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Fix validation error when Bundle has no type

This commit is contained in:
James Agnew 2017-10-11 10:20:12 -04:00
parent fddda443a2
commit 78b7188fbc
9 changed files with 204 additions and 39 deletions
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10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java
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@ -71,10 +71,12 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
private void deleteSearch(final Long theSearchPid) {
Search searchToDelete = mySearchDao.findOne(theSearchPid);
ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), searchToDelete.getCreated(), searchToDelete.getSearchLastReturned());
mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
mySearchResultDao.deleteForSearch(searchToDelete.getId());
mySearchDao.delete(searchToDelete);
if (searchToDelete != null) {
ourLog.info("Deleting search {}/{} - Created[{}] -- Last returned[{}]", searchToDelete.getId(), searchToDelete.getUuid(), searchToDelete.getCreated(), searchToDelete.getSearchLastReturned());
mySearchIncludeDao.deleteForSearch(searchToDelete.getId());
mySearchResultDao.deleteForSearch(searchToDelete.getId());
mySearchDao.delete(searchToDelete);
}
}
@Override

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SubscriptionsRequireManualActivationInterceptorDstu2.java
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@ -42,7 +42,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class SubscriptionsRequireManualActivationInterceptorDstu2 extends ServerOperationInterceptorAdapter {
@Autowired
@Qualifier("mySubscriptionDaoR4")
@Qualifier("mySubscriptionDaoDstu2")
private IFhirResourceDao<Subscription> myDao;
@Override

43
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/validation/InstanceValidator.java
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@ -13,8 +13,8 @@ import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult;
@ -105,6 +105,7 @@ import org.w3c.dom.Node;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
import com.google.gson.stream.JsonWriter;
import ca.uhn.fhir.util.ObjectUtil;
@ -292,8 +293,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
source = Source.InstanceValidator;
}
@Override
public boolean isNoInvariantChecks() {
return noInvariantChecks;
@ -1358,33 +1357,19 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
checkFixedValue(errors, path + ".denominator", focus.getNamedChild("denominator"), fixed.getDenominator(), "denominator", focus);
}
private Reference readAsReference(Element item) {
Reference r = new Reference();
r.setDisplay(item.getNamedChildValue("display"));
r.setReference(item.getNamedChildValue("reference"));
List<Element> identifier = item.getChildrenByName("identifier");
if (identifier.isEmpty() == false) {
r.setIdentifier(readAsIdentifier(identifier.get(0)));
}
return r;
}
private Identifier readAsIdentifier(Element item) {
Identifier r = new Identifier();
r.setSystem(item.getNamedChildValue("system"));
r.setValue(item.getNamedChildValue("value"));
return r;
}
private void checkReference(Object appContext, List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition container, String parentType, NodeStack stack) throws FHIRException, IOException {
Reference reference = readAsReference(element);
String ref = null;
try {
// Do this inside a try because invalid instances might provide more than one reference.
ref = element.getNamedChildValue("reference");
} catch (Error e) {
String ref = reference.getReference();
if (Utilities.noString(ref)) {
if (Utilities.noString(reference.getIdentifier().getSystem()) && Utilities.noString(reference.getIdentifier().getValue())) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference or identifier should have a display");
}
return;
}
}
if (Utilities.noString(ref)) {
// todo - what should we do in this case?
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference should have a display");
return;
}
Element we = localResolve(ref, stack, errors, path);
String refType;
@ -2816,6 +2801,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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")), "Documents or Messages must contain at least one entry");
} else {

10
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/validation/InstanceValidator.java
View File

@ -667,9 +667,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
try {
if (context.fetchResourceWithException(ValueSet.class, system) != null) {
rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Invalid System URI: "+system+" - cannot use a value set URI as a system");
return false;
} else
return true;
// Lloyd: This error used to prohibit checking for downstream issues, but there are some cases where that checking needs to occur. Please talk to me before changing the code back.
}
return true;
}
catch (Exception e) {
return true;
@ -1445,7 +1445,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
refType = "bundle";
}
}
ReferenceValidationPolicy pol = refType.equals("contained") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.appContext, path, ref);
ReferenceValidationPolicy pol = refType.equals("contained") || refType.equals("bundle") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.appContext, path, ref);
if (pol.checkExists()) {
if (we == null) {
@ -2783,6 +2783,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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")), "Documents or Messages must contain at least one entry");
} else {

17
hapi-fhir-validation/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorR4Test.java → hapi-fhir-validation/src/test/java/ca/uhn/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.validation;
package ca.uhn.fhir.r4.validation;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
@ -17,7 +17,12 @@ import java.io.InputStream;
import java.util.*;
import java.util.zip.GZIPInputStream;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidatorDstu3Test;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.hapi.ctx.*;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport.CodeValidationResult;
@ -533,6 +538,16 @@ public class FhirInstanceValidatorR4Test {
assertEquals(output.toString(), 0, output.getMessages().size());
}
@Test
public void testValidateBundleWithNoType() throws Exception {
String vsContents = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/r4/bundle-with-no-type.json"), "UTF-8");
ValidationResult output = myVal.validateWithResult(vsContents);
logResultsAndReturnNonInformationalOnes(output);
assertThat(output.getMessages().toString(), containsString("Element 'Bundle.type': minimum required = 1"));
}
@Test
public void testValidateRawXmlResourceWithEmptyPrimitive() {
// @formatter:off

9
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java
View File

@ -336,6 +336,15 @@ public class FhirInstanceValidatorDstu3Test {
assertTrue(output.isSuccessful());
}
@Test
public void testValidateBundleWithNoType() throws Exception {
String vsContents = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/dstu3/bundle-with-no-type.json"), "UTF-8");
ValidationResult output = myVal.validateWithResult(vsContents);
logResultsAndReturnNonInformationalOnes(output);
assertThat(output.getMessages().toString(), containsString("Element 'Bundle.type': minimum required = 1"));
}
/**
* See #739
*/

73
hapi-fhir-validation/src/test/resources/dstu3/bundle-with-no-type.json Normal file
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@ -0,0 +1,73 @@
{
"resourceType": "Bundle",
"entry": [
{
"fullUrl": "http://localhost:5555/phr/baseDstu3/Person/PERSON1",
"resource": {
"resourceType": "Person",
"id": "PERSON1",
"meta": {
"versionId": "1",
"lastUpdated": "2017-08-17T16:19:40.109+03:00"
},
"identifier": [
{
"value": "081181-9984"
}
],
"name": [
{
"text": "Anna Testi",
"family": "Testi",
"given": [
"Anna"
]
},
{
"family": "asdfas"
}
],
"telecom": [
{
"use": "home"
},
{
"system": "phone",
"value": "(044) 1234567",
"use": "work"
}
],
"gender": "female",
"birthDate": "1981-11-08",
"address": [
{
"line": [
"Osuuspankkitie 2"
],
"city": "Helsinki",
"postalCode": "00120",
"country": "Suomi"
},
{
"city": "Blo-49847020"
}
],
"active": true,
"link": [
{
"target": {
"reference": "Patient/PATIENT1",
"display": "Anna Testi"
}
}
]
},
"request": {
"method": "PUT",
"url": "Person/PERSON1",
"ifMatch": "1"
}
}
]
}

73
hapi-fhir-validation/src/test/resources/r4/bundle-with-no-type.json Normal file
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@ -0,0 +1,73 @@
{
"resourceType": "Bundle",
"entry": [
{
"fullUrl": "http://localhost:5555/phr/baseDstu3/Person/PERSON1",
"resource": {
"resourceType": "Person",
"id": "PERSON1",
"meta": {
"versionId": "1",
"lastUpdated": "2017-08-17T16:19:40.109+03:00"
},
"identifier": [
{
"value": "081181-9984"
}
],
"name": [
{
"text": "Anna Testi",
"family": "Testi",
"given": [
"Anna"
]
},
{
"family": "asdfas"
}
],
"telecom": [
{
"use": "home"
},
{
"system": "phone",
"value": "(044) 1234567",
"use": "work"
}
],
"gender": "female",
"birthDate": "1981-11-08",
"address": [
{
"line": [
"Osuuspankkitie 2"
],
"city": "Helsinki",
"postalCode": "00120",
"country": "Suomi"
},
{
"city": "Blo-49847020"
}
],
"active": true,
"link": [
{
"target": {
"reference": "Patient/PATIENT1",
"display": "Anna Testi"
}
}
]
},
"request": {
"method": "PUT",
"url": "Person/PERSON1",
"ifMatch": "1"
}
}
]
}

4
src/changes/changes.xml
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@ -55,6 +55,10 @@
the ID of the search, meaning that if a search returns results from the Query
cache, it will reuse the ID of the previously returned Bundle
</action>
<action type="fix">
Fix a NullPointerException when validating a Bundle (in DSTU3/R4) with no
<![CDATA[<code>Bundle.type</code>]]> value
</action>
</release>
<release version="3.0.0" date="2017-09-27">
<action type="add">