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FIx deadlock in transaction processing, and put transaction outcome 

in the right spot
This commit is contained in:
James 2017-07-21 07:39:11 -04:00
parent 6a178b08bd
commit a13c78d6cc
6 changed files with 426 additions and 280 deletions
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478
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java
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@ -19,48 +19,21 @@ 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 static org.apache.commons.lang3.StringUtils.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.*;
import java.util.Map.Entry;
import java.util.Set;
import javax.persistence.TypedQuery;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.hl7.fhir.dstu3.model.Bundle;
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.IdType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.OperationOutcome;
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.dstu3.model.Resource;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
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.*;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallback;
@ -69,10 +42,7 @@ import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.collect.ArrayListMultimap;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
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.dao.*;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TagDefinition;
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
@ -80,19 +50,12 @@ 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.PreferReturnEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.BaseMethodBinding;
import ca.uhn.fhir.rest.method.BaseResourceReturningMethodBinding;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.method.*;
import ca.uhn.fhir.rest.method.BaseResourceReturningMethodBinding.ResourceOrDstu1Bundle;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
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.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
@ -121,6 +84,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
for (final BundleEntryComponent nextRequestEntry : theRequest.getEntry()) {
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
TransactionCallback<Bundle> callback = new TransactionCallback<Bundle>() {
@Override
public Bundle doInTransaction(TransactionStatus theStatus) {
@ -133,13 +98,12 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
};
BaseServerResponseException caughtEx;
try {
Bundle nextResponseBundle = txTemplate.execute(callback);
caughtEx = null;
Bundle nextResponseBundle = callback.doInTransaction(null);
BundleEntryComponent subResponseEntry = nextResponseBundle.getEntry().get(0);
resp.addEntry(subResponseEntry);
/*
* If the individual entry didn't have a resource in its response, bring the sub-transaction's OperationOutcome across so the client can see it
*/
@ -148,21 +112,19 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
} catch (BaseServerResponseException e) {
caughtEx = e;
caughtEx.setException(e);
} catch (Throwable t) {
ourLog.error("Failure during BATCH sub transaction processing", t);
caughtEx = new InternalErrorException(t);
caughtEx.setException(new InternalErrorException(t));
}
if (caughtEx != null) {
if (caughtEx.getException() != null) {
BundleEntryComponent nextEntry = resp.addEntry();
OperationOutcome oo = new OperationOutcome();
oo.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics(caughtEx.getMessage());
nextEntry.setResource(oo);
populateEntryWithOperationOutcome(caughtEx.getException(), nextEntry);
BundleEntryResponseComponent nextEntryResp = nextEntry.getResponse();
nextEntryResp.setStatus(toStatusString(caughtEx.getStatusCode()));
nextEntryResp.setStatus(toStatusString(caughtEx.getException().getStatusCode()));
}
}
@ -173,117 +135,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
return resp;
}
private String extractTransactionUrlOrThrowException(BundleEntryComponent nextEntry, HTTPVerb verb) {
String url = nextEntry.getRequest().getUrl();
if (isBlank(url)) {
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionMissingUrl", verb.name()));
}
return url;
}
/**
* This method is called for nested bundles (e.g. if we received a transaction with an entry that
* 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.
*
* 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) {
IParser p = getContext().newJsonParser();
RestfulServerUtils.configureResponseParser(theRequestDetails, p);
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) {
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails);
notifyInterceptors(RestOperationTypeEnum.META, requestDetails);
String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t)";
TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
List<TagDefinition> tagDefinitions = q.getResultList();
Meta retVal = toMeta(tagDefinitions);
return retVal;
}
protected Meta toMeta(Collection<TagDefinition> tagDefinitions) {
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;
}
}
return retVal;
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> toDao(UrlParts theParts, String theVerb, String theUrl) {
RuntimeResourceDefinition resType;
try {
resType = getContext().getResourceDefinition(theParts.getResourceType());
} catch (DataFormatException e) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
throw new InvalidRequestException(msg);
}
IFhirResourceDao<? extends IBaseResource> dao = null;
if (resType != null) {
dao = getDao(resType.getImplementingClass());
}
if (dao == null) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
throw new InvalidRequestException(msg);
}
// if (theParts.getResourceId() == null && theParts.getParams() == null) {
// String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
// throw new InvalidRequestException(msg);
// }
return dao;
}
@Transactional(propagation = Propagation.REQUIRED)
@Override
public Bundle transaction(RequestDetails theRequestDetails, Bundle theRequest) {
if (theRequestDetails != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theRequest, "Bundle", null);
notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
}
String actionName = "Transaction";
return transaction((ServletRequestDetails) theRequestDetails, theRequest, actionName);
}
private Bundle transaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
super.markRequestAsProcessingSubRequest(theRequestDetails);
try {
return doTransaction(theRequestDetails, theRequest, theActionName);
} finally {
super.clearRequestAsProcessingSubRequest(theRequestDetails);
}
}
@SuppressWarnings("unchecked")
private Bundle doTransaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
private Bundle doTransaction(final ServletRequestDetails theRequestDetails, final Bundle theRequest, final String theActionName) {
BundleType transactionType = theRequest.getTypeElement().getValue();
if (transactionType == BundleType.BATCH) {
return batch(theRequestDetails, theRequest);
@ -301,11 +153,11 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
ourLog.info("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
long start = System.currentTimeMillis();
Date updateTime = new Date();
final Date updateTime = new Date();
Set<IdType> allIds = new LinkedHashSet<IdType>();
Map<IdType, IdType> idSubstitutions = new HashMap<IdType, IdType>();
Map<IdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<IdType, DaoMethodOutcome>();
final Set<IdType> allIds = new LinkedHashSet<IdType>();
final Map<IdType, IdType> idSubstitutions = new HashMap<IdType, IdType>();
final Map<IdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<IdType, DaoMethodOutcome>();
// Do all entries have a verb?
for (int i = 0; i < theRequest.getEntry().size(); i++) {
@ -326,9 +178,9 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
* are saved in a two-phase way in order to deal with interdependencies, and
* we want the GET processing to use the final indexing state
*/
Bundle response = new Bundle();
final Bundle response = new Bundle();
List<BundleEntryComponent> getEntries = new ArrayList<BundleEntryComponent>();
IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder = new IdentityHashMap<Bundle.BundleEntryComponent, Integer>();
final IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder = new IdentityHashMap<Bundle.BundleEntryComponent, Integer>();
for (int i = 0; i < theRequest.getEntry().size(); i++) {
originalRequestOrder.put(theRequest.getEntry().get(i), i);
response.addEntry();
@ -338,6 +190,108 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
Collections.sort(theRequest.getEntry(), new TransactionSorter());
/*
* 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
* 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.
*/
TransactionTemplate txManager = new TransactionTemplate(myTxManager);
Map<BundleEntryComponent, ResourceTable> entriesToProcess = txManager.execute(new TransactionCallback<Map<BundleEntryComponent, ResourceTable>>() {
@Override
public Map<BundleEntryComponent, ResourceTable> doInTransaction(TransactionStatus status) {
return doTransactionWriteOperations(theRequestDetails, theRequest, theActionName, updateTime, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder);
}
});
for (Entry<BundleEntryComponent, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
String responseLocation = nextEntry.getValue().getIdDt().toUnqualified().getValue();
String responseEtag = nextEntry.getValue().getIdDt().getVersionIdPart();
nextEntry.getKey().getResponse().setLocation(responseLocation);
nextEntry.getKey().getResponse().setEtag(responseEtag);
}
/*
* Loop through the request and process any entries of type GET
*/
for (int i = 0; i < getEntries.size(); i++) {
BundleEntryComponent nextReqEntry = getEntries.get(i);
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
BundleEntryComponent nextRespEntry = response.getEntry().get(originalOrder);
ServletSubRequestDetails requestDetails = new ServletSubRequestDetails();
requestDetails.setServletRequest(theRequestDetails.getServletRequest());
requestDetails.setRequestType(RequestTypeEnum.GET);
requestDetails.setServer(theRequestDetails.getServer());
String url = extractTransactionUrlOrThrowException(nextReqEntry, HTTPVerb.GET);
int qIndex = url.indexOf('?');
ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
requestDetails.setParameters(new HashMap<String, String[]>());
if (qIndex != -1) {
String params = url.substring(qIndex);
List<NameValuePair> parameters = translateMatchUrl(params);
for (NameValuePair next : parameters) {
paramValues.put(next.getName(), next.getValue());
}
for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
requestDetails.getParameters().put(nextParamEntry.getKey(), nextValue);
}
url = url.substring(0, qIndex);
}
requestDetails.setRequestPath(url);
requestDetails.setFhirServerBase(theRequestDetails.getFhirServerBase());
theRequestDetails.getServer().populateRequestDetailsFromRequestPath(requestDetails, url);
BaseMethodBinding<?> method = theRequestDetails.getServer().determineResourceMethod(requestDetails, url);
if (method == null) {
throw new IllegalArgumentException("Unable to handle GET " + url);
}
if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
requestDetails.addHeader(Constants.HEADER_IF_MATCH, nextReqEntry.getRequest().getIfMatch());
}
if (isNotBlank(nextReqEntry.getRequest().getIfNoneExist())) {
requestDetails.addHeader(Constants.HEADER_IF_NONE_EXIST, nextReqEntry.getRequest().getIfNoneExist());
}
if (isNotBlank(nextReqEntry.getRequest().getIfNoneMatch())) {
requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, nextReqEntry.getRequest().getIfNoneMatch());
}
Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {}", url);
try {
ResourceOrDstu1Bundle responseData = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
IBaseResource resource = responseData.getResource();
if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
resource = filterNestedBundle(requestDetails, resource);
}
nextRespEntry.setResource((Resource) resource);
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
} catch (NotModifiedException e) {
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_304_NOT_MODIFIED));
} catch (BaseServerResponseException e) {
ourLog.info("Failure processing transaction GET {}: {}", url, e.toString());
nextRespEntry.getResponse().setStatus(toStatusString(e.getStatusCode()));
populateEntryWithOperationOutcome(e, nextRespEntry);
}
}
long delay = System.currentTimeMillis() - start;
ourLog.info(theActionName + " completed in {}ms", new Object[] { delay });
response.setType(BundleType.TRANSACTIONRESPONSE);
return response;
}
@SuppressWarnings("unchecked")
private Map<BundleEntryComponent, ResourceTable> doTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date updateTime, Set<IdType> allIds,
Map<IdType, IdType> idSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, Bundle response, IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder) {
Set<String> deletedResources = new HashSet<String>();
List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<BundleEntryComponent, ResourceTable>();
@ -562,87 +516,122 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
ourLog.info("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
}
return entriesToProcess;
}
/*
* Loop through the request and process any entries of type GET
private String extractTransactionUrlOrThrowException(BundleEntryComponent nextEntry, HTTPVerb verb) {
String url = nextEntry.getRequest().getUrl();
if (isBlank(url)) {
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionMissingUrl", verb.name()));
}
return url;
}
/**
* This method is called for nested bundles (e.g. if we received a transaction with an entry that
* 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.
*
* TODO: This isn't the most efficient way of doing this.. hopefully we can come up with something better in the future.
*/
for (int i = 0; i < getEntries.size(); i++) {
BundleEntryComponent nextReqEntry = getEntries.get(i);
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
BundleEntryComponent nextRespEntry = response.getEntry().get(originalOrder);
ServletSubRequestDetails requestDetails = new ServletSubRequestDetails();
requestDetails.setServletRequest(theRequestDetails.getServletRequest());
requestDetails.setRequestType(RequestTypeEnum.GET);
requestDetails.setServer(theRequestDetails.getServer());
String url = extractTransactionUrlOrThrowException(nextReqEntry, HTTPVerb.GET);
int qIndex = url.indexOf('?');
ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
requestDetails.setParameters(new HashMap<String, String[]>());
if (qIndex != -1) {
String params = url.substring(qIndex);
List<NameValuePair> parameters = translateMatchUrl(params);
for (NameValuePair next : parameters) {
paramValues.put(next.getName(), next.getValue());
}
for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
requestDetails.getParameters().put(nextParamEntry.getKey(), nextValue);
}
url = url.substring(0, qIndex);
private IBaseResource filterNestedBundle(RequestDetails theRequestDetails, IBaseResource theResource) {
IParser p = getContext().newJsonParser();
RestfulServerUtils.configureResponseParser(theRequestDetails, p);
return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
}
requestDetails.setRequestPath(url);
requestDetails.setFhirServerBase(theRequestDetails.getFhirServerBase());
theRequestDetails.getServer().populateRequestDetailsFromRequestPath(requestDetails, url);
BaseMethodBinding<?> method = theRequestDetails.getServer().determineResourceMethod(requestDetails, url);
if (method == null) {
throw new IllegalArgumentException("Unable to handle GET " + url);
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;
}
if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
requestDetails.addHeader(Constants.HEADER_IF_MATCH, nextReqEntry.getRequest().getIfMatch());
}
if (isNotBlank(nextReqEntry.getRequest().getIfNoneExist())) {
requestDetails.addHeader(Constants.HEADER_IF_NONE_EXIST, nextReqEntry.getRequest().getIfNoneExist());
}
if (isNotBlank(nextReqEntry.getRequest().getIfNoneMatch())) {
requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, nextReqEntry.getRequest().getIfNoneMatch());
@Override
public Meta metaGetOperation(RequestDetails theRequestDetails) {
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails);
notifyInterceptors(RestOperationTypeEnum.META, requestDetails);
String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t)";
TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
List<TagDefinition> tagDefinitions = q.getResultList();
Meta retVal = toMeta(tagDefinitions);
return retVal;
}
if (method instanceof BaseResourceReturningMethodBinding) {
private void populateEntryWithOperationOutcome(BaseServerResponseException caughtEx, BundleEntryComponent nextEntry) {
OperationOutcome oo = new OperationOutcome();
oo.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics(caughtEx.getMessage());
nextEntry.getResponse().setOutcome(oo);
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> toDao(UrlParts theParts, String theVerb, String theUrl) {
RuntimeResourceDefinition resType;
try {
ResourceOrDstu1Bundle responseData = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
IBaseResource resource = responseData.getResource();
if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
resource = filterNestedBundle(requestDetails, resource);
resType = getContext().getResourceDefinition(theParts.getResourceType());
} catch (DataFormatException e) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
throw new InvalidRequestException(msg);
}
nextRespEntry.setResource((Resource) resource);
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
} catch (NotModifiedException e) {
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_304_NOT_MODIFIED));
IFhirResourceDao<? extends IBaseResource> dao = null;
if (resType != null) {
dao = getDao(resType.getImplementingClass());
}
} else {
throw new IllegalArgumentException("Unable to handle GET " + url);
if (dao == null) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
throw new InvalidRequestException(msg);
}
// if (theParts.getResourceId() == null && theParts.getParams() == null) {
// String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
// throw new InvalidRequestException(msg);
// }
return dao;
}
for (Entry<BundleEntryComponent, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
String responseLocation = nextEntry.getValue().getIdDt().toUnqualified().getValue();
String responseEtag = nextEntry.getValue().getIdDt().getVersionIdPart();
nextEntry.getKey().getResponse().setLocation(responseLocation);
nextEntry.getKey().getResponse().setEtag(responseEtag);
protected Meta toMeta(Collection<TagDefinition> tagDefinitions) {
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;
}
}
return retVal;
}
long delay = System.currentTimeMillis() - start;
ourLog.info(theActionName + " completed in {}ms", new Object[] { delay });
@Transactional(propagation = Propagation.NEVER)
@Override
public Bundle transaction(RequestDetails theRequestDetails, Bundle theRequest) {
if (theRequestDetails != null) {
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theRequest, "Bundle", null);
notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
}
response.setType(BundleType.TRANSACTIONRESPONSE);
return response;
String actionName = "Transaction";
return transaction((ServletRequestDetails) theRequestDetails, theRequest, actionName);
}
private Bundle transaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
super.markRequestAsProcessingSubRequest(theRequestDetails);
try {
return doTransaction(theRequestDetails, theRequest, theActionName);
} finally {
super.clearRequestAsProcessingSubRequest(theRequestDetails);
}
}
private static void handleTransactionCreateOrUpdateOutcome(Map<IdType, IdType> idSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, IdType nextResourceId, DaoMethodOutcome outcome,
@ -693,6 +682,19 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
}
private static class BaseServerResponseExceptionHolder
{
private BaseServerResponseException myException;
public BaseServerResponseException getException() {
return myException;
}
public void setException(BaseServerResponseException myException) {
this.myException = myException;
}
}
//@formatter:off
/**
* Transaction Order, per the spec:

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

@ -34,12 +34,10 @@ import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.UniqueConstraint;
//@formatter:off
@Entity
@Table(name = "HFJ_SEARCH_RESULT", uniqueConstraints= {
@UniqueConstraint(name="IDX_SEARCHRES_ORDER", columnNames= {"SEARCH_PID", "SEARCH_ORDER"})
})
//@formatter:on
public class SearchResult implements Serializable {
private static final long serialVersionUID = 1L;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.search;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 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%
*/
import java.util.Date;
import org.apache.commons.lang3.time.DateUtils;

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -44,6 +44,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
* starvation
*/
int maxThreads = (int)(Math.random() * 6) + 2;
maxThreads = 2;
retVal.setMaxTotal(maxThreads);
DataSource dataSource = ProxyDataSourceBuilder

168
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -26,31 +26,14 @@ import java.nio.charset.StandardCharsets;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Appointment;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryRequestComponent;
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.Coding;
import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.DiagnosticReport;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.EpisodeOfCare;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Medication;
import org.hl7.fhir.dstu3.model.MedicationRequest;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu3.model.Organization;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.After;
@ -497,9 +480,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertThat(resp.getEntry().get(0).getResponse().getLocation(), startsWith("Patient/"));
// Bundle.entry[1] is failed read response
assertEquals(OperationOutcome.class, resp.getEntry().get(1).getResource().getClass());
assertEquals(IssueSeverity.ERROR, ((OperationOutcome) resp.getEntry().get(1).getResource()).getIssue().get(0).getSeverityElement().getValue());
assertEquals("Resource Patient/THIS_ID_DOESNT_EXIST is not known", ((OperationOutcome) resp.getEntry().get(1).getResource()).getIssue().get(0).getDiagnostics());
Resource oo = resp.getEntry().get(1).getResponse().getOutcome();
assertEquals(OperationOutcome.class, oo.getClass());
assertEquals(IssueSeverity.ERROR, ((OperationOutcome) oo).getIssue().get(0).getSeverityElement().getValue());
assertEquals("Resource Patient/THIS_ID_DOESNT_EXIST is not known", ((OperationOutcome) oo).getIssue().get(0).getDiagnostics());
assertEquals("404 Not Found", resp.getEntry().get(1).getResponse().getStatus());
// Check POST
@ -891,6 +875,143 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
}
}
@Test
public void testTransactionCreateWithBadRead() {
Bundle request = new Bundle();
request.setType(BundleType.TRANSACTION);
Patient p;
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("FOO");
request
.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.POST)
.setUrl("Patient");
request
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient/BABABABA");
Bundle response = mySystemDao.transaction(mySrd, request);
assertEquals(2, response.getEntry().size());
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
assertThat(response.getEntry().get(0).getResponse().getLocation(), matchesPattern(".*Patient/[0-9]+.*"));
assertEquals("404 Not Found", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertEquals("Resource Patient/BABABABA is not known", oo.getIssue().get(0).getDiagnostics());
}
@Test
public void testTransactionCreateWithBadSearch() {
Bundle request = new Bundle();
request.setType(BundleType.TRANSACTION);
Patient p;
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("FOO");
request
.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.POST)
.setUrl("Patient");
request
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?foobadparam=1");
Bundle response = mySystemDao.transaction(mySrd, request);
assertEquals(2, response.getEntry().size());
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
assertThat(response.getEntry().get(0).getResponse().getLocation(), matchesPattern(".*Patient/[0-9]+.*"));
assertEquals("400 Bad Request", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("Unknown search parameter"));
}
@Test
public void testBatchCreateWithBadRead() {
Bundle request = new Bundle();
request.setType(BundleType.BATCH);
Patient p;
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("FOO");
request
.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.POST)
.setUrl("Patient");
request
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient/BABABABA");
Bundle response = mySystemDao.transaction(mySrd, request);
assertEquals(2, response.getEntry().size());
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
assertThat(response.getEntry().get(0).getResponse().getLocation(), matchesPattern(".*Patient/[0-9]+.*"));
assertEquals("404 Not Found", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertEquals("Resource Patient/BABABABA is not known", oo.getIssue().get(0).getDiagnostics());
}
@Test
public void testBatchCreateWithBadSearch() {
Bundle request = new Bundle();
request.setType(BundleType.BATCH);
Patient p;
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("FOO");
request
.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.POST)
.setUrl("Patient");
request
.addEntry()
.getRequest()
.setMethod(HTTPVerb.GET)
.setUrl("Patient?foobadparam=1");
Bundle response = mySystemDao.transaction(mySrd, request);
assertEquals(2, response.getEntry().size());
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
assertThat(response.getEntry().get(0).getResponse().getLocation(), matchesPattern(".*Patient/[0-9]+.*"));
assertEquals("400 Bad Request", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("Unknown search parameter"));
}
@Test
public void testTransactionCreateWithDuplicateMatchUrl02() {
String methodName = "testTransactionCreateWithDuplicateMatchUrl02";
@ -1331,9 +1452,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
@Test
public void testTransactionDoesNotLeavePlaceholderIds() throws Exception {
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
String input;
try {
input = IOUtils.toString(getClass().getResourceAsStream("/cdr-bundle.json"), StandardCharsets.UTF_8);
@ -1343,8 +1461,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
}
Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
mySystemDao.transaction(mySrd, bundle);
}
});
IBundleProvider history = mySystemDao.history(null, null, null);
Bundle list = toBundle(history);

11
src/changes/changes.xml
View File

@ -177,8 +177,17 @@
GitHub user @CarthageKing for the pull request!
</action>
<action type="fix">
Fix potential deadlock in stale search deleting task in JPA server
Fix potential deadlock in stale search deleting task in JPA server, as well
as potential deadlock when executing transactions containing nested
searches when operating under extremely heavy load.
</action>
<action type="add">
JPA server transaction operations now put OperationOutcome resources resulting
from actions in
<![CDATA[<code>Bundle.entry.response.outcome</code>]]>
instead of the previous
<![CDATA[<code>Bundle.entry.resource</code>]]>
<action>
</release>
<release version="2.5" date="2017-06-08">
<action type="fix">