Examples with GENERATED org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus.GENERATED used on opensource projects

Example 26 with GENERATED

use of org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus.GENERATED in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method generateByProfile.

private boolean generateByProfile(ResourceContext rc, StructureDefinition profile, boolean showCodeDetails) {
    XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
    x.para().b().tx("Generated Narrative" + (showCodeDetails ? " with Details" : ""));
    try {
        generateByProfile(rc.resourceResource, profile, rc.resourceResource, profile.getSnapshot().getElement(), profile.getSnapshot().getElement().get(0), getChildrenForPath(profile.getSnapshot().getElement(), rc.resourceResource.getResourceType().toString()), x, rc.resourceResource.getResourceType().toString(), showCodeDetails, rc);
    } catch (Exception e) {
        e.printStackTrace();
        x.para().b().setAttribute("style", "color: maroon").tx("Exception generating Narrative: " + e.getMessage());
    }
    inject(rc.resourceResource, x, NarrativeStatus.GENERATED);
    return true;
}

Example 27 with GENERATED

use of org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus.GENERATED in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method generateSnapshot.

/**
 * Given a base (snapshot) profile structure, and a differential profile, generate a new snapshot profile
 *
 * @param base - the base structure on which the differential will be applied
 * @param differential - the differential to apply to the base
 * @param url - where the base has relative urls for profile references, these need to be converted to absolutes by prepending this URL (e.g. the canonical URL)
 * @param webUrl - where the base has relative urls in markdown, these need to be converted to absolutes by prepending this URL (this is not the same as the canonical URL)
 * @param trimDifferential - if this is true, then the snap short generator will remove any material in the element definitions that is not different to the base
 * @return
 * @throws FHIRException
 * @throws DefinitionException
 * @throws Exception
 */
public void generateSnapshot(StructureDefinition base, StructureDefinition derived, String url, String webUrl, String profileName) throws DefinitionException, FHIRException {
    if (base == null) {
        throw new DefinitionException(context.formatMessage(I18nConstants.NO_BASE_PROFILE_PROVIDED));
    }
    if (derived == null) {
        throw new DefinitionException(context.formatMessage(I18nConstants.NO_DERIVED_STRUCTURE_PROVIDED));
    }
    checkNotGenerating(base, "Base for generating a snapshot for the profile " + derived.getUrl());
    checkNotGenerating(derived, "Focus for generating a snapshot");
    if (!base.hasType()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.BASE_PROFILE__HAS_NO_TYPE, base.getUrl()));
    }
    if (!derived.hasType()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_TYPE, derived.getUrl()));
    }
    if (!derived.hasDerivation()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_DERIVATION_VALUE_AND_SO_CANT_BE_PROCESSED, derived.getUrl()));
    }
    if (!base.getType().equals(derived.getType()) && derived.getDerivation() == TypeDerivationRule.CONSTRAINT) {
        throw new DefinitionException(context.formatMessage(I18nConstants.BASE__DERIVED_PROFILES_HAVE_DIFFERENT_TYPES____VS___, base.getUrl(), base.getType(), derived.getUrl(), derived.getType()));
    }
    if (snapshotStack.contains(derived.getUrl())) {
        throw new DefinitionException(context.formatMessage(I18nConstants.CIRCULAR_SNAPSHOT_REFERENCES_DETECTED_CANNOT_GENERATE_SNAPSHOT_STACK__, snapshotStack.toString()));
    }
    derived.setUserData("profileutils.snapshot.generating", true);
    snapshotStack.add(derived.getUrl());
    try {
        if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
            webUrl = webUrl + '/';
        if (defWebRoot == null)
            defWebRoot = webUrl;
        derived.setSnapshot(new StructureDefinitionSnapshotComponent());
        try {
            checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
            checkDifferentialBaseType(derived);
            // so we have two lists - the base list, and the differential list
            // the differential list is only allowed to include things that are in the base list, but
            // is allowed to include them multiple times - thereby slicing them
            // our approach is to walk through the base list, and see whether the differential
            // says anything about them.
            int baseCursor = 0;
            // we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
            int diffCursor = 0;
            for (ElementDefinition e : derived.getDifferential().getElement()) e.clearUserData(GENERATED_IN_SNAPSHOT);
            // we actually delegate the work to a subroutine so we can re-enter it with a different cursors
            // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
            StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential());
            StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                String derivedType = derived.getType();
                if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
                    derivedType = derivedType.substring(derivedType.lastIndexOf("/") + 1);
                }
                baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
            }
            // if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
            // debug = true;
            // }
            processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size() - 1, derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size() - 1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
            checkGroupConstraints(derived);
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                for (ElementDefinition e : diff.getElement()) {
                    if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
                        ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
                        e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
                        derived.getSnapshot().addElement(outcome);
                    }
                }
            }
            if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
                throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
            updateMaps(base, derived);
            setIds(derived, false);
            if (debug) {
                System.out.println("Differential: ");
                for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println("  " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                System.out.println("Snapshot: ");
                for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println("  " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
            }
            CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
            // Check that all differential elements have a corresponding snapshot element
            int ce = 0;
            for (ElementDefinition e : diff.getElement()) {
                if (!e.hasUserData("diff-source"))
                    throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
                else {
                    if (e.hasUserData(DERIVATION_EQUALS))
                        ((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
                    if (e.hasUserData(DERIVATION_POINTER))
                        ((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
                }
                if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
                    b.append(e.hasId() ? "id: " + e.getId() : "path: " + e.getPath());
                    ce++;
                    if (e.hasId()) {
                        String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
                        messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
                    }
                }
            }
            if (!Utilities.noString(b.toString())) {
                String msg = "The profile " + derived.getUrl() + " has " + ce + " " + Utilities.pluralize("element", ce) + " in the differential (" + b.toString() + ") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
                System.out.println("Error in snapshot generation: " + msg);
                if (!debug) {
                    System.out.println("Differential: ");
                    for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println("  " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                    System.out.println("Snapshot: ");
                    for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println("  " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                }
                if (exception)
                    throw new DefinitionException(msg);
                else
                    messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
            }
            // hack around a problem in R4 definitions (somewhere?)
            for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
                    if (mm.hasMap()) {
                        mm.setMap(mm.getMap().trim());
                    }
                }
                for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
                    if (s.hasSource()) {
                        String ref = s.getSource();
                        if (!Utilities.isAbsoluteUrl(ref)) {
                            if (ref.contains(".")) {
                                s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref.substring(0, ref.indexOf(".")) + "#" + ref);
                            } else {
                                s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref);
                            }
                        }
                    }
                }
            }
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                    if (!ed.hasBase()) {
                        ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
                    }
                }
            }
            // last, check for wrong profiles or target profiles
            for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                for (TypeRefComponent t : ed.getType()) {
                    for (UriType u : t.getProfile()) {
                        StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
                        if (sd == null) {
                            if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
                                sd = xver.makeDefinition(u.getValue());
                            }
                        }
                        if (sd == null) {
                            if (messages != null) {
                                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), "The type of profile " + u.getValue() + " cannot be checked as the profile is not known", IssueSeverity.WARNING));
                            }
                        } else {
                            String wt = t.getWorkingCode();
                            if (ed.getPath().equals("Bundle.entry.response.outcome")) {
                                wt = "OperationOutcome";
                            }
                            if (!sd.getType().equals(wt)) {
                                boolean ok = isCompatibleType(wt, sd);
                                if (!ok) {
                                    String smsg = "The profile " + u.getValue() + " has type " + sd.getType() + " which is not consistent with the stated type " + wt;
                                    if (exception)
                                        throw new DefinitionException(smsg);
                                    else
                                        messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), smsg, IssueSeverity.ERROR));
                                }
                            }
                        }
                    }
                }
            }
        } catch (Exception e) {
            // if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
            derived.setSnapshot(null);
            derived.clearUserData("profileutils.snapshot.generating");
            throw e;
        }
    } finally {
        derived.clearUserData("profileutils.snapshot.generating");
        snapshotStack.remove(derived.getUrl());
    }
}

Example 28 with GENERATED

use of org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus.GENERATED 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 29 with GENERATED

use of org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus.GENERATED in project org.hl7.fhir.core by hapifhir.

the class XmlSchemaGenerator method start.

private String start(StructureDefinition sd, String ns) throws IOException, FHIRException {
    String lang = "en";
    if (sd.hasLanguage())
        lang = sd.getLanguage();
    if (single && writer != null) {
        if (!ns.equals(getNs(sd)))
            throw new FHIRException("namespace inconsistency: " + ns + " vs " + getNs(sd));
        return lang;
    }
    close();
    writer = new OutputStreamWriter(new FileOutputStream(Utilities.path(folder, tail(sd.getType() + ".xsd"))), "UTF-8");
    ln("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
    ln("<!-- ");
    ln(license);
    ln("");
    ln("  Generated on " + genDate + " for FHIR v" + version + " ");
    ln("");
    ln("  Note: this schema does not contain all the knowledge represented in the underlying content model");
    ln("");
    ln("-->");
    ln("<xs:schema xmlns:xs=\"http://www.w3.org/2001/XMLSchema\" xmlns:fhir=\"http://hl7.org/fhir\" xmlns:xhtml=\"http://www.w3.org/1999/xhtml\" " + "xmlns:lm=\"" + ns + "\" targetNamespace=\"" + ns + "\" elementFormDefault=\"qualified\" version=\"1.0\">");
    ln("  <xs:import schemaLocation=\"fhir-common.xsd\" namespace=\"http://hl7.org/fhir\"/>");
    if (useNarrative) {
        if (ns.equals("urn:hl7-org:v3"))
            ln("  <xs:include schemaLocation=\"cda-narrative.xsd\"/>");
        else
            ln("  <xs:import schemaLocation=\"cda-narrative.xsd\" namespace=\"urn:hl7-org:v3\"/>");
    }
    namespaces.clear();
    namespaces.put(ns, "lm");
    namespaces.put("http://hl7.org/fhir", "fhir");
    typeNames.clear();
    return lang;
}

Example 30 with GENERATED

use of org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus.GENERATED in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method generateSnapshot.

/**
 * Given a base (snapshot) profile structure, and a differential profile, generate a new snapshot profile
 *
 * @param base - the base structure on which the differential will be applied
 * @param differential - the differential to apply to the base
 * @param url - where the base has relative urls for profile references, these need to be converted to absolutes by prepending this URL (e.g. the canonical URL)
 * @param webUrl - where the base has relative urls in markdown, these need to be converted to absolutes by prepending this URL (this is not the same as the canonical URL)
 * @param trimDifferential - if this is true, then the snap short generator will remove any material in the element definitions that is not different to the base
 * @return
 * @throws FHIRException
 * @throws DefinitionException
 * @throws Exception
 */
public void generateSnapshot(StructureDefinition base, StructureDefinition derived, String url, String webUrl, String profileName) throws DefinitionException, FHIRException {
    if (base == null) {
        throw new DefinitionException(context.formatMessage(I18nConstants.NO_BASE_PROFILE_PROVIDED));
    }
    if (derived == null) {
        throw new DefinitionException(context.formatMessage(I18nConstants.NO_DERIVED_STRUCTURE_PROVIDED));
    }
    checkNotGenerating(base, "Base for generating a snapshot for the profile " + derived.getUrl());
    checkNotGenerating(derived, "Focus for generating a snapshot");
    if (!base.hasType()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.BASE_PROFILE__HAS_NO_TYPE, base.getUrl()));
    }
    if (!derived.hasType()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_TYPE, derived.getUrl()));
    }
    if (!derived.hasDerivation()) {
        throw new DefinitionException(context.formatMessage(I18nConstants.DERIVED_PROFILE__HAS_NO_DERIVATION_VALUE_AND_SO_CANT_BE_PROCESSED, derived.getUrl()));
    }
    if (!base.getType().equals(derived.getType()) && derived.getDerivation() == TypeDerivationRule.CONSTRAINT) {
        throw new DefinitionException(context.formatMessage(I18nConstants.BASE__DERIVED_PROFILES_HAVE_DIFFERENT_TYPES____VS___, base.getUrl(), base.getType(), derived.getUrl(), derived.getType()));
    }
    if (snapshotStack.contains(derived.getUrl())) {
        throw new DefinitionException(context.formatMessage(I18nConstants.CIRCULAR_SNAPSHOT_REFERENCES_DETECTED_CANNOT_GENERATE_SNAPSHOT_STACK__, snapshotStack.toString()));
    }
    derived.setUserData("profileutils.snapshot.generating", true);
    snapshotStack.add(derived.getUrl());
    try {
        if (!Utilities.noString(webUrl) && !webUrl.endsWith("/"))
            webUrl = webUrl + '/';
        if (defWebRoot == null)
            defWebRoot = webUrl;
        derived.setSnapshot(new StructureDefinitionSnapshotComponent());
        try {
            checkDifferential(derived.getDifferential().getElement(), typeName(derived.getType()), derived.getUrl());
            checkDifferentialBaseType(derived);
            // so we have two lists - the base list, and the differential list
            // the differential list is only allowed to include things that are in the base list, but
            // is allowed to include them multiple times - thereby slicing them
            // our approach is to walk through the base list, and see whether the differential
            // says anything about them.
            int baseCursor = 0;
            // we need a diff cursor because we can only look ahead, in the bound scoped by longer paths
            int diffCursor = 0;
            for (ElementDefinition e : derived.getDifferential().getElement()) e.clearUserData(GENERATED_IN_SNAPSHOT);
            // we actually delegate the work to a subroutine so we can re-enter it with a different cursors
            // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
            StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential());
            StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                String derivedType = derived.getType();
                if (StructureDefinitionKind.LOGICAL.equals(derived.getKind()) && derived.getType().contains("/")) {
                    derivedType = derivedType.substring(derivedType.lastIndexOf("/") + 1);
                }
                baseSnapshot = cloneSnapshot(baseSnapshot, base.getType(), derivedType);
            }
            // if (derived.getId().equals("2.16.840.1.113883.10.20.22.2.1.1")) {
            // debug = true;
            // }
            processPaths("", derived.getSnapshot(), baseSnapshot, diff, baseCursor, diffCursor, baseSnapshot.getElement().size() - 1, derived.getDifferential().hasElement() ? derived.getDifferential().getElement().size() - 1 : -1, url, webUrl, derived.present(), null, null, false, base.getUrl(), null, false, null, null, new ArrayList<ElementRedirection>(), base);
            checkGroupConstraints(derived);
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                for (ElementDefinition e : diff.getElement()) {
                    if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
                        ElementDefinition outcome = updateURLs(url, webUrl, e.copy());
                        e.setUserData(GENERATED_IN_SNAPSHOT, outcome);
                        derived.getSnapshot().addElement(outcome);
                    }
                }
            }
            if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
                throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
            updateMaps(base, derived);
            setIds(derived, false);
            if (debug) {
                System.out.println("Differential: ");
                for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println("  " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                System.out.println("Snapshot: ");
                for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println("  " + ed.getId() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
            }
            CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
            // Check that all differential elements have a corresponding snapshot element
            int ce = 0;
            for (ElementDefinition e : diff.getElement()) {
                if (!e.hasUserData("diff-source"))
                    throw new Error(context.formatMessage(I18nConstants.UNXPECTED_INTERNAL_CONDITION__NO_SOURCE_ON_DIFF_ELEMENT));
                else {
                    if (e.hasUserData(DERIVATION_EQUALS))
                        ((Base) e.getUserData("diff-source")).setUserData(DERIVATION_EQUALS, e.getUserData(DERIVATION_EQUALS));
                    if (e.hasUserData(DERIVATION_POINTER))
                        ((Base) e.getUserData("diff-source")).setUserData(DERIVATION_POINTER, e.getUserData(DERIVATION_POINTER));
                }
                if (!e.hasUserData(GENERATED_IN_SNAPSHOT)) {
                    b.append(e.hasId() ? "id: " + e.getId() : "path: " + e.getPath());
                    ce++;
                    if (e.hasId()) {
                        String msg = "No match found in the generated snapshot: check that the path and definitions are legal in the differential (including order)";
                        messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + e.getId(), msg, ValidationMessage.IssueSeverity.ERROR));
                    }
                }
            }
            if (!Utilities.noString(b.toString())) {
                String msg = "The profile " + derived.getUrl() + " has " + ce + " " + Utilities.pluralize("element", ce) + " in the differential (" + b.toString() + ") that don't have a matching element in the snapshot: check that the path and definitions are legal in the differential (including order)";
                System.out.println("Error in snapshot generation: " + msg);
                if (!debug) {
                    System.out.println("Differential: ");
                    for (ElementDefinition ed : derived.getDifferential().getElement()) System.out.println("  " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                    System.out.println("Snapshot: ");
                    for (ElementDefinition ed : derived.getSnapshot().getElement()) System.out.println("  " + ed.getId() + " = " + ed.getPath() + " : " + typeSummaryWithProfile(ed) + "[" + ed.getMin() + ".." + ed.getMax() + "]" + sliceSummary(ed) + "  " + constraintSummary(ed));
                }
                if (exception)
                    throw new DefinitionException(msg);
                else
                    messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
            }
            // hack around a problem in R4 definitions (somewhere?)
            for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
                    if (mm.hasMap()) {
                        mm.setMap(mm.getMap().trim());
                    }
                }
                for (ElementDefinitionConstraintComponent s : ed.getConstraint()) {
                    if (s.hasSource()) {
                        String ref = s.getSource();
                        if (!Utilities.isAbsoluteUrl(ref)) {
                            if (ref.contains(".")) {
                                s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref.substring(0, ref.indexOf(".")) + "#" + ref);
                            } else {
                                s.setSource("http://hl7.org/fhir/StructureDefinition/" + ref);
                            }
                        }
                    }
                }
            }
            if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
                for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                    if (!ed.hasBase()) {
                        ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
                    }
                }
            }
            // last, check for wrong profiles or target profiles
            for (ElementDefinition ed : derived.getSnapshot().getElement()) {
                for (TypeRefComponent t : ed.getType()) {
                    for (UriType u : t.getProfile()) {
                        StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
                        if (sd == null) {
                            if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
                                sd = xver.makeDefinition(u.getValue());
                            }
                        }
                        if (sd == null) {
                            if (messages != null) {
                                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), "The type of profile " + u.getValue() + " cannot be checked as the profile is not known", IssueSeverity.WARNING));
                            }
                        } else {
                            String wt = t.getWorkingCode();
                            if (ed.getPath().equals("Bundle.entry.response.outcome")) {
                                wt = "OperationOutcome";
                            }
                            if (!sd.getType().equals(wt)) {
                                boolean ok = isCompatibleType(wt, sd);
                                if (!ok) {
                                    String smsg = "The profile " + u.getValue() + " has type " + sd.getType() + " which is not consistent with the stated type " + wt;
                                    if (exception)
                                        throw new DefinitionException(smsg);
                                    else
                                        messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url + "#" + ed.getId(), smsg, IssueSeverity.ERROR));
                                }
                            }
                        }
                    }
                }
            }
        } catch (Exception e) {
            // if we had an exception generating the snapshot, make sure we don't leave any half generated snapshot behind
            derived.setSnapshot(null);
            derived.clearUserData("profileutils.snapshot.generating");
            throw e;
        }
    } finally {
        derived.clearUserData("profileutils.snapshot.generating");
        snapshotStack.remove(derived.getUrl());
    }
}