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Fixed package loading to enable loading of binary package files into the default partition when partitioning is enabled.

This commit is contained in:
ianmarshall 2021-01-05 17:51:04 -05:00
parent 86f254cd66
commit 446dd5c782
5 changed files with 193 additions and 14 deletions
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37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
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@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionResourceDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.NpmPackageEntity;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionResourceEntity;
@ -54,6 +55,7 @@ import org.apache.http.impl.conn.BasicHttpClientConnectionManager;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseBinary;
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.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -115,6 +117,8 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
private FhirContext myCtx;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private PartitionSettings myPartitionSettings;
@Override
public NpmPackage loadPackageFromCacheOnly(String theId, @Nullable String theVersion) {
@ -205,7 +209,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
return newTxTemplate().execute(tx -> {
ResourceTable persistedPackage = (ResourceTable) getBinaryDao().create(binary).getEntity();
ResourceTable persistedPackage = createResourceBinary(binary);
NpmPackageEntity pkg = myPackageDao.findByPackageId(thePackageId).orElseGet(() -> createPackage(npmPackage));
NpmPackageVersionEntity packageVersion = myPackageVersionDao.findByPackageIdAndVersion(thePackageId, packageVersionId).orElse(null);
if (packageVersion != null) {
@ -282,7 +286,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
byte[] minimizedContents = packageContext.newJsonParser().encodeResourceToString(resource).getBytes(StandardCharsets.UTF_8);
IBaseBinary resourceBinary = createPackageResourceBinary(nextFile, minimizedContents, contentType);
ResourceTable persistedResource = (ResourceTable) getBinaryDao().create(resourceBinary).getEntity();
ResourceTable persistedResource = createResourceBinary(resourceBinary);
NpmPackageVersionResourceEntity resourceEntity = new NpmPackageVersionResourceEntity();
resourceEntity.setPackageVersion(packageVersion);
@ -319,6 +323,16 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
}
private ResourceTable createResourceBinary(IBaseBinary theResourceBinary) {
if (myPartitionSettings.isPartitioningEnabled()) {
PackageBinaryRequestDetails myRequestDetails = new PackageBinaryRequestDetails();
return (ResourceTable) getBinaryDao().create(theResourceBinary, myRequestDetails).getEntity();
} else {
return (ResourceTable) getBinaryDao().create(theResourceBinary).getEntity();
}
}
private boolean updateCurrentVersionFlagForAllPackagesBasedOnNewIncomingVersion(String thePackageId, String thePackageVersion) {
Collection<NpmPackageVersionEntity> existingVersions = myPackageVersionDao.findByPackageId(thePackageId);
boolean retVal = true;
@ -578,16 +592,14 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
ExpungeOptions options = new ExpungeOptions();
options.setExpungeDeletedResources(true).setExpungeOldVersions(true);
getBinaryDao().delete(next.getResourceBinary().getIdDt().toVersionless());
getBinaryDao().forceExpungeInExistingTransaction(next.getResourceBinary().getIdDt().toVersionless(), options, null);
deleteAndExpungeResourceBinary(next.getResourceBinary().getIdDt().toVersionless(), options);
}
myPackageVersionDao.delete(packageVersion.get());
ExpungeOptions options = new ExpungeOptions();
options.setExpungeDeletedResources(true).setExpungeOldVersions(true);
getBinaryDao().delete(packageVersion.get().getPackageBinary().getIdDt().toVersionless());
getBinaryDao().forceExpungeInExistingTransaction(packageVersion.get().getPackageBinary().getIdDt().toVersionless(), options, null);
deleteAndExpungeResourceBinary(packageVersion.get().getPackageBinary().getIdDt().toVersionless(), options);
Collection<NpmPackageVersionEntity> remainingVersions = myPackageVersionDao.findByPackageId(thePackageId);
if (remainingVersions.size() == 0) {
@ -622,6 +634,19 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
return retVal;
}
private void deleteAndExpungeResourceBinary(IIdType theResourceBinaryId, ExpungeOptions theOptions) {
if (myPartitionSettings.isPartitioningEnabled()) {
PackageBinaryRequestDetails myRequestDetails = new PackageBinaryRequestDetails();
getBinaryDao().delete(theResourceBinaryId, myRequestDetails).getEntity();
getBinaryDao().forceExpungeInExistingTransaction(theResourceBinaryId, theOptions, myRequestDetails);
} else {
getBinaryDao().delete(theResourceBinaryId).getEntity();
getBinaryDao().forceExpungeInExistingTransaction(theResourceBinaryId, theOptions, null);
}
}
@Nonnull
public List<Predicate> createSearchPredicates(PackageSearchSpec thePackageSearchSpec, CriteriaBuilder theCb, Root<NpmPackageVersionEntity> theRoot) {
List<Predicate> predicates = new ArrayList<>();

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageBinaryRequestDetails.java Normal file
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@ -0,0 +1,35 @@
package ca.uhn.fhir.jpa.packages;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
public class PackageBinaryRequestDetails extends SystemRequestDetails {
/**
* Constructor
*
*/
public PackageBinaryRequestDetails() {
super(new MyInterceptorBroadcaster());
}
private static class MyInterceptorBroadcaster implements IInterceptorBroadcaster {
@Override
public boolean callHooks(Pointcut thePointcut, HookParams theParams) {
return true;
}
@Override
public Object callHooksAndReturnObject(Pointcut thePointcut, HookParams theParams) {
return null;
}
@Override
public boolean hasHooks(Pointcut thePointcut) {
return false;
}
}
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvc.java
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@ -28,6 +28,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.packages.PackageBinaryRequestDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -68,14 +69,20 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
myPartitioningBlacklist.add("Subscription");
myPartitioningBlacklist.add("SearchParameter");
// Validation
// Validation and Conformance
myPartitioningBlacklist.add("StructureDefinition");
myPartitioningBlacklist.add("Questionnaire");
myPartitioningBlacklist.add("CapabilityStatement");
myPartitioningBlacklist.add("CompartmentDefinition");
myPartitioningBlacklist.add("OperationDefinition");
// Terminology
myPartitioningBlacklist.add("ConceptMap");
myPartitioningBlacklist.add("CodeSystem");
myPartitioningBlacklist.add("ValueSet");
myPartitioningBlacklist.add("NamingSystem");
myPartitioningBlacklist.add("StructureMap");
}
/**
@ -91,7 +98,7 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
if (myPartitionSettings.isPartitioningEnabled()) {
// Handle system requests
if (theRequest == null && myPartitioningBlacklist.contains(theResourceType)) {
if ((theRequest == null && myPartitioningBlacklist.contains(theResourceType)) || theRequest instanceof SystemRequestDetails) {
return RequestPartitionId.defaultPartition();
}
@ -123,7 +130,7 @@ public class RequestPartitionHelperSvc implements IRequestPartitionHelperSvc {
if (myPartitionSettings.isPartitioningEnabled()) {
// Handle system requests
if (theRequest == null && myPartitioningBlacklist.contains(theResourceType)) {
if ((theRequest == null && myPartitioningBlacklist.contains(theResourceType)) || theRequest instanceof SystemRequestDetails) {
return RequestPartitionId.defaultPartition();
}

73
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/SystemRequestDetails.java Normal file
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@ -0,0 +1,73 @@
package ca.uhn.fhir.jpa.partition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.nio.charset.Charset;
import java.util.List;
public class SystemRequestDetails extends RequestDetails {
public SystemRequestDetails(IInterceptorBroadcaster theInterceptorBroadcaster) {
super(theInterceptorBroadcaster);
}
@Override
protected byte[] getByteStreamRequestContents() {
return new byte[0];
}
@Override
public Charset getCharset() {
return null;
}
@Override
public FhirContext getFhirContext() {
return null;
}
@Override
public String getHeader(String name) {
return null;
}
@Override
public List<String> getHeaders(String name) {
return null;
}
@Override
public Object getAttribute(String theAttributeName) {
return null;
}
@Override
public void setAttribute(String theAttributeName, Object theAttributeValue) {
}
@Override
public InputStream getInputStream() throws IOException {
return null;
}
@Override
public Reader getReader() throws IOException {
return null;
}
@Override
public IRestfulServerDefaults getServer() {
return null;
}
@Override
public String getServerBaseForRequest() {
return null;
}
}

49
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/JpaPackageCacheTest.java
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@ -1,21 +1,20 @@
package ca.uhn.fhir.jpa.packages;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.JsonUtil;
import org.hl7.fhir.utilities.npm.IPackageCacheManager;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
@ -28,6 +27,16 @@ public class JpaPackageCacheTest extends BaseJpaR4Test {
private INpmPackageDao myPackageDao;
@Autowired
private INpmPackageVersionDao myPackageVersionDao;
@Autowired
private IInterceptorService myInterceptorService;
@Autowired
private RequestTenantPartitionInterceptor myRequestTenantPartitionInterceptor;
@AfterEach
public void disablePartitioning() {
myPartitionSettings.setPartitioningEnabled(false);
myInterceptorService.unregisterInterceptor(myRequestTenantPartitionInterceptor);
}
@Test
@ -53,6 +62,36 @@ public class JpaPackageCacheTest extends BaseJpaR4Test {
}
@Test
public void testSaveAndDeletePackagePartitionsEnabled() throws IOException {
myPartitionSettings.setPartitioningEnabled(true);
myInterceptorService.registerInterceptor(myRequestTenantPartitionInterceptor);
try (InputStream stream = IgInstallerDstu3Test.class.getResourceAsStream("/packages/basisprofil.de.tar.gz")) {
myPackageCacheManager.addPackageToCache("basisprofil.de", "0.2.40", stream, "basisprofil.de");
}
NpmPackage pkg;
pkg = myPackageCacheManager.loadPackage("basisprofil.de", null);
assertEquals("0.2.40", pkg.version());
pkg = myPackageCacheManager.loadPackage("basisprofil.de", "0.2.40");
assertEquals("0.2.40", pkg.version());
try {
myPackageCacheManager.loadPackage("basisprofil.de", "99");
fail();
} catch (ResourceNotFoundException e) {
assertEquals("Unable to locate package basisprofil.de#99", e.getMessage());
}
PackageDeleteOutcomeJson deleteOutcomeJson = myPackageCacheManager.uninstallPackage("basisprofil.de", "0.2.40");
List<String> deleteOutcomeMsgs = deleteOutcomeJson.getMessage();
assertEquals("Deleting package basisprofil.de#0.2.40", deleteOutcomeMsgs.get(0));
}
@Test
public void testSavePackageWithLongDescription() throws IOException {
try (InputStream stream = IgInstallerDstu3Test.class.getResourceAsStream("/packages/package-davinci-cdex-0.2.0.tgz")) {