use of org.hl7.fhir.dstu3.conformance.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method compareElements.
/**
* 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
*/
private boolean compareElements(ProfileComparison outcome, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException {
// 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:
// can't be bothered even testing this one
subset.getRepresentation().addAll(left.current().getRepresentation());
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.setComments(mergeText(subset, outcome, path, "comments", left.current().getComments(), right.current().getComments()));
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);
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);
}
use of org.hl7.fhir.dstu3.conformance.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method mergeText.
// result.addAll(left);
// for (TypeRefComponent r : right) {
// boolean found = false;
// TypeRefComponent c = r.copy();
// for (TypeRefComponent l : left)
// if (Utilities.equals(l.getCode(), r.getCode())) {
//
// }
// if (l.getCode().equals("Reference") && r.getCode().equals("Reference")) {
// if (Base.compareDeep(l.getProfile(), r.getProfile(), false)) {
// found = true;
// }
// } else
// found = true;
// // todo: compare profiles
// // todo: compare aggregation values
// }
// if (!found)
// result.add(c);
// }
// }
private String mergeText(ElementDefinition ed, ProfileComparison outcome, String path, String name, String left, String right) {
if (left == null && right == null)
return null;
if (left == null)
return right;
if (right == null)
return left;
if (left.equalsIgnoreCase(right))
return left;
if (path != null) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path, "Elements differ in definition for " + name + ":\r\n \"" + left + "\"\r\n \"" + right + "\"", "Elements differ in definition for " + name + ":<br/>\"" + Utilities.escapeXml(left) + "\"<br/>\"" + Utilities.escapeXml(right) + "\"", IssueSeverity.INFORMATION));
status(ed, ProfileUtilities.STATUS_HINT);
}
return "left: " + left + "; right: " + right;
}
use of org.hl7.fhir.dstu3.conformance.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilitiesTests method execute.
public void execute(String[] args) throws FileNotFoundException, IOException, FHIRException {
System.out.println("loading context");
context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation.zip"));
comp = new ProfileComparer(context);
compare("patient-daf-dafpatient.profile.xml", "patient-qicore-qicore-patient.profile.xml");
compare("encounter-daf-dafencounter.profile.xml", "encounter-qicore-qicore-encounter.profile.xml");
compare("substance-daf-dafsubstance.profile.xml", "substance-qicore-qicore-substance.profile.xml");
compare("medication-daf-dafmedication.profile.xml", "medication-qicore-qicore-medication.profile.xml");
compare("procedure-daf-dafprocedure.profile.xml", "procedure-qicore-qicore-procedure.profile.xml");
compare("familymemberhistory-daf-daffamilymemberhistory.profile.xml", "familymemberhistory-qicore-qicore-familymemberhistory.profile.xml");
compare("immunization-daf-dafimmunization.profile.xml", "immunization-qicore-qicore-immunization.profile.xml");
compare("condition-daf-dafcondition.profile.xml", "condition-qicore-qicore-condition.profile.xml");
compare("allergyintolerance-daf-dafallergyintolerance.profile.xml", "allergyintolerance-qicore-qicore-allergyintolerance.profile.xml");
compare("medicationadministration-daf-dafmedicationadministration.profile.xml", "medicationadministration-qicore-qicore-medicationadministration.profile.xml");
compare("medicationdispense-daf-dafmedicationdispense.profile.xml", "medicationdispense-qicore-qicore-medicationdispense.profile.xml");
compare("medicationprescription-daf-dafmedicationprescription.profile.xml", "medicationprescription-qicore-qicore-medicationprescription.profile.xml");
compare("medicationstatement-daf-dafmedicationstatement.profile.xml", "medicationstatement-qicore-qicore-medicationstatement.profile.xml");
compare("observation-daf-smokingstatus-dafsmokingstatus.profile.xml", "observation-qicore-qicore-observation.profile.xml");
compare("observation-daf-vitalsigns-dafvitalsigns.profile.xml", "observation-qicore-qicore-observation.profile.xml");
// compare("observation-daf-results-dafresultobs.profile.xml", "observation-qicore-qicore-observation.profile.xml");
// compare("diagnosticorder-daf-dafdiagnosticorder.profile.xml", "diagnosticorder-qicore-qicore-diagnosticorder.profile.xml");
// compare("diagnosticreport-daf-dafdiagnosticreport.profile.xml", "diagnosticreport-qicore-qicore-diagnosticreport.profile.xml");
System.out.println("processing output");
for (ProfileComparison outcome : comp.getComparisons()) {
if (outcome.getSubset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")), outcome.getSubset());
if (outcome.getSuperset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
System.out.println("\r\n" + outcome.getId() + ": Comparison of " + outcome.getLeft().getUrl() + " and " + outcome.getRight().getUrl());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.INFORMATION)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.WARNING)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.ERROR)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.FATAL)
System.out.println(vm.summary());
System.out.println("done. " + Integer.toString(outcome.getMessages().size()) + " messages");
System.out.println("=================================================================");
}
}
use of org.hl7.fhir.dstu3.conformance.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method compareBindings.
private boolean compareBindings(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError, DefinitionException, IOException {
assert (lDef.hasBinding() || rDef.hasBinding());
if (!lDef.hasBinding()) {
subset.setBinding(rDef.getBinding());
// technically, the super set is unbound, but that's not very useful - so we use the provided on as an example
superset.setBinding(rDef.getBinding().copy());
superset.getBinding().setStrength(BindingStrength.EXAMPLE);
return true;
}
if (!rDef.hasBinding()) {
subset.setBinding(lDef.getBinding());
superset.setBinding(lDef.getBinding().copy());
superset.getBinding().setStrength(BindingStrength.EXAMPLE);
return true;
}
ElementDefinitionBindingComponent left = lDef.getBinding();
ElementDefinitionBindingComponent right = rDef.getBinding();
if (Base.compareDeep(left, right, false)) {
subset.setBinding(left);
superset.setBinding(right);
}
// superset:
if (isPreferredOrExample(left) && isPreferredOrExample(right)) {
if (right.getStrength() == BindingStrength.PREFERRED && left.getStrength() == BindingStrength.EXAMPLE && !Base.compareDeep(left.getValueSet(), right.getValueSet(), false)) {
vm(IssueSeverity.INFORMATION, "Example/preferred bindings differ at " + path + " using binding from " + comp.getRight().getName(), path, comp.getMessages(), res.getMessages());
subset.setBinding(right);
superset.setBinding(unionBindings(comp, res, path, left, right));
} else {
if ((right.getStrength() != BindingStrength.EXAMPLE || left.getStrength() != BindingStrength.EXAMPLE) && !Base.compareDeep(left.getValueSet(), right.getValueSet(), false)) {
vm(IssueSeverity.INFORMATION, "Example/preferred bindings differ at " + path + " using binding from " + comp.getLeft().getName(), path, comp.getMessages(), res.getMessages());
}
subset.setBinding(left);
superset.setBinding(unionBindings(comp, res, path, left, right));
}
return true;
}
// if either of them are extensible/required, then it wins
if (isPreferredOrExample(left)) {
subset.setBinding(right);
superset.setBinding(unionBindings(comp, res, path, left, right));
return true;
}
if (isPreferredOrExample(right)) {
subset.setBinding(left);
superset.setBinding(unionBindings(comp, res, path, left, right));
return true;
}
// ok, both are extensible or required.
ElementDefinitionBindingComponent subBinding = new ElementDefinitionBindingComponent();
subset.setBinding(subBinding);
ElementDefinitionBindingComponent superBinding = new ElementDefinitionBindingComponent();
superset.setBinding(superBinding);
subBinding.setDescription(mergeText(comp, res, path, "description", left.getDescription(), right.getDescription(), false));
superBinding.setDescription(mergeText(comp, res, path, "description", left.getDescription(), right.getDescription(), false));
if (left.getStrength() == BindingStrength.REQUIRED || right.getStrength() == BindingStrength.REQUIRED)
subBinding.setStrength(BindingStrength.REQUIRED);
else
subBinding.setStrength(BindingStrength.EXTENSIBLE);
if (left.getStrength() == BindingStrength.EXTENSIBLE || right.getStrength() == BindingStrength.EXTENSIBLE)
superBinding.setStrength(BindingStrength.EXTENSIBLE);
else
superBinding.setStrength(BindingStrength.REQUIRED);
if (Base.compareDeep(left.getValueSet(), right.getValueSet(), false)) {
subBinding.setValueSet(left.getValueSet());
superBinding.setValueSet(left.getValueSet());
return true;
} else if (!left.hasValueSet()) {
vm(IssueSeverity.ERROR, "No left Value set at " + path, path, comp.getMessages(), res.getMessages());
return true;
} else if (!right.hasValueSet()) {
vm(IssueSeverity.ERROR, "No right Value set at " + path, path, comp.getMessages(), res.getMessages());
return true;
} else {
// ok, now we compare the value sets. This may be unresolvable.
ValueSet lvs = resolveVS(comp.getLeft(), left.getValueSet(), session.getContextLeft());
ValueSet rvs = resolveVS(comp.getRight(), right.getValueSet(), session.getContextRight());
if (lvs == null) {
vm(IssueSeverity.ERROR, "Unable to resolve left value set " + left.getValueSet().toString() + " at " + path, path, comp.getMessages(), res.getMessages());
return true;
} else if (rvs == null) {
vm(IssueSeverity.ERROR, "Unable to resolve right value set " + right.getValueSet().toString() + " at " + path, path, comp.getMessages(), res.getMessages());
return true;
} else if (sameValueSets(lvs, rvs)) {
subBinding.setValueSet(lvs.getUrl());
superBinding.setValueSet(lvs.getUrl());
} else {
ValueSetComparison compP = (ValueSetComparison) session.compare(lvs, rvs);
if (compP != null) {
subBinding.setValueSet(compP.getIntersection().getUrl());
superBinding.setValueSet(compP.getUnion().getUrl());
}
}
}
return false;
}
use of org.hl7.fhir.dstu3.conformance.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method intersectTypes.
private Collection<? extends TypeRefComponent> intersectTypes(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, ElementDefinition ed, String path, List<TypeRefComponent> left, List<TypeRefComponent> right) throws DefinitionException, IOException, FHIRFormatError {
List<TypeRefComponent> result = new ArrayList<TypeRefComponent>();
for (TypeRefComponent l : left) {
if (l.hasAggregation())
throw new DefinitionException("Aggregation not supported: " + path);
boolean pfound = false;
boolean tfound = false;
TypeRefComponent c = l.copy();
for (TypeRefComponent r : right) {
if (r.hasAggregation())
throw new DefinitionException("Aggregation not supported: " + path);
if (!l.hasProfile() && !r.hasProfile()) {
pfound = true;
} else if (!r.hasProfile()) {
pfound = true;
} else if (!l.hasProfile()) {
pfound = true;
c.setProfile(r.getProfile());
} else {
StructureDefinition sdl = resolveProfile(comp, res, path, l.getProfile().get(0).getValue(), comp.getLeft().getName(), session.getContextLeft());
StructureDefinition sdr = resolveProfile(comp, res, path, r.getProfile().get(0).getValue(), comp.getRight().getName(), session.getContextRight());
if (sdl != null && sdr != null) {
if (sdl == sdr) {
pfound = true;
} else if (derivesFrom(sdl, sdr, session.getContextLeft())) {
pfound = true;
} else if (derivesFrom(sdr, sdl, session.getContextRight())) {
c.setProfile(r.getProfile());
pfound = true;
} else if (sdl.getType().equals(sdr.getType())) {
ProfileComparison compP = (ProfileComparison) session.compare(sdl, sdr);
if (compP != null && compP.getIntersection() != null) {
pfound = true;
c.addProfile("#" + compP.getId());
}
}
}
}
if (!l.hasTargetProfile() && !r.hasTargetProfile()) {
tfound = true;
} else if (!r.hasTargetProfile()) {
tfound = true;
} else if (!l.hasTargetProfile()) {
tfound = true;
c.setTargetProfile(r.getTargetProfile());
} else {
StructureDefinition sdl = resolveProfile(comp, res, path, l.getTargetProfile().get(0).getValue(), comp.getLeft().getName(), session.getContextLeft());
StructureDefinition sdr = resolveProfile(comp, res, path, r.getTargetProfile().get(0).getValue(), comp.getRight().getName(), session.getContextRight());
if (sdl != null && sdr != null) {
if (matches(sdl, sdr)) {
tfound = true;
} else if (derivesFrom(sdl, sdr, session.getContextLeft())) {
tfound = true;
} else if (derivesFrom(sdr, sdl, session.getContextRight())) {
c.setTargetProfile(r.getTargetProfile());
tfound = true;
} else if (sdl.getType().equals(sdr.getType())) {
ProfileComparison compP = (ProfileComparison) session.compare(sdl, sdr);
if (compP != null && compP.getIntersection() != null) {
tfound = true;
c.addTargetProfile("#" + compP.getId());
}
}
}
}
}
if (pfound && tfound)
result.add(c);
}
return result;
}
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