From c0e929dacb7391074c11b574c8a0d9864edc4ab0 Mon Sep 17 00:00:00 2001 From: James Agnew Date: Tue, 21 Jan 2020 06:09:06 +0900 Subject: [PATCH] Copy identifiers to placeholder resources (#1675) * Copy identifiers to placeholder resources * Add tests * Maven cleanup * Still messing around with azure * Adding to logging * More azure work * One more attempt * More messing around with azure * Test fix * Another caching attempt * More work on azure pipeline * Fix pipeline file * Keep working on pipeline * More work on azure * More azure * More azure work * More azure --- azure-pipelines.yml | 16 +- .../instance/model/api/IBaseReference.java | 5 + .../1675-copy-identifiers-to-placeholder.yaml | 5 + .../ca/uhn/fhir/jpa/dao/BaseStorageDao.java | 4 +- .../java/ca/uhn/fhir/jpa/dao/DaoConfig.java | 180 ++++++++++++++---- .../dao/expunge/ResourceExpungeService.java | 2 +- .../dao/index/DaoResourceLinkResolver.java | 103 +++++++--- ...rchParamWithInlineReferencesExtractor.java | 33 ++-- ...irResourceDaoCreatePlaceholdersR4Test.java | 98 +++++++++- .../extractor/IResourceLinkResolver.java | 3 +- .../extractor/ResourceLinkExtractor.java | 18 +- .../matcher/InlineResourceLinkResolver.java | 5 +- .../ClientServerValidationDstu2Test.java | 4 +- 13 files changed, 382 insertions(+), 94 deletions(-) create mode 100644 hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/1675-copy-identifiers-to-placeholder.yaml diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 80ed24303bd..538bd413388 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -2,7 +2,9 @@ variables: MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository - MAVEN_OPTS: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)' + #MAVEN_CACHE_FOLDER: $(Agent.TempDirectory)/.m2/repository + #MAVEN_OPTS: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)' + MAVEN_OPTS: '' trigger: - master @@ -15,17 +17,21 @@ jobs: timeoutInMinutes: 360 container: maven:3-jdk-11 steps: - - task: CacheBeta@0 + - task: Cache@2 inputs: - key: maven + key: 'maven | "$(Agent.OS)" | **/pom.xml' path: $(MAVEN_CACHE_FOLDER) + - task: Bash@3 + inputs: + targetType: 'inline' + script: mkdir -p $(MAVEN_CACHE_FOLDER); pwd; ls -al $(MAVEN_CACHE_FOLDER) - task: Maven@3 env: JAVA_HOME_11_X64: /usr/local/openjdk-11 inputs: - goals: 'clean dependency:resolve install' + goals: 'clean install' # These are Maven CLI options (and show up in the build logs) - "-nsu"=Don't update snapshots. We can remove this when Maven OSS is more healthy - options: '-P ALLMODULES,JACOCO,CI,ERRORPRONE -nsu' + options: '-P ALLMODULES,JACOCO,CI,ERRORPRONE -nsu -e -B -Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)' # These are JVM options (and don't show up in the build logs) mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto' jdkVersionOption: 1.11 diff --git a/hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseReference.java b/hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseReference.java index 10e5e3c53e3..ea662f49b32 100644 --- a/hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseReference.java +++ b/hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseReference.java @@ -34,4 +34,9 @@ public interface IBaseReference extends ICompositeType { IBase setDisplay(String theValue); IPrimitiveType getDisplayElement(); + + default boolean hasIdentifier() { + return false; + } + } diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/1675-copy-identifiers-to-placeholder.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/1675-copy-identifiers-to-placeholder.yaml new file mode 100644 index 00000000000..df80a4ff2f4 --- /dev/null +++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/1675-copy-identifiers-to-placeholder.yaml @@ -0,0 +1,5 @@ +--- +type: add +title: "In the JPA server, a new setting called `setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean)` has + been added to the DaoConfig. If this setting is enabled, when creating placeholder resources, the Reference.identifier + value is copied to the target resource if possible." diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java index 1667b1264c5..b845ea07598 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java @@ -53,6 +53,7 @@ import java.util.Set; import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_ERROR; import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_INFO; +import static org.apache.commons.lang3.StringUtils.defaultString; import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank; @@ -95,7 +96,8 @@ public abstract class BaseStorageDao { if ("Bundle".equals(type)) { Set allowedBundleTypes = getConfig().getBundleTypesAllowedForStorage(); String bundleType = BundleUtil.getBundleType(getContext(), (IBaseBundle) theResource); - if (isBlank(bundleType) || !allowedBundleTypes.contains(bundleType)) { + bundleType = defaultString(bundleType); + if (!allowedBundleTypes.contains(bundleType)) { String message = "Unable to store a Bundle resource on this server with a Bundle.type value of: " + (isNotBlank(bundleType) ? bundleType : "(missing)"); throw new UnprocessableEntityException(message); } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java index 1c78f6fcaed..6168d8fe5e4 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java @@ -15,7 +15,12 @@ import org.hl7.fhir.r4.model.Bundle; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.Set; +import java.util.TreeSet; /* * #%L @@ -53,12 +58,6 @@ public class DaoConfig { * See {@link #setStatusBasedReindexingDisabled(boolean)} */ public static final String DISABLE_STATUS_BASED_REINDEX = "disable_status_based_reindex"; - /** - * Default value for {@link #setMaximumSearchResultCountInTransaction(Integer)} - * - * @see #setMaximumSearchResultCountInTransaction(Integer) - */ - private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null; /** * Default {@link #setBundleTypesAllowedForStorage(Set)} value: *
    @@ -73,12 +72,16 @@ public class DaoConfig { Bundle.BundleType.DOCUMENT.toCode(), Bundle.BundleType.MESSAGE.toCode() ))); - private static final Logger ourLog = LoggerFactory.getLogger(DaoConfig.class); - private static final int DEFAULT_EXPUNGE_BATCH_SIZE = 800; - // update setter javadoc if default changes public static final int DEFAULT_MAX_EXPANSION_SIZE = 1000; - + /** + * Default value for {@link #setMaximumSearchResultCountInTransaction(Integer)} + * + * @see #setMaximumSearchResultCountInTransaction(Integer) + */ + private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null; + private static final Logger ourLog = LoggerFactory.getLogger(DaoConfig.class); + private static final int DEFAULT_EXPUNGE_BATCH_SIZE = 800; private IndexEnabledEnum myIndexMissingFieldsEnabled = IndexEnabledEnum.DISABLED; /** @@ -175,6 +178,11 @@ public class DaoConfig { */ private int myPreExpandValueSetsMaxCount = 1000; + /** + * @since 4.2.0 + */ + private boolean myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets; + /** * Constructor */ @@ -570,7 +578,7 @@ public class DaoConfig { * the operation will be failed as too costly. Note that this setting applies only to * in-memory expansions and does not apply to expansions that are being pre-calculated. *

    - * The default value for this setting is 1000. + * The default value for this setting is 1000. *

    */ public void setMaximumExpansionSize(int theMaximumExpansionSize) { @@ -993,6 +1001,108 @@ public class DaoConfig { myAutoCreatePlaceholderReferenceTargets = theAutoCreatePlaceholderReferenceTargets; } + /** + * When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this + * setting is set to true (default is false) and the source + * reference has an identifier populated, the identifier will be copied to the target + * resource. + *

    + * When enabled, if an Observation contains a reference like the one below, + * and no existing resource was found that matches the given ID, a new + * one will be created and its Patient.identifier value will be + * populated using the value from Observation.subject.identifier. + *

    + * 
    +	 * {
+	 *   "resourceType": "Observation",
+	 *   "subject": {
+	 *     "reference": "Patient/ABC",
+	 *     "identifier": {
+	 *       "system": "http://foo",
+	 *       "value": "123"
+	 *     }
+	 *   }
+	 * }
+	 *
    + *

    + * This method is often combined with {@link #setAllowInlineMatchUrlReferences(boolean)}. + *

    + *

    + * In other words if an Observation contains a reference like the one below, + * and no existing resource was found that matches the given match URL, a new + * one will be created and its Patient.identifier value will be + * populated using the value from Observation.subject.identifier. + *

    + * 
    +	 * {
+	 *   "resourceType": "Observation",
+	 *   "subject": {
+	 *     "reference": "Patient?identifier=http://foo|123",
+	 *     "identifier": {
+	 *       "system": "http://foo",
+	 *       "value": "123"
+	 *     }
+	 *   }
+	 * }
+	 *
    + * + * @since 4.2.0 + */ + public boolean isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets() { + return myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets; + } + + /** + * When {@link #setAutoCreatePlaceholderReferenceTargets(boolean)} is enabled, if this + * setting is set to true (default is false) and the source + * reference has an identifier populated, the identifier will be copied to the target + * resource. + *

    + * When enabled, if an Observation contains a reference like the one below, + * and no existing resource was found that matches the given ID, a new + * one will be created and its Patient.identifier value will be + * populated using the value from Observation.subject.identifier. + *

    + * 
    +	 * {
+	 *   "resourceType": "Observation",
+	 *   "subject": {
+	 *     "reference": "Patient/ABC",
+	 *     "identifier": {
+	 *       "system": "http://foo",
+	 *       "value": "123"
+	 *     }
+	 *   }
+	 * }
+	 *
    + *

    + * This method is often combined with {@link #setAllowInlineMatchUrlReferences(boolean)}. + *

    + *

    + * In other words if an Observation contains a reference like the one below, + * and no existing resource was found that matches the given match URL, a new + * one will be created and its Patient.identifier value will be + * populated using the value from Observation.subject.identifier. + *

    + * 
    +	 * {
+	 *   "resourceType": "Observation",
+	 *   "subject": {
+	 *     "reference": "Patient?identifier=http://foo|123",
+	 *     "identifier": {
+	 *       "system": "http://foo",
+	 *       "value": "123"
+	 *     }
+	 *   }
+	 * }
+	 *
    + * + * @since 4.2.0 + */ + public void setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(boolean thePopulateIdentifierInAutoCreatedPlaceholderReferenceTargets) { + myPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets = thePopulateIdentifierInAutoCreatedPlaceholderReferenceTargets; + } + /** * If set to false (default is true) resources will be permitted to be * deleted even if other resources currently contain references to them. @@ -1682,29 +1792,6 @@ public class DaoConfig { myStoreMetaSourceInformation = theStoreMetaSourceInformation; } - public enum StoreMetaSourceInformationEnum { - NONE(false, false), - SOURCE_URI(true, false), - REQUEST_ID(false, true), - SOURCE_URI_AND_REQUEST_ID(true, true); - - private final boolean myStoreSourceUri; - private final boolean myStoreRequestId; - - StoreMetaSourceInformationEnum(boolean theStoreSourceUri, boolean theStoreRequestId) { - myStoreSourceUri = theStoreSourceUri; - myStoreRequestId = theStoreRequestId; - } - - public boolean isStoreSourceUri() { - return myStoreSourceUri; - } - - public boolean isStoreRequestId() { - return myStoreRequestId; - } - } - /** *

    * If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate @@ -1820,6 +1907,29 @@ public class DaoConfig { setPreExpandValueSetsDefaultCount(Math.min(getPreExpandValueSetsDefaultCount(), getPreExpandValueSetsMaxCount())); } + public enum StoreMetaSourceInformationEnum { + NONE(false, false), + SOURCE_URI(true, false), + REQUEST_ID(false, true), + SOURCE_URI_AND_REQUEST_ID(true, true); + + private final boolean myStoreSourceUri; + private final boolean myStoreRequestId; + + StoreMetaSourceInformationEnum(boolean theStoreSourceUri, boolean theStoreRequestId) { + myStoreSourceUri = theStoreSourceUri; + myStoreRequestId = theStoreRequestId; + } + + public boolean isStoreSourceUri() { + return myStoreSourceUri; + } + + public boolean isStoreRequestId() { + return myStoreRequestId; + } + } + public enum IndexEnabledEnum { ENABLED, DISABLED diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java index a0ffa1a0dd3..b66dc9b048f 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java @@ -159,7 +159,7 @@ class ResourceExpungeService implements IResourceExpungeService { private void callHooks(RequestDetails theRequestDetails, AtomicInteger theRemainingCount, ResourceHistoryTable theVersion, IdDt theId) { final AtomicInteger counter = new AtomicInteger(); if (JpaInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE, myInterceptorBroadcaster, theRequestDetails)) { - IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theId.getResourceType()); + IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theId.getResourceType()); IBaseResource resource = resourceDao.toResource(theVersion, false); HookParams params = new HookParams() .add(AtomicInteger.class, counter) diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java index cefc7325423..072e98b7470 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java @@ -20,6 +20,9 @@ package ca.uhn.fhir.jpa.dao.index; * #L% */ +import ca.uhn.fhir.context.BaseRuntimeChildDefinition; +import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition; +import ca.uhn.fhir.context.BaseRuntimeElementDefinition; import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.RuntimeResourceDefinition; import ca.uhn.fhir.context.RuntimeSearchParam; @@ -33,19 +36,24 @@ import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; +import org.hl7.fhir.instance.model.api.IBase; +import org.hl7.fhir.instance.model.api.IBaseReference; import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IIdType; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; +import javax.annotation.Nullable; import javax.persistence.EntityManager; import javax.persistence.PersistenceContext; import javax.persistence.PersistenceContextType; +import java.util.Optional; @Service public class DaoResourceLinkResolver implements IResourceLinkResolver { private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DaoResourceLinkResolver.class); - + @PersistenceContext(type = PersistenceContextType.TRANSACTION) + protected EntityManager myEntityManager; @Autowired private DaoConfig myDaoConfig; @Autowired @@ -55,38 +63,37 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver { @Autowired private DaoRegistry myDaoRegistry; - @PersistenceContext(type = PersistenceContextType.TRANSACTION) - protected EntityManager myEntityManager; - @Override - public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class theType, String theId, RequestDetails theRequest) { + public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class theType, IBaseReference theReference, RequestDetails theRequest) { ResourceTable target; ResourcePersistentId valueOf; + String idPart = theNextId.getIdPart(); try { - valueOf = myIdHelperService.translateForcedIdToPid(theTypeString, theId, theRequest); - ourLog.trace("Translated {}/{} to resource PID {}", theType, theId, valueOf); + valueOf = myIdHelperService.translateForcedIdToPid(theTypeString, idPart, theRequest); + ourLog.trace("Translated {}/{} to resource PID {}", theType, idPart, valueOf); } catch (ResourceNotFoundException e) { - if (myDaoConfig.isEnforceReferentialIntegrityOnWrite() == false) { - return null; - } - RuntimeResourceDefinition missingResourceDef = myContext.getResourceDefinition(theType); - String resName = missingResourceDef.getName(); - if (myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) { - IBaseResource newResource = missingResourceDef.newInstance(); - newResource.setId(resName + "/" + theId); - IFhirResourceDao placeholderResourceDao = (IFhirResourceDao) myDaoRegistry.getResourceDao(newResource.getClass()); - ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue()); - valueOf = placeholderResourceDao.update(newResource).getEntity().getPersistentId(); - } else { - throw new InvalidRequestException("Resource " + resName + "/" + theId + " not found, specified in path: " + theNextPathsUnsplit); + Optional pidOpt = createPlaceholderTargetIfConfiguredToDoSo(theType, theReference, idPart); + if (!pidOpt.isPresent()) { + + if (myDaoConfig.isEnforceReferentialIntegrityOnWrite() == false) { + return null; + } + + RuntimeResourceDefinition missingResourceDef = myContext.getResourceDefinition(theType); + String resName = missingResourceDef.getName(); + throw new InvalidRequestException("Resource " + resName + "/" + idPart + " not found, specified in path: " + theNextPathsUnsplit); + } + + valueOf = pidOpt.get(); } + target = myEntityManager.find(ResourceTable.class, valueOf.getIdAsLong()); RuntimeResourceDefinition targetResourceDef = myContext.getResourceDefinition(theType); if (target == null) { String resName = targetResourceDef.getName(); - throw new InvalidRequestException("Resource " + resName + "/" + theId + " not found, specified in path: " + theNextPathsUnsplit); + throw new InvalidRequestException("Resource " + resName + "/" + idPart + " not found, specified in path: " + theNextPathsUnsplit); } ourLog.trace("Resource PID {} is of type {}", valueOf, target.getResourceType()); @@ -98,7 +105,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver { if (target.getDeleted() != null) { String resName = targetResourceDef.getName(); - throw new InvalidRequestException("Resource " + resName + "/" + theId + " is deleted, specified in path: " + theNextPathsUnsplit); + throw new InvalidRequestException("Resource " + resName + "/" + idPart + " is deleted, specified in path: " + theNextPathsUnsplit); } if (!theNextSpDef.hasTargets() && theNextSpDef.getTargets().contains(theTypeString)) { @@ -107,8 +114,60 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver { return target; } + /** + * @param theIdToAssignToPlaceholder If specified, the placeholder resource created will be given a specific ID + */ + public Optional createPlaceholderTargetIfConfiguredToDoSo(Class theType, IBaseReference theReference, @Nullable String theIdToAssignToPlaceholder) { + ResourcePersistentId valueOf = null; + + if (myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) { + RuntimeResourceDefinition missingResourceDef = myContext.getResourceDefinition(theType); + String resName = missingResourceDef.getName(); + + @SuppressWarnings("unchecked") + T newResource = (T) missingResourceDef.newInstance(); + + IFhirResourceDao placeholderResourceDao = myDaoRegistry.getResourceDao(theType); + ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue()); + + if (myDaoConfig.isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets()) { + tryToCopyIdentifierFromReferenceToTargetResource(theReference, missingResourceDef, newResource); + } + + if (theIdToAssignToPlaceholder != null) { + newResource.setId(resName + "/" + theIdToAssignToPlaceholder); + valueOf = placeholderResourceDao.update(newResource).getEntity().getPersistentId(); + } else { + valueOf = placeholderResourceDao.create(newResource).getEntity().getPersistentId(); + } + } + + return Optional.ofNullable(valueOf); + } + + private void tryToCopyIdentifierFromReferenceToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) { + boolean referenceHasIdentifier = theSourceReference.hasIdentifier(); + if (referenceHasIdentifier) { + BaseRuntimeChildDefinition targetIdentifier = theTargetResourceDef.getChildByName("identifier"); + if (targetIdentifier != null) { + BaseRuntimeElementDefinition identifierElement = targetIdentifier.getChildByName("identifier"); + String identifierElementName = identifierElement.getName(); + boolean targetHasIdentifierElement = identifierElementName.equals("Identifier"); + if (targetHasIdentifierElement) { + + BaseRuntimeElementCompositeDefinition referenceElement = (BaseRuntimeElementCompositeDefinition) myContext.getElementDefinition(theSourceReference.getClass()); + BaseRuntimeChildDefinition referenceIdentifierChild = referenceElement.getChildByName("identifier"); + Optional identifierOpt = referenceIdentifierChild.getAccessor().getFirstValueOrNull(theSourceReference); + identifierOpt.ifPresent(theIBase -> targetIdentifier.getMutator().addValue(theTargetResource, theIBase)); + + } + } + } + } + @Override public void validateTypeOrThrowException(Class theType) { myDaoRegistry.getDaoOrThrowException(theType); } + } diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java index b9d54e86c3b..a540c0ab1b3 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java @@ -26,8 +26,8 @@ import ca.uhn.fhir.context.RuntimeSearchParam; import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao; import ca.uhn.fhir.jpa.dao.DaoConfig; import ca.uhn.fhir.jpa.dao.MatchResourceUrlService; -import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId; import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao; +import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId; import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam; import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique; import ca.uhn.fhir.jpa.model.entity.ResourceLink; @@ -61,6 +61,7 @@ import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; +import java.util.Optional; import java.util.Set; import static org.apache.commons.lang3.StringUtils.isNotBlank; @@ -81,17 +82,16 @@ public class SearchParamWithInlineReferencesExtractor { @Autowired private ISearchParamRegistry mySearchParamRegistry; @Autowired - SearchParamExtractorService mySearchParamExtractorService; + private SearchParamExtractorService mySearchParamExtractorService; @Autowired - ResourceLinkExtractor myResourceLinkExtractor; + private ResourceLinkExtractor myResourceLinkExtractor; @Autowired - DaoResourceLinkResolver myDaoResourceLinkResolver; + private DaoResourceLinkResolver myDaoResourceLinkResolver; @Autowired - DaoSearchParamSynchronizer myDaoSearchParamSynchronizer; + private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer; @Autowired private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao; - @PersistenceContext(type = PersistenceContextType.TRANSACTION) protected EntityManager myEntityManager; @@ -246,16 +246,25 @@ public class SearchParamWithInlineReferencesExtractor { } Class matchResourceType = matchResourceDef.getImplementingClass(); Set matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theRequest); + + ResourcePersistentId match; if (matches.isEmpty()) { - String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", nextId.getValue()); - throw new ResourceNotFoundException(msg); - } - if (matches.size() > 1) { + + Optional placeholderOpt = myDaoResourceLinkResolver.createPlaceholderTargetIfConfiguredToDoSo(matchResourceType, nextRef, null); + if (placeholderOpt.isPresent()) { + match = placeholderOpt.get(); + } else { + String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", nextId.getValue()); + throw new ResourceNotFoundException(msg); + } + } else if (matches.size() > 1) { String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlMultipleMatches", nextId.getValue()); throw new PreconditionFailedException(msg); + } else { + match = matches.iterator().next(); } - ResourcePersistentId next = matches.iterator().next(); - String newId = myIdHelperService.translatePidIdToForcedId(resourceTypeString, next); + + String newId = myIdHelperService.translatePidIdToForcedId(resourceTypeString, match); ourLog.debug("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId); nextRef.setReference(newId); } diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java index ef1fa4282aa..ee797ed0504 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java @@ -8,10 +8,14 @@ import ca.uhn.fhir.rest.param.TokenParam; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; import ca.uhn.fhir.util.TestUtil; +import com.google.common.collect.Sets; import org.hl7.fhir.instance.model.api.IIdType; +import org.hl7.fhir.r4.model.AuditEvent; import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.Observation; import org.hl7.fhir.r4.model.Observation.ObservationStatus; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.Reference; import org.hl7.fhir.r4.model.Task; import org.junit.After; import org.junit.AfterClass; @@ -21,9 +25,12 @@ import java.util.List; import static org.hamcrest.CoreMatchers.startsWith; import static org.hamcrest.Matchers.contains; -import static org.junit.Assert.*; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertThat; +import static org.junit.Assert.fail; -@SuppressWarnings({"unchecked", "deprecation"}) +@SuppressWarnings({"ConstantConditions"}) public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test { private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCreatePlaceholdersR4Test.class); @@ -32,6 +39,9 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test { public final void afterResetDao() { myDaoConfig.setAutoCreatePlaceholderReferenceTargets(new DaoConfig().isAutoCreatePlaceholderReferenceTargets()); myDaoConfig.setResourceClientIdStrategy(new DaoConfig().getResourceClientIdStrategy()); + myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(new DaoConfig().isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets()); + myDaoConfig.setBundleTypesAllowedForStorage(new DaoConfig().getBundleTypesAllowedForStorage()); + } @Test @@ -163,6 +173,90 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test { assertEquals("Patient/999999999999999", outcome.getResources(0,1).get(0).getIdElement().toUnqualifiedVersionless().getValue()); } + @Test + public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedByDefault() { + myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true); + myDaoConfig.setAllowInlineMatchUrlReferences(true); + + Observation obsToCreate = new Observation(); + obsToCreate.setStatus(ObservationStatus.FINAL); + obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123"); + obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123"); + IIdType id = myObservationDao.create(obsToCreate, mySrd).getId(); + + Observation createdObs = myObservationDao.read(id); + ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs)); + + Patient patient = myPatientDao.read(new IdType(createdObs.getSubject().getReference())); + ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient)); + assertEquals(0, patient.getIdentifier().size()); + } + + + @Test + public void testCreatePlaceholderWithMatchUrl_IdentifierCopied_NotPreExisting() { + myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true); + myDaoConfig.setAllowInlineMatchUrlReferences(true); + myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true); + + Observation obsToCreate = new Observation(); + obsToCreate.setStatus(ObservationStatus.FINAL); + obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123"); + obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123"); + IIdType id = myObservationDao.create(obsToCreate, mySrd).getId(); + + Observation createdObs = myObservationDao.read(id); + ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs)); + + Patient patient = myPatientDao.read(new IdType(createdObs.getSubject().getReference())); + ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient)); + assertEquals(1, patient.getIdentifier().size()); + assertEquals("http://foo", patient.getIdentifier().get(0).getSystem()); + assertEquals("123", patient.getIdentifier().get(0).getValue()); + } + + @Test + public void testCreatePlaceholderWithMatchUrl_IdentifierNotCopiedBecauseNoFieldMatches() { + myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true); + myDaoConfig.setAllowInlineMatchUrlReferences(true); + myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true); + myDaoConfig.setBundleTypesAllowedForStorage(Sets.newHashSet("")); + + AuditEvent eventToCreate = new AuditEvent(); + Reference what = eventToCreate.addEntity().getWhat(); + what.setReference("Bundle/ABC"); + what.getIdentifier().setSystem("http://foo"); + what.getIdentifier().setValue("123"); + IIdType id = myAuditEventDao.create(eventToCreate, mySrd).getId(); + + AuditEvent createdEvent = myAuditEventDao.read(id); + ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEvent)); + + } + + @Test + public void testCreatePlaceholderWithMatchUrl_PreExisting() { + myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true); + myDaoConfig.setAllowInlineMatchUrlReferences(true); + myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(true); + + Patient patient = new Patient(); + patient.setId("ABC"); + patient.addIdentifier().setSystem("http://foo").setValue("123"); + myPatientDao.update(patient); + + Observation obsToCreate = new Observation(); + obsToCreate.setStatus(ObservationStatus.FINAL); + obsToCreate.getSubject().setReference("Patient?identifier=http://foo|123"); + obsToCreate.getSubject().getIdentifier().setSystem("http://foo").setValue("123"); + IIdType id = myObservationDao.create(obsToCreate, mySrd).getId(); + + Observation createdObs = myObservationDao.read(id); + ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs)); + assertEquals("Patient/ABC", obsToCreate.getSubject().getReference()); + + } + @AfterClass public static void afterClassClearContext() { TestUtil.clearAllStaticFieldsForUnitTest(); diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/IResourceLinkResolver.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/IResourceLinkResolver.java index 47402bc246c..fa04e0784b8 100644 --- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/IResourceLinkResolver.java +++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/IResourceLinkResolver.java @@ -23,11 +23,12 @@ package ca.uhn.fhir.jpa.searchparam.extractor; import ca.uhn.fhir.context.RuntimeSearchParam; import ca.uhn.fhir.jpa.model.entity.ResourceTable; import ca.uhn.fhir.rest.api.server.RequestDetails; +import org.hl7.fhir.instance.model.api.IBaseReference; import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IIdType; public interface IResourceLinkResolver { - ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class theType, String theId, RequestDetails theRequest); + ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class theType, IBaseReference theReference, RequestDetails theRequest); void validateTypeOrThrowException(Class theType); } diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java index 58725b639a2..dbd8f79f9d9 100644 --- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java +++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java @@ -39,7 +39,6 @@ import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Service; import java.util.Date; -import java.util.Map; import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank; @@ -73,8 +72,8 @@ public class ResourceLinkExtractor { } private void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest) { - IBaseReference nextObject = thePathAndRef.getRef(); - IIdType nextId = nextObject.getReferenceElement(); + IBaseReference nextReference = thePathAndRef.getRef(); + IIdType nextId = nextReference.getReferenceElement(); String path = thePathAndRef.getPath(); /* @@ -82,8 +81,8 @@ public class ResourceLinkExtractor { * programmatically with a Bundle (not through the FHIR REST API) * but Smile does this */ - if (nextId.isEmpty() && nextObject.getResource() != null) { - nextId = nextObject.getResource().getIdElement(); + if (nextId.isEmpty() && nextReference.getResource() != null) { + nextId = nextReference.getResource().getIdElement(); } theParams.myPopulatedResourceLinkParameters.add(thePathAndRef.getSearchParamName()); @@ -152,15 +151,15 @@ public class ResourceLinkExtractor { } theResourceLinkResolver.validateTypeOrThrowException(type); - ResourceLink resourceLink = createResourceLink(theEntity, theUpdateTime, theResourceLinkResolver, theRuntimeSearchParam, path, thePathAndRef, nextId, typeString, type, id, theRequest); + ResourceLink resourceLink = createResourceLink(theEntity, theUpdateTime, theResourceLinkResolver, theRuntimeSearchParam, path, thePathAndRef, nextId, typeString, type, nextReference, theRequest); if (resourceLink == null) { return; } theParams.myLinks.add(resourceLink); } - private ResourceLink createResourceLink(ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam nextSpDef, String theNextPathsUnsplit, PathAndRef nextPathAndRef, IIdType theNextId, String theTypeString, Class theType, String theId, RequestDetails theRequest) { - ResourceTable targetResource = theResourceLinkResolver.findTargetResource(nextSpDef, theNextPathsUnsplit, theNextId, theTypeString, theType, theId, theRequest); + private ResourceLink createResourceLink(ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam nextSpDef, String theNextPathsUnsplit, PathAndRef nextPathAndRef, IIdType theNextId, String theTypeString, Class theType, IBaseReference theReference, RequestDetails theRequest) { + ResourceTable targetResource = theResourceLinkResolver.findTargetResource(nextSpDef, theNextPathsUnsplit, theNextId, theTypeString, theType, theReference, theRequest); if (targetResource == null) { return null; @@ -169,7 +168,4 @@ public class ResourceLinkExtractor { return new ResourceLink(nextPathAndRef.getPath(), theEntity, targetResource, theUpdateTime); } - private String toResourceName(Class theResourceType) { - return myContext.getResourceDefinition(theResourceType).getName(); - } } diff --git a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InlineResourceLinkResolver.java b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InlineResourceLinkResolver.java index 0618d4665b7..2830a85dd58 100644 --- a/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InlineResourceLinkResolver.java +++ b/hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InlineResourceLinkResolver.java @@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.model.entity.ForcedId; import ca.uhn.fhir.jpa.model.entity.ResourceTable; import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver; import ca.uhn.fhir.rest.api.server.RequestDetails; +import org.hl7.fhir.instance.model.api.IBaseReference; import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IIdType; import org.springframework.stereotype.Service; @@ -33,7 +34,7 @@ import org.springframework.stereotype.Service; public class InlineResourceLinkResolver implements IResourceLinkResolver { @Override - public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class theType, String theId, RequestDetails theRequest) { + public ResourceTable findTargetResource(RuntimeSearchParam theNextSpDef, String theNextPathsUnsplit, IIdType theNextId, String theTypeString, Class theType, IBaseReference theReference, RequestDetails theRequest) { ResourceTable target; target = new ResourceTable(); target.setResourceType(theTypeString); @@ -41,7 +42,7 @@ public class InlineResourceLinkResolver implements IResourceLinkResolver { target.setId(theNextId.getIdPartAsLong()); } else { ForcedId forcedId = new ForcedId(); - forcedId.setForcedId(theId); + forcedId.setForcedId(theNextId.getIdPart()); target.setForcedId(forcedId); } return target; diff --git a/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationDstu2Test.java b/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationDstu2Test.java index 6400f939e23..4028e8c3c1a 100644 --- a/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationDstu2Test.java +++ b/hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationDstu2Test.java @@ -265,7 +265,7 @@ public class ClientServerValidationDstu2Test { @Test public void testServerReturnsWrongVersionForDstu2() throws Exception { - String wrongFhirVersion = "3.0.1"; + String wrongFhirVersion = FhirVersionEnum.DSTU3.getFhirVersionString(); assertThat(wrongFhirVersion, is(FhirVersionEnum.DSTU3.getFhirVersionString())); // asserting that what we assume to be the DSTU3 FHIR version is still correct Conformance conf = new Conformance(); conf.setFhirVersion(wrongFhirVersion); @@ -285,7 +285,7 @@ public class ClientServerValidationDstu2Test { fail(); } catch (FhirClientInappropriateForServerException e) { String out = e.toString(); - String want = "The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"3.0.1\" which corresponds to DSTU3, but this client is configured to use DSTU2 (via the FhirContext)"; + String want = "The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"" + wrongFhirVersion + "\" which corresponds to DSTU3, but this client is configured to use DSTU2 (via the FhirContext)"; ourLog.info(out); ourLog.info(want); assertThat(out, containsString(want));