use of org.hl7.fhir.dstu2.utils.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method resolveProfile.
private StructureDefinition resolveProfile(ElementDefinition ed, ProfileComparison outcome, String path, String url, String name) {
StructureDefinition res = context.fetchResource(StructureDefinition.class, url);
if (res == null) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path, "Unable to resolve profile " + url + " in profile " + name, IssueSeverity.WARNING));
status(ed, ProfileUtilities.STATUS_HINT);
}
return res;
}
use of org.hl7.fhir.dstu2.utils.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method compareProfiles.
/**
* Compare left and right structure definitions to see whether they are consistent or not
*
* Note that left and right are arbitrary choices. In one respect, left
* is 'preferred' - the left's example value and data sets will be selected
* over the right ones in the common structure definition
* @throws DefinitionException
* @throws IOException
*
* @
*/
public ProfileComparison compareProfiles(StructureDefinition left, StructureDefinition right) throws DefinitionException, IOException {
ProfileComparison outcome = new ProfileComparison();
outcome.left = left;
outcome.right = right;
if (left == null)
throw new DefinitionException("No StructureDefinition provided (left)");
if (right == null)
throw new DefinitionException("No StructureDefinition provided (right)");
if (!left.hasSnapshot())
throw new DefinitionException("StructureDefinition has no snapshot (left: " + outcome.leftName() + ")");
if (!right.hasSnapshot())
throw new DefinitionException("StructureDefinition has no snapshot (right: " + outcome.rightName() + ")");
if (left.getSnapshot().getElement().isEmpty())
throw new DefinitionException("StructureDefinition snapshot is empty (left: " + outcome.leftName() + ")");
if (right.getSnapshot().getElement().isEmpty())
throw new DefinitionException("StructureDefinition snapshot is empty (right: " + outcome.rightName() + ")");
for (ProfileComparison pc : comparisons) if (pc.left.getUrl().equals(left.getUrl()) && pc.right.getUrl().equals(right.getUrl()))
return pc;
outcome.id = Integer.toString(comparisons.size() + 1);
comparisons.add(outcome);
DefinitionNavigator ln = new DefinitionNavigator(context, left);
DefinitionNavigator rn = new DefinitionNavigator(context, right);
// from here on in, any issues go in messages
outcome.superset = new StructureDefinition();
outcome.subset = new StructureDefinition();
if (outcome.ruleEqual(ln.path(), null, ln.path(), rn.path(), "Base Type is not compatible", false)) {
if (compareElements(outcome, ln.path(), ln, rn)) {
outcome.subset.setName("intersection of " + outcome.leftName() + " and " + outcome.rightName());
outcome.subset.setStatus(ConformanceResourceStatus.DRAFT);
outcome.subset.setKind(outcome.left.getKind());
outcome.subset.setConstrainedType(outcome.left.getConstrainedType());
outcome.subset.setBase("http://hl7.org/fhir/StructureDefinition/" + outcome.subset.getConstrainedType());
outcome.subset.setAbstract(false);
outcome.superset.setName("union of " + outcome.leftName() + " and " + outcome.rightName());
outcome.superset.setStatus(ConformanceResourceStatus.DRAFT);
outcome.superset.setKind(outcome.left.getKind());
outcome.superset.setConstrainedType(outcome.left.getConstrainedType());
outcome.superset.setBase("http://hl7.org/fhir/StructureDefinition/" + outcome.subset.getConstrainedType());
outcome.superset.setAbstract(false);
} else {
outcome.subset = null;
outcome.superset = null;
}
}
return outcome;
}
use of org.hl7.fhir.dstu2.utils.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method unite.
private ValueSet unite(ElementDefinition ed, ProfileComparison outcome, String path, ValueSet lvs, ValueSet rvs) {
ValueSet vs = new ValueSet();
if (lvs.hasCodeSystem())
vs.getCompose().addInclude().setSystem(lvs.getCodeSystem().getSystem());
if (rvs.hasCodeSystem())
vs.getCompose().addInclude().setSystem(rvs.getCodeSystem().getSystem());
if (lvs.hasCompose()) {
for (UriType imp : lvs.getCompose().getImport()) vs.getCompose().getImport().add(imp);
for (ConceptSetComponent inc : lvs.getCompose().getInclude()) vs.getCompose().getInclude().add(inc);
if (lvs.getCompose().hasExclude()) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "The value sets " + lvs.getUrl() + " has exclude statements, and no union involving it can be correctly determined", IssueSeverity.ERROR));
status(ed, ProfileUtilities.STATUS_ERROR);
}
}
if (rvs.hasCompose()) {
for (UriType imp : rvs.getCompose().getImport()) if (!vs.getCompose().hasImport(imp.getValue()))
vs.getCompose().getImport().add(imp);
for (ConceptSetComponent inc : rvs.getCompose().getInclude()) if (!mergeIntoExisting(vs.getCompose().getInclude(), inc))
vs.getCompose().getInclude().add(inc);
if (rvs.getCompose().hasExclude()) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "The value sets " + lvs.getUrl() + " has exclude statements, and no union involving it can be correctly determined", IssueSeverity.ERROR));
status(ed, ProfileUtilities.STATUS_ERROR);
}
}
return vs;
}
use of org.hl7.fhir.dstu2.utils.ProfileComparer.ProfileComparison in project org.hl7.fhir.core by hapifhir.
the class ProfileComparer method compareBindings.
private boolean compareBindings(ProfileComparison outcome, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) {
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)) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "Example/preferred bindings differ at " + path + " using binding from " + outcome.rightName(), IssueSeverity.INFORMATION));
status(subset, ProfileUtilities.STATUS_HINT);
subset.setBinding(right);
superset.setBinding(unionBindings(superset, outcome, path, left, right));
} else {
if ((right.getStrength() != BindingStrength.EXAMPLE || left.getStrength() != BindingStrength.EXAMPLE) && !Base.compareDeep(left.getValueSet(), right.getValueSet(), false)) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "Example/preferred bindings differ at " + path + " using binding from " + outcome.leftName(), IssueSeverity.INFORMATION));
status(subset, ProfileUtilities.STATUS_HINT);
}
subset.setBinding(left);
superset.setBinding(unionBindings(superset, outcome, path, left, right));
}
return true;
}
// if either of them are extensible/required, then it wins
if (isPreferredOrExample(left)) {
subset.setBinding(right);
superset.setBinding(unionBindings(superset, outcome, path, left, right));
return true;
}
if (isPreferredOrExample(right)) {
subset.setBinding(left);
superset.setBinding(unionBindings(superset, outcome, 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(subset, outcome, path, "description", left.getDescription(), right.getDescription()));
superBinding.setDescription(mergeText(subset, outcome, null, "description", left.getDescription(), right.getDescription()));
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()) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "No left Value set at " + path, IssueSeverity.ERROR));
return true;
} else if (!right.hasValueSet()) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "No right Value set at " + path, IssueSeverity.ERROR));
return true;
} else {
// ok, now we compare the value sets. This may be unresolvable.
ValueSet lvs = resolveVS(outcome.left, left.getValueSet());
ValueSet rvs = resolveVS(outcome.right, right.getValueSet());
if (lvs == null) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "Unable to resolve left value set " + left.getValueSet().toString() + " at " + path, IssueSeverity.ERROR));
return true;
} else if (rvs == null) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "Unable to resolve right value set " + right.getValueSet().toString() + " at " + path, IssueSeverity.ERROR));
return true;
} else {
// first, we'll try to do it by definition
ValueSet cvs = intersectByDefinition(lvs, rvs);
if (cvs == null) {
// if that didn't work, we'll do it by expansion
ValueSetExpansionOutcome le;
ValueSetExpansionOutcome re;
try {
le = context.expandVS(lvs, true);
re = context.expandVS(rvs, true);
if (!closed(le.getValueset()) || !closed(re.getValueset()))
throw new DefinitionException("unclosed value sets are not handled yet");
cvs = intersectByExpansion(lvs, rvs);
if (!cvs.getCompose().hasInclude()) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "The value sets " + lvs.getUrl() + " and " + rvs.getUrl() + " do not intersect", IssueSeverity.ERROR));
status(subset, ProfileUtilities.STATUS_ERROR);
return false;
}
} catch (Exception e) {
outcome.messages.add(new ValidationMessage(Source.ProfileComparer, IssueType.STRUCTURE, path, "Unable to expand or process value sets " + lvs.getUrl() + " and " + rvs.getUrl() + ": " + e.getMessage(), IssueSeverity.ERROR));
status(subset, ProfileUtilities.STATUS_ERROR);
return false;
}
}
subBinding.setValueSet(new Reference().setReference("#" + addValueSet(cvs)));
superBinding.setValueSet(new Reference().setReference("#" + addValueSet(unite(superset, outcome, path, lvs, rvs))));
}
}
return false;
}
use of org.hl7.fhir.dstu2.utils.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("=================================================================");
}
}
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