Examples with ValidationMessage org.hl7.fhir.utilities.validation.ValidationMessage used on opensource projects

Example 46 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project org.hl7.fhir.core by hapifhir.

the class OperationOutcomeUtilities method convertToIssue.

public static OperationOutcomeIssueComponent convertToIssue(ValidationMessage message, OperationOutcome op) {
    OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
    issue.setUserData("source.vm", message);
    issue.setCode(convert(message.getType()));
    if (message.getLocation() != null) {
        // message location has a fhirPath in it. We need to populate the expression
        issue.addExpression(message.getLocation());
    }
    // pass through line/col if they're present
    if (message.getLine() >= 0)
        issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_LINE).setValue(new IntegerType(message.getLine()));
    if (message.getCol() >= 0)
        issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_COL).setValue(new IntegerType(message.getCol()));
    issue.setSeverity(convert(message.getLevel()));
    CodeableConcept c = new CodeableConcept();
    c.setText(message.getMessage());
    issue.setDetails(c);
    if (message.getSource() != null) {
        issue.getExtension().add(ToolingExtensions.makeIssueSource(message.getSource()));
    }
    issue.setUserData("source.msg", message);
    return issue;
}

Example 47 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project org.hl7.fhir.core by hapifhir.

the class ToolingExtensions method readValidationMessage.

public static ValidationMessage readValidationMessage(OperationOutcomeIssueComponent issue, Source source) {
    ValidationMessage vm = new ValidationMessage();
    vm.setSource(source);
    vm.setLevel(mapSeverity(issue.getSeverity()));
    vm.setType(mapType(issue.getCode()));
    if (issue.hasExtension(ToolingExtensions.EXT_ISSUE_LINE))
        vm.setLine(ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, 0));
    if (issue.hasExtension(ToolingExtensions.EXT_ISSUE_COL))
        vm.setCol(ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, 0));
    if (issue.hasExpression())
        vm.setLocation(issue.getExpression().get(0).asStringValue());
    vm.setMessage(issue.getDetails().getText());
    if (issue.hasExtension("http://hl7.org/fhir/StructureDefinition/rendering-xhtml"))
        vm.setHtml(ToolingExtensions.readStringExtension(issue, "http://hl7.org/fhir/StructureDefinition/rendering-xhtml"));
    return vm;
}

Example 48 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage 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 49 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method generateIds.

private void generateIds(List<ElementDefinition> list, String name, String type) throws DefinitionException {
    if (list.isEmpty())
        return;
    Map<String, String> idList = new HashMap<String, String>();
    Map<String, String> replacedIds = new HashMap<String, String>();
    SliceList sliceInfo = new SliceList();
    // first pass, update the element ids
    for (ElementDefinition ed : list) {
        List<String> paths = new ArrayList<String>();
        if (!ed.hasPath())
            throw new DefinitionException(context.formatMessage(I18nConstants.NO_PATH_ON_ELEMENT_DEFINITION__IN_, Integer.toString(list.indexOf(ed)), name));
        sliceInfo.seeElement(ed);
        String[] pl = ed.getPath().split("\\.");
        for (// -1 because the last path is in focus
        int i = paths.size(); // -1 because the last path is in focus
        i < pl.length; // -1 because the last path is in focus
        i++) paths.add(pl[i]);
        String[] slices = sliceInfo.analyse(paths);
        StringBuilder b = new StringBuilder();
        b.append(paths.get(0));
        for (int i = 1; i < paths.size(); i++) {
            b.append(".");
            String s = paths.get(i);
            String p = slices[i];
            b.append(fixChars(s));
            if (p != null) {
                b.append(":");
                b.append(p);
            }
        }
        String bs = b.toString();
        if (ed.hasId()) {
            replacedIds.put(ed.getId(), ed.getPath());
        }
        ed.setId(bs);
        if (idList.containsKey(bs)) {
            if (exception || messages == null) {
                throw new DefinitionException(context.formatMessage(I18nConstants.SAME_ID_ON_MULTIPLE_ELEMENTS__IN_, bs, idList.get(bs), ed.getPath(), name));
            } else
                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, name + "." + bs, "Duplicate Element id " + bs, ValidationMessage.IssueSeverity.ERROR));
        }
        idList.put(bs, ed.getPath());
        if (ed.hasContentReference() && ed.getContentReference().startsWith("#")) {
            String s = ed.getContentReference();
            if (replacedIds.containsKey(s.substring(1))) {
                ed.setContentReference("http://hl7.org/fhir/StructureDefinition/" + type + "#" + replacedIds.get(s.substring(1)));
            } else {
                ed.setContentReference("http://hl7.org/fhir/StructureDefinition/" + type + s);
            }
        }
    }
// second path - fix up any broken path based id references
}

Example 50 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project org.hl7.fhir.core by hapifhir.

the class SimpleWorkerContext method generateSnapshot.

@Override
public void generateSnapshot(StructureDefinition p, boolean logical) throws FHIRException {
    if ((!p.hasSnapshot() || isProfileNeedsRegenerate(p)) && (logical || p.getKind() != StructureDefinitionKind.LOGICAL)) {
        if (!p.hasBaseDefinition())
            throw new DefinitionException(formatMessage(I18nConstants.PROFILE___HAS_NO_BASE_AND_NO_SNAPSHOT, p.getName(), p.getUrl()));
        StructureDefinition sd = fetchResource(StructureDefinition.class, p.getBaseDefinition());
        if (sd == null && "http://hl7.org/fhir/StructureDefinition/Base".equals(p.getBaseDefinition())) {
            sd = ProfileUtilities.makeBaseDefinition(p.getFhirVersion());
        }
        if (sd == null) {
            throw new DefinitionException(formatMessage(I18nConstants.PROFILE___BASE__COULD_NOT_BE_RESOLVED, p.getName(), p.getUrl(), p.getBaseDefinition()));
        }
        List<ValidationMessage> msgs = new ArrayList<ValidationMessage>();
        List<String> errors = new ArrayList<String>();
        ProfileUtilities pu = new ProfileUtilities(this, msgs, this);
        pu.setAutoFixSliceNames(true);
        pu.setThrowException(false);
        if (xverManager == null) {
            xverManager = new XVerExtensionManager(this);
        }
        pu.setXver(xverManager);
        if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
            pu.sortDifferential(sd, p, p.getUrl(), errors, true);
        }
        pu.setDebug(false);
        for (String err : errors) msgs.add(new ValidationMessage(Source.ProfileValidator, IssueType.EXCEPTION, p.getUserString("path"), "Error sorting Differential: " + err, ValidationMessage.IssueSeverity.ERROR));
        pu.generateSnapshot(sd, p, p.getUrl(), sd.getUserString("webroot"), p.getName());
        for (ValidationMessage msg : msgs) {
            if ((!ignoreProfileErrors && msg.getLevel() == ValidationMessage.IssueSeverity.ERROR) || msg.getLevel() == ValidationMessage.IssueSeverity.FATAL)
                throw new DefinitionException(formatMessage(I18nConstants.PROFILE___ELEMENT__ERROR_GENERATING_SNAPSHOT_, p.getName(), p.getUrl(), msg.getLocation(), msg.getMessage()));
        }
        if (!p.hasSnapshot())
            throw new FHIRException(formatMessage(I18nConstants.PROFILE___ERROR_GENERATING_SNAPSHOT, p.getName(), p.getUrl()));
        pu = null;
    }
}