Java Code Examples for org.hl7.fhir.dstu3.model.Base#compareDeep()

private boolean ruleCompares(ElementDefinition ed, Type vLeft, Type vRight, String path, int nullStatus) throws IOException {
  if (vLeft == null && vRight == null && nullStatus == BOTH_NULL)
    return true;
  if (vLeft == null && vRight == null) {
    messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Must be the same and not null (null/null)", ValidationMessage.IssueSeverity.ERROR));
    status(ed, ProfileUtilities.STATUS_ERROR);
  }
  if (vLeft == null && nullStatus == EITHER_NULL)
    return true;
  if (vRight == null && nullStatus == EITHER_NULL)
    return true;
  if (vLeft == null || vRight == null || !Base.compareDeep(vLeft, vRight, false)) {
    messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Must be the same ("+toString(vLeft)+"/"+toString(vRight)+")", ValidationMessage.IssueSeverity.ERROR));
    status(ed, ProfileUtilities.STATUS_ERROR);
  }
  return true;
}
 

private ElementDefinitionBindingComponent unionBindings(ElementDefinition ed, ProfileComparison outcome, String path, ElementDefinitionBindingComponent left, ElementDefinitionBindingComponent right) throws FHIRFormatError {
  ElementDefinitionBindingComponent union = new ElementDefinitionBindingComponent();
  if (left.getStrength().compareTo(right.getStrength()) < 0)
    union.setStrength(left.getStrength());
  else
    union.setStrength(right.getStrength());
  union.setDescription(mergeText(ed, outcome, path, "binding.description", left.getDescription(), right.getDescription()));
  if (Base.compareDeep(left.getValueSet(), right.getValueSet(), false))
    union.setValueSet(left.getValueSet());
  else {
    ValueSet lvs = resolveVS(outcome.left, left.getValueSet());
    ValueSet rvs = resolveVS(outcome.left, right.getValueSet());
    if (lvs != null && rvs != null)
      union.setValueSet(new Reference().setReference("#"+addValueSet(unite(ed, outcome, path, lvs, rvs))));
    else if (lvs != null)
      union.setValueSet(new Reference().setReference("#"+addValueSet(lvs)));
    else if (rvs != null)
      union.setValueSet(new Reference().setReference("#"+addValueSet(rvs)));
  }
  return union;
}
 

private boolean equalsDeep(org.hl7.fhir.dstu3.model.Property p, org.hl7.fhir.dstu3.model.Property o) {
  if (o == null || p == null)
    return false;
  if (p.getValues().size() != o.getValues().size())
    return false;
  for (int i = 0; i < p.getValues().size(); i++)
    if (!Base.compareDeep(p.getValues().get(i), o.getValues().get(i), true))
      return false;
  return true;
}
 

private boolean mergeIntoExisting(List<ConceptSetComponent> include, ConceptSetComponent inc) {
  for (ConceptSetComponent dst : include) {
    if (Base.compareDeep(dst,  inc, false))
      return true; // they're actually the same
    if (dst.getSystem().equals(inc.getSystem())) {
      if (inc.hasFilter() || dst.hasFilter()) {
        return false; // just add the new one as a a parallel
      } else if (inc.hasConcept() && dst.hasConcept()) {
        for (ConceptReferenceComponent cc : inc.getConcept()) {
          boolean found = false;
          for (ConceptReferenceComponent dd : dst.getConcept()) {
            if (dd.getCode().equals(cc.getCode()))
              found = true;
            if (found) {
              if (cc.hasDisplay() && !dd.hasDisplay())
                dd.setDisplay(cc.getDisplay());
              break;
            }
          }
          if (!found)
            dst.getConcept().add(cc.copy());
        }
      } else
        dst.getConcept().clear(); // one of them includes the entire code system 
    }
  }
  return false;
}
 

/**
 * 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");
}
 

/**
 * This is simple: we just create an empty differential, generate the snapshot, and then insist it must match the base. for a different resource with recursion 
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testSimple2() throws EOperationOutcome, Exception {
  StructureDefinition focus = new StructureDefinition();
  StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet").copy();
  focus.setUrl(Utilities.makeUuidUrn());
  focus.setBaseDefinition(base.getUrl());
  focus.setType(base.getType());
  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");
}
 

/**
 * 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");
}
 

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 (ContactDetail 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;
}
 

/**
 * 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");
}
 

/**
 * check that narrowing types is working
 * this one doesn't rename the path
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void textTypeNarrowing1() 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.deceased[x]");
  id.addType().setCode("dateTime");
  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.deceasedDateTime")) {
          ok = f.getType().size() == 1 && f.getType().get(0).getCode().equals("dateTime");
          if (ok) {
            f.getType().clear();
            b.getType().clear();
            f.setPath(b.getPath());
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation narrow type 1 failed");
  } else 
    System.out.println("Snap shot generation narrow type 1 test passed");
}
 

/**
 * check that narrowing types is working
 * this one renames the path
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void textTypeNarrowing2() 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.deceasedDateTime");
  id.addType().setCode("dateTime");
  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.deceasedDateTime")) {
          ok = f.getType().size() == 1 && f.getType().get(0).getCode().equals("dateTime");
          if (ok) {
            f.getType().clear();
            b.getType().clear();
            f.setPath(b.getPath());
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation narrow type 2 failed");
  } else 
    System.out.println("Snap shot generation narrow type 2 test passed");
}
 

/**
 * check that mapping resolution is working
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testMapping() 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.addMapping().setIdentity("rim").setMap("test");
  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.getMapping().size() > b.getMapping().size();
          if (ok) {
            f.getMapping().clear();
            b.getMapping().clear();
          }
        }
        ok = ok && Base.compareDeep(b, f, true);
      }
    }
  }
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation mapping changes failed");
  } else 
    System.out.println("Snap shot generation mapping changes test passed");
}
 

/**
 * Walking into a type 
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testTypeWalk() 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.setMustSupport(true);
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier.system");
  id.setMustSupport(true);
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // the derived should be 8 longer
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 8;
  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 <= 9 ? i : i + 8);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getMustSupport() && !b.getMustSupport();
          if (ok) {
            f.setMustSupportElement(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");
}
 

/**
 * Walking into a type, without explicitly doing so 
 * 
 * note: this currently fails.
 * 
 * @param context2
 * @
 * @throws EOperationOutcome 
 */
private void testTypeWalk2() 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.system");
  id.setMustSupport(true);
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // the derived should be 8 longer
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 8;
  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 <= 9 ? i : i + 8);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.getMustSupport() && !b.getMustSupport();
          if (ok) {
            f.setMustSupportElement(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");
}
 

/**
 * we're going to slice Patient.identifier
 */
private void testSlicingSimple() 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 = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator().setPath("use").setType(DiscriminatorType.VALUE);
  
  // first slice: 
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setSliceName("name1");
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier.use");
  id.setFixed(new CodeType("usual"));
  
  // second slice:
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier");
  id.setSliceName("name2");
  id = focus.getDifferential().addElement();
  id.setPath("Patient.identifier.use");
  id.setFixed(new CodeType("official"));
  
  
  List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
  new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );

  // 18 different: identifier + 8 inner children * 2 
  boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 18;
  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 <= 9 ? i : i + 18);
      if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath())) 
        ok = false;
      else {
        f.setBase(null);
        if (f.getPath().equals("Patient.identifier")) {
          ok = f.hasSlicing();
          if (ok)
            f.setSlicing(null);
        }            
        ok = Base.compareDeep(b, f, true);
      }
    }
  }
  // now, check that the slices we skipped are correct:
  for (int i = 10; i <= 18; i++) {
    if (ok) {
      ElementDefinition d1 = focus.getSnapshot().getElement().get(i);
      ElementDefinition d2 = focus.getSnapshot().getElement().get(i+9);
      if (d1.getPath().equals("Patient.identifier.use")) {
        ok = d1.hasFixed() && d2.hasFixed() && !Base.compareDeep(d1.getFixed(), d2.getFixed(), true);
        if (ok) {
          d1.setFixed(null);
          d2.setFixed(null);
        }
      }
      if (d1.getPath().equals("Patient.identifier")) {
        ok = d1.hasSliceName() && d2.hasSliceName() && !Base.compareDeep(d1.getSliceNameElement(), d2.getSliceNameElement(), true);
        if (ok) {
          d1.setSliceName(null);
          d2.setSliceName(null);
        }
      }
      ok = Base.compareDeep(d1, d2, true);
    }
  }
  // for throughness, we could check against identifier too, but this is not done now.
  
  if (!ok) {
    compareXml(base, focus);
    throw new FHIRException("Snap shot generation slicing failed");
  } else 
    System.out.println("Snap shot generation slicing passed");
  
}
 

/**
 * 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");
}