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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
jamesagnew 2018-05-23 16:09:34 -04:00
parent 92dc258c6e ba8827091a
commit b146a80502
8 changed files with 150 additions and 123 deletions
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30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -98,6 +98,7 @@ import java.text.Normalizer;
import java.util.*;
import java.util.Map.Entry;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.*;
@ -704,6 +705,27 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@SuppressWarnings("unchecked")
public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> resourceTypeToDao = getDaos();
IFhirResourceDao<R> dao = (IFhirResourceDao<R>) resourceTypeToDao.get(theType);
return dao;
}
protected IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IBaseResource> theClass) {
IFhirResourceDao<? extends IBaseResource> retVal = getDao(theClass);
if (retVal == null) {
List<String> supportedResourceTypes = getDaos()
.keySet()
.stream()
.map(t->myContext.getResourceDefinition(t).getName())
.sorted()
.collect(Collectors.toList());
throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName() + " - Can handle: " + supportedResourceTypes);
}
return retVal;
}
private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> getDaos() {
if (myResourceTypeToDao == null) {
Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> theResourceTypeToDao = new HashMap<>();
Map<String, IFhirResourceDao> daos = myApplicationContext.getBeansOfType(IFhirResourceDao.class, false, false);
@ -719,8 +741,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
myResourceTypeToDao = theResourceTypeToDao;
}
IFhirResourceDao<R> dao = (IFhirResourceDao<R>) myResourceTypeToDao.get(theType);
return dao;
return Collections.unmodifiableMap(myResourceTypeToDao);
}
@ -1227,10 +1248,13 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
case JSON:
bytes = encoded.getBytes(Charsets.UTF_8);
break;
default:
case JSONC:
bytes = GZipUtil.compress(encoded);
break;
default:
case DEL:
bytes = new byte[0];
break;
}
ourLog.debug("Encoded {} chars of resource body as {} bytes", encoded.length(), bytes.length);

68
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -13,6 +13,7 @@ import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.StopWatch;
import org.apache.commons.lang3.concurrent.BasicThreadFactory;
@ -281,36 +282,51 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
public void run() {
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.afterPropertiesSet();
Throwable reindexFailure = txTemplate.execute(new TransactionCallback<Throwable>() {
@Override
public Throwable doInTransaction(TransactionStatus theStatus) {
ResourceTable resourceTable = myResourceTableDao.findOne(myNextId);
try {
/*
* This part is because from HAPI 1.5 - 1.6 we changed the format of forced ID to be "type/id" instead of just "id"
*/
ForcedId forcedId = resourceTable.getForcedId();
if (forcedId != null) {
if (isBlank(forcedId.getResourceType())) {
ourLog.info("Updating resource {} forcedId type to {}", forcedId.getForcedId(), resourceTable.getResourceType());
forcedId.setResourceType(resourceTable.getResourceType());
myForcedIdDao.save(forcedId);
Throwable reindexFailure;
try {
reindexFailure = txTemplate.execute(new TransactionCallback<Throwable>() {
@Override
public Throwable doInTransaction(TransactionStatus theStatus) {
ResourceTable resourceTable = myResourceTableDao.findOne(myNextId);
try {
/*
* This part is because from HAPI 1.5 - 1.6 we changed the format of forced ID to be "type/id" instead of just "id"
*/
ForcedId forcedId = resourceTable.getForcedId();
if (forcedId != null) {
if (isBlank(forcedId.getResourceType())) {
ourLog.info("Updating resource {} forcedId type to {}", forcedId.getForcedId(), resourceTable.getResourceType());
forcedId.setResourceType(resourceTable.getResourceType());
myForcedIdDao.save(forcedId);
}
}
final IBaseResource resource = toResource(resourceTable, false);
@SuppressWarnings("rawtypes") final IFhirResourceDao dao = getDao(resource.getClass());
dao.reindex(resource, resourceTable);
return null;
} catch (Exception e) {
ourLog.error("Failed to index resource {}: {}", resourceTable.getIdDt(), e.toString(), e);
theStatus.setRollbackOnly();
return e;
}
final IBaseResource resource = toResource(resourceTable, false);
@SuppressWarnings("rawtypes") final IFhirResourceDao dao = getDao(resource.getClass());
dao.reindex(resource, resourceTable);
return null;
} catch (Exception e) {
ourLog.error("Failed to index resource {}: {}", resourceTable.getIdDt(), e.toString(), e);
return e;
}
}
});
});
} catch (ResourceVersionConflictException e) {
/*
* We reindex in multiple threads, so it's technically possible that two threads try
* to index resources that cause a constraint error now (i.e. because a unique index has been
* added that didn't previously exist). In this case, one of the threads would succeed and
* not get this error, so we'll let the other one fail and try
* again later.
*/
ourLog.info("Failed to reindex {} because of a version conflict. Leaving in unindexed state: {}", e.getMessage());
reindexFailure = null;
}
if (reindexFailure != null) {
txTemplate.execute(new TransactionCallbackWithoutResult() {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
View File

@ -547,14 +547,6 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
}
private IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IResource> theClass) {
IFhirResourceDao<? extends IResource> retVal = getDao(theClass);
if (retVal == null) {
throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName());
}
return retVal;
}
@Override
public MetaDt metaGetOperation(RequestDetails theRequestDetails) {
// Notify interceptors

147
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* 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.
@ -19,34 +19,12 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.*;
import java.util.Map.Entry;
import javax.persistence.TypedQuery;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.param.ParameterUtil;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.instance.model.api.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.*;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.collect.ArrayListMultimap;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao;
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TagDefinition;
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
@ -54,18 +32,49 @@ import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.PreferReturnEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.UrlUtil.UrlParts;
import com.google.common.collect.ArrayListMultimap;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryResponseComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.instance.model.api.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import javax.persistence.TypedQuery;
import java.util.*;
import java.util.Map.Entry;
import static org.apache.commons.lang3.StringUtils.*;
public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
@ -90,8 +99,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
for (final BundleEntryComponent nextRequestEntry : theRequest.getEntry()) {
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
TransactionCallback<Bundle> callback = new TransactionCallback<Bundle>() {
@Override
public Bundle doInTransaction(TransactionStatus theStatus) {
@ -136,7 +145,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
long delay = System.currentTimeMillis() - start;
ourLog.info("Batch completed in {}ms", new Object[] { delay });
ourLog.info("Batch completed in {}ms", new Object[] {delay});
return resp;
}
@ -178,7 +187,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
* We want to execute the transaction request bundle elements in the order
* specified by the FHIR specification (see TransactionSorter) so we save the
* original order in the request, then sort it.
*
*
* Entries with a type of GET are removed from the bundle so that they
* can be processed at the very end. We do this because the incoming resources
* are saved in a two-phase way in order to deal with interdependencies, and
@ -212,11 +221,11 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
/*
* All of the write operations in the transaction (PUT, POST, etc.. basically anything
* except GET) are performed in their own database transaction before we do the reads.
* We do this because the reads (specifically the searches) often spawn their own
* secondary database transaction and if we allow that within the primary
* We do this because the reads (specifically the searches) often spawn their own
* secondary database transaction and if we allow that within the primary
* database transaction we can end up with deadlocks if the server is under
* heavy load with lots of concurrent transactions using all available
* database connections.
* database connections.
*/
TransactionTemplate txManager = new TransactionTemplate(myTxManager);
Map<BundleEntryComponent, ResourceTable> entriesToProcess = txManager.execute(new TransactionCallback<Map<BundleEntryComponent, ResourceTable>>() {
@ -605,7 +614,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
* was a GET search, this method is called on the bundle for the search result, that will be placed in the
* outer bundle). This method applies the _summary and _content parameters to the output of
* that bundle.
*
* <p>
* TODO: This isn't the most efficient way of doing this.. hopefully we can come up with something better in the future.
*/
private IBaseResource filterNestedBundle(RequestDetails theRequestDetails, IBaseResource theResource) {
@ -614,13 +623,6 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
}
private IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IBaseResource> theClass) {
IFhirResourceDao<? extends IBaseResource> retVal = getDao(theClass);
if (retVal == null) {
throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName());
}
return retVal;
}
@Override
public Meta metaGetOperation(RequestDetails theRequestDetails) {
@ -689,15 +691,15 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
Meta retVal = new Meta();
for (TagDefinition next : tagDefinitions) {
switch (next.getTagType()) {
case PROFILE:
retVal.addProfile(next.getCode());
break;
case SECURITY_LABEL:
retVal.addSecurity().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
break;
case TAG:
retVal.addTag().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
break;
case PROFILE:
retVal.addProfile(next.getCode());
break;
case SECURITY_LABEL:
retVal.addSecurity().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
break;
case TAG:
retVal.addTag().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
break;
}
}
return retVal;
@ -725,7 +727,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
private static void handleTransactionCreateOrUpdateOutcome(Map<IdType, IdType> idSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, IdType nextResourceId, DaoMethodOutcome outcome,
BundleEntryComponent newEntry, String theResourceType, IBaseResource theRes, ServletRequestDetails theRequestDetails) {
BundleEntryComponent newEntry, String theResourceType, IBaseResource theRes, ServletRequestDetails theRequestDetails) {
IdType newId = (IdType) outcome.getId().toUnqualifiedVersionless();
IdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
if (newId.equals(resourceId) == false) {
@ -774,7 +776,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
/**
* Transaction Order, per the spec:
*
* <p>
* Process any DELETE interactions
* Process any POST interactions
* Process any PUT interactions
@ -853,21 +855,21 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
int o1 = 0;
if (theO1.getRequest().getMethodElement().getValue() != null) {
switch (theO1.getRequest().getMethodElement().getValue()) {
case DELETE:
o1 = 1;
break;
case POST:
o1 = 2;
break;
case PUT:
o1 = 3;
break;
case GET:
o1 = 4;
break;
case NULL:
o1 = 0;
break;
case DELETE:
o1 = 1;
break;
case POST:
o1 = 2;
break;
case PUT:
o1 = 3;
break;
case GET:
o1 = 4;
break;
case NULL:
o1 = 0;
break;
}
}
return o1;
@ -877,8 +879,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
//@formatter:off
private static class BaseServerResponseExceptionHolder
{
private static class BaseServerResponseExceptionHolder {
private BaseServerResponseException myException;
public BaseServerResponseException getException() {

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java
View File

@ -603,13 +603,6 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
}
private IFhirResourceDao<?> getDaoOrThrowException(Class<? extends IBaseResource> theClass) {
IFhirResourceDao<? extends IBaseResource> retVal = getDao(theClass);
if (retVal == null) {
throw new InvalidRequestException("Unable to process request, this server does not know how to handle resources of type " + getContext().getResourceDefinition(theClass).getName());
}
return retVal;
}
@Override
public Meta metaGetOperation(RequestDetails theRequestDetails) {

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java
View File

@ -29,8 +29,7 @@ import java.util.Collections;
import java.util.List;
import java.util.UUID;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
@SuppressWarnings({"unchecked", "deprecation"})
@ -465,7 +464,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
uniques = myResourceIndexedCompositeStringUniqueDao.findAll();
assertEquals(uniques.toString(), 1, uniques.size());
assertEquals("Observation/" + id2.getIdPart(), uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue());
assertThat(uniques.get(0).getResource().getIdDt().toUnqualifiedVersionless().getValue(), either(equalTo("Observation/" + id2.getIdPart())).or(equalTo("Observation/" + id3.getIdPart())));
assertEquals("Observation?code=foo%7Cbar&date=2011-01-01&subject=Patient%2F" + id1.getIdPart(), uniques.get(0).getIndexString());
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/ResourceIndexedSearchParamStringTest.java
View File

@ -25,7 +25,7 @@ public class ResourceIndexedSearchParamStringTest {
assertEquals(6598082761639188617L, token.getHashNormalizedPrefix().longValue());
// Should be different from testHashFunctions()
assertEquals(-1970227166134682431L, token.getHashExact().longValue());
assertEquals(7045214018927566109L, token.getHashExact().longValue());
}
}

6
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
View File

@ -158,8 +158,10 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
* </p>
*/
public void addHeadersToResponse(HttpServletResponse theHttpResponse) {
String b = createPoweredByHeader();
theHttpResponse.addHeader(Constants.POWERED_BY_HEADER, b);
String poweredByHeader = createPoweredByHeader();
if (isNotBlank(poweredByHeader)) {
theHttpResponse.addHeader(Constants.POWERED_BY_HEADER, poweredByHeader);
}
}
private void addLocationHeader(RequestDetails theRequest, HttpServletResponse theResponse, MethodOutcome response, String headerLocation, String resourceName) {