItemType.CHOICE, element.getPath(), "_type", "type", null, makeTypeList(profile, types, element.getPath()));
        for (TypeRefComponent t : types) {
          Questionnaire.QuestionnaireItemComponent sub = q.addItem();
          sub.setType(QuestionnaireItemType.GROUP);
          sub.setLinkId(element.getPath()+"._"+t.getUserData("text"));
          sub.setText((String) t.getUserData("text"));
          // always optional, never repeats

          List<QuestionnaireResponse.QuestionnaireResponseItemComponent> selected = new ArrayList<QuestionnaireResponse.QuestionnaireResponseItemComponent>();
          selectTypes(profile, sub, t, answerGroups, selected);
          processDataType(profile, sub, element, element.getPath()+"._"+t.getUserData("text"), t, selected);
        }
    } else
      // now we have to build the question panel for each different data type
      processDataType(profile, group, element, element.getPath(), element.getType().get(0), answerGroups);

}
 

/**
 * we're going to slice Patient.extension and refer to extension by profile
 * 
 * implicit: whether to rely on implicit extension slicing
 */
private void testSlicingExtension(boolean implicit) 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);
  
  // set the slice up
  ElementDefinition id;
  if (!implicit) {
    id = focus.getDifferential().addElement();
    id.setPath("Patient.extension");
    id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator().setPath("url").setType(DiscriminatorType.VALUE);
    id.setMax("3");
  }
  // first slice: 
  id = focus.getDifferential().addElement();
  id.setPath("Patient.extension");
  id.setSliceName("name1");
  id.addType().setCode("Extension").setProfile("http://hl7.org/fhir/StructureDefinition/patient-birthTime");
  id.setMin(1);
  
  // second slice:
  id = focus.getDifferential().addElement();
  id.setPath("Patient.extension");
  id.setSliceName("name2");
  id.addType().setCode("Extension").setProfile("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");    
  
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  ProfileUtilities pu = new ProfileUtilities(context, messages, null);
  pu.generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // 2 different: extension slices 
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 2;
  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 <= 7 ? i : i + 2);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.extension")) {
          ok = f.hasSlicing() && (implicit || f.getMax().equals("3"));
          if (ok) {
            f.setSlicing(null);
            f.setMaxElement(b.getMaxElement());
          }
        }            
        if (!f.getPath().equals("Patient.extension")) // no compare that because the definitions get overwritten 
          ok = Base.compareDeep(b, f, true);
      }
    }
  }
  // now, check that the slices we skipped are correct:
  if (ok) {
    ElementDefinition d1 = focus.getSnapshot().getElement().get(8);
    ElementDefinition d2 = focus.getSnapshot().getElement().get(9);
    ok = d1.hasType() && d1.getType().get(0).hasProfile() && d2.hasType() && d2.getType().get(0).hasProfile() && !Base.compareDeep(d1.getType(), d2.getType(), true) &&
          d1.getMin() == 1 && d2.getMin() == 0 && d1.getMax().equals("1") && d2.getMax().equals("1");
    if (ok) {
      d1.getType().clear();
      d2.getType().clear();
      d1.setSliceName("x");
      d2.setSliceName("x");
      d1.setMin(0);
    }
    ok = Base.compareDeep(d1, d2, true);
    // for throughness, we could check against extension too, but this is not done now.
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation slicing extensions simple ("+(implicit ? "implicit" : "not implicit")+") failed");
  } else 
    System.out.println("Snap shot generation slicing extensions simple ("+(implicit ? "implicit" : "not implicit")+") passed");
}