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Merge pull request #686 from hapifhir/gg-202112-validation-fixes-tx 

Gg 202112 validation fixes tx
This commit is contained in:
Grahame Grieve 2021-12-13 21:11:35 +11:00 committed by GitHub
parent e310c8c1ef ac5e2b14a2
commit 67d8d8c076
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
12 changed files with 370 additions and 94 deletions
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15
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -111,6 +111,7 @@ import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorCla
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.ToolingClientLogger;
@ -927,6 +928,12 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
@Override
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs) {
ValidationContextCarrier ctxt = new ValidationContextCarrier();
return validateCode(options, code, vs, ctxt);
}
@Override
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs, ValidationContextCarrier ctxt) {
if (options == null) {
options = ValidationOptions.defaults();
}
@ -946,7 +953,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
if (options.isUseClient()) {
// ok, first we try to validate locally
try {
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this);
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this, ctxt);
if (!vsc.isServerSide(code.getSystem())) {
res = vsc.validateCode(code);
if (txCache != null) {
@ -1066,13 +1073,15 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
}
if (vs != null) {
if (isTxCaching && cacheId != null && cached.contains(vs.getUrl()+"|"+vs.getVersion())) {
if (isTxCaching && cacheId != null && vs.getUrl() != null && cached.contains(vs.getUrl()+"|"+vs.getVersion())) {
pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()+(vs.hasVersion() ? "|"+vs.getVersion() : "")));
} else if (options.getVsAsUrl()){
pin.addParameter().setName("url").setValue(new StringType(vs.getUrl()));
} else {
pin.addParameter().setName("valueSet").setResource(vs);
cached.add(vs.getUrl()+"|"+vs.getVersion());
if (vs.getUrl() != null) {
cached.add(vs.getUrl()+"|"+vs.getVersion());
}
}
cache = true;
addDependentResources(pin, vs);

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
View File

@ -45,6 +45,7 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.model.Bundle;
@ -64,11 +65,13 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import com.google.gson.JsonSyntaxException;
@ -193,13 +196,14 @@ public interface IWorkerContext {
}
}
public interface ICanonicalResourceLocator {
void findResource(Object caller, String url); // if it can be found, put it in the context
}
public interface IContextResourceLoader {
/**
* @return List of the resource types that shoud be loaded
* @return List of the resource types that should be loaded
*/
String[] getTypes();
@ -244,7 +248,6 @@ public interface IWorkerContext {
IContextResourceLoader getNewLoader(NpmPackage npm) throws JsonSyntaxException, IOException;
}
/**
* Get the versions of the definitions loaded in context
* @return
@ -745,6 +748,8 @@ public interface IWorkerContext {
* @return
*/
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs);
public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs, ValidationContextCarrier ctxt);
public void validateCodeBatch(ValidationOptions options, List<? extends CodingValidationRequest> codes, ValueSet vs);

69
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -56,6 +56,9 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier.ValidationContextResourceProxy;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@ -69,12 +72,52 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
private IWorkerContext context;
private Map<String, ValueSetCheckerSimple> inner = new HashMap<>();
private ValidationOptions options;
private ValidationContextCarrier localContext;
private List<CodeSystem> localSystems = new ArrayList<>();
public ValueSetCheckerSimple(ValidationOptions options, ValueSet source, IWorkerContext context) {
this.valueset = source;
this.context = context;
this.options = options;
}
public ValueSetCheckerSimple(ValidationOptions options, ValueSet source, IWorkerContext context, ValidationContextCarrier ctxt) {
this.valueset = source;
this.context = context;
this.options = options;
this.localContext = ctxt;
analyseValueSet();
}
private void analyseValueSet() {
if (localContext != null) {
if (valueset != null) {
for (ConceptSetComponent i : valueset.getCompose().getInclude()) {
analyseComponent(i);
}
for (ConceptSetComponent i : valueset.getCompose().getExclude()) {
analyseComponent(i);
}
}
}
}
private void analyseComponent(ConceptSetComponent i) {
if (i.getSystemElement().hasExtension(ToolingExtensions.EXT_VALUESET_SYSTEM)) {
String ref = i.getSystemElement().getExtensionString(ToolingExtensions.EXT_VALUESET_SYSTEM);
if (ref.startsWith("#")) {
String id = ref.substring(1);
for (ValidationContextResourceProxy t : localContext.getResources()) {
CodeSystem cs = (CodeSystem) t.loadContainedResource(id, CodeSystem.class);
if (cs != null) {
localSystems.add(cs);
}
}
} else {
throw new Error("Not done yet #2: "+ref);
}
}
}
public ValidationResult validateCode(CodeableConcept code) throws FHIRException {
// first, we validate the codings themselves
@ -85,7 +128,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (!c.hasSystem()) {
warnings.add(context.formatMessage(I18nConstants.CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE));
}
CodeSystem cs = context.fetchCodeSystem(c.getSystem());
CodeSystem cs = resolveCodeSystem(c.getSystem());
ValidationResult res = null;
if (cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) {
res = context.validateCode(options.noClient(), c, null);
@ -124,6 +167,19 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
}
public CodeSystem resolveCodeSystem(String system) {
for (CodeSystem t : localSystems) {
if (t.getUrl().equals(system)) {
return t;
}
}
CodeSystem cs = context.fetchCodeSystem(system);
if (cs == null) {
cs = findSpecialCodeSystem(system);
}
return cs;
}
public ValidationResult validateCode(Coding code) throws FHIRException {
String warningMessage = null;
// first, we validate the concept itself
@ -144,10 +200,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
inExpansion = checkExpansion(code);
inInclude = checkInclude(code);
CodeSystem cs = context.fetchCodeSystem(system);
if (cs == null) {
cs = findSpecialCodeSystem(system);
}
CodeSystem cs = resolveCodeSystem(system);
if (cs == null) {
warningMessage = "Unable to resolve system "+system;
if (!inExpansion) {
@ -498,7 +551,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (vsi.hasFilter()) {
return null;
}
CodeSystem cs = context.fetchCodeSystem(vsi.getSystem());
CodeSystem cs = resolveCodeSystem(vsi.getSystem());
if (cs == null) {
return null;
}
@ -604,7 +657,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (!system.equals(vsi.getSystem()))
return false;
// ok, we need the code system
CodeSystem cs = context.fetchCodeSystem(system);
CodeSystem cs = resolveCodeSystem(system);
if (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT)) {
// make up a transient value set with
ValueSet vs = new ValueSet();
@ -709,7 +762,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
return inner.get(url);
}
ValueSet vs = context.fetchResource(ValueSet.class, url);
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, context);
ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, context, localContext);
inner.put(url, vsc);
return vsc;
}

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ToolingExtensions.java
View File

@ -197,6 +197,7 @@ public class ToolingExtensions {
public static final String EXT_BINARY_FORMAT = "http://hl7.org/fhir/StructureDefinition/implementationguide-resource-format";
public static final String EXT_TARGET_ID = "http://hl7.org/fhir/StructureDefinition/targetElement";
public static final String EXT_TARGET_PATH = "http://hl7.org/fhir/StructureDefinition/targetPath";
public static final String EXT_VALUESET_SYSTEM = "http://hl7.org/fhir/StructureDefinition/valueset-system";
// specific extension helpers

81
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/validation/ValidationContextCarrier.java Normal file
View File

@ -0,0 +1,81 @@
package org.hl7.fhir.r5.utils.validation;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.utilities.validation.ValidationMessage;
public class ValidationContextCarrier {
/**
*
* When the validator is calling validateCode, it typically has a partially loaded resource that may provide
* additional resources that are relevant to the validation. This is a handle back into the validator context
* to ask for the resource to be fully loaded if it becomes relevant. Note that the resource may fail to load
* (e.g. if it's part of what's being validated) and if it does, the validator will record the validation
* issues before throwing an error
*
* This is a reference back int
*
*/
public interface IValidationContextResourceLoader {
public Resource loadContainedResource(List<ValidationMessage> errors, String path, Element resource, String id, Class<? extends Resource> class1) throws FHIRException;
}
/**
* A list of resources that provide context - typically, a container resource, and a bundle resource.
* iterate these in order looking for contained resources
*
*/
public static class ValidationContextResourceProxy {
// either a resource
private Resource resource;
// or an element and a loader
private Element element;
private IValidationContextResourceLoader loader;
private List<ValidationMessage> errors;
private String path;
public ValidationContextResourceProxy(Resource resource) {
this.resource = resource;
}
public ValidationContextResourceProxy(List<ValidationMessage> errors, String path, Element element, IValidationContextResourceLoader loader) {
this.errors = errors;
this.path = path;
this.element = element;
this.loader = loader;
}
public Resource loadContainedResource(String id, Class<? extends Resource> class1) throws FHIRException {
if (resource == null) {
Resource res = loader.loadContainedResource(errors, path, element, id, class1);
return res;
} else {
if (resource instanceof DomainResource) {
for (Resource r : ((DomainResource) resource).getContained()) {
if (r.getId().equals(id)) {
if (class1.isInstance(r))
return r;
}
}
}
return null;
}
}
}
private List<ValidationContextResourceProxy> resources = new ArrayList<>();
public List<ValidationContextResourceProxy> getResources() {
return resources;
}
}

38
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/SIDUtilities.java
View File

@ -10,11 +10,9 @@ public class SIDUtilities {
public static List<String> codeSystemList() {
List<String> codeSystems = new ArrayList<>();
codeSystems.add("http://hl7.org/fhir/sid/ndc");
codeSystems.add("http://hl7.org/fhir/sid/icd-10");
codeSystems.add("http://hl7.org/fhir/sid/icpc2");
codeSystems.add("http://hl7.org/fhir/sid/icd-9");
codeSystems.add("http://hl7.org/fhir/sid/icd-10");
codeSystems.add("http://hl7.org/fhir/sid/icpc2");
codeSystems.add("http://hl7.org/fhir/sid/cvx");
codeSystems.add("http://hl7.org/fhir/sid/srt");
codeSystems.add("http://hl7.org/fhir/sid/icd-10-vn");
@ -55,8 +53,38 @@ public class SIDUtilities {
allSystems.addAll(idSystemList());
return allSystems;
}
public static boolean isInvalidVersion(String u, String v) {
if (v == null) {
return false;
} else {
if (idSystemList().contains(u)) {
return true;
} else {
switch (u) {
case "http://hl7.org/fhir/sid/ndc":
return v.matches("[\\d]{8}");
case "http://hl7.org/fhir/sid/icpc2":
return false;
case "http://hl7.org/fhir/sid/icd-10":
return false;
case "http://hl7.org/fhir/sid/icd-9":
return false;
case "http://hl7.org/fhir/sid/cvx":
return v.matches("[\\d]{8}");
case "http://hl7.org/fhir/sid/srt":
return false;
case "http://hl7.org/fhir/sid/icd-10-vn":
return false;
case "http://hl7.org/fhir/sid/icd-10-cm":
return false;
case "http://hl7.org/fhir/sid/icd-9-cm":
return false;
default:
return true;
}
}
}
}
}

33
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
View File

@ -397,7 +397,6 @@ public class VersionUtilities {
}
if (isR4Ver(version)) {
res.add("CodeSystem");
res.add("ActivityDefinition");
res.add("CapabilityStatement");
@ -429,6 +428,38 @@ public class VersionUtilities {
res.add("TestScript");
res.add("ValueSet");
}
if (isR4BVer(version)) {
res.add("ActivityDefinition");
res.add("CapabilityStatement");
res.add("ChargeItemDefinition");
res.add("Citation");
res.add("CodeSystem");
res.add("CompartmentDefinition");
res.add("ConceptMap");
res.add("EventDefinition");
res.add("Evidence");
res.add("EvidenceReport");
res.add("EvidenceVariable");
res.add("ExampleScenario");
res.add("GraphDefinition");
res.add("ImplementationGuide");
res.add("Library");
res.add("Measure");
res.add("MessageDefinition");
res.add("NamingSystem");
res.add("OperationDefinition");
res.add("PlanDefinition");
res.add("Questionnaire");
res.add("ResearchDefinition");
res.add("ResearchElementDefinition");
res.add("SearchParameter");
res.add("StructureDefinition");
res.add("StructureMap");
res.add("SubscriptionTopic");
res.add("TerminologyCapabilities");
res.add("TestScript");
res.add("ValueSet");
}
if (isR5Ver(version) || "current".equals(version)) {

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -514,6 +514,7 @@ public class I18nConstants {
public static final String TYPE_SPECIFIC_CHECKS_DT_URL_EXAMPLE = "TYPE_SPECIFIC_CHECKS_DT_URL_EXAMPLE";
public static final String TYPE_SPECIFIC_CHECKS_DT_CANONICAL_TYPE = "TYPE_SPECIFIC_CHECKS_DT_CANONICAL_TYPE";
public static final String TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE = "TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE";
public static final String TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE_NC = "TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE_NC";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_STRAT = "Type_Specific_Checks_DT_UUID_Strat";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_VALID = "Type_Specific_Checks_DT_UUID_Valid";
public static final String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER = "Unable_to_connect_to_terminology_server";

1
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -645,6 +645,7 @@ SD_ED_BIND_NO_BINDABLE = The element {0} has a binding, but no bindable types ar
DISCRIMINATOR_BAD_PATH = Error processing path expression for discriminator: {0} (src = ''{1}'')
SLICING_CANNOT_BE_EVALUATED = Slicing cannot be evaluated: {0}
TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE = Canonical URL ''{0}'' does not resolve
TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE_NC = Canonical URL ''{0}'' exists, but can't be loaded, so it can't be checked for validity
TYPE_SPECIFIC_CHECKS_DT_CANONICAL_TYPE = Canonical URL ''{0}'' refers to a resource that has the wrong type. Found {1} expecting one of {2}
CODESYSTEM_CS_NO_SUPPLEMENT = CodeSystem {0} is a supplement, so can't be used as a value in Coding.system
CODESYSTEM_CS_SUPP_CANT_CHECK = CodeSystem {0} cannot be found, so can't check if concepts are valid

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
View File

@ -44,6 +44,7 @@ import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.terminologies.ValueSetUtilities;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.r5.utils.XVerExtensionManager.XVerExtensionStatus;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier.IValidationContextResourceLoader;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
@ -61,7 +62,8 @@ import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class BaseValidator {
public class BaseValidator implements IValidationContextResourceLoader {
public class TrackedLocationRelatedMessage {
private Object location;
private ValidationMessage vmsg;
@ -996,7 +998,8 @@ public class BaseValidator {
}
}
protected Resource loadContainedResource(List<ValidationMessage> errors, String path, Element resource, String id, Class class1) throws FHIRException {
@Override
public Resource loadContainedResource(List<ValidationMessage> errors, String path, Element resource, String id, Class<? extends Resource> class1) throws FHIRException {
for (Element contained : resource.getChildren("contained")) {
if (contained.getIdBase().equals(id)) {
return loadFoundResource(errors, path, contained, class1);
@ -1005,7 +1008,7 @@ public class BaseValidator {
return null;
}
protected Resource loadFoundResource(List<ValidationMessage> errors, String path, Element resource, Class class1) throws FHIRException {
protected Resource loadFoundResource(List<ValidationMessage> errors, String path, Element resource, Class<? extends Resource> class1) throws FHIRException {
try {
FhirPublication v = FhirPublication.fromCode(context.getVersion());
ByteArrayOutputStream bs = new ByteArrayOutputStream();

125
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -2114,52 +2114,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isAbsoluteUrl(url),
node.isContained() ? I18nConstants.TYPE_SPECIFIC_CHECKS_CANONICAL_CONTAINED : I18nConstants.TYPE_SPECIFIC_CHECKS_CANONICAL_ABSOLUTE, url);
} else {
// now, do we check the URI target?
if (fetcher != null && !type.equals("uuid")) {
boolean found;
try {
found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) || (url.startsWith("http://hl7.org/fhir/tools")) ||
SpecialExtensions.isKnownExtension(url) || isXverUrl(url) || fetcher.resolveURL(this, hostContext, path, url, type);
} catch (IOException e1) {
found = false;
}
if (!found) {
if (type.equals("canonical")) {
ReferenceValidationPolicy rp = policyAdvisor == null ? ReferenceValidationPolicy.CHECK_VALID : policyAdvisor.policyForReference(this, hostContext, path, url);
if (rp == ReferenceValidationPolicy.CHECK_EXISTS || rp == ReferenceValidationPolicy.CHECK_EXISTS_AND_TYPE) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE, url);
} else {
hint(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE, url);
}
} else {
if (url.contains("hl7.org") || url.contains("fhir.org")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URL_RESOLVE, url);
} else if (url.contains("example.org") || url.contains("acme.com")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URL_EXAMPLE, url);
} else {
warning(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URL_RESOLVE, url);
}
}
} else {
if (type.equals("canonical")) {
ReferenceValidationPolicy rp = policyAdvisor == null ? ReferenceValidationPolicy.CHECK_VALID : policyAdvisor.policyForReference(this, hostContext, path, url);
if (rp == ReferenceValidationPolicy.CHECK_EXISTS_AND_TYPE || rp == ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS || rp == ReferenceValidationPolicy.CHECK_VALID) {
try {
Resource r = fetcher.fetchCanonicalResource(this, url);
if (r == null) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE, url);
} else if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, isCorrectCanonicalType(r, context), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_TYPE, url, r.fhirType(), listExpectedCanonicalTypes(context))) {
if (rp == ReferenceValidationPolicy.CHECK_VALID) {
// todo....
}
}
} catch (Exception ex) {
// won't happen
}
}
}
}
}
validateReference(hostContext, errors, path, type, context, e, url);
}
}
if (type.equals(ID) && !"Resource.id".equals(context.getBase().getPath())) {
@ -2323,6 +2278,67 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// for nothing to check
}
public void validateReference(ValidatorHostContext hostContext, List<ValidationMessage> errors, String path, String type, ElementDefinition context, Element e, String url) {
// now, do we check the URI target?
if (fetcher != null && !type.equals("uuid")) {
boolean found;
try {
found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com")) || url.contains("acme.org")) || (url.startsWith("http://hl7.org/fhir/tools")) ||
SpecialExtensions.isKnownExtension(url) || isXverUrl(url);
if (!found) {
found = fetcher.resolveURL(this, hostContext, path, url, type);
}
} catch (IOException e1) {
found = false;
}
if (!found) {
if (type.equals("canonical")) {
ReferenceValidationPolicy rp = policyAdvisor == null ? ReferenceValidationPolicy.CHECK_VALID : policyAdvisor.policyForReference(this, hostContext, path, url);
if (rp == ReferenceValidationPolicy.CHECK_EXISTS || rp == ReferenceValidationPolicy.CHECK_EXISTS_AND_TYPE) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE, url);
} else {
hint(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE, url);
}
} else {
if (url.contains("hl7.org") || url.contains("fhir.org")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URL_RESOLVE, url);
} else if (url.contains("example.org") || url.contains("acme.com")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URL_EXAMPLE, url);
} else {
warning(errors, IssueType.INVALID, e.line(), e.col(), path, false, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_URL_RESOLVE, url);
}
}
} else {
if (type.equals("canonical")) {
ReferenceValidationPolicy rp = policyAdvisor == null ? ReferenceValidationPolicy.CHECK_VALID : policyAdvisor.policyForReference(this, hostContext, path, url);
if (rp == ReferenceValidationPolicy.CHECK_EXISTS_AND_TYPE || rp == ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS || rp == ReferenceValidationPolicy.CHECK_VALID) {
try {
Resource r = null;
if (url.startsWith("#")) {
r = loadContainedResource(errors, path, hostContext.getRootResource(), url.substring(1), Resource.class);
}
if (r == null) {
fetcher.fetchCanonicalResource(this, url);
}
if (r == null) {
r = this.context.fetchResource(Resource.class, url);
}
if (r == null) {
warning(errors, IssueType.INVALID, e.line(), e.col(), path, rp != ReferenceValidationPolicy.CHECK_VALID, I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE_NC, url);
} else if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, isCorrectCanonicalType(r, context), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_CANONICAL_TYPE, url, r.fhirType(), listExpectedCanonicalTypes(context))) {
if (rp == ReferenceValidationPolicy.CHECK_VALID) {
// todo....
}
}
} catch (Exception ex) {
// won't happen
}
}
}
}
}
}
private List<String> listExpectedCanonicalTypes(ElementDefinition context) {
List<String> res = new ArrayList<>();
TypeRefComponent tr = context.getType("canonical");
@ -2354,11 +2370,20 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private boolean isCorrectCanonicalType(Resource r, CanonicalType p) {
String url = p.getValue();
if (url != null && url.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
url = url.substring("http://hl7.org/fhir/StructureDefinition/".length());
return Utilities.existsInList(url, "Resource", "CanonicalResource") || url.equals(r.fhirType());
String t = null;
if (url.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
t = url.substring("http://hl7.org/fhir/StructureDefinition/".length());
} else {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
if (sd != null) {
t = sd.getType();
}
}
if (t == null ) {
return false;
} else {
return Utilities.existsInList(t, "Resource", "CanonicalResource") || t.equals(r.fhirType());
}
return false;
}
private boolean isCanonicalURLElement(Element e) {

82
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/QuestionnaireValidator.java
View File

@ -10,6 +10,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.attoparser.config.ParseConfiguration.ElementBalancing;
import org.hl7.fhir.convertors.conv10_50.VersionConvertor_10_50;
import org.hl7.fhir.convertors.conv14_50.VersionConvertor_14_50;
import org.hl7.fhir.convertors.conv30_50.VersionConvertor_30_50;
@ -40,6 +41,8 @@ import org.hl7.fhir.r5.model.TimeType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier.ValidationContextResourceProxy;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@ -52,6 +55,7 @@ import org.hl7.fhir.validation.cli.utils.QuestionnaireMode;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.EnableWhenEvaluator;
import org.hl7.fhir.validation.instance.EnableWhenEvaluator.QStack;
import org.hl7.fhir.validation.instance.type.QuestionnaireValidator.ElementWithIndex;
import org.hl7.fhir.validation.instance.type.QuestionnaireValidator.QuestionnaireWithContext;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
@ -60,6 +64,26 @@ import ca.uhn.fhir.util.ObjectUtil;
public class QuestionnaireValidator extends BaseValidator {
public class ElementWithIndex {
private Element element;
private int index;
public ElementWithIndex(Element element, int index) {
this.element = element;
this.index = index;
}
public Element getElement() {
return element;
}
public int getIndex() {
return index;
}
}
public static class QuestionnaireWithContext {
private Questionnaire q;
private Element container;
@ -88,7 +112,7 @@ public class QuestionnaireValidator extends BaseValidator {
public Questionnaire q() {
return q;
}
}
private EnableWhenEvaluator myEnableWhenEvaluator;
@ -263,8 +287,9 @@ public class QuestionnaireValidator extends BaseValidator {
if (answers.size() > 1)
rule(errors, IssueType.INVALID, answers.get(1).line(), answers.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), I18nConstants.QUESTIONNAIRE_QR_ITEM_ONLYONEA);
int i = 0;
for (Element answer : answers) {
NodeStack ns = stack.push(answer, -1, null, null);
NodeStack ns = stack.push(answer, i, null, null);
if (qItem.getType() != null) {
switch (qItem.getType()) {
case GROUP:
@ -337,12 +362,15 @@ public class QuestionnaireValidator extends BaseValidator {
case NULL:
// no validation
break;
case QUESTION:
throw new Error("Shouldn't get here?");
}
}
if (qItem.getType() != QuestionnaireItemType.GROUP) {
// if it's a group, we already have an error before getting here, so no need to hammer away on that
validateQuestionannaireResponseItems(hostContext, qsrc, qItem.getItem(), errors, answer, stack, inProgress, questionnaireResponseRoot, qstack);
}
i++;
}
if (qItem.getType() == null) {
fail(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, I18nConstants.QUESTIONNAIRE_QR_ITEM_NOTYPE, qItem.getLinkId());
@ -363,14 +391,13 @@ public class QuestionnaireValidator extends BaseValidator {
return !answers.isEmpty() || !qItem.getRequired() || qItem.getType() == QuestionnaireItemType.GROUP;
}
private void validateQuestionnaireResponseItem(ValidatorHostContext hostcontext, QuestionnaireWithContext qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, List<Element> elements, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) {
if (elements.size() > 1)
rule(errors, IssueType.INVALID, elements.get(1).line(), elements.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), I18nConstants.QUESTIONNAIRE_QR_ITEM_ONLYONEI, qItem.getLinkId());
int i = 0;
for (Element element : elements) {
NodeStack ns = stack.push(element, i, null, null);
validateQuestionnaireResponseItem(hostcontext, qsrc, qItem, errors, element, ns, inProgress, questionnaireResponseRoot, qstack.push(qItem, element));
i++;
private void validateQuestionnaireResponseItem(ValidatorHostContext hostcontext, QuestionnaireWithContext qsrc, QuestionnaireItemComponent qItem, List<ValidationMessage> errors, List<ElementWithIndex> elements, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) {
if (elements.size() > 1) {
rule(errors, IssueType.INVALID, elements.get(1).getElement().line(), elements.get(1).getElement().col(), stack.getLiteralPath(), qItem.getRepeats(), I18nConstants.QUESTIONNAIRE_QR_ITEM_ONLYONEI, qItem.getLinkId());
}
for (ElementWithIndex element : elements) {
NodeStack ns = stack.push(element.getElement(), element.getIndex(), null, null);
validateQuestionnaireResponseItem(hostcontext, qsrc, qItem, errors, element.getElement(), ns, inProgress, questionnaireResponseRoot, qstack.push(qItem, element.getElement()));
}
}
@ -386,8 +413,9 @@ public class QuestionnaireValidator extends BaseValidator {
List<Element> items = new ArrayList<Element>();
element.getNamedChildren("item", items);
// now, sort into stacks
Map<String, List<Element>> map = new HashMap<String, List<Element>>();
Map<String, List<ElementWithIndex>> map = new HashMap<String, List<ElementWithIndex>>();
int lastIndex = -1;
int counter = 0;
for (Element item : items) {
String linkId = item.getNamedChildValue("linkId");
if (rule(errors, IssueType.REQUIRED, item.line(), item.col(), stack.getLiteralPath(), !Utilities.noString(linkId), I18nConstants.QUESTIONNAIRE_QR_ITEM_NOLINKID)) {
@ -396,7 +424,7 @@ public class QuestionnaireValidator extends BaseValidator {
QuestionnaireItemComponent qItem = findQuestionnaireItem(qsrc, linkId);
if (qItem != null) {
rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index > -1, misplacedItemError(qItem));
NodeStack ns = stack.push(item, -1, null, null);
NodeStack ns = stack.push(item, counter, null, null);
validateQuestionnaireResponseItem(hostContext, qsrc, qItem, errors, item, ns, inProgress, questionnaireResponseRoot, qstack.push(qItem, item));
} else
rule(errors, IssueType.NOTFOUND, item.line(), item.col(), stack.getLiteralPath(), index > -1, I18nConstants.QUESTIONNAIRE_QR_ITEM_NOTFOUND, linkId);
@ -407,29 +435,28 @@ public class QuestionnaireValidator extends BaseValidator {
// If an item has a child called "linkId" but no child called "answer",
// we'll treat it as not existing for the purposes of enableWhen validation
if (item.hasChildren("answer") || item.hasChildren("item")) {
List<Element> mapItem = map.computeIfAbsent(linkId, key -> new ArrayList<>());
mapItem.add(item);
List<ElementWithIndex> mapItem = map.computeIfAbsent(linkId, key -> new ArrayList<>());
mapItem.add(new ElementWithIndex(item, counter));
}
}
}
counter++;
}
// ok, now we have a list of known items, grouped by linkId. We've made an error for anything out of order
for (QuestionnaireItemComponent qItem : qItems) {
List<Element> mapItem = map.get(qItem.getLinkId());
List<ElementWithIndex> mapItem = map.get(qItem.getLinkId());
validateQuestionnaireResponseItem(hostContext, qsrc, errors, element, stack, inProgress, questionnaireResponseRoot, qItem, mapItem, qstack);
}
}
public void validateQuestionnaireResponseItem(ValidatorHostContext hostContext, QuestionnaireWithContext qsrc, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QuestionnaireItemComponent qItem, List<Element> mapItem, QStack qstack) {
public void validateQuestionnaireResponseItem(ValidatorHostContext hostContext, QuestionnaireWithContext qsrc, List<ValidationMessage> errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QuestionnaireItemComponent qItem, List<ElementWithIndex> mapItem, QStack qstack) {
boolean enabled = myEnableWhenEvaluator.isQuestionEnabled(hostContext, qItem, qstack, fpe);
if (mapItem != null) {
if (!enabled) {
int i = 0;
for (Element e : mapItem) {
NodeStack ns = stack.push(e, i, e.getProperty().getDefinition(), e.getProperty().getDefinition());
rule(errors, IssueType.INVALID, e.line(), e.col(), ns.getLiteralPath(), enabled, I18nConstants.QUESTIONNAIRE_QR_ITEM_NOTENABLED2, qItem.getLinkId());
i++;
for (ElementWithIndex e : mapItem) {
NodeStack ns = stack.push(e.getElement(), e.getElement().getIndex(), e.getElement().getProperty().getDefinition(), e.getElement().getProperty().getDefinition());
rule(errors, IssueType.INVALID, e.getElement().line(), e.getElement().col(), ns.getLiteralPath(), enabled, I18nConstants.QUESTIONNAIRE_QR_ITEM_NOTENABLED2, qItem.getLinkId());
}
}
@ -516,7 +543,8 @@ public class QuestionnaireValidator extends BaseValidator {
}
long t = System.nanoTime();
ValidationResult res = context.validateCode(new ValidationOptions(stack.getWorkingLang()), c, vs);
ValidationContextCarrier vc = makeValidationContext(errors, qSrc);
ValidationResult res = context.validateCode(new ValidationOptions(stack.getWorkingLang()), c, vs, vc);
timeTracker.tx(t, "vc "+c.getSystem()+"#"+c.getCode()+" '"+c.getDisplay()+"'");
if (!res.isOk()) {
txRule(errors, res.getTxLink(), IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, I18nConstants.QUESTIONNAIRE_QR_ITEM_BADOPTION, c.getSystem(), c.getCode());
@ -529,6 +557,16 @@ public class QuestionnaireValidator extends BaseValidator {
}
}
private ValidationContextCarrier makeValidationContext(List<ValidationMessage> errors, QuestionnaireWithContext qSrc) {
ValidationContextCarrier vc = new ValidationContextCarrier();
if (qSrc.container == null) {
vc.getResources().add(new ValidationContextResourceProxy(qSrc.q));
} else {
vc.getResources().add(new ValidationContextResourceProxy(errors, qSrc.containerPath, qSrc.container, this));
}
return vc;
}
private void validateAnswerCode(List<ValidationMessage> errors, Element answer, NodeStack stack, QuestionnaireWithContext qSrc, QuestionnaireItemComponent qItem, boolean theOpenChoice) {
Element v = answer.getNamedChild("valueCoding");
NodeStack ns = stack.push(v, -1, null, null);