Examples with DefinitionNavigator org.hl7.fhir.r4b.utils.DefinitionNavigator used on opensource projects

Example 11 with DefinitionNavigator

use of org.hl7.fhir.r4b.utils.DefinitionNavigator in project org.hl7.fhir.core by hapifhir.

the class ProfileComparer method compareElements.

private void compareElements(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, String sliceName, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, FHIRFormatError, IOException {
    assert (path != null);
    assert (left != null);
    assert (right != null);
    assert (left.path().equals(right.path()));
    if (session.isDebug()) {
        System.out.println("Compare elements at " + path);
    }
    // not allowed to be different:
    // ruleEqual(comp, res, left.current().getDefaultValue(), right.current().getDefaultValue(), "defaultValue", path);
    // ruleEqual(comp, res, left.current().getMeaningWhenMissingElement(), right.current().getMeaningWhenMissingElement(), "meaningWhenMissing", path);
    // ruleEqual(comp, res, left.current().getIsModifierElement(), right.current().getIsModifierElement(), "isModifier", path); - this check belongs in the core
    // ruleEqual(comp, res, left.current().getIsSummaryElement(), right.current().getIsSummaryElement(), "isSummary", path); - so does this
    // 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());
    if (sliceName != null)
        subset.setSliceName(sliceName);
    // can't be bothered even testing this one
    subset.getRepresentation().addAll(left.current().getRepresentation());
    subset.setDefaultValue(left.current().getDefaultValue());
    subset.setMeaningWhenMissing(left.current().getMeaningWhenMissing());
    subset.setIsModifier(left.current().getIsModifier());
    subset.setIsSummary(left.current().getIsSummary());
    // descriptive properties from ElementDefinition - merge them:
    subset.setLabel(mergeText(comp, res, path, "label", left.current().getLabel(), right.current().getLabel(), false));
    subset.setShort(mergeText(comp, res, path, "short", left.current().getShort(), right.current().getShort(), false));
    subset.setDefinition(mergeText(comp, res, path, "definition", left.current().getDefinition(), right.current().getDefinition(), false));
    subset.setComment(mergeText(comp, res, path, "comments", left.current().getComment(), right.current().getComment(), false));
    subset.setRequirements(mergeText(comp, res, path, "requirements", left.current().getRequirements(), right.current().getRequirements(), false));
    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());
    if (left.current().getMustSupport() != right.current().getMustSupport()) {
        vm(IssueSeverity.WARNING, "Elements differ in definition for mustSupport: '" + left.current().getMustSupport() + "' vs '" + right.current().getMustSupport() + "'", path, comp.getMessages(), res.getMessages());
    }
    subset.setMustSupport(left.current().getMustSupport() || right.current().getMustSupport());
    ElementDefinition superset = subset.copy();
    // compare and intersect
    int leftMin = left.current().getMin();
    int rightMin = right.current().getMin();
    int leftMax = "*".equals(left.current().getMax()) ? Integer.MAX_VALUE : Integer.parseInt(left.current().getMax());
    int rightMax = "*".equals(right.current().getMax()) ? Integer.MAX_VALUE : Integer.parseInt(right.current().getMax());
    checkMinMax(comp, res, path, leftMin, rightMin, leftMax, rightMax);
    superset.setMin(unionMin(leftMin, rightMin));
    superset.setMax(unionMax(leftMax, rightMax, left.current().getMax(), right.current().getMax()));
    subset.setMin(intersectMin(leftMin, rightMin));
    subset.setMax(intersectMax(leftMax, rightMax, left.current().getMax(), right.current().getMax()));
    superset.getType().addAll(unionTypes(comp, res, path, left.current().getType(), right.current().getType()));
    subset.getType().addAll(intersectTypes(comp, res, subset, path, left.current().getType(), right.current().getType()));
    rule(comp, res, !subset.getType().isEmpty() || (!left.current().hasType() && !right.current().hasType()), path, "Type Mismatch: " + typeCode(left) + " vs " + 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(comp, res, 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(comp, res, path, left.current().getConstraint(), right.current().getConstraint()));
    comp.getIntersection().getSnapshot().getElement().add(subset);
    comp.getUnion().getSnapshot().getElement().add(superset);
    // add the children
    compareChildren(comp, res, path, left, right);
// 
// // now process the slices
// if (left.current().hasSlicing() || right.current().hasSlicing()) {
// assert sliceName == null;
// if (isExtension(left.path()))
// return compareExtensions(outcome, path, superset, subset, left, right);
// //      return true;
// else {
// ElementDefinitionSlicingComponent slicingL = left.current().getSlicing();
// ElementDefinitionSlicingComponent slicingR = right.current().getSlicing();
// // well, this is tricky. If one is sliced, and the other is not, then in general, the union just ignores the slices, and the intersection is the slices.
// if (left.current().hasSlicing() && !right.current().hasSlicing()) {
// // the super set is done. Any restrictions in the slices are irrelevant to what the super set says, except that we're going sum up the value sets if we can (for documentation purposes) (todo)
// // the minimum set is the slicing specified in the slicer
// subset.setSlicing(slicingL);
// // stick everything from the right to do with the slices to the subset
// copySlices(outcome.subset.getSnapshot().getElement(), left.getStructure().getSnapshot().getElement(), left.slices());
// } else if (!left.current().hasSlicing() && right.current().hasSlicing()) {
// // the super set is done. Any restrictions in the slices are irrelevant to what the super set says, except that we're going sum up the value sets if we can (for documentation purposes) (todo)
// // the minimum set is the slicing specified in the slicer
// subset.setSlicing(slicingR);
// // stick everything from the right to do with the slices to the subset
// copySlices(outcome.subset.getSnapshot().getElement(), right.getStructure().getSnapshot().getElement(), right.slices());
// } else if (isTypeSlicing(slicingL) || isTypeSlicing(slicingR)) {
// superset.getSlicing().setRules(SlicingRules.OPEN).setOrdered(false).addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
// subset.getSlicing().setRules(slicingL.getRules() == SlicingRules.CLOSED || slicingR.getRules() == SlicingRules.CLOSED ? SlicingRules.OPEN : SlicingRules.CLOSED).setOrdered(false).addDiscriminator().setType(DiscriminatorType.TYPE).setPath("$this");
// 
// // the superset is the union of the types
// // the subset is the intersection of them
// List<DefinitionNavigator> handled = new ArrayList<>();
// for (DefinitionNavigator t : left.slices()) {
// DefinitionNavigator r = findMatchingSlice(right.slices(), t);
// if (r == null) {
// copySlice(outcome.superset.getSnapshot().getElement(), left.getStructure().getSnapshot().getElement(), t);
// } else {
// handled.add(r);
// ret = compareElements(outcome, path+":"+t.current().getSliceName(), t, r, t.current().getSliceName()) && ret;
// }
// }
// for (DefinitionNavigator t : right.slices()) {
// if (!handled.contains(t)) {
// copySlice(outcome.superset.getSnapshot().getElement(), right.getStructure().getSnapshot().getElement(), t);
// }
// }
// } else if (slicingMatches(slicingL, slicingR)) {
// // if it's the same, we can try matching the slices - though we might have to give up without getting matches correct
// // there amy be implied consistency we can't reason about
// throw new DefinitionException("Slicing matches but is not handled yet at "+left.current().getId()+": ("+ProfileUtilities.summarizeSlicing(slicingL)+")");
// } else  {
// // if the slicing is different, we can't compare them - or can we?
// throw new DefinitionException("Slicing doesn't match at "+left.current().getId()+": ("+ProfileUtilities.summarizeSlicing(slicingL)+" / "+ProfileUtilities.summarizeSlicing(slicingR)+")");
// }
// }
// // todo: name
// }
// return ret;
// 
// // TODO Auto-generated method stub
// return null;
}

Example 12 with DefinitionNavigator

use of org.hl7.fhir.r4b.utils.DefinitionNavigator in project org.hl7.fhir.core by hapifhir.

the class ProfileComparer method compareChildren.

private void compareChildren(ProfileComparison comp, StructuralMatch<ElementDefinitionNode> res, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
    List<DefinitionNavigator> lc = left.children();
    List<DefinitionNavigator> rc = right.children();
    // walk into it
    if (lc.isEmpty() && !rc.isEmpty() && right.current().getType().size() == 1 && left.hasTypeChildren(right.current().getType().get(0)))
        lc = left.childrenFromType(right.current().getType().get(0));
    if (rc.isEmpty() && !lc.isEmpty() && left.current().getType().size() == 1 && right.hasTypeChildren(left.current().getType().get(0)))
        rc = right.childrenFromType(left.current().getType().get(0));
    List<DefinitionNavigator> matchR = new ArrayList<>();
    for (DefinitionNavigator l : lc) {
        DefinitionNavigator r = findInList(rc, l);
        if (r == null) {
            comp.getUnion().getSnapshot().getElement().add(l.current().copy());
            res.getChildren().add(new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(l.getStructure(), l.current()), vmI(IssueSeverity.INFORMATION, "Removed this element", path)));
        } else {
            matchR.add(r);
            StructuralMatch<ElementDefinitionNode> sm = new StructuralMatch<ElementDefinitionNode>(new ElementDefinitionNode(l.getStructure(), l.current()), new ElementDefinitionNode(r.getStructure(), r.current()));
            res.getChildren().add(sm);
            compareElements(comp, sm, l.path(), null, l, r);
        }
    }
    for (DefinitionNavigator r : rc) {
        if (!matchR.contains(r)) {
            comp.getUnion().getSnapshot().getElement().add(r.current().copy());
            res.getChildren().add(new StructuralMatch<ElementDefinitionNode>(vmI(IssueSeverity.INFORMATION, "Added this element", path), new ElementDefinitionNode(r.getStructure(), r.current())));
        }
    }
}

Example 13 with DefinitionNavigator

use of org.hl7.fhir.r4b.utils.DefinitionNavigator in project org.hl7.fhir.core by hapifhir.

the class DefinitionNavigator method loadChildren.

private void loadChildren() throws DefinitionException {
    children = new ArrayList<DefinitionNavigator>();
    String prefix = current().getPath() + ".";
    Map<String, DefinitionNavigator> nameMap = new HashMap<String, DefinitionNavigator>();
    for (int i = index + 1; i < structure.getSnapshot().getElement().size(); i++) {
        String path = structure.getSnapshot().getElement().get(i).getPath();
        if (path.startsWith(prefix) && !path.substring(prefix.length()).contains(".")) {
            DefinitionNavigator dn = new DefinitionNavigator(context, structure, i, this.path + "." + tail(path), names, null);
            if (nameMap.containsKey(path)) {
                DefinitionNavigator master = nameMap.get(path);
                if (!master.current().hasSlicing())
                    throw new DefinitionException("Found slices with no slicing details at " + dn.current().getPath());
                if (master.slices == null)
                    master.slices = new ArrayList<DefinitionNavigator>();
                master.slices.add(dn);
            } else {
                nameMap.put(path, dn);
                children.add(dn);
            }
        } else if (path.length() < prefix.length())
            break;
    }
}

Example 14 with DefinitionNavigator

use of org.hl7.fhir.r4b.utils.DefinitionNavigator 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
 * @throws FHIRFormatError
 *
 * @
 */
public ProfileComparison compareProfiles(StructureDefinition left, StructureDefinition right) throws DefinitionException, IOException, FHIRFormatError {
    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(PublicationStatus.DRAFT);
            outcome.subset.setKind(outcome.left.getKind());
            outcome.subset.setType(outcome.left.getType());
            outcome.subset.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/" + outcome.subset.getType());
            outcome.subset.setDerivation(TypeDerivationRule.CONSTRAINT);
            outcome.subset.setAbstract(false);
            outcome.superset.setName("union of " + outcome.leftName() + " and " + outcome.rightName());
            outcome.superset.setStatus(PublicationStatus.DRAFT);
            outcome.superset.setKind(outcome.left.getKind());
            outcome.superset.setType(outcome.left.getType());
            outcome.superset.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/" + outcome.subset.getType());
            outcome.superset.setAbstract(false);
            outcome.superset.setDerivation(TypeDerivationRule.CONSTRAINT);
        } else {
            outcome.subset = null;
            outcome.superset = null;
        }
    }
    return outcome;
}

Example 15 with DefinitionNavigator

use of org.hl7.fhir.r4b.utils.DefinitionNavigator in project org.hl7.fhir.core by hapifhir.

the class ProfileComparer method compareChildren.

private boolean compareChildren(ElementDefinition ed, ProfileComparison outcome, String path, DefinitionNavigator left, DefinitionNavigator right) throws DefinitionException, IOException, FHIRFormatError {
    List<DefinitionNavigator> lc = left.children();
    List<DefinitionNavigator> rc = right.children();
    // walk into it
    if (lc.isEmpty() && !rc.isEmpty() && right.current().getType().size() == 1 && left.hasTypeChildren(right.current().getType().get(0)))
        lc = left.childrenFromType(right.current().getType().get(0));
    if (rc.isEmpty() && !lc.isEmpty() && left.current().getType().size() == 1 && right.hasTypeChildren(left.current().getType().get(0)))
        rc = right.childrenFromType(left.current().getType().get(0));
    if (lc.size() != rc.size()) {
        outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Different number of children at " + path + " (" + Integer.toString(lc.size()) + "/" + Integer.toString(rc.size()) + ")", ValidationMessage.IssueSeverity.ERROR));
        status(ed, ProfileUtilities.STATUS_ERROR);
        return false;
    } else {
        for (int i = 0; i < lc.size(); i++) {
            DefinitionNavigator l = lc.get(i);
            DefinitionNavigator r = rc.get(i);
            String cpath = comparePaths(l.path(), r.path(), path, l.nameTail(), r.nameTail());
            if (cpath != null) {
                if (!compareElements(outcome, cpath, l, r))
                    return false;
            } else {
                outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Different path at " + path + "[" + Integer.toString(i) + "] (" + l.path() + "/" + r.path() + ")", ValidationMessage.IssueSeverity.ERROR));
                status(ed, ProfileUtilities.STATUS_ERROR);
                return false;
            }
        }
    }
    return true;
}