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Merge branch 'master' into add-attribution-for-gotoguy

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Tadgh 2021-09-01 16:42:19 -04:00 committed by GitHub
parent ae2c752c55 7e80461e77
commit ee956929f9
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5 changed files with 164 additions and 72 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2935-Search-with-trailing-percent-sign.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 2935
jira: SMILE-3022
title: "No resource returned when search with percent sign. Problem is now fixed"

154
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
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@ -65,6 +65,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -100,6 +101,9 @@ public class ExpungeEverythingService {
private TransactionTemplate myTxTemplate;
@Autowired
private MemoryCacheService myMemoryCacheService;
@PostConstruct
public void initTxTemplate() {
myTxTemplate = new TransactionTemplate(myPlatformTransactionManager);
@ -122,37 +126,37 @@ public class ExpungeEverythingService {
counter.addAndGet(doExpungeEverythingQuery("UPDATE " + TermCodeSystem.class.getSimpleName() + " d SET d.myCurrentVersion = null"));
return null;
});
counter.addAndGet(expungeEverythingByType(NpmPackageVersionResourceEntity.class));
counter.addAndGet(expungeEverythingByType(NpmPackageVersionEntity.class));
counter.addAndGet(expungeEverythingByType(NpmPackageEntity.class));
counter.addAndGet(expungeEverythingByType(SearchParamPresent.class));
counter.addAndGet(expungeEverythingByType(BulkImportJobFileEntity.class));
counter.addAndGet(expungeEverythingByType(BulkImportJobEntity.class));
counter.addAndGet(expungeEverythingByType(ForcedId.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamDate.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamNumber.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamQuantity.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamQuantityNormalized.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamString.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamToken.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamUri.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamCoords.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedComboStringUnique.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedComboTokenNonUnique.class));
counter.addAndGet(expungeEverythingByType(ResourceLink.class));
counter.addAndGet(expungeEverythingByType(SearchResult.class));
counter.addAndGet(expungeEverythingByType(SearchInclude.class));
counter.addAndGet(expungeEverythingByType(TermValueSetConceptDesignation.class));
counter.addAndGet(expungeEverythingByType(TermValueSetConcept.class));
counter.addAndGet(expungeEverythingByType(TermValueSet.class));
counter.addAndGet(expungeEverythingByType(TermConceptParentChildLink.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElementTarget.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElement.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroup.class));
counter.addAndGet(expungeEverythingByType(TermConceptMap.class));
counter.addAndGet(expungeEverythingByType(TermConceptProperty.class));
counter.addAndGet(expungeEverythingByType(TermConceptDesignation.class));
counter.addAndGet(expungeEverythingByType(TermConcept.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageVersionResourceEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageVersionEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchParamPresent.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(BulkImportJobFileEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(BulkImportJobEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ForcedId.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamDate.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamNumber.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamQuantity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamQuantityNormalized.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamString.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamToken.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamUri.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamCoords.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedComboStringUnique.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedComboTokenNonUnique.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceLink.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchResult.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchInclude.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermValueSetConceptDesignation.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermValueSetConcept.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermValueSet.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptParentChildLink.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMapGroupElementTarget.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMapGroupElement.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMapGroup.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMap.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptProperty.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptDesignation.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConcept.class));
myTxTemplate.execute(t -> {
for (TermCodeSystem next : myEntityManager.createQuery("SELECT c FROM " + TermCodeSystem.class.getName() + " c", TermCodeSystem.class).getResultList()) {
next.setCurrentVersion(null);
@ -160,52 +164,66 @@ public class ExpungeEverythingService {
}
return null;
});
counter.addAndGet(expungeEverythingByType(TermCodeSystemVersion.class));
counter.addAndGet(expungeEverythingByType(TermCodeSystem.class));
counter.addAndGet(expungeEverythingByType(SubscriptionTable.class));
counter.addAndGet(expungeEverythingByType(ResourceHistoryTag.class));
counter.addAndGet(expungeEverythingByType(ResourceTag.class));
counter.addAndGet(expungeEverythingByType(TagDefinition.class));
counter.addAndGet(expungeEverythingByType(ResourceHistoryProvenanceEntity.class));
counter.addAndGet(expungeEverythingByType(ResourceHistoryTable.class));
counter.addAndGet(expungeEverythingByType(ResourceTable.class));
counter.addAndGet(expungeEverythingByType(PartitionEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermCodeSystemVersion.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermCodeSystem.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SubscriptionTable.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceHistoryTag.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceTag.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TagDefinition.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceHistoryProvenanceEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceHistoryTable.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceTable.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(PartitionEntity.class));
myTxTemplate.execute(t -> {
counter.addAndGet(doExpungeEverythingQuery("DELETE from " + Search.class.getSimpleName() + " d"));
return null;
});
purgeAllCaches();
ourLog.info("COMPLETED GLOBAL $expunge - Deleted {} rows", counter.get());
}
private void purgeAllCaches() {
myTxTemplate.execute(t -> {
myMemoryCacheService.invalidateAllCaches();
return null;
});
}
private int expungeEverythingByTypeWithoutPurging(Class<?> theEntityType) {
int outcome = 0;
while (true) {
StopWatch sw = new StopWatch();
@SuppressWarnings("ConstantConditions")
int count = myTxTemplate.execute(t -> {
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<?> cq = cb.createQuery(theEntityType);
cq.from(theEntityType);
TypedQuery<?> query = myEntityManager.createQuery(cq);
query.setMaxResults(1000);
List<?> results = query.getResultList();
for (Object result : results) {
myEntityManager.remove(result);
}
return results.size();
});
outcome += count;
if (count == 0) {
break;
}
ourLog.info("Have deleted {} entities of type {} in {}", outcome, theEntityType.getSimpleName(), sw.toString());
}
return outcome;
}
public int expungeEverythingByType(Class<?> theEntityType) {
int outcome = 0;
while (true) {
StopWatch sw = new StopWatch();
@SuppressWarnings("ConstantConditions")
int count = myTxTemplate.execute(t -> {
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<?> cq = cb.createQuery(theEntityType);
cq.from(theEntityType);
TypedQuery<?> query = myEntityManager.createQuery(cq);
query.setMaxResults(1000);
List<?> results = query.getResultList();
for (Object result : results) {
myEntityManager.remove(result);
}
return results.size();
});
outcome += count;
if (count == 0) {
break;
}
ourLog.info("Have deleted {} entities of type {} in {}", outcome, theEntityType.getSimpleName(), sw.toString());
}
return outcome;
int result = expungeEverythingByTypeWithoutPurging(theEntityType);
purgeAllCaches();
return result;
}
private int doExpungeEverythingQuery(String theQuery) {

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/StringPredicateBuilder.java
View File

@ -225,15 +225,15 @@ public class StringPredicateBuilder extends BaseSearchParamPredicateBuilder {
}
public static String createLeftAndRightMatchLikeExpression(String likeExpression) {
return "%" + likeExpression.replace("%", "[%]") + "%";
return "%" + likeExpression.replace("%", "\\%") + "%";
}
public static String createLeftMatchLikeExpression(String likeExpression) {
return likeExpression.replace("%", "[%]") + "%";
return likeExpression.replace("%", "\\%") + "%";
}
public static String createRightMatchLikeExpression(String likeExpression) {
return "%" + likeExpression.replace("%", "[%]");
return "%" + likeExpression.replace("%", "\\%");
}

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeHookTest.java
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@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.test.concurrency.PointcutLatch;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@ -40,6 +41,8 @@ public class ExpungeHookTest extends BaseJpaDstu3Test {
@BeforeEach
public void before() {
myDaoConfig.setExpungeEnabled(true);
myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ALPHANUMERIC);
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_EVERYTHING, myEverythingLatch);
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE, myExpungeResourceLatch);
}
@ -65,6 +68,42 @@ public class ExpungeHookTest extends BaseJpaDstu3Test {
assertPatientGone(id);
}
@Test
public void expungeEverythingAndRecreate() throws InterruptedException {
// Create a patient.
Patient thePatient = new Patient();
thePatient.setId("ABC123");
Meta theMeta = new Meta();
theMeta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient");
thePatient.setMeta(theMeta);
IIdType id = myPatientDao.update(thePatient, mySrd).getId();
assertNotNull(myPatientDao.read(id));
// Expunge it directly.
myPatientDao.delete(id);
ExpungeOptions options = new ExpungeOptions();
options.setExpungeEverything(true);
options.setExpungeDeletedResources(true);
options.setExpungeOldVersions(true);
myPatientDao.expunge(id.toUnqualifiedVersionless(), options, mySrd);
assertPatientGone(id);
// Create it a second time.
myPatientDao.update(thePatient, mySrd);
assertNotNull(myPatientDao.read(id));
// Expunge everything with the service.
myEverythingLatch.setExpectedCount(1);
myExpungeService.expunge(null, null, null, options, mySrd);
myEverythingLatch.awaitExpected();
assertPatientGone(id);
// Create it a third time.
myPatientDao.update(thePatient, mySrd);
assertNotNull(myPatientDao.read(id));
}
private void assertPatientGone(IIdType theId) {
try {
myPatientDao.read(theId);

32
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
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@ -295,7 +295,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myCaptureQueriesListener.logSelectQueries();
}
@Test
public void testSearchWithContainsLowerCase() {
myDaoConfig.setAllowContainsSearches(true);
@ -333,6 +332,37 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
@Test
public void testSearchWithPercentSign() {
myDaoConfig.setAllowContainsSearches(true);
Patient pt1 = new Patient();
pt1.addName().setFamily("Smith%");
String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
Bundle output = myClient
.search()
.forResource("Patient")
.where(Patient.NAME.contains().value("Smith%"))
.returnBundle(Bundle.class)
.execute();
List<String> ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
assertThat(ids, containsInAnyOrder(pt1id));
Patient pt2 = new Patient();
pt2.addName().setFamily("Sm%ith");
String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
output = myClient
.search()
.forResource("Patient")
.where(Patient.NAME.contains().value("Sm%ith"))
.returnBundle(Bundle.class)
.execute();
ids = output.getEntry().stream().map(t -> t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).collect(Collectors.toList());
assertThat(ids, containsInAnyOrder(pt2id));
}
@Test
public void testSearchWithDateInvalid() throws IOException {
HttpGet get = new HttpGet(ourServerBase + "/Condition?onset-date=junk");