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Merge remote-tracking branch 'upstream/master'

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This commit is contained in:
bdenton 2018-11-09 14:03:51 -08:00
commit 0f39cc2d71
11 changed files with 161 additions and 63 deletions
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7
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java
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@ -404,8 +404,8 @@ class ModelScanner {
if (paramType == null) {
throw new ConfigurationException("Search param " + searchParam.name() + " has an invalid type: " + searchParam.type());
}
Set<String> providesMembershipInCompartments = null;
providesMembershipInCompartments = new HashSet<String>();
Set<String> providesMembershipInCompartments;
providesMembershipInCompartments = new HashSet<>();
for (Compartment next : searchParam.providesMembershipIn()) {
if (paramType != RestSearchParameterTypeEnum.REFERENCE) {
StringBuilder b = new StringBuilder();
@ -427,7 +427,8 @@ class ModelScanner {
}
RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), paramType, providesMembershipInCompartments, toTargetList(searchParam.target()), RuntimeSearchParamStatusEnum.ACTIVE);
Collection<String> base = Collections.singletonList(theResourceDef.getName());
RuntimeSearchParam param = new RuntimeSearchParam(null, null, searchParam.name(), searchParam.description(), searchParam.path(), paramType, null, providesMembershipInCompartments, toTargetList(searchParam.target()), RuntimeSearchParamStatusEnum.ACTIVE, base);
theResourceDef.addSearchParam(param);
nameToParam.put(param.getName(), param);
}

20
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/RequestFormatParamStyleEnum.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.rest.api;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2018 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public enum RequestFormatParamStyleEnum {
/**
* Do not include a _format parameter on requests

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -638,7 +638,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
if (myDaoConfig.isMarkResourcesForReindexingUponSearchParameterChange()) {
if (isNotBlank(theExpression)) {
if (isNotBlank(theExpression) && theExpression.contains(".")) {
final String resourceType = theExpression.substring(0, theExpression.indexOf('.'));
ourLog.debug("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", resourceType, theExpression);

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java
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@ -13,7 +13,11 @@ import ca.uhn.fhir.util.ElementUtil;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.utils.FHIRLexer;
import org.hl7.fhir.r4.utils.FHIRPathEngine;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
@ -42,6 +46,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
public static final DefaultProfileValidationSupport VALIDATION_SUPPORT = new DefaultProfileValidationSupport();
@Autowired
private IFhirSystemDao<Bundle, Meta> mySystemDao;
@ -88,7 +93,7 @@ public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchPa
throw new UnprocessableEntityException("SearchParameter.status is missing or invalid");
}
if (ElementUtil.isEmpty(theBase)) {
if (ElementUtil.isEmpty(theBase) && (theType == null || !Enumerations.SearchParamType.COMPOSITE.name().equals(theType.name()))) {
throw new UnprocessableEntityException("SearchParameter.base is missing");
}
@ -104,6 +109,7 @@ public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchPa
theExpression = theExpression.trim();
if (!theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
String[] expressionSplit = BaseSearchParamExtractor.SPLIT.split(theExpression);
for (String nextPath : expressionSplit) {
nextPath = nextPath.trim();
@ -133,6 +139,16 @@ public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchPa
}
}
} else {
FHIRPathEngine fhirPathEngine = new FHIRPathEngine(new HapiWorkerContext(theContext, VALIDATION_SUPPORT));
try {
fhirPathEngine.parse(theExpression);
} catch (FHIRLexer.FHIRLexerException e) {
throw new UnprocessableEntityException("Invalid SearchParameter.expression value \"" + theExpression + "\": " + e.getMessage());
}
}
} // if have expression
}

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
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@ -14,10 +14,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Appointment.AppointmentStatus;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.*;
import org.mockito.internal.util.collections.ListUtil;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
@ -61,6 +58,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
}
@Test
@Ignore
public void testCreateInvalidParamInvalidResourceName() {
SearchParameter fooSp = new SearchParameter();
fooSp.addBase("Patient");
@ -96,6 +94,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
}
@Test
@Ignore
public void testCreateInvalidParamNoResourceName() {
SearchParameter fooSp = new SearchParameter();
fooSp.addBase("Patient");
@ -243,29 +242,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
}
@Test
public void testIndexFailsIfInvalidSearchParameterExists() {
myDaoConfig.setValidateSearchParameterExpressionsOnSave(false);
SearchParameter threadIdSp = new SearchParameter();
threadIdSp.addBase("Communication");
threadIdSp.setCode("has-attachments");
threadIdSp.setType(Enumerations.SearchParamType.REFERENCE);
threadIdSp.setExpression("Communication.payload[1].contentAttachment is not null");
threadIdSp.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
threadIdSp.setStatus(Enumerations.PublicationStatus.ACTIVE);
mySearchParameterDao.create(threadIdSp, mySrd);
mySearchParamRegsitry.forceRefresh();
Communication com = new Communication();
com.setStatus(Communication.CommunicationStatus.INPROGRESS);
try {
myCommunicationDao.create(com, mySrd);
fail();
} catch (InternalErrorException e) {
assertThat(e.getMessage(), startsWith("Failed to extract values from resource using FHIRPath \"Communication.payload[1].contentAttachment is not null\": org.hl7.fhir"));
}
}
@Test
public void testOverrideAndDisableBuiltInSearchParametersWithOverridingDisabled() {
@ -430,7 +407,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
mySearchParameterDao.create(threadIdSp, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), startsWith("The expression \"Communication.payload[1].contentAttachment is not null\" can not be evaluated and may be invalid: "));
assertThat(e.getMessage(), startsWith("Invalid SearchParameter.expression value \"Communication.payload[1].contentAttachment is not null\""));
}
}

80
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4Test.java Normal file
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@ -0,0 +1,80 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.Before;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
public class FhirResourceDaoSearchParameterR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoSearchParameterR4Test.class);
private FhirContext myCtx;
private FhirResourceDaoSearchParameterR4 myDao;
@Before
public void before() {
myCtx = FhirContext.forR4();
myDao = new FhirResourceDaoSearchParameterR4();
myDao.setContext(myCtx);
myDao.setConfig(new DaoConfig());
}
@Test
public void testValidateAllBuiltInSearchParams() {
for (String nextResource : myCtx.getResourceNames()) {
RuntimeResourceDefinition nextResDef = myCtx.getResourceDefinition(nextResource);
for (RuntimeSearchParam nextp : nextResDef.getSearchParams()) {
if (nextp.getName().equals("_id")) {
continue;
}
if (nextp.getName().equals("_language")) {
continue;
}
if (isBlank(nextp.getPath())) {
continue;
}
SearchParameter nextSearchParameter = new SearchParameter();
nextSearchParameter.setExpression(nextp.getPath());
nextSearchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
nextSearchParameter.setType(Enumerations.SearchParamType.fromCode(nextp.getParamType().getCode()));
nextp.getBase().forEach(t -> nextSearchParameter.addBase(t));
ourLog.info("Validating {}.{}", nextResource, nextp.getName());
myDao.validateResourceForStorage(nextSearchParameter, null);
}
}
}
@Test
public void testValidateInvalidExpression() {
SearchParameter nextSearchParameter = new SearchParameter();
nextSearchParameter.setExpression("Patient////");
nextSearchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
nextSearchParameter.setType(Enumerations.SearchParamType.STRING);
nextSearchParameter.addBase("Patient");
try {
myDao.validateResourceForStorage(nextSearchParameter, null);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Invalid SearchParameter.expression value \"Patient////\": Error at 1, 1: Premature ExpressionNode termination at unexpected token \"////\"", e.getMessage());
}
}
}

4
src/changes/changes.xml
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@ -177,6 +177,10 @@
<![CDATA[<code>_format</code>]]>
parameter should be included in requests.
</action>
<action type="add">
JPA server R4 SearchParameter custom expression validation is now done using the
actual FHIRPath evaluator, meaning it is more rigorous in what it can find.
</action>
</release>
<release version="3.5.0" date="2018-09-17">