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hapi-fhir
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Squashed commit of the following: 

commit 7ff895de77
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 15:25:06 2017 -0400

    More test fixes

commit c9fee23e48
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 15:14:52 2017 -0400

    More tests work

commit c796e19458
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 15:00:26 2017 -0400

    Get tests passing

commit eb2787d30c
Author: James Agnew <jamesagnew@gmail.com>
Date:   Fri Oct 6 14:08:23 2017 -0400

    Add an optimistic lock to the ResourceTable

commit ff85503acb
Author: James <jamesagnew@gmail.com>
Date:   Fri Oct 6 08:56:35 2017 -0400

    Add a test
This commit is contained in:
James Agnew 2017-10-06 15:33:24 -04:00
parent b4127674e4
commit bacd0bfbbb
19 changed files with 431 additions and 183 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -1011,14 +1011,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
changed = true;
}
if (theResource instanceof IResource) {
String title = ResourceMetadataKeyEnum.TITLE.get((IResource) theResource);
if (title != null && title.length() > BaseHasResource.MAX_TITLE_LENGTH) {
title = title.substring(0, BaseHasResource.MAX_TITLE_LENGTH);
}
theEntity.setTitle(title);
}
return changed;
}
@ -1052,10 +1044,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
ResourceMetadataKeyEnum.UPDATED.put(res, theEntity.getUpdated());
IDao.RESOURCE_PID.put(res, theEntity.getId());
if (theEntity.getTitle() != null) {
ResourceMetadataKeyEnum.TITLE.put(res, theEntity.getTitle());
}
Collection<? extends BaseTag> tags = theEntity.getTags();
if (theEntity.isHasTags()) {
TagList tagList = new TagList();

90
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseHasResource.java
View File

@ -20,52 +20,54 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import java.util.Collection;
import java.util.Date;
import javax.persistence.*;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import org.hibernate.annotations.OptimisticLock;
import javax.persistence.*;
import java.util.Collection;
import java.util.Date;
@MappedSuperclass
public abstract class BaseHasResource {
public static final int MAX_TITLE_LENGTH = 100;
@Column(name = "RES_DELETED_AT", nullable = true)
@Temporal(TemporalType.TIMESTAMP)
private Date myDeleted;
@Column(name = "RES_ENCODING", nullable = false, length = 5)
@Enumerated(EnumType.STRING)
@OptimisticLock(excluded = true)
private ResourceEncodingEnum myEncoding;
@Column(name = "RES_VERSION", nullable = true, length = 7)
@Enumerated(EnumType.STRING)
@OptimisticLock(excluded = true)
private FhirVersionEnum myFhirVersion;
@OneToOne(optional = true, fetch = FetchType.EAGER, cascade = {}, orphanRemoval = false)
@JoinColumn(name = "FORCED_ID_PID")
@OptimisticLock(excluded = true)
private ForcedId myForcedId;
@Column(name = "HAS_TAGS", nullable = false)
@OptimisticLock(excluded = true)
private boolean myHasTags;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "RES_PUBLISHED", nullable = false)
@OptimisticLock(excluded = true)
private Date myPublished;
@Column(name = "RES_TEXT", length = Integer.MAX_VALUE - 1, nullable = false)
@Lob()
@OptimisticLock(excluded = true)
private byte[] myResource;
@Column(name = "RES_TITLE", nullable = true, length = MAX_TITLE_LENGTH)
private String myTitle;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "RES_UPDATED", nullable = false)
@OptimisticLock(excluded = true)
private Date myUpdated;
public abstract BaseTag addTag(TagDefinition theDef);
@ -74,18 +76,36 @@ public abstract class BaseHasResource {
return myDeleted;
}
public void setDeleted(Date theDate) {
myDeleted = theDate;
}
public ResourceEncodingEnum getEncoding() {
return myEncoding;
}
public void setEncoding(ResourceEncodingEnum theEncoding) {
myEncoding = theEncoding;
}
public FhirVersionEnum getFhirVersion() {
return myFhirVersion;
}
public void setFhirVersion(FhirVersionEnum theFhirVersion) {
myFhirVersion = theFhirVersion;
}
public ForcedId getForcedId() {
return myForcedId;
}
public void setForcedId(ForcedId theForcedId) {
myForcedId = theForcedId;
}
public abstract Long getId();
public abstract IdDt getIdDt();
public InstantDt getPublished() {
@ -96,22 +116,30 @@ public abstract class BaseHasResource {
}
}
public void setPublished(InstantDt thePublished) {
myPublished = thePublished.getValue();
}
public byte[] getResource() {
return myResource;
}
public void setResource(byte[] theResource) {
myResource = theResource;
}
public abstract String getResourceType();
public abstract Collection<? extends BaseTag> getTags();
public String getTitle() {
return myTitle;
}
public InstantDt getUpdated() {
return new InstantDt(myUpdated);
}
public void setUpdated(InstantDt theUpdated) {
myUpdated = theUpdated.getValue();
}
public Date getUpdatedDate() {
return myUpdated;
}
@ -122,24 +150,6 @@ public abstract class BaseHasResource {
return myHasTags;
}
public void setDeleted(Date theDate) {
myDeleted = theDate;
}
public abstract Long getId();
public void setEncoding(ResourceEncodingEnum theEncoding) {
myEncoding = theEncoding;
}
public void setFhirVersion(FhirVersionEnum theFhirVersion) {
myFhirVersion = theFhirVersion;
}
public void setForcedId(ForcedId theForcedId) {
myForcedId = theForcedId;
}
public void setHasTags(boolean theHasTags) {
myHasTags = theHasTags;
}
@ -148,24 +158,8 @@ public abstract class BaseHasResource {
myPublished = thePublished;
}
public void setPublished(InstantDt thePublished) {
myPublished = thePublished.getValue();
}
public void setResource(byte[] theResource) {
myResource = theResource;
}
public void setTitle(String theTitle) {
myTitle = theTitle;
}
public void setUpdated(Date theUpdated) {
myUpdated = theUpdated;
}
public void setUpdated(InstantDt theUpdated) {
myUpdated = theUpdated.getValue();
}
}

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java
View File

@ -37,6 +37,7 @@ import org.apache.lucene.analysis.snowball.SnowballPorterFilterFactory;
import org.apache.lucene.analysis.standard.StandardFilterFactory;
import org.apache.lucene.analysis.standard.StandardTokenizerFactory;
import org.hibernate.annotations.ColumnDefault;
import org.hibernate.annotations.OptimisticLock;
import org.hibernate.search.annotations.*;
import org.hibernate.search.annotations.Parameter;
@ -124,12 +125,15 @@ public class ResourceTable extends BaseHasResource implements Serializable {
@Field(name = "myContentTextNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteNGramAnalyzer")),
@Field(name = "myContentTextPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
})
@OptimisticLock(excluded = true)
private String myContentText;
@Column(name = "HASH_SHA256", length = 64, nullable = true)
@OptimisticLock(excluded = true)
private String myHashSha256;
@Column(name = "SP_HAS_LINKS")
@OptimisticLock(excluded = true)
private boolean myHasLinks;
@Id
@ -139,12 +143,15 @@ public class ResourceTable extends BaseHasResource implements Serializable {
private Long myId;
@OneToMany(mappedBy = "myTargetResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceLink> myIncomingResourceLinks;
@Column(name = "SP_INDEX_STATUS", nullable = true)
@OptimisticLock(excluded = true)
private Long myIndexStatus;
@Column(name = "RES_LANGUAGE", length = MAX_LANGUAGE_LENGTH, nullable = true)
@OptimisticLock(excluded = true)
private String myLanguage;
/**
@ -157,69 +164,100 @@ public class ResourceTable extends BaseHasResource implements Serializable {
@Field(name = "myNarrativeTextNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteNGramAnalyzer")),
@Field(name = "myNarrativeTextPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
})
@OptimisticLock(excluded = true)
private String myNarrativeText;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedSearchParamCoords> myParamsCoords;
@Column(name = "SP_COORDS_PRESENT")
@OptimisticLock(excluded = true)
private boolean myParamsCoordsPopulated;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedSearchParamDate> myParamsDate;
@Column(name = "SP_DATE_PRESENT")
@OptimisticLock(excluded = true)
private boolean myParamsDatePopulated;
@OptimisticLock(excluded = true)
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
private Collection<ResourceIndexedSearchParamNumber> myParamsNumber;
@Column(name = "SP_NUMBER_PRESENT")
@OptimisticLock(excluded = true)
private boolean myParamsNumberPopulated;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedSearchParamQuantity> myParamsQuantity;
@Column(name = "SP_QUANTITY_PRESENT")
@OptimisticLock(excluded = true)
private boolean myParamsQuantityPopulated;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedSearchParamString> myParamsString;
@Column(name = "SP_STRING_PRESENT")
@OptimisticLock(excluded = true)
private boolean myParamsStringPopulated;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedSearchParamToken> myParamsToken;
@Column(name = "SP_TOKEN_PRESENT")
@OptimisticLock(excluded = true)
private boolean myParamsTokenPopulated;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedSearchParamUri> myParamsUri;
@Column(name = "SP_URI_PRESENT")
@OptimisticLock(excluded = true)
private boolean myParamsUriPopulated;
@Column(name = "RES_PROFILE", length = MAX_PROFILE_LENGTH, nullable = true)
@OptimisticLock(excluded = true)
private String myProfile;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
private Collection<ResourceIndexedCompositeStringUnique> myParamsCompositeStringUnique;
// Added in 3.0.0 - Should make this a primitive Boolean at some point
@OptimisticLock(excluded = true)
@Column(name = "SP_CMPSTR_UNIQ_PRESENT")
private Boolean myParamsCompositeStringUniquePresent = false;
@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@OptimisticLock(excluded = true)
private Collection<ResourceIndexedCompositeStringUnique> myParamsCompositeStringUnique;
@OneToMany(mappedBy = "mySourceResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
@IndexedEmbedded()
@OptimisticLock(excluded = true)
private Collection<ResourceLink> myResourceLinks;
@Column(name = "RES_TYPE", length = RESTYPE_LEN)
@Field
@OptimisticLock(excluded = true)
private String myResourceType;
@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
@OptimisticLock(excluded = true)
private Collection<SearchParamPresent> mySearchParamPresents;
@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
@OptimisticLock(excluded = true)
private Set<ResourceTag> myTags;
@Transient
private transient boolean myUnchangedInCurrentOperation;
@Version
@Column(name = "RES_VER")
private long myVersion;
@ -555,7 +593,6 @@ public class ResourceTable extends BaseHasResource implements Serializable {
retVal.setResourceType(myResourceType);
retVal.setVersion(myVersion);
retVal.setTitle(getTitle());
retVal.setPublished(getPublished());
retVal.setUpdated(getUpdated());
retVal.setEncoding(getEncoding());

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

@ -89,7 +89,7 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
searchParam = new SearchParam();
searchParam.setResourceName(resourceType);
searchParam.setParamName(paramName);
searchParam = mySearchParamDao.saveAndFlush(searchParam);
searchParam = mySearchParamDao.save(searchParam);
ourLog.info("Added search param {} with pid {}", paramName, searchParam.getId());
// Don't add the newly saved entity to the map in case the save fails
}

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionInterceptor.java
View File

@ -36,6 +36,7 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.interceptor.ServerOperationInterceptorAdapter;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.concurrent.BasicThreadFactory;
import org.hl7.fhir.exceptions.FHIRException;
@ -51,8 +52,12 @@ import org.springframework.messaging.MessageHandler;
import org.springframework.messaging.SubscribableChannel;
import org.springframework.messaging.support.ExecutorSubscribableChannel;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionSynchronizationAdapter;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
@ -87,6 +92,9 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
@Autowired(required = false)
@Qualifier("myEventDefinitionDaoR4")
private IFhirResourceDao<org.hl7.fhir.r4.model.EventDefinition> myEventDefinitionDaoR4;
@Autowired
private PlatformTransactionManager myTxManager;
/**
* Constructor
*/
@ -368,6 +376,11 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
myResourceDaos = theResourceDaos;
}
@VisibleForTesting
public void setTxManager(PlatformTransactionManager theTxManager) {
myTxManager = theTxManager;
}
@PostConstruct
public void start() {
for (IFhirResourceDao<?> next : myResourceDaos) {
@ -452,8 +465,14 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
registerSubscriptionCheckingSubscriber();
registerDeliverySubscriber();
TransactionTemplate transactionTemplate = new TransactionTemplate(myTxManager);
transactionTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus status) {
initSubscriptions();
}
});
}
protected void submitResourceModified(final ResourceModifiedMessage theMsg) {
mySubscriptionActivatingSubscriber.handleMessage(theMsg.getOperationType(), theMsg.getId(myCtx), theMsg.getNewPayload(myCtx));

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/SubscriptionActivatingSubscriber.java
View File

@ -32,6 +32,8 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.messaging.Message;
import org.springframework.messaging.MessagingException;
import org.springframework.transaction.support.TransactionSynchronizationAdapter;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import java.util.concurrent.ConcurrentHashMap;
@ -53,22 +55,27 @@ public class SubscriptionActivatingSubscriber {
myCtx = theSubscriptionDao.getContext();
}
public void activateAndRegisterSubscriptionIfRequired(IBaseResource theSubscription) {
public void activateAndRegisterSubscriptionIfRequired(final IBaseResource theSubscription) {
boolean subscriptionTypeApplies = BaseSubscriptionSubscriber.subscriptionTypeApplies(myCtx, theSubscription, myChannelType);
if (subscriptionTypeApplies == false) {
return;
}
IPrimitiveType<?> status = myCtx.newTerser().getSingleValueOrNull(theSubscription, BaseSubscriptionInterceptor.SUBSCRIPTION_STATUS, IPrimitiveType.class);
final IPrimitiveType<?> status = myCtx.newTerser().getSingleValueOrNull(theSubscription, BaseSubscriptionInterceptor.SUBSCRIPTION_STATUS, IPrimitiveType.class);
String statusString = status.getValueAsString();
String requestedStatus = Subscription.SubscriptionStatus.REQUESTED.toCode();
String activeStatus = Subscription.SubscriptionStatus.ACTIVE.toCode();
final String requestedStatus = Subscription.SubscriptionStatus.REQUESTED.toCode();
final String activeStatus = Subscription.SubscriptionStatus.ACTIVE.toCode();
if (requestedStatus.equals(statusString)) {
TransactionSynchronizationManager.registerSynchronization(new TransactionSynchronizationAdapter() {
@Override
public void afterCommit() {
status.setValueAsString(activeStatus);
ourLog.info("Activating and registering subscription {} from status {} to {}", theSubscription.getIdElement().toUnqualified().getValue(), requestedStatus, activeStatus);
mySubscriptionDao.update(theSubscription);
mySubscriptionInterceptor.registerSubscription(theSubscription.getIdElement(), theSubscription);
}
});
} else if (activeStatus.equals(statusString)) {
if (!mySubscriptionInterceptor.hasSubscription(theSubscription.getIdElement())) {
ourLog.info("Registering active subscription {}", theSubscription.getIdElement().toUnqualified().getValue());

16
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -8,6 +8,7 @@ import java.util.concurrent.TimeUnit;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.springframework.context.annotation.*;
@ -35,7 +36,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
}
@Bean()
public DataSource dataSource() {
public BasicDataSource basicDataSource() {
BasicDataSource retVal = new BasicDataSource() {
@ -92,13 +93,20 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
* and catch any potential deadlocks caused by database connection
* starvation
*/
int maxThreads = (int) (Math.random() * 6) + 1;
int maxThreads = (int) (Math.random() * 6.0) + 1;
retVal.setMaxTotal(maxThreads);
return retVal;
}
@Bean()
@Primary()
public DataSource dataSource() {
DataSource dataSource = ProxyDataSourceBuilder
.create(retVal)
.create(basicDataSource())
// .logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
.logSlowQueryBySlf4j(100, TimeUnit.MILLISECONDS)
.logSlowQueryBySlf4j(1000, TimeUnit.MILLISECONDS)
.countQuery()
.build();

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -94,12 +94,12 @@ public class TestR4Config extends BaseJavaConfigR4 {
* and catch any potential deadlocks caused by database connection
* starvation
*/
int maxThreads = (int) (Math.random() * 6) + 1;
int maxThreads = (int) (Math.random() * 6.0) + 1;
retVal.setMaxTotal(maxThreads);
DataSource dataSource = ProxyDataSourceBuilder
.create(retVal)
.logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
// .logQueryBySlf4j(SLF4JLogLevel.INFO, "SQL")
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
.countQuery(new ThreadQueryCountHolder())
.build();

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java
View File

@ -921,7 +921,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
List<Patient> patients = toList(myPatientDao.search(params));
assertEquals(1, patients.size());
assertEquals(id1.getIdPart(), patients.get(0).getId().getIdPart());
assertEquals("P1TITLE", ResourceMetadataKeyEnum.TITLE.get(patients.get(0)));
// Given name shouldn't return for family param
params = new SearchParameterMap();

153
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirDaoConcurrencyDstu3Test.java Normal file
View File

@ -0,0 +1,153 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.util.TestUtil;
import com.phloc.commons.compare.ReverseComparator;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hl7.fhir.dstu3.model.Bundle;
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.Organization;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.util.comparator.ComparableComparator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.concurrent.Future;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import static org.junit.Assert.*;
public class FhirDaoConcurrencyDstu3Test extends BaseJpaDstu3SystemTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirDaoConcurrencyDstu3Test.class);
@Autowired
public BasicDataSource myBasicDataSource;
private int myMaxTotal;
@After
public void afterResetConnectionPool() {
myBasicDataSource.setMaxTotal(myMaxTotal);
}
@Before
public void beforeSetUpConnectionPool() {
myMaxTotal = myBasicDataSource.getMaxTotal();
myBasicDataSource.setMaxTotal(5);
}
@Test
public void testMultipleConcurrentWritesToSameResource() throws InterruptedException {
ThreadPoolExecutor exec = new ThreadPoolExecutor(10, 10,
0L, TimeUnit.MILLISECONDS,
new LinkedBlockingQueue<Runnable>());
final AtomicInteger errors = new AtomicInteger();
List<Future> futures = new ArrayList<>();
for (int i = 0; i < 50; i++) {
final Patient p = new Patient();
p.setId("PID");
p.setActive(true);
p.setBirthDate(new Date());
p.addIdentifier().setSystem("foo1");
p.addIdentifier().setSystem("foo2");
p.addIdentifier().setSystem("foo3");
p.addIdentifier().setSystem("foo4");
p.addName().setFamily("FOO" + i);
p.addName().addGiven("AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBB1");
p.addName().addGiven("AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBB2");
p.addName().addGiven("AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBB3");
p.addName().addGiven("AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBB4");
p.addName().addGiven("AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBB5");
p.addName().addGiven("AAAAABBBBBBBBBBBBBBBBBBBBBBBBBBBB6");
Organization o = new Organization();
o.setName("ORG" + i);
final Bundle t = new Bundle();
t.setType(BundleType.TRANSACTION);
t.addEntry()
.setResource(p)
.getRequest()
.setUrl("Patient/PID")
.setMethod(HTTPVerb.PUT);
t.addEntry()
.setResource(o)
.getRequest()
.setUrl("Organization")
.setMethod(HTTPVerb.POST);
if (i == 0) {
mySystemDao.transaction(mySrd, t);
}
futures.add(exec.submit(new Runnable() {
@Override
public void run() {
try {
mySystemDao.transaction(mySrd, t);
} catch (Exception e) {
ourLog.error("Failed to update", e);
errors.incrementAndGet();
}
}
}));
}
ourLog.info("Shutting down excutor");
StopWatch sw = new StopWatch();
for (Future next : futures) {
while (!next.isDone()) {
Thread.sleep(20);
}
}
exec.shutdown();
ourLog.info("Shut down excutor in {}ms", sw.getMillis());
ourLog.info("Had {} errors", errors.get());
Patient currentPatient = myPatientDao.read(new IdType("Patient/PID"));
Long currentVersion = currentPatient.getIdElement().getVersionIdPartAsLong();
ourLog.info("Current version: {}", currentVersion);
IBundleProvider historyBundle = myPatientDao.history(new IdType("Patient/PID"),null,null,mySrd);
List<IBaseResource> resources = historyBundle.getResources(0, 1000);
List<Long> versions = new ArrayList<>();
for (IBaseResource next : resources) {
versions.add(next.getIdElement().getVersionIdPartAsLong());
}
String message = "Current version is " + currentVersion + " - History is: " + versions;
ourLog.info(message);
Collections.sort(versions, new ReverseComparator<>(new ComparableComparator<Long>()));
Long lastVersion = versions.get(0);
ourLog.info("Last version: {}", lastVersion);
//assertEquals(message, currentVersion.intValue(), versions.size());
assertEquals(message, currentVersion, lastVersion);
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java
View File

@ -252,6 +252,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
p.setId("Patient/A");
String id = myPatientDao.update(p).getId().getValue();
assertThat(id, endsWith("Patient/A/_history/1"));
assertEquals("1", myPatientDao.read(new IdType("Patient/A")).getIdElement().getVersionIdPart());
// Second time should not result in an update
p = new Patient();
@ -259,6 +260,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
p.setId("Patient/A");
id = myPatientDao.update(p).getId().getValue();
assertThat(id, endsWith("Patient/A/_history/1"));
assertEquals("1", myPatientDao.read(new IdType("Patient/A")).getIdElement().getVersionIdPart());
// And third time should not result in an update
p = new Patient();
@ -266,6 +268,7 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
p.setId("Patient/A");
id = myPatientDao.update(p).getId().getValue();
assertThat(id, endsWith("Patient/A/_history/1"));
assertEquals("1", myPatientDao.read(new IdType("Patient/A")).getIdElement().getVersionIdPart());
myPatientDao.read(new IdType("Patient/A"));
myPatientDao.read(new IdType("Patient/A/_history/1"));

82
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -62,43 +62,6 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
public void testTransactionWhichFailsPersistsNothing() {
// Run a transaction which points to that practitioner
// in a field that isn't allowed to refer to a practitioner
Bundle input = new Bundle();
input.setType(BundleType.TRANSACTION);
Patient pt = new Patient();
pt.setId("PT");
pt.setActive(true);
pt.addName().setFamily("FAMILY");
input.addEntry()
.setResource(pt)
.getRequest().setMethod(HTTPVerb.PUT).setUrl("Patient/PT");
Observation obs = new Observation();
obs.setId("OBS");
obs.getCode().addCoding().setSystem("foo").setCode("bar");
obs.addPerformer().setReference("Practicioner/AAAAA");
input.addEntry()
.setResource(obs)
.getRequest().setMethod(HTTPVerb.PUT).setUrl("Observation/OBS");
try {
mySystemDao.transaction(mySrd, input);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Resource type 'Practicioner' is not valid for this path"));
}
assertThat(myResourceTableDao.findAll(), empty());
assertThat(myResourceIndexedSearchParamStringDao.findAll(), empty());
}
private Bundle createInputTransactionWithPlaceholderIdInMatchUrl(HTTPVerb theVerb) {
Patient pat = new Patient();
@ -209,6 +172,11 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
return null;
}
private Bundle loadBundle(String theFileName) throws IOException {
String req = IOUtils.toString(FhirSystemDaoDstu3Test.class.getResourceAsStream(theFileName), StandardCharsets.UTF_8);
return myFhirCtx.newXmlParser().parseResource(Bundle.class, req);
}
@Test
public void testBatchCreateWithBadRead() {
Bundle request = new Bundle();
@ -1222,8 +1190,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
@Test
public void testTransactionCreateWithPutUsingUrl2() throws Exception {
String req = IOUtils.toString(FhirSystemDaoDstu3Test.class.getResourceAsStream("/bundle-dstu3.xml"), StandardCharsets.UTF_8);
Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, req);
Bundle request = loadBundle("/bundle-dstu3.xml");
mySystemDao.transaction(mySrd, request);
}
@ -2147,6 +2114,42 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
}
}
@Test
public void testTransactionWhichFailsPersistsNothing() {
// Run a transaction which points to that practitioner
// in a field that isn't allowed to refer to a practitioner
Bundle input = new Bundle();
input.setType(BundleType.TRANSACTION);
Patient pt = new Patient();
pt.setId("PT");
pt.setActive(true);
pt.addName().setFamily("FAMILY");
input.addEntry()
.setResource(pt)
.getRequest().setMethod(HTTPVerb.PUT).setUrl("Patient/PT");
Observation obs = new Observation();
obs.setId("OBS");
obs.getCode().addCoding().setSystem("foo").setCode("bar");
obs.addPerformer().setReference("Practicioner/AAAAA");
input.addEntry()
.setResource(obs)
.getRequest().setMethod(HTTPVerb.PUT).setUrl("Observation/OBS");
try {
mySystemDao.transaction(mySrd, input);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Resource type 'Practicioner' is not valid for this path"));
}
assertThat(myResourceTableDao.findAll(), empty());
assertThat(myResourceIndexedSearchParamStringDao.findAll(), empty());
}
/**
* Format changed, source isn't valid
*/
@ -2815,6 +2818,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java
View File

@ -303,7 +303,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
Patient pt1 = new Patient();
pt1.setGender(Enumerations.AdministrativeGender.MALE);
pt1.setBirthDateElement(new DateType("2011-01-01"));
IIdType id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
String id1 = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
Patient pt2 = new Patient();
pt2.setGender(Enumerations.AdministrativeGender.MALE);
@ -316,7 +316,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
params.add("birthdate", new DateParam("2011-01-01"));
IBundleProvider results = myPatientDao.search(params);
String searchId = results.getUuid();
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1));
assertEquals(SearchBuilder.HandlerTypeEnum.UNIQUE_INDEX, SearchBuilder.getLastHandlerMechanismForUnitTest());
// Other order
@ -326,7 +326,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
results = myPatientDao.search(params);
assertEquals(searchId, results.getUuid());
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1.getValue()));
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1));
// Null because we just reuse the last search
assertEquals(null, SearchBuilder.getLastHandlerMechanismForUnitTest());

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/BaseResourceProviderDstu2Test.java
View File

@ -24,6 +24,7 @@ import org.eclipse.jetty.servlet.ServletHolder;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.web.context.ContextLoader;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
@ -47,6 +48,7 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
protected static GenericWebApplicationContext ourWebApplicationContext;
protected static SubscriptionRestHookInterceptor ourRestHookSubscriptionInterceptor;
protected static DatabaseBackedPagingProvider ourPagingProvider;
protected static PlatformTransactionManager ourTxManager;
public BaseResourceProviderDstu2Test() {
super();
@ -98,6 +100,7 @@ public abstract class BaseResourceProviderDstu2Test extends BaseJpaDstu2Test {
ourWebApplicationContext.refresh();
ourRestHookSubscriptionInterceptor = ourWebApplicationContext.getBean(SubscriptionRestHookInterceptor.class);
ourTxManager = ourWebApplicationContext.getBean(PlatformTransactionManager.class);
proxyHandler.getServletContext().setAttribute(WebApplicationContext.ROOT_WEB_APPLICATION_CONTEXT_ATTRIBUTE, ourWebApplicationContext);

45
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/StressTestDstu3Test.java
View File

@ -1,33 +1,43 @@
package ca.uhn.fhir.jpa.stresstest;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import java.util.List;
import java.util.UUID;
import ca.uhn.fhir.jpa.provider.dstu3.BaseResourceProviderDstu3Test;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
import org.junit.*;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Patient;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import java.util.List;
import java.util.UUID;
import ca.uhn.fhir.jpa.provider.dstu3.BaseResourceProviderDstu3Test;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.TestUtil;
import static org.junit.Assert.*;
public class StressTestDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StressTestDstu3Test.class);
private RequestValidatingInterceptor myRequestValidatingInterceptor;
@After
public void after() throws Exception {
super.after();
ourRestServer.unregisterInterceptor(myRequestValidatingInterceptor);
}
@Before
public void before() throws Exception {
super.before();
@ -38,13 +48,6 @@ public class StressTestDstu3Test extends BaseResourceProviderDstu3Test {
myRequestValidatingInterceptor.addValidatorModule(module);
}
@After
public void after() throws Exception {
super.after();
ourRestServer.unregisterInterceptor(myRequestValidatingInterceptor);
}
@Test
public void testMultithreadedSearch() throws Exception {
@ -75,7 +78,6 @@ public class StressTestDstu3Test extends BaseResourceProviderDstu3Test {
}
/**
* This test prevents a deadlock that was detected with a large number of
* threads creating resources and blocking on the searchparamcache refreshing
@ -226,4 +228,5 @@ public class StressTestDstu3Test extends BaseResourceProviderDstu3Test {
}
}
}

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/EmailSubscriptionDstu2Test.java
View File

@ -71,6 +71,7 @@ public class EmailSubscriptionDstu2Test extends BaseResourceProviderDstu2Test {
mySubscriber.setEmailSender(emailSender);
mySubscriber.setResourceDaos(myResourceDaos);
mySubscriber.setFhirContext(myFhirCtx);
mySubscriber.setTxManager(ourTxManager);
mySubscriber.start();
ourRestServer.registerInterceptor(mySubscriber);

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/r4/RestHookTestR4Test.java
View File

@ -51,7 +51,9 @@ public class RestHookTestR4Test extends BaseResourceProviderR4Test {
@After
public void afterUnregisterRestHookListener() {
for (IIdType next : mySubscriptionIds) {
ourClient.delete().resourceById(next).execute();
IIdType nextId = next.toUnqualifiedVersionless();
ourLog.info("Deleting: {}", nextId);
ourClient.delete().resourceById(nextId).execute();
}
mySubscriptionIds.clear();

20
hapi-fhir-jpaserver-uhnfhirtest/derby_maintenance.txt
View File

@ -74,4 +74,24 @@ drop table trm_concept cascade constraints;
drop table trm_concept_pc_link cascade constraints;
drop table trm_concept_property cascade constraints;
# Delete all resources
update hfj_res_ver set forced_id_pid = null where res_id in (select res_id from hfj_resource);
update hfj_resource set forced_id_pid = null where res_id in (select res_id from hfj_resource);
delete from hfj_history_tag where res_id in (select res_id from hfj_resource);
delete from hfj_res_ver where res_id in (select res_id from hfj_resource);
delete from hfj_forced_id where resource_pid in (select res_id from hfj_resource);
delete from hfj_res_link where src_resource_id in (select res_id from hfj_resource);
delete from hfj_res_link where target_resource_id in (select res_id from hfj_resource);
delete from hfj_spidx_coords where res_id in (select res_id from hfj_resource);
delete from hfj_spidx_date where res_id in (select res_id from hfj_resource);
delete from hfj_spidx_number where res_id in (select res_id from hfj_resource);
delete from hfj_spidx_quantity where res_id in (select res_id from hfj_resource);
delete from hfj_spidx_string where res_id in (select res_id from hfj_resource);
delete from hfj_spidx_token where res_id in (select res_id from hfj_resource);
delete from hfj_spidx_uri where res_id in (select res_id from hfj_resource);
delete from hfj_res_tag where res_id in (select res_id from hfj_resource);
delete from hfj_search_result where resource_pid in (select res_id from hfj_resource);
delete from hfj_res_param_present where res_id in (select res_id from hfj_resource);
delete from hfj_resource where res_id in (select res_id from hfj_resource);

7
src/changes/changes.xml
View File

@ -42,6 +42,13 @@
<![CDATA[<a href="http://hapifhir.io/doc_jpa.html">JPA Page</a>]]>
for more information.
</action>
<action type="fix">
In certain cases in the JPA server, if multiple threads all attempted to
update the same resource simultaneously, the optimistic lock failure caused
a "gap" in the history numbers to occur. This would then cause a mysterious
failure when trying to update this resource further. This has been
resolved.
</action>
</release>
<release version="3.0.0" date="2017-09-27">
<action type="add">