Address use case where packages include non-conformance resources. Update documentation as well.
This commit is contained in:
ianmarshall
parent
d01c775b99
commit
659e83f451
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@ -139,3 +139,5 @@ None of the limitations listed here are considered permanent. Over time the HAPI
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* **Cross-partition History Operations are not supported**: It is not possible to perform a `_history` operation that spans all partitions (`_history` does work when applied to a single partition however).
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* **Bulk Operations are not partition aware**: Bulk export operations will export data across all partitions.
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* **Package Operations are not partition aware**: Package operations will only affect resources defined in the default partition.
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@ -326,7 +326,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
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private ResourceTable createResourceBinary(IBaseBinary theResourceBinary) {
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if (myPartitionSettings.isPartitioningEnabled()) {
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PackageBinaryRequestDetails myRequestDetails = new PackageBinaryRequestDetails();
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PackageSystemRequestDetails myRequestDetails = new PackageSystemRequestDetails();
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return (ResourceTable) getBinaryDao().create(theResourceBinary, myRequestDetails).getEntity();
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} else {
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return (ResourceTable) getBinaryDao().create(theResourceBinary).getEntity();
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@ -637,7 +637,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
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private void deleteAndExpungeResourceBinary(IIdType theResourceBinaryId, ExpungeOptions theOptions) {
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if (myPartitionSettings.isPartitioningEnabled()) {
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PackageBinaryRequestDetails myRequestDetails = new PackageBinaryRequestDetails();
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PackageSystemRequestDetails myRequestDetails = new PackageSystemRequestDetails();
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getBinaryDao().delete(theResourceBinaryId, myRequestDetails).getEntity();
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getBinaryDao().forceExpungeInExistingTransaction(theResourceBinaryId, theOptions, myRequestDetails);
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} else {
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@ -31,6 +31,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
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import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
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import ca.uhn.fhir.jpa.model.config.PartitionSettings;
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import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
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@ -50,12 +51,12 @@ import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.hl7.fhir.r4.model.Identifier;
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import org.hl7.fhir.utilities.npm.IPackageCacheManager;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.support.TransactionTemplate;
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import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
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import org.hl7.fhir.utilities.npm.NpmPackage;
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import javax.annotation.PostConstruct;
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@ -102,7 +103,8 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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private INpmPackageVersionDao myPackageVersionDao;
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@Autowired
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private ISearchParamRegistry mySearchParamRegistry;
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@Autowired
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private PartitionSettings myPartitionSettings;
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/**
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* Constructor
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*/
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@ -316,19 +318,19 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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private void create(IBaseResource theResource, PackageInstallOutcomeJson theOutcome) {
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IFhirResourceDao dao = myDaoRegistry.getResourceDao(theResource.getClass());
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SearchParameterMap map = createSearchParameterMapFor(theResource);
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IBundleProvider searchResult = dao.search(map);
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IBundleProvider searchResult = searchResource(dao, map);
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if (validForUpload(theResource)) {
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if (searchResult.isEmpty()) {
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ourLog.info("Creating new resource matching {}", map.toNormalizedQueryString(myFhirContext));
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theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
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dao.create(theResource);
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createResource(dao, theResource);
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} else {
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ourLog.info("Updating existing resource matching {}", map.toNormalizedQueryString(myFhirContext));
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theResource.setId(searchResult.getResources(0, 1).get(0).getIdElement().toUnqualifiedVersionless());
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DaoMethodOutcome outcome = dao.update(theResource);
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DaoMethodOutcome outcome = updateResource(dao, theResource);
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if (!outcome.isNop()) {
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theOutcome.incrementResourcesInstalled(myFhirContext.getResourceType(theResource));
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}
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@ -337,6 +339,33 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
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}
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}
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private IBundleProvider searchResource(IFhirResourceDao theDao, SearchParameterMap theMap) {
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if (myPartitionSettings.isPartitioningEnabled()) {
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PackageSystemRequestDetails myRequestDetails = new PackageSystemRequestDetails();
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return theDao.search(theMap, myRequestDetails);
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} else {
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return theDao.search(theMap);
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}
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}
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private void createResource(IFhirResourceDao theDao, IBaseResource theResource) {
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if (myPartitionSettings.isPartitioningEnabled()) {
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PackageSystemRequestDetails myRequestDetails = new PackageSystemRequestDetails();
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theDao.create(theResource, myRequestDetails);
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} else {
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theDao.create(theResource);
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}
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}
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private DaoMethodOutcome updateResource(IFhirResourceDao theDao, IBaseResource theResource) {
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if (myPartitionSettings.isPartitioningEnabled()) {
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PackageSystemRequestDetails myRequestDetails = new PackageSystemRequestDetails();
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return theDao.update(theResource, myRequestDetails);
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} else {
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return theDao.update(theResource);
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}
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}
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boolean validForUpload(IBaseResource theResource) {
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String resourceType = myFhirContext.getResourceType(theResource);
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if ("SearchParameter".equals(resourceType)) {
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@ -5,12 +5,12 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
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import ca.uhn.fhir.interceptor.api.Pointcut;
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import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
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public class PackageBinaryRequestDetails extends SystemRequestDetails {
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/**
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* Constructor
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*
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*/
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public PackageBinaryRequestDetails() {
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/**
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* A RequestDetails implementation to be used when processing resources defined in a package to ensure
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* that they are always queried or updated in the DEFAULT partition if partitioning is enabled.
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*/
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public class PackageSystemRequestDetails extends SystemRequestDetails {
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public PackageSystemRequestDetails() {
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super(new MyInterceptorBroadcaster());
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}
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@ -28,7 +28,6 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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import ca.uhn.fhir.jpa.entity.PartitionEntity;
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import ca.uhn.fhir.jpa.model.config.PartitionSettings;
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import ca.uhn.fhir.jpa.model.util.JpaConstants;
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import ca.uhn.fhir.jpa.packages.PackageBinaryRequestDetails;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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@ -1,9 +1,16 @@
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package ca.uhn.fhir.jpa.partition;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.api.AddProfileTagEnum;
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import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
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import ca.uhn.fhir.interceptor.api.IInterceptorService;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.server.ETagSupportEnum;
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import ca.uhn.fhir.rest.server.ElementsSupportEnum;
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import ca.uhn.fhir.rest.server.IPagingProvider;
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import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
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import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
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import java.io.IOException;
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import java.io.InputStream;
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@ -11,6 +18,12 @@ import java.io.Reader;
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import java.nio.charset.Charset;
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import java.util.List;
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/**
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* A default RequestDetails implementation that can be used for system calls to
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* Resource DAO methods when partitioning is enabled. Using a SystemRequestDetails
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* instance for system calls will ensure that any resource queries or updates will
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* use the DEFAULT partition when partitioninbg is enabled.
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*/
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public class SystemRequestDetails extends RequestDetails {
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public SystemRequestDetails(IInterceptorBroadcaster theInterceptorBroadcaster) {
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super(theInterceptorBroadcaster);
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@ -63,11 +76,59 @@ public class SystemRequestDetails extends RequestDetails {
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@Override
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public IRestfulServerDefaults getServer() {
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return null;
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return new MyRestfulServerDefaults();
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}
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@Override
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public String getServerBaseForRequest() {
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return null;
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}
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private static class MyRestfulServerDefaults implements IRestfulServerDefaults {
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@Override
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public AddProfileTagEnum getAddProfileTag() {
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return null;
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}
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@Override
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public EncodingEnum getDefaultResponseEncoding() {
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return null;
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}
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@Override
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public ETagSupportEnum getETagSupport() {
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return null;
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}
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@Override
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public ElementsSupportEnum getElementsSupport() {
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return null;
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}
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@Override
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public FhirContext getFhirContext() {
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return null;
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}
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@Override
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public List<IServerInterceptor> getInterceptors_() {
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return null;
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}
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@Override
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public IPagingProvider getPagingProvider() {
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return null;
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}
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@Override
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public boolean isDefaultPrettyPrint() {
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return false;
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}
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@Override
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public IInterceptorService getInterceptorService() {
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return null;
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}
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}
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}
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@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.packages;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
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import ca.uhn.fhir.interceptor.api.IInterceptorService;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
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import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
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@ -10,13 +12,18 @@ import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
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import ca.uhn.fhir.jpa.model.entity.NpmPackageEntity;
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import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionEntity;
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import ca.uhn.fhir.jpa.model.entity.NpmPackageVersionResourceEntity;
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import ca.uhn.fhir.jpa.model.util.JpaConstants;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.UriParam;
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import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
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import ca.uhn.fhir.rest.server.RestfulServer;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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import ca.uhn.fhir.test.utilities.JettyUtil;
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import ca.uhn.fhir.test.utilities.ProxyUtil;
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import ca.uhn.fhir.util.JsonUtil;
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@ -63,6 +70,8 @@ import static org.junit.jupiter.api.Assertions.assertArrayEquals;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNull;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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public class NpmR4Test extends BaseJpaR4Test {
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@ -81,6 +90,10 @@ public class NpmR4Test extends BaseJpaR4Test {
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@Autowired
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private INpmPackageVersionResourceDao myPackageVersionResourceDao;
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private FakeNpmServlet myFakeNpmServlet;
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@Autowired
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private IInterceptorService myInterceptorService;
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@Autowired
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private RequestTenantPartitionInterceptor myRequestTenantPartitionInterceptor;
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@BeforeEach
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public void before() throws Exception {
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@ -105,6 +118,8 @@ public class NpmR4Test extends BaseJpaR4Test {
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public void after() throws Exception {
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JettyUtil.closeServer(myServer);
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myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
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myPartitionSettings.setPartitioningEnabled(false);
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myInterceptorService.unregisterInterceptor(myRequestTenantPartitionInterceptor);
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}
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@ -273,6 +288,47 @@ public class NpmR4Test extends BaseJpaR4Test {
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}
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@Test
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public void testInstallR4Package_NonConformanceResources_Partitioned() throws Exception {
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myPartitionSettings.setPartitioningEnabled(true);
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myInterceptorService.registerInterceptor(myRequestTenantPartitionInterceptor);
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myDaoConfig.setAllowExternalReferences(true);
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byte[] bytes = loadClasspathBytes("/packages/test-organizations-package.tgz");
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myFakeNpmServlet.myResponses.put("/test-organizations/1.0.0", bytes);
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List<String> resourceList = new ArrayList<>();
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resourceList.add("Organization");
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PackageInstallationSpec spec = new PackageInstallationSpec().setName("test-organizations").setVersion("1.0.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
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spec.setInstallResourceTypes(resourceList);
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PackageInstallOutcomeJson outcome = igInstaller.install(spec);
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assertEquals(3, outcome.getResourcesInstalled().get("Organization"));
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// Be sure no further communication with the server
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JettyUtil.closeServer(myServer);
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// Search for the installed resources
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mySrd = mock(ServletRequestDetails.class);
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when(mySrd.getTenantId()).thenReturn(JpaConstants.DEFAULT_PARTITION_NAME);
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when(mySrd.getServer()).thenReturn(mock(RestfulServer.class));
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when(mySrd.getInterceptorBroadcaster()).thenReturn(mock(IInterceptorBroadcaster.class));
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runInTransaction(() -> {
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SearchParameterMap map = SearchParameterMap.newSynchronous();
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map.add(Organization.SP_IDENTIFIER, new TokenParam("https://github.com/synthetichealth/synthea", "organization1"));
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IBundleProvider result = myOrganizationDao.search(map, mySrd);
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assertEquals(1, result.sizeOrThrowNpe());
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map = SearchParameterMap.newSynchronous();
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map.add(Organization.SP_IDENTIFIER, new TokenParam("https://github.com/synthetichealth/synthea", "organization2"));
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result = myOrganizationDao.search(map, mySrd);
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assertEquals(1, result.sizeOrThrowNpe());
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map = SearchParameterMap.newSynchronous();
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map.add(Organization.SP_IDENTIFIER, new TokenParam("https://github.com/synthetichealth/synthea", "organization3"));
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result = myOrganizationDao.search(map, mySrd);
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assertEquals(1, result.sizeOrThrowNpe());
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});
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}
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@Test
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public void testInstallR4Package_NoIdentifierNoUrl() throws Exception {
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myDaoConfig.setAllowExternalReferences(true);
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