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Enable Package Loader when partitioning is enabled with unnamed partitions (#2808) 

* Enable Package Loader when partitioning is enabled with unnamed partitions.

* Enable Package Loader when partitioning is enabled with unnamed partitions.

* Additional package loading problems found with partitioning.

* Additional package loading problems found with partitioning.

Co-authored-by: ianmarshall <ian@simpatico.ai>
This commit is contained in:
IanMMarshall 2021-07-22 05:17:17 -04:00 committed by GitHub
parent 6d37749be8
commit 8b8db82666
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5 changed files with 108 additions and 4 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2808-allow-package-loading-with-unnamed-partitions.yaml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 2808
title: "Loading packages would fail when partitioning was enabled with unnamed partitions. This has been fixed."

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
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@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.packages;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
@ -331,7 +332,11 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
if (myPartitionSettings.isPartitioningEnabled()) {
SystemRequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
if (myPartitionSettings.isUnnamedPartitionMode() && myPartitionSettings.getDefaultPartitionId() != null) {
requestDetails.setRequestPartitionId(RequestPartitionId.fromPartitionId(myPartitionSettings.getDefaultPartitionId()));
} else {
requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
}
return (ResourceTable) getBinaryDao().create(theResourceBinary, requestDetails).getEntity();
} else {
return (ResourceTable) getBinaryDao().create(theResourceBinary).getEntity();

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageInstallerSvcImpl.java
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@ -359,7 +359,6 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
private IBundleProvider searchResource(IFhirResourceDao theDao, SearchParameterMap theMap) {
if (myPartitionSettings.isPartitioningEnabled()) {
SystemRequestDetails requestDetails = new SystemRequestDetails();
// requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
return theDao.search(theMap, requestDetails);
} else {
return theDao.search(theMap);
@ -369,7 +368,6 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
private void createResource(IFhirResourceDao theDao, IBaseResource theResource) {
if (myPartitionSettings.isPartitioningEnabled()) {
SystemRequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
theDao.create(theResource, requestDetails);
} else {
theDao.create(theResource);
@ -379,7 +377,6 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
private DaoMethodOutcome updateResource(IFhirResourceDao theDao, IBaseResource theResource) {
if (myPartitionSettings.isPartitioningEnabled()) {
SystemRequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setTenantId(JpaConstants.DEFAULT_PARTITION_NAME);
return theDao.update(theResource, requestDetails);
} else {
return theDao.update(theResource);

33
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/JpaPackageCacheTest.java
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@ -45,6 +45,7 @@ public class JpaPackageCacheTest extends BaseJpaR4Test {
public void disablePartitioning() {
myPartitionSettings.setPartitioningEnabled(false);
myPartitionSettings.setDefaultPartitionId(new PartitionSettings().getDefaultPartitionId());
myPartitionSettings.setUnnamedPartitionMode(false);
myInterceptorService.unregisterInterceptor(myRequestTenantPartitionInterceptor);
}
@ -103,6 +104,38 @@ public class JpaPackageCacheTest extends BaseJpaR4Test {
assertEquals("Deleting package basisprofil.de#0.2.40", deleteOutcomeMsgs.get(0));
}
@Test
public void testSaveAndDeletePackageUnnamedPartitionsEnabled() throws IOException {
myPartitionSettings.setPartitioningEnabled(true);
myPartitionSettings.setDefaultPartitionId(0);
myPartitionSettings.setUnnamedPartitionMode(true);
myInterceptorService.registerInterceptor(new PatientIdPartitionInterceptor());
myInterceptorService.registerInterceptor(myRequestTenantPartitionInterceptor);
try (InputStream stream = ClasspathUtil.loadResourceAsStream("/packages/hl7.fhir.uv.shorthand-0.12.0.tgz")) {
myPackageCacheManager.addPackageToCache("hl7.fhir.uv.shorthand", "0.12.0", stream, "hl7.fhir.uv.shorthand");
}
NpmPackage pkg;
pkg = myPackageCacheManager.loadPackage("hl7.fhir.uv.shorthand", null);
assertEquals("0.12.0", pkg.version());
pkg = myPackageCacheManager.loadPackage("hl7.fhir.uv.shorthand", "0.12.0");
assertEquals("0.12.0", pkg.version());
try {
myPackageCacheManager.loadPackage("hl7.fhir.uv.shorthand", "99");
fail();
} catch (ResourceNotFoundException e) {
assertEquals("Unable to locate package hl7.fhir.uv.shorthand#99", e.getMessage());
}
PackageDeleteOutcomeJson deleteOutcomeJson = myPackageCacheManager.uninstallPackage("hl7.fhir.uv.shorthand", "0.12.0");
List<String> deleteOutcomeMsgs = deleteOutcomeJson.getMessage();
assertEquals("Deleting package hl7.fhir.uv.shorthand#0.12.0", deleteOutcomeMsgs.get(0));
}
@Test
public void testSavePackageWithLongDescription() throws IOException {
try (InputStream stream = ClasspathUtil.loadResourceAsStream("/packages/package-davinci-cdex-0.2.0.tgz")) {

65
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
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@ -10,6 +10,7 @@ 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.dao.r4.BaseJpaR4Test;
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;
@ -127,6 +128,8 @@ public class NpmR4Test extends BaseJpaR4Test {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(new DaoConfig().isAutoCreatePlaceholderReferenceTargets());
myPartitionSettings.setPartitioningEnabled(false);
myPartitionSettings.setUnnamedPartitionMode(false);
myPartitionSettings.setDefaultPartitionId(new PartitionSettings().getDefaultPartitionId());
myInterceptorService.unregisterInterceptor(myRequestTenantPartitionInterceptor);
}
@ -451,6 +454,31 @@ public class NpmR4Test extends BaseJpaR4Test {
}
@Test
public void testInstallR4Package_Twice_partitioningEnabled() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
myPartitionSettings.setPartitioningEnabled(true);
myInterceptorService.registerInterceptor(myRequestTenantPartitionInterceptor);
byte[] bytes = loadClasspathBytes("/packages/hl7.fhir.uv.shorthand-0.12.0.tgz");
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
PackageInstallOutcomeJson outcome;
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
outcome = myPackageInstallerSvc.install(spec);
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
myPackageInstallerSvc.install(spec);
outcome = myPackageInstallerSvc.install(spec);
assertEquals(null, outcome.getResourcesInstalled().get("CodeSystem"));
// Ensure that we loaded the contents
IBundleProvider searchResult = myCodeSystemDao.search(SearchParameterMap.newSynchronous("url", new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system")));
assertEquals(1, searchResult.sizeOrThrowNpe());
}
@Test
public void testInstallR4PackageWithNoDescription() throws Exception {
@ -801,6 +829,43 @@ public class NpmR4Test extends BaseJpaR4Test {
});
}
@Test
public void testInstallPkgContainingNonPartitionedResourcesPartitionsEnabled() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
myPartitionSettings.setPartitioningEnabled(true);
myInterceptorService.registerInterceptor(myRequestTenantPartitionInterceptor);
byte[] bytes = loadClasspathBytes("/packages/test-logical-structuredefinition.tgz");
myFakeNpmServlet.myResponses.put("/test-logical-structuredefinition/1.0.0", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-logical-structuredefinition").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
assertEquals(2, outcome.getResourcesInstalled().get("StructureDefinition"));
// Be sure no further communication with the server
JettyUtil.closeServer(myServer);
// Search for the installed resource
runInTransaction(() -> {
// Confirm that Laborbefund (a logical StructureDefinition) was created without a snapshot.
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add(StructureDefinition.SP_URL, new UriParam("https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/LogicalModel/Laborbefund"));
IBundleProvider result = myStructureDefinitionDao.search(map);
assertEquals(1, result.sizeOrThrowNpe());
List<IBaseResource> resources = result.getResources(0,1);
assertFalse(((StructureDefinition)resources.get(0)).hasSnapshot());
// Confirm that DiagnosticLab (a resource StructureDefinition with differential but no snapshot) was created with a generated snapshot.
map = SearchParameterMap.newSynchronous();
map.add(StructureDefinition.SP_URL, new UriParam("https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/DiagnosticReportLab"));
result = myStructureDefinitionDao.search(map);
assertEquals(1, result.sizeOrThrowNpe());
resources = result.getResources(0,1);
assertTrue(((StructureDefinition)resources.get(0)).hasSnapshot());
});
}
static class FakeNpmServlet extends HttpServlet {
private final Map<String, byte[]> myResponses = new HashMap<>();