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* fix fatal NPE validating bundles when resource is missing 

* fix tests for R5 changes
This commit is contained in:
Grahame Grieve 2020-05-13 09:45:29 +10:00
parent 463a557402
commit d688f9254d
6 changed files with 579 additions and 522 deletions
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12
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageCacheManager.java vendored
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@ -329,8 +329,6 @@ public class PackageCacheManager {
}
private InputStreamWithSrc loadFromPackageServer(String id, String v) {
// release hack:
if ("4.4.0".equals(v)) {v = "4.2.0"; };
PackageClient pc = new PackageClient(PRIMARY_SERVER);
String u = null;
InputStream stream;
@ -861,6 +859,16 @@ public class PackageCacheManager {
return null;
}
public List<String> listPackages() {
List<String> res = new ArrayList<>();
for (File f : new File(cacheFolder).listFiles()) {
if (f.isDirectory() && f.getName().contains("#")) {
res.add(f.getName());
}
}
return res;
}
//public List<String> getUrls() throws IOException {

4
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/PackageCacheTests.java
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@ -14,11 +14,10 @@ import java.io.IOException;
public class PackageCacheTests {
@Test
@Disabled // This test is currently set to always fail.
public void testPath() throws IOException {
PackageCacheManager cache = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
cache.clear();
Assertions.assertTrue(false);
Assertions.assertTrue(cache.listPackages().isEmpty());
NpmPackage npm = cache.loadPackage("hl7.fhir.pubpack", "0.0.3");
npm.loadAllFiles();
Assertions.assertNotNull(npm);
@ -31,5 +30,6 @@ public class PackageCacheTests {
npm.save(dir);
NpmPackage npm2 = cache.loadPackage("hl7.fhir.pubpack", "file:" + dir.getAbsolutePath());
Assertions.assertNotNull(npm2);
Assertions.assertFalse(cache.listPackages().isEmpty());
}
}

182
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
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@ -2,6 +2,8 @@ package org.hl7.fhir.validation;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.ArrayList;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
@ -64,18 +66,35 @@ POSSIBILITY OF SUCH DAMAGE.
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.ValueSetUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.instance.utils.IndexedElement;
public class BaseValidator {
protected final String META = "meta";
protected final String ENTRY = "entry";
protected final String DOCUMENT = "document";
protected final String RESOURCE = "resource";
protected final String MESSAGE = "message";
protected final String ID = "id";
protected final String FULL_URL = "fullUrl";
protected final String PATH_ARG = ":0";
protected final String TYPE = "type";
protected final String BUNDLE = "Bundle";
protected final String LAST_UPDATED = "lastUpdated";
protected Source source;
protected IWorkerContext context;
protected TimeTracker timeTracker = new TimeTracker();
@ -616,5 +635,168 @@ public class BaseValidator {
return reference;
}
protected Base resolveInBundle(String url, Element bnd) {
if (bnd == null)
return null;
if (bnd.fhirType().equals(BUNDLE)) {
for (Element be : bnd.getChildrenByName(ENTRY)) {
Element res = be.getNamedChild(RESOURCE);
if (res != null) {
String fullUrl = be.getChildValue(FULL_URL);
String rt = res.fhirType();
String id = res.getChildValue(ID);
if (url.equals(fullUrl))
return res;
if (url.equals(rt + "/" + id))
return res;
}
}
}
return null;
}
protected Element resolveInBundle(List<Element> entries, String ref, String fullUrl, String type, String id) {
if (Utilities.isAbsoluteUrl(ref)) {
// if the reference is absolute, then you resolve by fullUrl. No other thinking is required.
for (Element entry : entries) {
String fu = entry.getNamedChildValue(FULL_URL);
if (ref.equals(fu))
return entry;
}
return null;
} else {
// split into base, type, and id
String u = null;
if (fullUrl != null && fullUrl.endsWith(type + "/" + id))
// fullUrl = complex
u = fullUrl.substring(0, fullUrl.length() - (type + "/" + id).length()) + ref;
// u = fullUrl.substring((type+"/"+id).length())+ref;
String[] parts = ref.split("\\/");
if (parts.length >= 2) {
String t = parts[0];
String i = parts[1];
for (Element entry : entries) {
String fu = entry.getNamedChildValue(FULL_URL);
if (fu != null && fu.equals(u))
return entry;
if (u == null) {
Element resource = entry.getNamedChild(RESOURCE);
if (resource != null) {
String et = resource.getType();
String eid = resource.getNamedChildValue(ID);
if (t.equals(et) && i.equals(eid))
return entry;
}
}
}
}
return null;
}
}
protected IndexedElement getFromBundle(Element bundle, String ref, String fullUrl, List<ValidationMessage> errors, String path, String type, boolean isTransaction) {
String targetUrl = null;
String version = "";
String resourceType = null;
if (ref.startsWith("http") || ref.startsWith("urn")) {
// We've got an absolute reference, no need to calculate
if (ref.contains("/_history/")) {
targetUrl = ref.substring(0, ref.indexOf("/_history/") - 1);
version = ref.substring(ref.indexOf("/_history/") + 10);
} else
targetUrl = ref;
} else if (fullUrl == null) {
//This isn't a problem for signatures - if it's a signature, we won't have a resolution for a relative reference. For anything else, this is an error
// but this rule doesn't apply for batches or transactions
rule(errors, IssueType.REQUIRED, -1, -1, path, Utilities.existsInList(type, "batch-response", "transaction-response") || path.startsWith("Bundle.signature"), I18nConstants.BUNDLE_BUNDLE_FULLURL_MISSING);
return null;
} else if (ref.split("/").length != 2 && ref.split("/").length != 4) {
if (isTransaction) {
rule(errors, IssueType.INVALID, -1, -1, path, isSearchUrl(ref), I18nConstants.REFERENCE_REF_FORMAT1, ref);
} else {
rule(errors, IssueType.INVALID, -1, -1, path, false, I18nConstants.REFERENCE_REF_FORMAT2, ref);
}
return null;
} else {
String base = "";
if (fullUrl.startsWith("urn")) {
String[] parts = fullUrl.split("\\:");
for (int i = 0; i < parts.length - 1; i++) {
base = base + parts[i] + ":";
}
} else {
String[] parts;
parts = fullUrl.split("/");
for (int i = 0; i < parts.length - 2; i++) {
base = base + parts[i] + "/";
}
}
String id = null;
if (ref.contains("/_history/")) {
version = ref.substring(ref.indexOf("/_history/") + 10);
String[] refBaseParts = ref.substring(0, ref.indexOf("/_history/")).split("/");
resourceType = refBaseParts[0];
id = refBaseParts[1];
} else if (base.startsWith("urn")) {
resourceType = ref.split("/")[0];
id = ref.split("/")[1];
} else
id = ref;
targetUrl = base + id;
}
List<Element> entries = new ArrayList<Element>();
bundle.getNamedChildren(ENTRY, entries);
Element match = null;
int matchIndex = -1;
for (int i = 0; i < entries.size(); i++) {
Element we = entries.get(i);
if (targetUrl.equals(we.getChildValue(FULL_URL))) {
Element r = we.getNamedChild(RESOURCE);
if (version.isEmpty()) {
rule(errors, IssueType.FORBIDDEN, -1, -1, path, match == null, I18nConstants.BUNDLE_BUNDLE_MULTIPLEMATCHES, ref);
match = r;
matchIndex = i;
} else {
try {
if (version.equals(r.getChildren(META).get(0).getChildValue("versionId"))) {
rule(errors, IssueType.FORBIDDEN, -1, -1, path, match == null, I18nConstants.BUNDLE_BUNDLE_MULTIPLEMATCHES, ref);
match = r;
matchIndex = i;
}
} catch (Exception e) {
warning(errors, IssueType.REQUIRED, -1, -1, path, r.getChildren(META).size() == 1 && r.getChildren(META).get(0).getChildValue("versionId") != null, I18nConstants.BUNDLE_BUNDLE_FULLURL_NEEDVERSION, targetUrl);
// If one of these things is null
}
}
}
}
if (match != null && resourceType != null)
rule(errors, IssueType.REQUIRED, -1, -1, path, match.getType().equals(resourceType), I18nConstants.REFERENCE_REF_RESOURCETYPE, ref, match.getType());
if (match == null)
warning(errors, IssueType.REQUIRED, -1, -1, path, !ref.startsWith("urn"), I18nConstants.BUNDLE_BUNDLE_NOT_LOCAL, ref);
return match == null ? null : new IndexedElement(matchIndex, match, entries.get(matchIndex));
}
private boolean isSearchUrl(String ref) {
if (Utilities.noString(ref) || !ref.contains("?")) {
return false;
}
String tn = ref.substring(0, ref.indexOf("?"));
String q = ref.substring(ref.indexOf("?") + 1);
if (!context.getResourceNames().contains(tn)) {
return false;
} else {
return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+))*");
}
}
}

524
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -149,6 +149,7 @@ import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.EnableWhenEvaluator.QStack;
import org.hl7.fhir.validation.instance.type.BundleValidator;
import org.hl7.fhir.validation.instance.type.CodeSystemValidator;
import org.hl7.fhir.validation.instance.type.MeasureValidator;
import org.hl7.fhir.validation.instance.type.QuestionnaireValidator;
@ -188,19 +189,9 @@ import ca.uhn.fhir.util.ObjectUtil;
*/
public class InstanceValidator extends BaseValidator implements IResourceValidator {
private final String META = "meta";
private final String ENTRY = "entry";
private final String DOCUMENT = "document";
private final String RESOURCE = "resource";
private final String MESSAGE = "message";
private final String ID = "id";
private final String PATH_ARG = ":0";
private final String FULL_URL = "fullUrl";
private final String TYPE = "type";
private final String BUNDLE = "Bundle";
private final String LAST_UPDATED = "lastUpdated";
private static final String EXECUTED_CONSTRAINT_LIST = "validator.executed.invariant.list";
private static final String EXECUTION_ID = "validator.execution.id";
private class ValidatorHostServices implements IEvaluationContext {
@Override
@ -278,26 +269,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
public Base resolveInBundle(String url, Element bnd) {
if (bnd == null)
return null;
if (bnd.fhirType().equals(BUNDLE)) {
for (Element be : bnd.getChildrenByName(ENTRY)) {
Element res = be.getNamedChild(RESOURCE);
if (res != null) {
String fullUrl = be.getChildValue(FULL_URL);
String rt = res.fhirType();
String id = res.getChildValue(ID);
if (url.equals(fullUrl))
return res;
if (url.equals(rt + "/" + id))
return res;
}
}
}
return null;
}
@Override
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
ValidatorHostContext ctxt = (ValidatorHostContext) appContext;
@ -2595,109 +2567,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return extensionDomains;
}
private IndexedElement getFromBundle(Element bundle, String ref, String fullUrl, List<ValidationMessage> errors, String path, String type, boolean isTransaction) {
String targetUrl = null;
String version = "";
String resourceType = null;
if (ref.startsWith("http") || ref.startsWith("urn")) {
// We've got an absolute reference, no need to calculate
if (ref.contains("/_history/")) {
targetUrl = ref.substring(0, ref.indexOf("/_history/") - 1);
version = ref.substring(ref.indexOf("/_history/") + 10);
} else
targetUrl = ref;
} else if (fullUrl == null) {
//This isn't a problem for signatures - if it's a signature, we won't have a resolution for a relative reference. For anything else, this is an error
// but this rule doesn't apply for batches or transactions
rule(errors, IssueType.REQUIRED, -1, -1, path, Utilities.existsInList(type, "batch-response", "transaction-response") || path.startsWith("Bundle.signature"), I18nConstants.BUNDLE_BUNDLE_FULLURL_MISSING);
return null;
} else if (ref.split("/").length != 2 && ref.split("/").length != 4) {
if (isTransaction) {
rule(errors, IssueType.INVALID, -1, -1, path, isSearchUrl(ref), I18nConstants.REFERENCE_REF_FORMAT1, ref);
} else {
rule(errors, IssueType.INVALID, -1, -1, path, false, I18nConstants.REFERENCE_REF_FORMAT2, ref);
}
return null;
} else {
String base = "";
if (fullUrl.startsWith("urn")) {
String[] parts = fullUrl.split("\\:");
for (int i = 0; i < parts.length - 1; i++) {
base = base + parts[i] + ":";
}
} else {
String[] parts;
parts = fullUrl.split("/");
for (int i = 0; i < parts.length - 2; i++) {
base = base + parts[i] + "/";
}
}
String id = null;
if (ref.contains("/_history/")) {
version = ref.substring(ref.indexOf("/_history/") + 10);
String[] refBaseParts = ref.substring(0, ref.indexOf("/_history/")).split("/");
resourceType = refBaseParts[0];
id = refBaseParts[1];
} else if (base.startsWith("urn")) {
resourceType = ref.split("/")[0];
id = ref.split("/")[1];
} else
id = ref;
targetUrl = base + id;
}
List<Element> entries = new ArrayList<Element>();
bundle.getNamedChildren(ENTRY, entries);
Element match = null;
int matchIndex = -1;
for (int i = 0; i < entries.size(); i++) {
Element we = entries.get(i);
if (targetUrl.equals(we.getChildValue(FULL_URL))) {
Element r = we.getNamedChild(RESOURCE);
if (version.isEmpty()) {
rule(errors, IssueType.FORBIDDEN, -1, -1, path, match == null, I18nConstants.BUNDLE_BUNDLE_MULTIPLEMATCHES, ref);
match = r;
matchIndex = i;
} else {
try {
if (version.equals(r.getChildren(META).get(0).getChildValue("versionId"))) {
rule(errors, IssueType.FORBIDDEN, -1, -1, path, match == null, I18nConstants.BUNDLE_BUNDLE_MULTIPLEMATCHES, ref);
match = r;
matchIndex = i;
}
} catch (Exception e) {
warning(errors, IssueType.REQUIRED, -1, -1, path, r.getChildren(META).size() == 1 && r.getChildren(META).get(0).getChildValue("versionId") != null, I18nConstants.BUNDLE_BUNDLE_FULLURL_NEEDVERSION, targetUrl);
// If one of these things is null
}
}
}
}
if (match != null && resourceType != null)
rule(errors, IssueType.REQUIRED, -1, -1, path, match.getType().equals(resourceType), I18nConstants.REFERENCE_REF_RESOURCETYPE, ref, match.getType());
if (match == null)
warning(errors, IssueType.REQUIRED, -1, -1, path, !ref.startsWith("urn"), I18nConstants.BUNDLE_BUNDLE_NOT_LOCAL, ref);
return match == null ? null : new IndexedElement(matchIndex, match, entries.get(matchIndex));
}
private boolean isSearchUrl(String ref) {
if (Utilities.noString(ref) || !ref.contains("?")) {
return false;
}
String tn = ref.substring(0, ref.indexOf("?"));
String q = ref.substring(ref.indexOf("?") + 1);
if (!context.getResourceNames().contains(tn)) {
return false;
} else {
return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+))*");
}
}
private StructureDefinition getProfileForType(String type, List<TypeRefComponent> list) {
for (TypeRefComponent tr : list) {
String url = tr.getWorkingCode();
@ -2964,45 +2833,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
private Element resolveInBundle(List<Element> entries, String ref, String fullUrl, String type, String id) {
if (Utilities.isAbsoluteUrl(ref)) {
// if the reference is absolute, then you resolve by fullUrl. No other thinking is required.
for (Element entry : entries) {
String fu = entry.getNamedChildValue(FULL_URL);
if (ref.equals(fu))
return entry;
}
return null;
} else {
// split into base, type, and id
String u = null;
if (fullUrl != null && fullUrl.endsWith(type + "/" + id))
// fullUrl = complex
u = fullUrl.substring(0, fullUrl.length() - (type + "/" + id).length()) + ref;
// u = fullUrl.substring((type+"/"+id).length())+ref;
String[] parts = ref.split("\\/");
if (parts.length >= 2) {
String t = parts[0];
String i = parts[1];
for (Element entry : entries) {
String fu = entry.getNamedChildValue(FULL_URL);
if (fu != null && fu.equals(u))
return entry;
if (u == null) {
Element resource = entry.getNamedChild(RESOURCE);
if (resource != null) {
String et = resource.getType();
String eid = resource.getNamedChildValue(ID);
if (t.equals(et) && i.equals(eid))
return entry;
}
}
}
}
return null;
}
}
private ElementDefinition resolveNameReference(StructureDefinitionSnapshotComponent snapshot, String contentReference) {
for (ElementDefinition ed : snapshot.getElement())
if (contentReference.equals("#" + ed.getId()))
@ -3486,7 +3316,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
public void checkSpecials(ValidatorHostContext hostContext, List<ValidationMessage> errors, Element element, NodeStack stack, boolean checkSpecials) {
// specific known special validations
if (element.getType().equals(BUNDLE)) {
validateBundle(errors, element, stack, checkSpecials);
new BundleValidator(context, serverBase).validateBundle(errors, element, stack, checkSpecials);
} else if (element.getType().equals("Observation")) {
validateObservation(errors, element, stack);
} else if (element.getType().equals("Questionnaire")) {
@ -3583,268 +3413,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
iRest++;
}
}
private void validateBundle(List<ValidationMessage> errors, Element bundle, NodeStack stack, boolean checkSpecials) {
List<Element> entries = new ArrayList<Element>();
bundle.getNamedChildren(ENTRY, entries);
String type = bundle.getNamedChildValue(TYPE);
type = StringUtils.defaultString(type);
if (entries.size() == 0) {
rule(errors, IssueType.INVALID, stack.getLiteralPath(), !(type.equals(DOCUMENT) || type.equals(MESSAGE)), I18nConstants.BUNDLE_BUNDLE_ENTRY_NOFIRST);
} else {
// Get the first entry, the MessageHeader
Element firstEntry = entries.get(0);
// Get the stack of the first entry
NodeStack firstStack = stack.push(firstEntry, 1, null, null);
String fullUrl = firstEntry.getNamedChildValue(FULL_URL);
if (type.equals(DOCUMENT)) {
Element resource = firstEntry.getNamedChild(RESOURCE);
String id = resource.getNamedChildValue(ID);
if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), resource != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOFIRSTRESOURCE)) {
validateDocument(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id);
}
if (!VersionUtilities.isThisOrLater(FHIRVersion._4_0_1.getDisplay(), bundle.getProperty().getStructure().getFhirVersion().getDisplay())) {
handleSpecialCaseForLastUpdated(bundle, errors, stack);
}
checkAllInterlinked(errors, entries, stack, bundle, true);
}
if (type.equals(MESSAGE)) {
Element resource = firstEntry.getNamedChild(RESOURCE);
String id = resource.getNamedChildValue(ID);
if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), resource != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOFIRSTRESOURCE)) {
validateMessage(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id);
}
checkAllInterlinked(errors, entries, stack, bundle, VersionUtilities.isR5Ver(context.getVersion()));
}
// We do not yet have rules requiring that the id and fullUrl match when dealing with messaging Bundles
// validateResourceIds(errors, entries, stack);
}
for (Element entry : entries) {
String fullUrl = entry.getNamedChildValue(FULL_URL);
String url = getCanonicalURLForEntry(entry);
String id = getIdForEntry(entry);
if (url != null) {
if (!(!url.equals(fullUrl) || (url.matches(uriRegexForVersion()) && url.endsWith("/" + id))) && !isV3orV2Url(url))
rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), false, I18nConstants.BUNDLE_BUNDLE_ENTRY_MISMATCHIDURL, url, fullUrl, id);
rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), !url.equals(fullUrl) || serverBase == null || (url.equals(Utilities.pathURL(serverBase, entry.getNamedChild(RESOURCE).fhirType(), id))), I18nConstants.BUNDLE_BUNDLE_ENTRY_CANONICAL, url, fullUrl);
}
// todo: check specials
}
}
/**
* As per outline for <a href=http://hl7.org/fhir/stu3/documents.html#content>Document Content</a>:
* <li>"The document date (mandatory). This is found in Bundle.meta.lastUpdated and identifies when the document bundle
* was assembled from the underlying resources"</li>
* <p></p>
* This check was not being done for release versions < r4.
* <p></p>
* Related JIRA ticket is <a href=https://jira.hl7.org/browse/FHIR-26544>FHIR-26544</a>
*
* @param bundle {@link org.hl7.fhir.r5.elementmodel}
* @param errors {@link List<ValidationMessage>}
* @param stack {@link NodeStack}
*/
private void handleSpecialCaseForLastUpdated(Element bundle, List<ValidationMessage> errors, NodeStack stack) {
boolean ok = bundle.hasChild(META)
&& bundle.getNamedChild(META).hasChild(LAST_UPDATED)
&& bundle.getNamedChild(META).getNamedChild(LAST_UPDATED).hasValue();
rule(errors, IssueType.REQUIRED, stack.getLiteralPath(), ok, I18nConstants.DOCUMENT_DATE_REQUIRED, I18nConstants.DOCUMENT_DATE_REQUIRED_HTML);
}
// hack for pre-UTG v2/v3
private boolean isV3orV2Url(String url) {
return url.startsWith("http://hl7.org/fhir/v3/") || url.startsWith("http://hl7.org/fhir/v2/");
}
public final static String URI_REGEX3 = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AllergyIntolerance|AdverseEvent|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BodySite|Bundle|CapabilityStatement|CarePlan|CareTeam|ChargeItem|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition (aka Problem)|Consent|Contract|Coverage|DataElement|DetectedIssue|Device|DeviceComponent|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EligibilityRequest|EligibilityResponse|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|ExpansionProfile|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingManifest|ImagingStudy|Immunization|ImmunizationRecommendation|ImplementationGuide|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationRequest|MedicationStatement|MessageDefinition|MessageHeader|NamingSystem|NutritionOrder|Observation|OperationDefinition|OperationOutcome|Organization|Parameters|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|ProcedureRequest|ProcessRequest|ProcessResponse|Provenance|Questionnaire|QuestionnaireResponse|ReferralRequest|RelatedPerson|RequestGroup|ResearchStudy|ResearchSubject|RiskAssessment|Schedule|SearchParameter|Sequence|ServiceDefinition|Slot|Specimen|StructureDefinition|StructureMap|Subscription|Substance|SupplyDelivery|SupplyRequest|Task|TestScript|TestReport|ValueSet|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?";
private static final String EXECUTED_CONSTRAINT_LIST = "validator.executed.invariant.list";
private static final String EXECUTION_ID = "validator.execution.id";
private String uriRegexForVersion() {
if (VersionUtilities.isR3Ver(context.getVersion()))
return URI_REGEX3;
else
return Constants.URI_REGEX;
}
private String getCanonicalURLForEntry(Element entry) {
Element e = entry.getNamedChild(RESOURCE);
if (e == null)
return null;
return e.getNamedChildValue("url");
}
private String getIdForEntry(Element entry) {
Element e = entry.getNamedChild(RESOURCE);
if (e == null)
return null;
return e.getNamedChildValue(ID);
}
/**
* Check each resource entry to ensure that the entry's fullURL includes the resource's id
* value. Adds an ERROR ValidationMessge to errors List for a given entry if it references
* a resource and fullURL does not include the resource's id.
*
* @param errors List of ValidationMessage objects that new errors will be added to.
* @param entries List of entry Element objects to be checked.
* @param stack Current NodeStack used to create path names in error detail messages.
*/
private void validateResourceIds(List<ValidationMessage> errors, List<Element> entries, NodeStack stack) {
// TODO: Need to handle _version
int i = 1;
for (Element entry : entries) {
String fullUrl = entry.getNamedChildValue(FULL_URL);
Element resource = entry.getNamedChild(RESOURCE);
String id = resource != null ? resource.getNamedChildValue(ID) : null;
if (id != null && fullUrl != null) {
String urlId = null;
if (fullUrl.startsWith("https://") || fullUrl.startsWith("http://")) {
urlId = fullUrl.substring(fullUrl.lastIndexOf('/') + 1);
} else if (fullUrl.startsWith("urn:uuid") || fullUrl.startsWith("urn:oid")) {
urlId = fullUrl.substring(fullUrl.lastIndexOf(':') + 1);
}
rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry[" + i + "]"), urlId.equals(id), I18nConstants.BUNDLE_BUNDLE_ENTRY_IDURLMISMATCH, id, fullUrl);
}
i++;
}
}
private void checkAllInterlinked(List<ValidationMessage> errors, List<Element> entries, NodeStack stack, Element bundle, boolean isError) {
List<EntrySummary> entryList = new ArrayList<>();
for (Element entry : entries) {
Element r = entry.getNamedChild(RESOURCE);
if (r != null) {
entryList.add(new EntrySummary(entry, r));
}
}
for (EntrySummary e : entryList) {
Set<String> references = findReferences(e.getEntry());
for (String ref : references) {
Element tgt = resolveInBundle(entries, ref, e.getEntry().getChildValue(FULL_URL), e.getResource().fhirType(), e.getResource().getIdBase());
if (tgt != null) {
EntrySummary t = entryForTarget(entryList, tgt);
if (t != null) {
e.getTargets().add(t);
}
}
}
}
Set<EntrySummary> visited = new HashSet<>();
visitLinked(visited, entryList.get(0));
boolean foundRevLinks;
do {
foundRevLinks = false;
for (EntrySummary e : entryList) {
if (!visited.contains(e)) {
boolean add = false;
for (EntrySummary t : e.getTargets()) {
if (visited.contains(t)) {
add = true;
}
}
if (add) {
foundRevLinks = true;
visitLinked(visited, e);
}
}
}
} while (foundRevLinks);
int i = 0;
for (EntrySummary e : entryList) {
Element entry = e.getEntry();
if (isError) {
rule(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY + '[' + (i + 1) + ']'), visited.contains(e), I18nConstants.BUNDLE_BUNDLE_ENTRY_ORPHAN, (entry.getChildValue(FULL_URL) != null ? "'" + entry.getChildValue(FULL_URL) + "'" : ""));
} else {
warning(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY + '[' + (i + 1) + ']'), visited.contains(e), I18nConstants.BUNDLE_BUNDLE_ENTRY_ORPHAN, (entry.getChildValue(FULL_URL) != null ? "'" + entry.getChildValue(FULL_URL) + "'" : ""));
}
i++;
}
}
private EntrySummary entryForTarget(List<EntrySummary> entryList, Element tgt) {
for (EntrySummary e : entryList) {
if (e.getEntry() == tgt) {
return e;
}
}
return null;
}
private void visitLinked(Set<EntrySummary> visited, EntrySummary t) {
if (!visited.contains(t)) {
visited.add(t);
for (EntrySummary e : t.getTargets()) {
visitLinked(visited, e);
}
}
}
private void followResourceLinks(Element entry, Map<String, Element> visitedResources, Map<Element, Element> candidateEntries, List<Element> candidateResources, List<ValidationMessage> errors, NodeStack stack) {
followResourceLinks(entry, visitedResources, candidateEntries, candidateResources, errors, stack, 0);
}
private void followResourceLinks(Element entry, Map<String, Element> visitedResources, Map<Element, Element> candidateEntries, List<Element> candidateResources, List<ValidationMessage> errors, NodeStack stack, int depth) {
Element resource = entry.getNamedChild(RESOURCE);
if (visitedResources.containsValue(resource))
return;
visitedResources.put(entry.getNamedChildValue(FULL_URL), resource);
String type = null;
Set<String> references = findReferences(resource);
for (String reference : references) {
// We don't want errors when just retrieving the element as they will be caught (with better path info) in subsequent processing
IndexedElement r = getFromBundle(stack.getElement(), reference, entry.getChildValue(FULL_URL), new ArrayList<ValidationMessage>(), stack.addToLiteralPath("entry[" + candidateResources.indexOf(resource) + "]"), type, "transaction".equals(stack.getElement().getChildValue(TYPE)));
if (r != null && !visitedResources.containsValue(r.getMatch())) {
followResourceLinks(candidateEntries.get(r.getMatch()), visitedResources, candidateEntries, candidateResources, errors, stack, depth + 1);
}
}
}
private Set<String> findReferences(Element start) {
Set<String> references = new HashSet<String>();
findReferences(start, references);
return references;
}
private void findReferences(Element start, Set<String> references) {
for (Element child : start.getChildren()) {
if (child.getType().equals("Reference")) {
String ref = child.getChildValue("reference");
if (ref != null && !ref.startsWith("#"))
references.add(ref);
}
if (child.getType().equals("url") || child.getType().equals("uri") || child.getType().equals("canonical")) {
String ref = child.primitiveValue();
if (ref != null && !ref.startsWith("#"))
references.add(ref);
}
findReferences(child, references);
}
}
private void validateBundleReference(List<ValidationMessage> errors, List<Element> entries, Element ref, String name, NodeStack stack, String fullUrl, String type, String id) {
String reference = null;
try {
reference = ref.getNamedChildValue("reference");
} catch (Error e) {
}
if (ref != null && !Utilities.noString(reference) && !reference.startsWith("#")) {
Element target = resolveInBundle(entries, reference, fullUrl, type, id);
rule(errors, IssueType.INVALID, ref.line(), ref.col(), stack.addToLiteralPath("reference"), target != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOTFOUND, reference, name);
}
}
private void validateContains(ValidatorHostContext hostContext, List<ValidationMessage> errors, String path, ElementDefinition child, ElementDefinition context, Element resource, Element element, NodeStack stack, IdStatus idstatus) throws FHIRException {
String resourceName = element.getType();
TypeRefComponent trr = null;
@ -3919,50 +3488,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return false;
}
private void validateDocument(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id) {
// first entry must be a composition
if (rule(errors, IssueType.INVALID, composition.line(), composition.col(), stack.getLiteralPath(), composition.getType().equals("Composition"), I18nConstants.BUNDLE_BUNDLE_ENTRY_DOCUMENT)) {
// the composition subject etc references must resolve in the bundle
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "subject", "Composition");
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, true, "author", "Composition");
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "encounter", "Composition");
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "custodian", "Composition");
validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "attester", false, "party");
validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "event", true, "detail");
validateSections(errors, entries, composition, stack, fullUrl, id);
}
}
public void validateDocumentSubReference(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id, String title, String parent, boolean repeats, String propName) {
List<Element> list = new ArrayList<>();
composition.getNamedChildren(parent, list);
int i = 1;
for (Element elem : list) {
validateDocumentReference(errors, entries, elem, stack.push(elem, i, null, null), fullUrl, id, repeats, propName, title + "." + parent);
i++;
}
}
public void validateDocumentReference(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id, boolean repeats, String propName, String title) {
if (repeats) {
List<Element> list = new ArrayList<>();
composition.getNamedChildren(propName, list);
int i = 1;
for (Element elem : list) {
validateBundleReference(errors, entries, elem, title + "." + propName, stack.push(elem, i, null, null), fullUrl, "Composition", id);
i++;
}
} else {
Element elem = composition.getNamedChild(propName);
if (elem != null) {
validateBundleReference(errors, entries, elem, title + "." + propName, stack.push(elem, -1, null, null), fullUrl, "Composition", id);
}
}
}
private void validateElement(ValidatorHostContext hostContext, List<ValidationMessage> errors, StructureDefinition profile, ElementDefinition definition, StructureDefinition cprofile, ElementDefinition context,
Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, String extensionUrl) throws FHIRException {
@ -4668,16 +4193,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
}
private void validateMessage(List<ValidationMessage> errors, List<Element> entries, Element messageHeader, NodeStack stack, String fullUrl, String id) {
// first entry must be a messageheader
if (rule(errors, IssueType.INVALID, messageHeader.line(), messageHeader.col(), stack.getLiteralPath(), messageHeader.getType().equals("MessageHeader"), I18nConstants.VALIDATION_BUNDLE_MESSAGE)) {
List<Element> elements = messageHeader.getChildren("focus");
for (Element elem : elements)
validateBundleReference(errors, entries, elem, "MessageHeader Data", stack.push(elem, -1, null, null), fullUrl, "MessageHeader", id);
}
}
private void validateObservation(List<ValidationMessage> errors, Element element, NodeStack stack) {
// all observations should have a subject, a performer, and a time
@ -4742,30 +4258,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
private void validateSections(List<ValidationMessage> errors, List<Element> entries, Element focus, NodeStack stack, String fullUrl, String id) {
List<Element> sections = new ArrayList<Element>();
focus.getNamedChildren("section", sections);
int i = 1;
for (Element section : sections) {
NodeStack localStack = stack.push(section, i, null, null);
// technically R4+, but there won't be matches from before that
validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "author", "Section");
validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "focus", "Section");
List<Element> sectionEntries = new ArrayList<Element>();
section.getNamedChildren(ENTRY, sectionEntries);
int j = 1;
for (Element sectionEntry : sectionEntries) {
NodeStack localStack2 = localStack.push(sectionEntry, j, null, null);
validateBundleReference(errors, entries, sectionEntry, "Section Entry", localStack2, fullUrl, "Composition", id);
j++;
}
validateSections(errors, entries, section, localStack, fullUrl, id);
i++;
}
}
private boolean valueMatchesCriteria(Element value, ElementDefinition criteria, StructureDefinition profile) throws FHIRException {
if (criteria.hasFixed()) {
List<ValidationMessage> msgs = new ArrayList<ValidationMessage>();

375
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/BundleValidator.java Normal file
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@ -0,0 +1,375 @@
package org.hl7.fhir.validation.instance.type;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.instance.utils.EntrySummary;
import org.hl7.fhir.validation.instance.utils.IndexedElement;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class BundleValidator extends BaseValidator{
public final static String URI_REGEX3 = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AllergyIntolerance|AdverseEvent|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BodySite|Bundle|CapabilityStatement|CarePlan|CareTeam|ChargeItem|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition (aka Problem)|Consent|Contract|Coverage|DataElement|DetectedIssue|Device|DeviceComponent|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EligibilityRequest|EligibilityResponse|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|ExpansionProfile|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingManifest|ImagingStudy|Immunization|ImmunizationRecommendation|ImplementationGuide|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationRequest|MedicationStatement|MessageDefinition|MessageHeader|NamingSystem|NutritionOrder|Observation|OperationDefinition|OperationOutcome|Organization|Parameters|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|ProcedureRequest|ProcessRequest|ProcessResponse|Provenance|Questionnaire|QuestionnaireResponse|ReferralRequest|RelatedPerson|RequestGroup|ResearchStudy|ResearchSubject|RiskAssessment|Schedule|SearchParameter|Sequence|ServiceDefinition|Slot|Specimen|StructureDefinition|StructureMap|Subscription|Substance|SupplyDelivery|SupplyRequest|Task|TestScript|TestReport|ValueSet|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?";
private String serverBase;
public BundleValidator(IWorkerContext context, String serverBase) {
super(context);
this.serverBase = serverBase;
}
public void validateBundle(List<ValidationMessage> errors, Element bundle, NodeStack stack, boolean checkSpecials) {
List<Element> entries = new ArrayList<Element>();
bundle.getNamedChildren(ENTRY, entries);
String type = bundle.getNamedChildValue(TYPE);
type = StringUtils.defaultString(type);
if (entries.size() == 0) {
rule(errors, IssueType.INVALID, stack.getLiteralPath(), !(type.equals(DOCUMENT) || type.equals(MESSAGE)), I18nConstants.BUNDLE_BUNDLE_ENTRY_NOFIRST);
} else {
// Get the first entry, the MessageHeader
Element firstEntry = entries.get(0);
// Get the stack of the first entry
NodeStack firstStack = stack.push(firstEntry, 1, null, null);
String fullUrl = firstEntry.getNamedChildValue(FULL_URL);
if (type.equals(DOCUMENT)) {
Element resource = firstEntry.getNamedChild(RESOURCE);
if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), resource != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOFIRSTRESOURCE)) {
String id = resource.getNamedChildValue(ID);
validateDocument(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id);
}
if (!VersionUtilities.isThisOrLater(FHIRVersion._4_0_1.getDisplay(), bundle.getProperty().getStructure().getFhirVersion().getDisplay())) {
handleSpecialCaseForLastUpdated(bundle, errors, stack);
}
checkAllInterlinked(errors, entries, stack, bundle, true);
}
if (type.equals(MESSAGE)) {
Element resource = firstEntry.getNamedChild(RESOURCE);
String id = resource.getNamedChildValue(ID);
if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), resource != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOFIRSTRESOURCE)) {
validateMessage(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id);
}
checkAllInterlinked(errors, entries, stack, bundle, VersionUtilities.isR5Ver(context.getVersion()));
}
// We do not yet have rules requiring that the id and fullUrl match when dealing with messaging Bundles
// validateResourceIds(errors, entries, stack);
}
for (Element entry : entries) {
String fullUrl = entry.getNamedChildValue(FULL_URL);
String url = getCanonicalURLForEntry(entry);
String id = getIdForEntry(entry);
if (url != null) {
if (!(!url.equals(fullUrl) || (url.matches(uriRegexForVersion()) && url.endsWith("/" + id))) && !isV3orV2Url(url))
rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), false, I18nConstants.BUNDLE_BUNDLE_ENTRY_MISMATCHIDURL, url, fullUrl, id);
rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY, PATH_ARG), !url.equals(fullUrl) || serverBase == null || (url.equals(Utilities.pathURL(serverBase, entry.getNamedChild(RESOURCE).fhirType(), id))), I18nConstants.BUNDLE_BUNDLE_ENTRY_CANONICAL, url, fullUrl);
}
// todo: check specials
}
}
private void validateDocument(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id) {
// first entry must be a composition
if (rule(errors, IssueType.INVALID, composition.line(), composition.col(), stack.getLiteralPath(), composition.getType().equals("Composition"), I18nConstants.BUNDLE_BUNDLE_ENTRY_DOCUMENT)) {
// the composition subject etc references must resolve in the bundle
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "subject", "Composition");
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, true, "author", "Composition");
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "encounter", "Composition");
validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "custodian", "Composition");
validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "attester", false, "party");
validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "event", true, "detail");
validateSections(errors, entries, composition, stack, fullUrl, id);
}
}
private void validateSections(List<ValidationMessage> errors, List<Element> entries, Element focus, NodeStack stack, String fullUrl, String id) {
List<Element> sections = new ArrayList<Element>();
focus.getNamedChildren("section", sections);
int i = 1;
for (Element section : sections) {
NodeStack localStack = stack.push(section, i, null, null);
// technically R4+, but there won't be matches from before that
validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "author", "Section");
validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "focus", "Section");
List<Element> sectionEntries = new ArrayList<Element>();
section.getNamedChildren(ENTRY, sectionEntries);
int j = 1;
for (Element sectionEntry : sectionEntries) {
NodeStack localStack2 = localStack.push(sectionEntry, j, null, null);
validateBundleReference(errors, entries, sectionEntry, "Section Entry", localStack2, fullUrl, "Composition", id);
j++;
}
validateSections(errors, entries, section, localStack, fullUrl, id);
i++;
}
}
public void validateDocumentSubReference(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id, String title, String parent, boolean repeats, String propName) {
List<Element> list = new ArrayList<>();
composition.getNamedChildren(parent, list);
int i = 1;
for (Element elem : list) {
validateDocumentReference(errors, entries, elem, stack.push(elem, i, null, null), fullUrl, id, repeats, propName, title + "." + parent);
i++;
}
}
public void validateDocumentReference(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id, boolean repeats, String propName, String title) {
if (repeats) {
List<Element> list = new ArrayList<>();
composition.getNamedChildren(propName, list);
int i = 1;
for (Element elem : list) {
validateBundleReference(errors, entries, elem, title + "." + propName, stack.push(elem, i, null, null), fullUrl, "Composition", id);
i++;
}
} else {
Element elem = composition.getNamedChild(propName);
if (elem != null) {
validateBundleReference(errors, entries, elem, title + "." + propName, stack.push(elem, -1, null, null), fullUrl, "Composition", id);
}
}
}
private void validateMessage(List<ValidationMessage> errors, List<Element> entries, Element messageHeader, NodeStack stack, String fullUrl, String id) {
// first entry must be a messageheader
if (rule(errors, IssueType.INVALID, messageHeader.line(), messageHeader.col(), stack.getLiteralPath(), messageHeader.getType().equals("MessageHeader"), I18nConstants.VALIDATION_BUNDLE_MESSAGE)) {
List<Element> elements = messageHeader.getChildren("focus");
for (Element elem : elements)
validateBundleReference(errors, entries, elem, "MessageHeader Data", stack.push(elem, -1, null, null), fullUrl, "MessageHeader", id);
}
}
private void validateBundleReference(List<ValidationMessage> errors, List<Element> entries, Element ref, String name, NodeStack stack, String fullUrl, String type, String id) {
String reference = null;
try {
reference = ref.getNamedChildValue("reference");
} catch (Error e) {
}
if (ref != null && !Utilities.noString(reference) && !reference.startsWith("#")) {
Element target = resolveInBundle(entries, reference, fullUrl, type, id);
rule(errors, IssueType.INVALID, ref.line(), ref.col(), stack.addToLiteralPath("reference"), target != null, I18nConstants.BUNDLE_BUNDLE_ENTRY_NOTFOUND, reference, name);
}
}
/**
* As per outline for <a href=http://hl7.org/fhir/stu3/documents.html#content>Document Content</a>:
* <li>"The document date (mandatory). This is found in Bundle.meta.lastUpdated and identifies when the document bundle
* was assembled from the underlying resources"</li>
* <p></p>
* This check was not being done for release versions < r4.
* <p></p>
* Related JIRA ticket is <a href=https://jira.hl7.org/browse/FHIR-26544>FHIR-26544</a>
*
* @param bundle {@link org.hl7.fhir.r5.elementmodel}
* @param errors {@link List<ValidationMessage>}
* @param stack {@link NodeStack}
*/
private void handleSpecialCaseForLastUpdated(Element bundle, List<ValidationMessage> errors, NodeStack stack) {
boolean ok = bundle.hasChild(META)
&& bundle.getNamedChild(META).hasChild(LAST_UPDATED)
&& bundle.getNamedChild(META).getNamedChild(LAST_UPDATED).hasValue();
rule(errors, IssueType.REQUIRED, stack.getLiteralPath(), ok, I18nConstants.DOCUMENT_DATE_REQUIRED, I18nConstants.DOCUMENT_DATE_REQUIRED_HTML);
}
private void checkAllInterlinked(List<ValidationMessage> errors, List<Element> entries, NodeStack stack, Element bundle, boolean isError) {
List<EntrySummary> entryList = new ArrayList<>();
for (Element entry : entries) {
Element r = entry.getNamedChild(RESOURCE);
if (r != null) {
entryList.add(new EntrySummary(entry, r));
}
}
for (EntrySummary e : entryList) {
Set<String> references = findReferences(e.getEntry());
for (String ref : references) {
Element tgt = resolveInBundle(entries, ref, e.getEntry().getChildValue(FULL_URL), e.getResource().fhirType(), e.getResource().getIdBase());
if (tgt != null) {
EntrySummary t = entryForTarget(entryList, tgt);
if (t != null) {
e.getTargets().add(t);
}
}
}
}
Set<EntrySummary> visited = new HashSet<>();
visitLinked(visited, entryList.get(0));
boolean foundRevLinks;
do {
foundRevLinks = false;
for (EntrySummary e : entryList) {
if (!visited.contains(e)) {
boolean add = false;
for (EntrySummary t : e.getTargets()) {
if (visited.contains(t)) {
add = true;
}
}
if (add) {
foundRevLinks = true;
visitLinked(visited, e);
}
}
}
} while (foundRevLinks);
int i = 0;
for (EntrySummary e : entryList) {
Element entry = e.getEntry();
if (isError) {
rule(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY + '[' + (i + 1) + ']'), visited.contains(e), I18nConstants.BUNDLE_BUNDLE_ENTRY_ORPHAN, (entry.getChildValue(FULL_URL) != null ? "'" + entry.getChildValue(FULL_URL) + "'" : ""));
} else {
warning(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath(ENTRY + '[' + (i + 1) + ']'), visited.contains(e), I18nConstants.BUNDLE_BUNDLE_ENTRY_ORPHAN, (entry.getChildValue(FULL_URL) != null ? "'" + entry.getChildValue(FULL_URL) + "'" : ""));
}
i++;
}
}
private String uriRegexForVersion() {
if (VersionUtilities.isR3Ver(context.getVersion()))
return URI_REGEX3;
else
return Constants.URI_REGEX;
}
private String getCanonicalURLForEntry(Element entry) {
Element e = entry.getNamedChild(RESOURCE);
if (e == null)
return null;
return e.getNamedChildValue("url");
}
private String getIdForEntry(Element entry) {
Element e = entry.getNamedChild(RESOURCE);
if (e == null)
return null;
return e.getNamedChildValue(ID);
}
/**
* Check each resource entry to ensure that the entry's fullURL includes the resource's id
* value. Adds an ERROR ValidationMessge to errors List for a given entry if it references
* a resource and fullURL does not include the resource's id.
*
* @param errors List of ValidationMessage objects that new errors will be added to.
* @param entries List of entry Element objects to be checked.
* @param stack Current NodeStack used to create path names in error detail messages.
*/
private void validateResourceIds(List<ValidationMessage> errors, List<Element> entries, NodeStack stack) {
// TODO: Need to handle _version
int i = 1;
for (Element entry : entries) {
String fullUrl = entry.getNamedChildValue(FULL_URL);
Element resource = entry.getNamedChild(RESOURCE);
String id = resource != null ? resource.getNamedChildValue(ID) : null;
if (id != null && fullUrl != null) {
String urlId = null;
if (fullUrl.startsWith("https://") || fullUrl.startsWith("http://")) {
urlId = fullUrl.substring(fullUrl.lastIndexOf('/') + 1);
} else if (fullUrl.startsWith("urn:uuid") || fullUrl.startsWith("urn:oid")) {
urlId = fullUrl.substring(fullUrl.lastIndexOf(':') + 1);
}
rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry[" + i + "]"), urlId.equals(id), I18nConstants.BUNDLE_BUNDLE_ENTRY_IDURLMISMATCH, id, fullUrl);
}
i++;
}
}
private EntrySummary entryForTarget(List<EntrySummary> entryList, Element tgt) {
for (EntrySummary e : entryList) {
if (e.getEntry() == tgt) {
return e;
}
}
return null;
}
private void visitLinked(Set<EntrySummary> visited, EntrySummary t) {
if (!visited.contains(t)) {
visited.add(t);
for (EntrySummary e : t.getTargets()) {
visitLinked(visited, e);
}
}
}
private void followResourceLinks(Element entry, Map<String, Element> visitedResources, Map<Element, Element> candidateEntries, List<Element> candidateResources, List<ValidationMessage> errors, NodeStack stack) {
followResourceLinks(entry, visitedResources, candidateEntries, candidateResources, errors, stack, 0);
}
private void followResourceLinks(Element entry, Map<String, Element> visitedResources, Map<Element, Element> candidateEntries, List<Element> candidateResources, List<ValidationMessage> errors, NodeStack stack, int depth) {
Element resource = entry.getNamedChild(RESOURCE);
if (visitedResources.containsValue(resource))
return;
visitedResources.put(entry.getNamedChildValue(FULL_URL), resource);
String type = null;
Set<String> references = findReferences(resource);
for (String reference : references) {
// We don't want errors when just retrieving the element as they will be caught (with better path info) in subsequent processing
IndexedElement r = getFromBundle(stack.getElement(), reference, entry.getChildValue(FULL_URL), new ArrayList<ValidationMessage>(), stack.addToLiteralPath("entry[" + candidateResources.indexOf(resource) + "]"), type, "transaction".equals(stack.getElement().getChildValue(TYPE)));
if (r != null && !visitedResources.containsValue(r.getMatch())) {
followResourceLinks(candidateEntries.get(r.getMatch()), visitedResources, candidateEntries, candidateResources, errors, stack, depth + 1);
}
}
}
private Set<String> findReferences(Element start) {
Set<String> references = new HashSet<String>();
findReferences(start, references);
return references;
}
private void findReferences(Element start, Set<String> references) {
for (Element child : start.getChildren()) {
if (child.getType().equals("Reference")) {
String ref = child.getChildValue("reference");
if (ref != null && !ref.startsWith("#"))
references.add(ref);
}
if (child.getType().equals("url") || child.getType().equals("uri") || child.getType().equals("canonical")) {
String ref = child.primitiveValue();
if (ref != null && !ref.startsWith("#"))
references.add(ref);
}
findReferences(child, references);
}
}
// hack for pre-UTG v2/v3
private boolean isV3orV2Url(String url) {
return url.startsWith("http://hl7.org/fhir/v3/") || url.startsWith("http://hl7.org/fhir/v2/");
}
}

4
release-notes-validator.md
View File

@ -6,11 +6,11 @@ title: FHIR Validator Release Notes
## Current (not released yet)
(no changes yet)
* fix fatal NPE validating bundles when resource is missing
* fix tests for R5 changes
## v4.2.30 (2020-05-12)
* Allow mailto: urls as absolute URIs
## v4.2.29 (2020-05-11)