Examples with ProfileComparison org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison used on opensource projects

Example 16 with ProfileComparison

use of org.hl7.fhir.r5.comparison.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);
}

Example 17 with ProfileComparison

use of org.hl7.fhir.r5.comparison.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;
}

Example 18 with ProfileComparison

use of org.hl7.fhir.r5.comparison.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("=================================================================");
    }
}

Example 19 with ProfileComparison

use of org.hl7.fhir.r5.comparison.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;
}

Example 20 with ProfileComparison

use of org.hl7.fhir.r5.comparison.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;
}