Examples with NodeStack org.hl7.fhir.validation.instance.utils.NodeStack used on opensource projects

Example 56 with NodeStack

use of org.hl7.fhir.validation.instance.utils.NodeStack in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method checkPrimitiveBinding.

private void checkPrimitiveBinding(ValidatorHostContext hostContext, List<ValidationMessage> errors, String path, String type, ElementDefinition elementContext, Element element, StructureDefinition profile, NodeStack stack) {
    // We ignore bindings that aren't on string, uri or code
    if (!element.hasPrimitiveValue() || !("code".equals(type) || "string".equals(type) || "uri".equals(type) || "url".equals(type) || "canonical".equals(type))) {
        return;
    }
    if (noTerminologyChecks)
        return;
    String value = element.primitiveValue();
    // System.out.println("check "+value+" in "+path);
    // firstly, resolve the value set
    ElementDefinitionBindingComponent binding = elementContext.getBinding();
    if (binding.hasValueSet()) {
        ValueSet vs = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl());
        if (vs == null) {
            CodeSystem cs = context.fetchCodeSystem(binding.getValueSet());
            if (rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, cs == null, I18nConstants.TERMINOLOGY_TX_VALUESET_NOTFOUND_CS, describeReference(binding.getValueSet()))) {
                warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, I18nConstants.TERMINOLOGY_TX_VALUESET_NOTFOUND, describeReference(binding.getValueSet()));
            }
        } else {
            CodedContentValidationPolicy validationPolicy = getPolicyAdvisor() == null ? CodedContentValidationPolicy.VALUESET : getPolicyAdvisor().policyForCodedContent(this, hostContext, stack.getLiteralPath(), elementContext, profile, BindingKind.PRIMARY, vs, new ArrayList<>());
            if (validationPolicy != CodedContentValidationPolicy.IGNORE) {
                long t = System.nanoTime();
                ValidationResult vr = null;
                if (binding.getStrength() != BindingStrength.EXAMPLE) {
                    ValidationOptions options = baseOptions.setLanguage(stack.getWorkingLang()).guessSystem();
                    if (validationPolicy == CodedContentValidationPolicy.CODE) {
                        options = options.noCheckValueSetMembership();
                    }
                    vr = checkCodeOnServer(stack, vs, value, options);
                }
                timeTracker.tx(t, "vc " + value + "");
                if (binding.getStrength() == BindingStrength.REQUIRED) {
                    removeTrackedMessagesForLocation(errors, element, path);
                }
                if (vr != null && !vr.isOk()) {
                    if (vr.IsNoService())
                        txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_15, value);
                    else if (binding.getStrength() == BindingStrength.REQUIRED)
                        txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_16, value, describeValueSet(binding.getValueSet()), getErrorMessage(vr.getMessage()));
                    else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
                        if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"))
                            checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), value, stack);
                        else if (!noExtensibleWarnings && !isOkExtension(value, vs))
                            txWarningForLaterRemoval(element, errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_17, value, describeValueSet(binding.getValueSet()), getErrorMessage(vr.getMessage()));
                    } else if (binding.getStrength() == BindingStrength.PREFERRED) {
                        if (baseOnly) {
                            txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_18, value, describeValueSet(binding.getValueSet()), getErrorMessage(vr.getMessage()));
                        }
                    }
                }
            }
        }
    } else if (!noBindingMsgSuppressed)
        hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !type.equals("code"), I18nConstants.TERMINOLOGY_TX_BINDING_NOSOURCE2);
}

Example 57 with NodeStack

use of org.hl7.fhir.validation.instance.utils.NodeStack in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method localResolve.

private ResolvedReference localResolve(String ref, NodeStack stack, List<ValidationMessage> errors, String path, Element rootResource, Element groupingResource, Element source) {
    if (ref.startsWith("#")) {
        // work back through the parent list.
        // really, there should only be one level for this (contained resources cannot contain
        // contained resources), but we'll leave that to some other code to worry about
        boolean wasContained = false;
        NodeStack nstack = stack;
        while (nstack != null && nstack.getElement() != null) {
            if (nstack.getElement().getProperty().isResource()) {
                // ok, we'll try to find the contained reference
                if (ref.equals("#") && nstack.getElement().getSpecial() != SpecialElement.CONTAINED && wasContained) {
                    ResolvedReference rr = new ResolvedReference();
                    rr.setResource(nstack.getElement());
                    rr.setFocus(nstack.getElement());
                    rr.setExternal(false);
                    rr.setStack(nstack);
                    // System.out.println("-->"+nstack.getLiteralPath());
                    return rr;
                }
                if (nstack.getElement().getSpecial() == SpecialElement.CONTAINED) {
                    wasContained = true;
                }
                IndexedElement res = getContainedById(nstack.getElement(), ref.substring(1));
                if (res != null) {
                    ResolvedReference rr = new ResolvedReference();
                    rr.setResource(nstack.getElement());
                    rr.setFocus(res.getMatch());
                    rr.setExternal(false);
                    rr.setStack(nstack.push(res.getMatch(), res.getIndex(), res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition()));
                    rr.getStack().qualifyPath(".ofType(" + nstack.getElement().fhirType() + ")");
                    return rr;
                }
            }
            if (nstack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || nstack.getElement().getSpecial() == SpecialElement.PARAMETER) {
                // we don't try to resolve contained references across this boundary
                return null;
            }
            nstack = nstack.getParent();
        }
        // try again, and work up the element parent list
        if (ref.equals("#")) {
            Element e = stack.getElement();
            while (e != null) {
                if (e.getProperty().isResource() && (e.getSpecial() != SpecialElement.CONTAINED)) {
                    ResolvedReference rr = new ResolvedReference();
                    rr.setResource(e);
                    rr.setFocus(e);
                    rr.setExternal(false);
                    rr.setStack(stack.push(e, -1, e.getProperty().getDefinition(), e.getProperty().getDefinition()));
                    rr.getStack().qualifyPath(".ofType(" + e.fhirType() + ")");
                    return rr;
                }
                e = e.getParentForValidator();
            }
        }
        return null;
    } else {
        // work back through the parent list - if any of them are bundles, try to resolve
        // the resource in the bundle
        // we're going to try to work this out as we go up
        String fullUrl = null;
        while (stack != null && stack.getElement() != null) {
            if (stack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY && fullUrl == null && stack.getParent() != null && stack.getParent().getElement().getName().equals(ENTRY)) {
                String type = stack.getParent().getParent().getElement().getChildValue(TYPE);
                // we don't try to resolve contained references across this boundary
                fullUrl = stack.getParent().getElement().getChildValue(FULL_URL);
                if (fullUrl == null)
                    rule(errors, IssueType.REQUIRED, stack.getParent().getElement().line(), stack.getParent().getElement().col(), stack.getParent().getLiteralPath(), Utilities.existsInList(type, "batch-response", "transaction-response") || fullUrl != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOFULLURL);
            }
            if (BUNDLE.equals(stack.getElement().getType())) {
                String type = stack.getElement().getChildValue(TYPE);
                IndexedElement res = getFromBundle(stack.getElement(), ref, fullUrl, errors, path, type, "transaction".equals(type));
                if (res == null) {
                    return null;
                } else {
                    ResolvedReference rr = new ResolvedReference();
                    rr.setResource(res.getMatch());
                    rr.setFocus(res.getMatch());
                    rr.setExternal(false);
                    rr.setStack(stack.push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition()));
                    rr.getStack().qualifyPath(".ofType(" + rr.getResource().fhirType() + ")");
                    return rr;
                }
            }
            if (stack.getElement().getSpecial() == SpecialElement.PARAMETER && stack.getParent() != null) {
                NodeStack tgt = findInParams(stack.getParent().getParent(), ref);
                if (tgt != null) {
                    ResolvedReference rr = new ResolvedReference();
                    rr.setResource(tgt.getElement());
                    rr.setFocus(tgt.getElement());
                    rr.setExternal(false);
                    rr.setStack(tgt);
                    rr.getStack().qualifyPath(".ofType(" + tgt.getElement().fhirType() + ")");
                    return rr;
                }
            }
            stack = stack.getParent();
        }
        // we can get here if we got called via FHIRPath conformsTo which breaks the stack continuity.
        if (groupingResource != null && BUNDLE.equals(groupingResource.fhirType())) {
            // it could also be a Parameters resource - that case isn't handled yet
            String type = groupingResource.getChildValue(TYPE);
            Element entry = getEntryForSource(groupingResource, source);
            fullUrl = entry.getChildValue(FULL_URL);
            IndexedElement res = getFromBundle(groupingResource, ref, fullUrl, errors, path, type, "transaction".equals(type));
            if (res == null) {
                return null;
            } else {
                ResolvedReference rr = new ResolvedReference();
                rr.setResource(res.getMatch());
                rr.setFocus(res.getMatch());
                rr.setExternal(false);
                rr.setStack(new NodeStack(context, null, rootResource, validationLanguage).push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition()));
                rr.getStack().qualifyPath(".ofType(" + rr.getResource().fhirType() + ")");
                return rr;
            }
        }
    }
    return null;
}

Example 58 with NodeStack

use of org.hl7.fhir.validation.instance.utils.NodeStack in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method checkExtension.

private StructureDefinition checkExtension(ValidatorHostContext hostContext, List<ValidationMessage> errors, String path, Element resource, Element container, Element element, ElementDefinition def, StructureDefinition profile, NodeStack stack, NodeStack containerStack, String extensionUrl) throws FHIRException {
    String url = element.getNamedChildValue("url");
    boolean isModifier = element.getName().equals("modifierExtension");
    assert def.getIsModifier() == isModifier;
    long t = System.nanoTime();
    StructureDefinition ex = Utilities.isAbsoluteUrl(url) ? context.fetchResource(StructureDefinition.class, url) : null;
    timeTracker.sd(t);
    if (ex == null) {
        ex = getXverExt(errors, path, element, url);
    }
    if (ex == null) {
        if (extensionUrl != null && !isAbsolute(url)) {
            if (extensionUrl.equals(profile.getUrl())) {
                rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", hasExtensionSlice(profile, url), I18nConstants.EXTENSION_EXT_SUBEXTENSION_INVALID, url, profile.getUrl());
            }
        } else if (SpecialExtensions.isKnownExtension(url)) {
            ex = SpecialExtensions.getDefinition(url);
        } else if (Utilities.existsInList(url, BuildExtensions.allConsts())) {
        // nothing
        } else if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowUnknownExtension(url), I18nConstants.EXTENSION_EXT_UNKNOWN_NOTHERE, url)) {
            hint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, isKnownExtension(url), I18nConstants.EXTENSION_EXT_UNKNOWN, url);
        }
    }
    if (ex != null) {
        trackUsage(ex, hostContext, element);
        // check internal definitions are coherent
        if (isModifier) {
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", def.getIsModifier() == isModifier, I18nConstants.EXTENSION_EXT_MODIFIER_MISMATCHY);
        } else {
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", def.getIsModifier() == isModifier, I18nConstants.EXTENSION_EXT_MODIFIER_MISMATCHN);
        }
        // two questions
        // 1. can this extension be used here?
        checkExtensionContext(errors, resource, container, ex, containerStack, hostContext, isModifier);
        if (isModifier)
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", ex.getSnapshot().getElement().get(0).getIsModifier(), I18nConstants.EXTENSION_EXT_MODIFIER_Y, url);
        else
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", !ex.getSnapshot().getElement().get(0).getIsModifier(), I18nConstants.EXTENSION_EXT_MODIFIER_N, url);
        // check the type of the extension:
        Set<String> allowedTypes = listExtensionTypes(ex);
        String actualType = getExtensionType(element);
        if (actualType == null)
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowedTypes.isEmpty(), I18nConstants.EXTENSION_EXT_SIMPLE, url);
        else
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowedTypes.contains(actualType), I18nConstants.EXTENSION_EXT_TYPE, url, allowedTypes.toString(), actualType);
        // 3. is the content of the extension valid?
        validateElement(hostContext, errors, ex, ex.getSnapshot().getElement().get(0), null, null, resource, element, "Extension", stack, false, true, url);
    }
    return ex;
}

Example 59 with NodeStack

use of org.hl7.fhir.validation.instance.utils.NodeStack in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method checkAttachment.

private void checkAttachment(List<ValidationMessage> errors, String path, Element element, StructureDefinition theProfile, ElementDefinition definition, boolean theInCodeableConcept, boolean theCheckDisplayInContext, NodeStack theStack) {
    long size = -1;
    // first check size
    String fetchError = null;
    if (element.hasChild("data")) {
        String b64 = element.getChildValue("data");
        // Note: If the value isn't valid, we're not adding an error here, as the test to the
        // child Base64Binary will catch it and we don't want to log it twice
        boolean ok = isValidBase64(b64);
        if (ok && element.hasChild("size")) {
            size = countBase64DecodedBytes(b64);
            String sz = element.getChildValue("size");
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, Long.toString(size).equals(sz), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_SIZE_CORRECT, sz, size);
        }
    } else if (element.hasChild("size")) {
        String sz = element.getChildValue("size");
        if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, Utilities.isLong(sz), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_SIZE_INVALID, sz)) {
            size = Long.parseLong(sz);
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, size >= 0, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_SIZE_INVALID, sz);
        }
    } else if (element.hasChild("url")) {
        String url = element.getChildValue("url");
        if (definition.hasExtension("http://hl7.org/fhir/StructureDefinition/maxSize")) {
            try {
                if (url.startsWith("http://") || url.startsWith("https://")) {
                    if (fetcher == null) {
                        fetchError = context.formatMessage(I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_NO_FETCHER, url);
                    } else {
                        byte[] cnt = fetcher.fetchRaw(this, url);
                        size = cnt.length;
                    }
                } else if (url.startsWith("file:")) {
                    size = new File(url.substring(5)).length();
                } else {
                    fetchError = context.formatMessage(I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_UNKNOWN_URL_SCHEME, url);
                }
            } catch (Exception e) {
                if (STACK_TRACE)
                    e.printStackTrace();
                fetchError = context.formatMessage(I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_URL_ERROR, url, e.getMessage());
            }
        }
    }
    if (definition.hasExtension("http://hl7.org/fhir/StructureDefinition/maxSize")) {
        if (warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, size >= 0, fetchError)) {
            long def = Long.parseLong(ToolingExtensions.readStringExtension(definition, "http://hl7.org/fhir/StructureDefinition/maxSize"));
            rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, size <= def, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_TOO_LONG, size, def);
        }
    }
    warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, (element.hasChild("data") || element.hasChild("url")) || (element.hasChild("contentType") || element.hasChild("language")), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ATT_NO_CONTENT);
}

Example 60 with NodeStack

use of org.hl7.fhir.validation.instance.utils.NodeStack in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method start.

// checkSpecials = we're only going to run these tests if we are actually validating this content (as opposed to we looked it up)
private void start(ValidatorHostContext hostContext, List<ValidationMessage> errors, Element resource, Element element, StructureDefinition defn, NodeStack stack) throws FHIRException {
    checkLang(resource, stack);
    if (crumbTrails) {
        element.addMessage(signpost(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), I18nConstants.VALIDATION_VAL_PROFILE_SIGNPOST, defn.getUrl()));
    }
    if (BUNDLE.equals(element.fhirType())) {
        resolveBundleReferences(element, new ArrayList<Element>());
    }
    startInner(hostContext, errors, resource, element, defn, stack, hostContext.isCheckSpecials());
    Element meta = element.getNamedChild(META);
    if (meta != null) {
        List<Element> profiles = new ArrayList<Element>();
        meta.getNamedChildren("profile", profiles);
        int i = 0;
        for (Element profile : profiles) {
            StructureDefinition sd = context.fetchResource(StructureDefinition.class, profile.primitiveValue());
            if (!defn.getUrl().equals(profile.primitiveValue())) {
                // is this a version specific reference?
                VersionURLInfo vu = VersionUtilities.parseVersionUrl(profile.primitiveValue());
                if (vu != null) {
                    if (!VersionUtilities.versionsCompatible(vu.getVersion(), context.getVersion())) {
                        hint(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_OTHER_VERSION, vu.getVersion());
                    } else if (vu.getUrl().equals(defn.getUrl())) {
                        hint(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_THIS_VERSION_OK);
                    } else {
                        StructureDefinition sdt = context.fetchResource(StructureDefinition.class, vu.getUrl());
                        rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_THIS_VERSION_OTHER, sdt == null ? "null" : sdt.getType());
                    }
                } else {
                    if (sd == null) {
                        // we'll try fetching it directly from it's source, but this is likely to fail later even if the resolution succeeds
                        if (fetcher == null) {
                            warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN, profile.primitiveValue());
                        } else if (!fetcher.fetchesCanonicalResource(this, profile.primitiveValue())) {
                            warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY, profile.primitiveValue());
                        } else {
                            try {
                                sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, profile.primitiveValue());
                            } catch (Exception e) {
                                if (STACK_TRACE)
                                    e.printStackTrace();
                                warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());
                            }
                            if (sd != null) {
                                context.cacheResource(sd);
                            }
                        }
                    }
                    if (sd != null) {
                        if (crumbTrails) {
                            element.addMessage(signpost(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), I18nConstants.VALIDATION_VAL_PROFILE_SIGNPOST_META, sd.getUrl()));
                        }
                        stack.resetIds();
                        startInner(hostContext, errors, resource, element, sd, stack, false);
                    }
                }
            }
            i++;
        }
    }
    String rt = element.fhirType();
    for (ImplementationGuide ig : igs) {
        for (ImplementationGuideGlobalComponent gl : ig.getGlobal()) {
            if (rt.equals(gl.getType())) {
                StructureDefinition sd = context.fetchResource(StructureDefinition.class, gl.getProfile());
                if (warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), sd != null, I18nConstants.VALIDATION_VAL_GLOBAL_PROFILE_UNKNOWN, gl.getProfile())) {
                    if (crumbTrails) {
                        element.addMessage(signpost(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), I18nConstants.VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL, sd.getUrl(), ig.getUrl()));
                    }
                    stack.resetIds();
                    startInner(hostContext, errors, resource, element, sd, stack, false);
                }
            }
        }
    }
}