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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
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@ -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 total;
int count; int count;
org.hl7.fhir.r4.model.Bundle bundle; org.hl7.fhir.r4.model.Bundle bundle;
ourLog.info("Uploading " + name); ourLog.info("Uploading " + theName);
String vsContents; String vsContents;
try { 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) { } catch (IOException e) {
throw new CommandFailureException(e.toString()); 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); filterBundle(bundle);
total = bundle.getEntry().size(); total = bundle.getEntry().size();
count = 1; count = 1;
@ -547,9 +547,9 @@ public class ValidationDataUploader extends BaseCommand {
continue; 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 { try {
client.update().resource(next).execute(); theClient.update().resource(next).execute();
} catch (BaseServerResponseException e) { } catch (BaseServerResponseException e) {
ourLog.warn("Server responded HTTP " + e.getStatusCode() + ": " + e.toString()); 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") @SuppressWarnings("unchecked")
protected Set<String> extractResourceLinks(ResourceTable theEntity, IBaseResource theResource, Set<ResourceLink> theLinks, Date theUpdateTime) { protected Set<String> extractResourceLinks(ResourceTable theEntity, IBaseResource theResource, Set<ResourceLink> theLinks, Date theUpdateTime) {
HashSet<String> retVal = new HashSet<>(); 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.. * 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")) { } else if (myContext.getElementDefinition((Class<? extends IBase>) nextObject.getClass()).getName().equals("uri")) {
continue; 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 { } else {
if (!multiType) { if (!multiType) {
if (nextSpDef.getName().equals("sourceuri")) { 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 @Override
public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) { 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); Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
for (RuntimeSearchParam nextSpDef : searchParams) { for (RuntimeSearchParam nextSpDef : searchParams) {
@ -164,6 +165,9 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
} else if (nextObject instanceof StringType) { } else if (nextObject instanceof StringType) {
// CarePlan.activitydate can be a string // CarePlan.activitydate can be a string
continue; 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 { } else {
if (!multiType) { if (!multiType) {
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass()); throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());

50
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao.r4;
* Licensed under the Apache License, Version 2.0 (the "License"); * Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License. * you may not use this file except in compliance with the License.
* You may obtain a copy of the License at * You may obtain a copy of the License at
* *
* http://www.apache.org/licenses/LICENSE-2.0 * http://www.apache.org/licenses/LICENSE-2.0
* *
* Unless required by applicable law or agreed to in writing, software * Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS, * distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -20,12 +20,28 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L% * #L%
*/ */
import static org.apache.commons.lang3.StringUtils.isNotBlank; import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import java.util.*; 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.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.IdType;
import org.hl7.fhir.r4.model.OperationOutcome; import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity; 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.Autowired;
import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.context.RuntimeResourceDefinition; import java.util.ArrayList;
import ca.uhn.fhir.context.RuntimeSearchParam; import java.util.List;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao; import static org.apache.commons.lang3.StringUtils.isNotBlank;
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.*;
public class FhirResourceDaoR4<T extends IAnyResource> extends BaseHapiFhirResourceDao<T> { public class FhirResourceDaoR4<T extends IAnyResource> extends BaseHapiFhirResourceDao<T> {
@ -107,7 +113,7 @@ public class FhirResourceDaoR4<T extends IAnyResource> extends BaseHapiFhirResou
IFhirResourceDao<? extends IBaseResource> dao = getDao(type); IFhirResourceDao<? extends IBaseResource> dao = getDao(type);
resourceToValidateById = dao.read(theId, theRequestDetails); resourceToValidateById = dao.read(theId, theRequestDetails);
} }
ValidationResult result; ValidationResult result;
if (theResource == null) { if (theResource == null) {
if (resourceToValidateById != null) { if (resourceToValidateById != null) {

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; continue;
} }
String resourceType = theEntity.getResourceType();
String nextPath = nextSpDef.getPath(); String nextPath = nextSpDef.getPath();
if (isBlank(nextPath)) { if (isBlank(nextPath)) {
continue; continue;
@ -478,8 +479,8 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
multiType = true; multiType = true;
} }
List<String> systems = new ArrayList<String>(); List<String> systems = new ArrayList<>();
List<String> codes = new ArrayList<String>(); List<String> codes = new ArrayList<>();
for (Object nextObject : extractValues(nextPath, theResource)) { for (Object nextObject : extractValues(nextPath, theResource)) {
@ -555,9 +556,15 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
} else if (nextObject instanceof LocationPositionComponent) { } else if (nextObject instanceof LocationPositionComponent) {
ourLog.warn("Position search not currently supported, not indexing location"); ourLog.warn("Position search not currently supported, not indexing location");
continue; 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 { } else {
if (!multiType) { 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 { } else {
continue; 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") @Qualifier("myOrganizationDaoDstu3")
protected IFhirResourceDao<Organization> myOrganizationDao; protected IFhirResourceDao<Organization> myOrganizationDao;
@Autowired @Autowired
@Qualifier("myConsentDaoDstu3")
protected IFhirResourceDao<Consent> myConsentDao;
@Autowired
protected DatabaseBackedPagingProvider myPagingProvider; protected DatabaseBackedPagingProvider myPagingProvider;
@Autowired @Autowired
@Qualifier("myPatientDaoDstu3") @Qualifier("myPatientDaoDstu3")

192
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -1,49 +1,53 @@
package ca.uhn.fhir.jpa.dao.dstu3; package ca.uhn.fhir.jpa.dao.dstu3;
import static org.apache.commons.lang3.StringUtils.defaultString; import ca.uhn.fhir.jpa.dao.*;
import static org.hamcrest.Matchers.*; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import static org.junit.Assert.*; import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import static org.mockito.Matchers.eq; import ca.uhn.fhir.model.api.Include;
import static org.mockito.Mockito.*; import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
import java.util.*; 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.io.IOUtils;
import org.apache.commons.lang3.RandomStringUtils; import org.apache.commons.lang3.RandomStringUtils;
import org.hamcrest.Matchers; import org.hamcrest.Matchers;
import org.hamcrest.core.StringContains; import org.hamcrest.core.StringContains;
import org.hl7.fhir.dstu3.model.*; 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.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus; import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus; import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity; import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueType; import org.hl7.fhir.dstu3.model.OperationOutcome.IssueType;
import org.hl7.fhir.dstu3.model.Quantity.QuantityComparator; 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.junit.*;
import org.mockito.ArgumentCaptor; import org.mockito.ArgumentCaptor;
import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult; import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate; import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.collect.Lists; import java.util.*;
import ca.uhn.fhir.jpa.dao.*; import static org.apache.commons.lang3.StringUtils.defaultString;
import ca.uhn.fhir.jpa.entity.*; import static org.hamcrest.Matchers.contains;
import ca.uhn.fhir.model.api.Include; import static org.hamcrest.Matchers.*;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum; import static org.junit.Assert.*;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum; import static org.mockito.Matchers.eq;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum; import static org.mockito.Mockito.*;
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;
@SuppressWarnings({ "unchecked", "deprecation" }) @SuppressWarnings({"unchecked", "deprecation"})
public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test { public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3Test.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3Test.class);
@ -78,7 +82,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
} }
} }
@Before @Before
public void beforeDisableResultReuse() { public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null); myDaoConfig.setReuseCachedSearchResultsForMillis(null);
@ -117,7 +121,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
} }
} }
private void sortCodings(List<Coding> theSecLabels) { private void sortCodings(List<Coding> theSecLabels) {
Collections.sort(theSecLabels, new Comparator<Coding>() { Collections.sort(theSecLabels, new Comparator<Coding>() {
@Override @Override
@ -126,7 +129,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
} }
}); });
} }
private List<UriType> sortIds(List<UriType> theProfiles) { private List<UriType> sortIds(List<UriType> theProfiles) {
ArrayList<UriType> retVal = new ArrayList<UriType>(theProfiles); ArrayList<UriType> retVal = new ArrayList<UriType>(theProfiles);
Collections.sort(retVal, new Comparator<UriType>() { Collections.sort(retVal, new Comparator<UriType>() {
@ -137,7 +140,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
}); });
return retVal; return retVal;
} }
@Test @Test
public void testCantSearchForDeletedResourceByLanguageOrTag() { public void testCantSearchForDeletedResourceByLanguageOrTag() {
String methodName = "testCantSearchForDeletedResourceByLanguageOrTag"; String methodName = "testCantSearchForDeletedResourceByLanguageOrTag";
@ -478,8 +481,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
myBundleDao.create(bundle, mySrd); myBundleDao.create(bundle, mySrd);
} }
@Test @Test
public void testCreateDifferentTypesWithSameForcedId() { public void testCreateDifferentTypesWithSameForcedId() {
String idName = "forcedId"; String idName = "forcedId";
@ -500,12 +502,11 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
obs = myObservationDao.read(obsId.toUnqualifiedVersionless(), mySrd); obs = myObservationDao.read(obsId.toUnqualifiedVersionless(), mySrd);
} }
@Test @Test
public void testCreateDuplicateTagsDoesNotCauseDuplicates() { public void testCreateDuplicateTagsDoesNotCauseDuplicates() {
Patient p = new Patient(); Patient p = new Patient();
p.setActive(true); p.setActive(true);
p.getMeta().addTag().setSystem("FOO").setCode("BAR"); p.getMeta().addTag().setSystem("FOO").setCode("BAR");
p.getMeta().addTag().setSystem("FOO").setCode("BAR"); p.getMeta().addTag().setSystem("FOO").setCode("BAR");
p.getMeta().addTag().setSystem("FOO").setCode("BAR"); p.getMeta().addTag().setSystem("FOO").setCode("BAR");
@ -513,9 +514,9 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
p.getMeta().addTag().setSystem("FOO").setCode("BAR"); p.getMeta().addTag().setSystem("FOO").setCode("BAR");
p.getMeta().addTag().setSystem("FOO").setCode("BAR"); p.getMeta().addTag().setSystem("FOO").setCode("BAR");
p.getMeta().addTag().setSystem("FOO").setCode("BAR"); p.getMeta().addTag().setSystem("FOO").setCode("BAR");
myPatientDao.create(p); myPatientDao.create(p);
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() { new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override @Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) { protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
@ -523,24 +524,24 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
assertThat(myTagDefinitionDao.findAll(), hasSize(1)); assertThat(myTagDefinitionDao.findAll(), hasSize(1));
} }
}); });
} }
@Test @Test
public void testCreateEmptyTagsIsIgnored() { public void testCreateEmptyTagsIsIgnored() {
Patient p = new Patient(); Patient p = new Patient();
p.setActive(true); p.setActive(true);
// Add an empty tag // Add an empty tag
p.getMeta().addTag(); p.getMeta().addTag();
// Add another empty tag // Add another empty tag
p.getMeta().addTag().setSystem(""); p.getMeta().addTag().setSystem("");
p.getMeta().addTag().setCode(""); p.getMeta().addTag().setCode("");
p.getMeta().addTag().setDisplay(""); p.getMeta().addTag().setDisplay("");
myPatientDao.create(p); myPatientDao.create(p);
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() { new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override @Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) { protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
@ -548,29 +549,29 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
assertThat(myTagDefinitionDao.findAll(), empty()); assertThat(myTagDefinitionDao.findAll(), empty());
} }
}); });
} }
@Test @Test
public void testCreateLongString() { public void testCreateLongString() {
//@formatter:off //@formatter:off
String input = "<NamingSystem>\n" + String input = "<NamingSystem>\n" +
" <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" + " <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" +
" <status value=\"draft\"/>\n" + " <status value=\"draft\"/>\n" +
" <kind value=\"codesystem\"/>\n" + " <kind value=\"codesystem\"/>\n" +
" <publisher value=\"HL7, Inc\"/>\n" + " <publisher value=\"HL7, Inc\"/>\n" +
" <date value=\"2015-08-21\"/>\n" + " <date value=\"2015-08-21\"/>\n" +
" <uniqueId>\n" + " <uniqueId>\n" +
" <type value=\"uri\"/>\n" + " <type value=\"uri\"/>\n" +
" <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" + " <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" +
" <preferred value=\"true\"/>\n" + " <preferred value=\"true\"/>\n" +
" </uniqueId>\n" + " </uniqueId>\n" +
" <uniqueId>\n" + " <uniqueId>\n" +
" <type value=\"oid\"/>\n" + " <type value=\"oid\"/>\n" +
" <value value=\"2.16.840.1.113883.6.209\"/>\n" + " <value value=\"2.16.840.1.113883.6.209\"/>\n" +
" <preferred value=\"false\"/>\n" + " <preferred value=\"false\"/>\n" +
" </uniqueId>\n" + " </uniqueId>\n" +
" </NamingSystem>"; " </NamingSystem>";
//@formatter:on //@formatter:on
NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input); NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input);
@ -633,9 +634,9 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
Organization org = new Organization(); Organization org = new Organization();
org.setActive(true); org.setActive(true);
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless(); IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
myOrganizationDao.delete(orgId); myOrganizationDao.delete(orgId);
Patient p = new Patient(); Patient p = new Patient();
p.getManagingOrganization().setReferenceElement(orgId); p.getManagingOrganization().setReferenceElement(orgId);
try { try {
@ -809,7 +810,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
} }
} }
@Test @Test
public void testCreateWithInvalidReferenceFailsGracefully() { public void testCreateWithInvalidReferenceFailsGracefully() {
Patient patient = new Patient(); Patient patient = new Patient();
@ -1088,7 +1088,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
patient.addIdentifier().setSystem("ZZZZZZZ").setValue("ZZZZZZZZZ"); patient.addIdentifier().setSystem("ZZZZZZZ").setValue("ZZZZZZZZZ");
id2b = myPatientDao.update(patient, mySrd).getId(); id2b = myPatientDao.update(patient, mySrd).getId();
} }
ourLog.info("ID1:{} ID2:{} ID2b:{}", new Object[] { id1, id2, id2b }); ourLog.info("ID1:{} ID2:{} ID2b:{}", new Object[] {id1, id2, id2b});
SearchParameterMap params = new SearchParameterMap(); SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true); params.setLoadSynchronous(true);
@ -1697,7 +1697,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
preDates.add(new Date()); preDates.add(new Date());
Thread.sleep(100); Thread.sleep(100);
patient.setId(id); patient.setId(id);
patient.getName().get(0).getFamilyElement().setValue(methodName + "_i"+i); patient.getName().get(0).getFamilyElement().setValue(methodName + "_i" + i);
ids.add(myPatientDao.update(patient, mySrd).getId().toUnqualified().getValue()); ids.add(myPatientDao.update(patient, mySrd).getId().toUnqualified().getValue());
} }
@ -2056,27 +2056,27 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
public void testOrganizationName() { public void testOrganizationName() {
//@formatter:off //@formatter:off
String inputStr = String inputStr =
"{" + "{" +
" \"resourceType\":\"Organization\",\n" + " \"resourceType\":\"Organization\",\n" +
" \"extension\":[\n" + " \"extension\":[\n" +
" {\n" + " {\n" +
" \"url\":\"http://fhir.connectinggta.ca/Profile/organization#providerIdPool\",\n" + " \"url\":\"http://fhir.connectinggta.ca/Profile/organization#providerIdPool\",\n" +
" \"valueUri\":\"urn:oid:2.16.840.1.113883.3.239.23.21.1\"\n" + " \"valueUri\":\"urn:oid:2.16.840.1.113883.3.239.23.21.1\"\n" +
" }\n" + " }\n" +
" ],\n" + " ],\n" +
" \"text\":{\n" + " \"text\":{\n" +
" \"status\":\"empty\",\n" + " \"status\":\"empty\",\n" +
" \"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">No narrative template available for resource profile: http://fhir.connectinggta.ca/Profile/organization</div>\"\n" + " \"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">No narrative template available for resource profile: http://fhir.connectinggta.ca/Profile/organization</div>\"\n" +
" },\n" + " },\n" +
" \"identifier\":[\n" + " \"identifier\":[\n" +
" {\n" + " {\n" +
" \"use\":\"official\",\n" + " \"use\":\"official\",\n" +
" \"system\":\"urn:cgta:hsp_ids\",\n" + " \"system\":\"urn:cgta:hsp_ids\",\n" +
" \"value\":\"urn:oid:2.16.840.1.113883.3.239.23.21\"\n" + " \"value\":\"urn:oid:2.16.840.1.113883.3.239.23.21\"\n" +
" }\n" + " }\n" +
" ],\n" + " ],\n" +
" \"name\":\"Peterborough Regional Health Centre\"\n" + " \"name\":\"Peterborough Regional Health Centre\"\n" +
"}\n"; "}\n";
//@formatter:on //@formatter:on
@ -2131,7 +2131,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
dr01.setSubject(new Reference(patientId01)); dr01.setSubject(new Reference(patientId01));
IIdType drId01 = myDiagnosticReportDao.create(dr01, mySrd).getId(); IIdType drId01 = myDiagnosticReportDao.create(dr01, mySrd).getId();
ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", new Object[] { patientId01, patientId02, obsId01, obsId02, drId01 }); ourLog.info("P1[{}] P2[{}] O1[{}] O2[{}] D1[{}]", new Object[] {patientId01, patientId02, obsId01, obsId02, drId01});
List<Observation> result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam(patientId01.getIdPart())).setLoadSynchronous(true))); List<Observation> result = toList(myObservationDao.search(new SearchParameterMap(Observation.SP_SUBJECT, new ReferenceParam(patientId01.getIdPart())).setLoadSynchronous(true)));
assertEquals(1, result.size()); assertEquals(1, result.size());
@ -2141,7 +2141,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
assertEquals(1, result.size()); assertEquals(1, result.size());
assertEquals(obsId02.getIdPart(), result.get(0).getIdElement().getIdPart()); 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()); assertEquals(0, result.size());
} }
@ -2224,7 +2225,8 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
long id = outcome.getId().getIdPartAsLong(); long id = outcome.getId().getIdPartAsLong();
TokenParam value = new TokenParam("urn:system", "001testPersistSearchParams"); 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(1, found.size());
assertEquals(id, found.get(0).getIdElement().getIdPartAsLong().longValue()); assertEquals(id, found.get(0).getIdElement().getIdPartAsLong().longValue());
@ -2797,7 +2799,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
pm.setSort(new SortSpec(Patient.SP_BIRTHDATE).setOrder(SortOrderEnum.DESC)); pm.setSort(new SortSpec(Patient.SP_BIRTHDATE).setOrder(SortOrderEnum.DESC));
actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm)); actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
assertEquals(4, actual.size()); assertEquals(4, actual.size());
// The first would be better, but JPA doesn't do NULLS LAST // The first would be better, but JPA doesn't do NULLS LAST
// assertThat(actual, contains(id3, id2, id1, id4)); // assertThat(actual, contains(id3, id2, id1, id4));
assertThat(actual, contains(id4, id3, id2, id1)); assertThat(actual, contains(id4, id3, id2, id1));
@ -3081,7 +3083,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.DESC)); pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.DESC));
actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm)); actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
assertEquals(4, actual.size()); assertEquals(4, actual.size());
// The first would be better, but JPA doesn't do NULLS LAST // The first would be better, but JPA doesn't do NULLS LAST
// assertThat(actual, contains(id3, id2, id1, id4)); // assertThat(actual, contains(id3, id2, id1, id4));
assertThat(actual, contains(id4, id3, id2, id1)); assertThat(actual, contains(id4, id3, id2, id1));
} }
@ -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 @AfterClass
public static void afterClassClearContext() { public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest(); TestUtil.clearAllStaticFieldsForUnitTest();
@ -3542,7 +3554,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
public static void assertConflictException(ResourceVersionConflictException e) { public static void assertConflictException(ResourceVersionConflictException e) {
assertThat(e.getMessage(), matchesPattern( assertThat(e.getMessage(), matchesPattern(
"Unable to delete [a-zA-Z]+/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource [a-zA-Z]+/[0-9]+ in path [a-zA-Z]+.[a-zA-Z]+")); "Unable to delete [a-zA-Z]+/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource [a-zA-Z]+/[0-9]+ in path [a-zA-Z]+.[a-zA-Z]+"));
} }
private static List<String> toStringList(List<UriType> theUriType) { private static List<String> toStringList(List<UriType> theUriType) {

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") @Qualifier("myStructureDefinitionDaoR4")
protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao; protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
@Autowired @Autowired
@Qualifier("myConsentDaoR4")
protected IFhirResourceDao<Consent> myConsentDao;
@Autowired
@Qualifier("mySubscriptionDaoR4") @Qualifier("mySubscriptionDaoR4")
protected IFhirResourceDaoSubscription<Subscription> mySubscriptionDao; protected IFhirResourceDaoSubscription<Subscription> mySubscriptionDao;
@Autowired @Autowired

25
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.io.IOUtils;
import org.apache.commons.lang3.RandomStringUtils; import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hamcrest.Matchers; import org.hamcrest.Matchers;
import org.hamcrest.core.StringContains; import org.hamcrest.core.StringContains;
import org.hl7.fhir.instance.model.api.IAnyResource; import org.hl7.fhir.instance.model.api.IAnyResource;
@ -2966,7 +2967,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
pm.setSort(new SortSpec(Patient.SP_BIRTHDATE).setOrder(SortOrderEnum.DESC)); pm.setSort(new SortSpec(Patient.SP_BIRTHDATE).setOrder(SortOrderEnum.DESC));
actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm)); actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
assertEquals(4, actual.size()); assertEquals(4, actual.size());
// The first would be better, but JPA doesn't do NULLS LAST // The first would be better, but JPA doesn't do NULLS LAST
// assertThat(actual, contains(id3, id2, id1, id4)); // assertThat(actual, contains(id3, id2, id1, id4));
assertThat(actual, contains(id4, id3, id2, id1)); assertThat(actual, contains(id4, id3, id2, id1));
@ -3284,7 +3285,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.DESC)); pm.setSort(new SortSpec(Patient.SP_FAMILY).setOrder(SortOrderEnum.DESC));
actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm)); actual = toUnqualifiedVersionlessIds(myPatientDao.search(pm));
assertEquals(4, actual.size()); assertEquals(4, actual.size());
// The first would be better, but JPA doesn't do NULLS LAST // The first would be better, but JPA doesn't do NULLS LAST
// assertThat(actual, contains(id3, id2, id1, id4)); // assertThat(actual, contains(id3, id2, id1, id4));
assertThat(actual, contains(id4, id3, id2, id1)); assertThat(actual, contains(id4, id3, id2, id1));
} }
@ -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 @AfterClass
public static void afterClassClearContext() { public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest(); 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 pull request! These have also been added to the list of definitions uploaded
by the CLI "upload-definitions" command. by the CLI "upload-definitions" command.
</action> </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>
<release version="3.3.0" date="2018-03-29"> <release version="3.3.0" date="2018-03-29">
<action type="add"> <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/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/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/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/