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Handle invalid paths in Consent resource

This commit is contained in:
James Agnew 2018-05-16 21:45:23 -04:00
parent 4fd868afae
commit c588e01a4d
11 changed files with 191 additions and 124 deletions
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12
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidationDataUploader.java
View File

@ -506,19 +506,19 @@ public class ValidationDataUploader extends BaseCommand {
}
}
private void uploadR4Profiles(FhirContext ctx, IGenericClient client, String name) throws CommandFailureException {
private void uploadR4Profiles(FhirContext theContext, IGenericClient theClient, String theName) throws CommandFailureException {
int total;
int count;
org.hl7.fhir.r4.model.Bundle bundle;
ourLog.info("Uploading " + name);
ourLog.info("Uploading " + theName);
String vsContents;
try {
vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/r4/model/profile/" + name + ".xml"), "UTF-8");
vsContents = IOUtils.toString(ValidationDataUploader.class.getResourceAsStream("/org/hl7/fhir/r4/model/" + theName + ".xml"), "UTF-8");
} catch (IOException e) {
throw new CommandFailureException(e.toString());
}
bundle = ctx.newXmlParser().parseResource(org.hl7.fhir.r4.model.Bundle.class, vsContents);
bundle = theContext.newXmlParser().parseResource(org.hl7.fhir.r4.model.Bundle.class, vsContents);
filterBundle(bundle);
total = bundle.getEntry().size();
count = 1;
@ -547,9 +547,9 @@ public class ValidationDataUploader extends BaseCommand {
continue;
}
ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {name, count, total, next.getIdElement().getValue()});
ourLog.info("Uploading {} StructureDefinition {}/{} : {}", new Object[] {theName, count, total, next.getIdElement().getValue()});
try {
client.update().resource(next).execute();
theClient.update().resource(next).execute();
} catch (BaseServerResponseException e) {
ourLog.warn("Server responded HTTP " + e.getStatusCode() + ": " + e.toString());
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -511,6 +511,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@SuppressWarnings("unchecked")
protected Set<String> extractResourceLinks(ResourceTable theEntity, IBaseResource theResource, Set<ResourceLink> theLinks, Date theUpdateTime) {
HashSet<String> retVal = new HashSet<>();
String resourceType = theEntity.getResourceType();
/*
* For now we don't try to load any of the links in a bundle if it's the actual bundle we're storing..
@ -580,6 +581,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
} else if (myContext.getElementDefinition((Class<? extends IBase>) nextObject.getClass()).getName().equals("uri")) {
continue;
} else if (resourceType.equals("Consent") && nextPathAndRef.getPath().equals("Consent.source")) {
// Consent#source-identifier has a path that isn't typed - This is a one-off to deal with that
continue;
} else {
if (!multiType) {
if (nextSpDef.getName().equals("sourceuri")) {

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamExtractorDstu3.java
View File

@ -105,7 +105,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
*/
@Override
public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<ResourceIndexedSearchParamDate>();
HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<>();
String resourceType = theEntity.getResourceType();
Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) {
@ -164,6 +165,9 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
} else if (nextObject instanceof StringType) {
// CarePlan.activitydate can be a string
continue;
} else if (resourceType.equals("Consent") && nextPath.equals("Consent.source")) {
// Consent#source-identifier has a path that isn't typed - This is a one-off to deal with that
continue;
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());

44
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4.java
View File

@ -20,12 +20,28 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.*;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
@ -33,20 +49,10 @@ import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.validation.*;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoR4<T extends IAnyResource> extends BaseHapiFhirResourceDao<T> {

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/SearchParamExtractorR4.java
View File

@ -468,6 +468,7 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
continue;
}
String resourceType = theEntity.getResourceType();
String nextPath = nextSpDef.getPath();
if (isBlank(nextPath)) {
continue;
@ -478,8 +479,8 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
multiType = true;
}
List<String> systems = new ArrayList<String>();
List<String> codes = new ArrayList<String>();
List<String> systems = new ArrayList<>();
List<String> codes = new ArrayList<>();
for (Object nextObject : extractValues(nextPath, theResource)) {
@ -555,9 +556,15 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
} else if (nextObject instanceof LocationPositionComponent) {
ourLog.warn("Position search not currently supported, not indexing location");
continue;
} else if (nextObject instanceof StructureDefinition.StructureDefinitionContextComponent) {
ourLog.warn("StructureDefinition context indexing not currently supported"); // TODO: implement this
continue;
} else if (resourceType.equals("Consent") && nextPath.equals("Consent.source")) {
// Consent#source-identifier has a path that isn't typed - This is a one-off to deal with that
continue;
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());
throw new ConfigurationException("Search param " + nextSpDef.getName() + " with path " + nextPath + " is of unexpected datatype: " + nextObject.getClass());
} else {
continue;
}

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -160,6 +160,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myOrganizationDaoDstu3")
protected IFhirResourceDao<Organization> myOrganizationDao;
@Autowired
@Qualifier("myConsentDaoDstu3")
protected IFhirResourceDao<Consent> myConsentDao;
@Autowired
protected DatabaseBackedPagingProvider myPagingProvider;
@Autowired
@Qualifier("myPatientDaoDstu3")

72
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -1,47 +1,51 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Matchers.eq;
import static org.mockito.Mockito.*;
import java.util.*;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.RandomStringUtils;
import org.hamcrest.Matchers;
import org.hamcrest.core.StringContains;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueType;
import org.hl7.fhir.dstu3.model.Quantity.QuantityComparator;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.mockito.ArgumentCaptor;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.collect.Lists;
import java.util.*;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Matchers.eq;
import static org.mockito.Mockito.*;
@SuppressWarnings({"unchecked", "deprecation"})
public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
@ -117,7 +121,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
}
}
private void sortCodings(List<Coding> theSecLabels) {
Collections.sort(theSecLabels, new Comparator<Coding>() {
@Override
@ -479,7 +482,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
}
@Test
public void testCreateDifferentTypesWithSameForcedId() {
String idName = "forcedId";
@ -500,7 +502,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
obs = myObservationDao.read(obsId.toUnqualifiedVersionless(), mySrd);
}
@Test
public void testCreateDuplicateTagsDoesNotCauseDuplicates() {
Patient p = new Patient();
@ -809,7 +810,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
}
}
@Test
public void testCreateWithInvalidReferenceFailsGracefully() {
Patient patient = new Patient();
@ -2141,7 +2141,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
assertEquals(1, result.size());
assertEquals(obsId02.getIdPart(), result.get(0).getIdElement().getIdPart());
result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam("999999999999")).setLoadSynchronous(true)));;
result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam("999999999999")).setLoadSynchronous(true)));
;
assertEquals(0, result.size());
}
@ -2224,7 +2225,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
long id = outcome.getId().getIdPartAsLong();
TokenParam value = new TokenParam("urn:system", "001testPersistSearchParams");
List<Patient> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_IDENTIFIER, value).setLoadSynchronous(true)));;
List<Patient> found = toList(myPatientDao.search(new SearchParameterMap(Patient.SP_IDENTIFIER, value).setLoadSynchronous(true)));
;
assertEquals(1, found.size());
assertEquals(id, found.get(0).getIdElement().getIdPartAsLong().longValue());
@ -3535,6 +3537,16 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
}
/**
* Make sure this can upload successfully (indexer failed at one point)
*/
@Test
public void testUploadConsentWithSourceAttachment() {
Consent consent = new Consent();
consent.setSource(new Attachment().setUrl("http://foo"));
myConsentDao.create(consent);
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -212,6 +212,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myStructureDefinitionDaoR4")
protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
@Autowired
@Qualifier("myConsentDaoR4")
protected IFhirResourceDao<Consent> myConsentDao;
@Autowired
@Qualifier("mySubscriptionDaoR4")
protected IFhirResourceDaoSubscription<Subscription> mySubscriptionDao;
@Autowired

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
View File

@ -21,6 +21,7 @@ import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hamcrest.Matchers;
import org.hamcrest.core.StringContains;
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -3738,6 +3739,26 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
}
/**
* Make sure this can upload successfully (indexer failed at one point)
*/
@Test
public void testUploadConsentWithSourceAttachment() {
Consent consent = new Consent();
consent.setSource(new Attachment().setUrl("http://foo"));
myConsentDao.create(consent);
}
/**
* Make sure this can upload successfully (indexer failed at one point)
*/
@Test
public void testUploadExtensionStructureDefinition() {
StructureDefinition ext = myValidationSupport.fetchStructureDefinition(myFhirCtx, "http://hl7.org/fhir/StructureDefinition/familymemberhistory-type");
Validate.notNull(ext);
myStructureDefinitionDao.update(ext);
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

6
src/changes/changes.xml
View File

@ -178,6 +178,12 @@
pull request! These have also been added to the list of definitions uploaded
by the CLI "upload-definitions" command.
</action>
<action type="fix">
A workaround for an invalid search parameter path in the R4 consent
resource has been implemented. This path was preventing some Consent
resources from successfully being uploaded to the JPA server. Thanks to
Anthony Sute for identifying this.
</action>
</release>
<release version="3.3.0" date="2018-03-29">
<action type="add">

1
sync_ri4.sh
View File

@ -60,3 +60,4 @@ cp ~/workspace/fhir/trunk/build/publish/profiles-*.xml hapi-fhir-validatio
cp ~/workspace/fhir/trunk/build/publish/v2-tables.xml hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/valueset/
cp ~/workspace/fhir/trunk/build/publish/v3-codesystems.xml hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/valueset/
cp ~/workspace/fhir/trunk/build/publish/valuesets.xml hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/valueset/
cp ~/workspace/fhir/trunk/build/publish/extension-definitions.xml hapi-fhir-validation-resources-r4/src/main/resources/org/hl7/fhir/r4/model/extension/