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Merge branch 'hapifhir:master' into fix_for_5.0.0-snapshot1

This commit is contained in:
Jens Kristian Villadsen 2022-04-25 11:02:50 +02:00 committed by GitHub
parent 5c564bc343 f7a31287b6
commit 8ad18915a1
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114 changed files with 1776 additions and 297 deletions
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2
hapi-deployable-pom/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/Msg.java
View File

@ -25,7 +25,7 @@ public final class Msg {
/**
* IMPORTANT: Please update the following comment after you add a new code
* Last code value: 2075
* Last code value: 2076
*/
private Msg() {}

28
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
View File

@ -1345,6 +1345,34 @@ public enum Pointcut implements IPointcut {
"ca.uhn.fhir.rest.api.server.storage.TransactionDetails"
),
/**
* <b>Storage Hook:</b>
* Invoked before client-assigned id is created.
* <p>
* Hooks will have access to the contents of the resource being created
* so that client-assigned ids can be allowed/denied. These changes will
* be reflected in permanent storage.
* </p>
* Hooks may accept the following parameters:
* <ul>
* <li>org.hl7.fhir.instance.model.api.IBaseResource</li>
* <li>
* ca.uhn.fhir.rest.api.server.RequestDetails - A bean containing details about the request that is about to be processed, including details such as the
* resource type and logical ID (if any) and other FHIR-specific aspects of the request which have been
* pulled out of the servlet request. Note that the bean
* properties are not all guaranteed to be populated, depending on how early during processing the
* exception occurred.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
* </p>
*/
STORAGE_PRESTORAGE_CLIENT_ASSIGNED_ID(void.class,
"org.hl7.fhir.instance.model.api.IBaseResource",
"ca.uhn.fhir.rest.api.server.RequestDetails"
),
/**
* <b>Storage Hook:</b>
* Invoked before a resource will be updated, immediately before the resource

1
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -159,6 +159,7 @@ ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotUpdateUrlOrVersionForValueSetReso
ca.uhn.fhir.jpa.patch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.invalidGraphqlArgument=Unknown GraphQL argument "{0}". Value GraphQL argument for this type are: {1}
ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.invalidGraphqlCursorArgument=GraphQL Cursor "{0}" does not exist and may have expired
ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.nonDefaultPartitionSelectedForNonPartitionable=Resource type {0} can not be partitioned
ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc.unknownPartitionId=Unknown partition ID: {0}

2
hapi-fhir-batch/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/BatchConstants.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.batch.config;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
public final class BatchConstants {
@ -90,6 +91,8 @@ public final class BatchConstants {
*/
public static final String JOB_EXECUTION_RESOURCE_TYPE = "resourceType";
public static final List<String> PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES = List.of("Practitioner", "Organization");
/**
* This Set contains the step names across all job types that are appropriate for
* someone to look at the write count for that given step in order to determine the

4
hapi-fhir-bom/pom.xml
View File

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3524-export-poll-status-returning-the-wrong-partition-in-the-url.yaml Normal file
View File

@ -0,0 +1,4 @@
type: fix
issue: 3524
jira: SMILE-3672
title: "Previously if partitioning was enabled, the URL returned from `$export-poll-status` provided a location in the wrong partition. This has been fixed and all Bulk Exports will be stored in the `DEFAULT` partition."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3547-interceptor-hook-for-client-assigned-ids.yaml Normal file
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@ -0,0 +1,4 @@
type: add
issue: 3547
jira: SMILE-4141
title: "Added a new pointcut: `STORAGE_PRESTORAGE_CLIENT_ASSIGNED_ID` which is invoked when a user attempts to create a resource with a client-assigned ID. "

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3548-has-query-parameter-resolution Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 3548
jira: SMILE-4023
title: "A recent change caused searches that use _has in conjuction with a `Resource` search param (e.g. _id, _text) to fail. This has been fixed."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3550-expunge-resource-ids.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: change
issue: 3550
title: "Method signatures on several interfaces and classes related to the `$expunge` operation have changed to support
the case where the primary identifier of a resource is not necessarily a `Long`."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3553-prevent-deexternalize.yaml Normal file
View File

@ -0,0 +1,4 @@
type: fix
issue: 3553
jira: SMILE-3964
title: "Added a new setting to BinaryStorageInterceptor which allows you to disable binary de-externalization during resource reads."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3557-group-export-forward-references.yaml Normal file
View File

@ -0,0 +1,4 @@
type: add
issue: 3557
jira: SMILE-4062
title: "Group Bulk Export (e.g. Group/123/$export) now additionally supports Organization and Practitioner as valid _type parameters. This works internally by querying using a `_has` parameter"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3561-bulk-export-premature-collection-removal.yaml Normal file
View File

@ -0,0 +1,5 @@
type: fix
issue: 3561
jira: SMILE-3728
title: "Previously, Bulk export jobs automatically cleared the collection after a hardcoded 2 hour time period from start of the job. This is now configurable via a new DaoConfig property,
`setBulkExportFileRetentionPeriodHours()`. If this is set to a value of 0 or below, then the collections will never be expired."

2
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/job/MdmLinkDeleter.java
View File

@ -25,11 +25,11 @@ import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
import ca.uhn.fhir.jpa.dao.expunge.PartitionRunner;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemProcessor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.SliceImpl;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
@ -58,14 +58,14 @@ public class MdmLinkDeleter implements ItemProcessor<List<Long>, List<Long>> {
public List<Long> process(List<Long> thePidList) throws Exception {
ConcurrentLinkedQueue<Long> goldenPidAggregator = new ConcurrentLinkedQueue<>();
PartitionRunner partitionRunner = new PartitionRunner(PROCESS_NAME, THREAD_PREFIX, myDaoConfig.getReindexBatchSize(), myDaoConfig.getReindexThreadCount());
partitionRunner.runInPartitionedThreads(thePidList, pids -> removeLinks(pids, goldenPidAggregator));
partitionRunner.runInPartitionedThreads(ResourcePersistentId.fromLongList(thePidList), pids -> removeLinks(pids, goldenPidAggregator));
return new ArrayList<>(goldenPidAggregator);
}
private void removeLinks(List<Long> pidList, ConcurrentLinkedQueue<Long> theGoldenPidAggregator) {
private void removeLinks(List<ResourcePersistentId> pidList, ConcurrentLinkedQueue<Long> theGoldenPidAggregator) {
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.executeWithoutResult(t -> theGoldenPidAggregator.addAll(deleteMdmLinksAndReturnGoldenResourcePids(pidList)));
txTemplate.executeWithoutResult(t -> theGoldenPidAggregator.addAll(deleteMdmLinksAndReturnGoldenResourcePids(ResourcePersistentId.toLongList(pidList))));
}
public List<Long> deleteMdmLinksAndReturnGoldenResourcePids(List<Long> thePids) {

48
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processor/GoldenResourceAnnotatingProcessor.java
View File

@ -34,14 +34,18 @@ import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.springframework.batch.item.ItemProcessor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.lang.NonNull;
import java.util.List;
import java.util.Optional;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES;
/**
* Reusable Item Processor which attaches an extension to any outgoing resource. This extension will contain a resource
* reference to the golden resource patient of the given resources' patient. (e.g. Observation.subject, Immunization.patient, etc)
@ -49,6 +53,7 @@ import java.util.Optional;
public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBaseResource>, List<IBaseResource>> {
private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
@Value("#{stepExecutionContext['resourceType']}")
private String myResourceType;
@ -79,21 +84,34 @@ public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBa
}
@Override
public List<IBaseResource> process(List<IBaseResource> theIBaseResources) throws Exception {
//If MDM expansion is enabled, add this magic new extension, otherwise, return the resource as is.
if (myMdmEnabled) {
if (myRuntimeSearchParam == null) {
populateRuntimeSearchParam();
}
if (myPatientFhirPath == null) {
populatePatientFhirPath();
}
theIBaseResources.forEach(this::annotateClinicalResourceWithRelatedGoldenResourcePatient);
public List<IBaseResource> process(@NonNull List<IBaseResource> theIBaseResources) throws Exception {
if (shouldAnnotateResource()) {
lazyLoadSearchParamsAndFhirPath();
theIBaseResources.forEach(this::annotateBackwardsReferences);
}
return theIBaseResources;
}
private void annotateClinicalResourceWithRelatedGoldenResourcePatient(IBaseResource iBaseResource) {
private void lazyLoadSearchParamsAndFhirPath() {
if (myRuntimeSearchParam == null) {
populateRuntimeSearchParam();
}
if (myPatientFhirPath == null) {
populatePatientFhirPath();
}
}
/**
* If the resource is added via a forward-reference from a patient, e.g. Patient.managingOrganization, we have no way to fetch the patient at this point in time.
* This is a shortcoming of including the forward reference types in a Group/Patient bulk export.
*
* @return true if the resource should be annotated with the golden resource patient reference
*/
private boolean shouldAnnotateResource() {
return myMdmEnabled && !PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(myResourceType);
}
private void annotateBackwardsReferences(IBaseResource iBaseResource) {
Optional<String> patientReference = getPatientReference(iBaseResource);
if (patientReference.isPresent()) {
addGoldenResourceExtension(iBaseResource, patientReference.get());
@ -104,13 +122,15 @@ public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBa
}
private Optional<String> getPatientReference(IBaseResource iBaseResource) {
//In the case of patient, we will just use the raw ID.
if (myResourceType.equalsIgnoreCase("Patient")) {
return Optional.of(iBaseResource.getIdElement().getIdPart());
//Otherwise, we will perform evaluation of the fhirPath.
} else {
Optional<IBaseReference> optionalReference = getFhirParser().evaluateFirst(iBaseResource, myPatientFhirPath, IBaseReference.class);
return optionalReference.map(theIBaseReference -> theIBaseReference.getReferenceElement().getIdPart());
if (optionalReference.isPresent()) {
return optionalReference.map(theIBaseReference -> theIBaseReference.getReferenceElement().getIdPart());
} else {
return Optional.empty();
}
}
}

59
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkItemReader.java
View File

@ -38,6 +38,8 @@ import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.HasOrListParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -58,6 +60,8 @@ import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES;
/**
* Bulk Item reader for the Group Bulk Export job.
* Instead of performing a normal query on the resource type using type filters, we instead
@ -87,13 +91,14 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
@Override
protected Iterator<ResourcePersistentId> getResourcePidIterator() {
Set<ResourcePersistentId> myReadPids = new HashSet<>();
//Short circuit out if we detect we are attempting to extract patients
if (myResourceType.equalsIgnoreCase("Patient")) {
return getExpandedPatientIterator();
}
//First lets expand the group so we get a list of all patient IDs of the group, and MDM-matched patient IDs of the group.
Set<String> expandedMemberResourceIds = expandAllPatientPidsFromGroup();
if (ourLog.isDebugEnabled()) {
@ -102,15 +107,16 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
//Next, let's search for the target resources, with their correct patient references, chunked.
//The results will be jammed into myReadPids
Set<ResourcePersistentId> myExpandedMemberPids = new HashSet<>();
QueryChunker<String> queryChunker = new QueryChunker<>();
queryChunker.chunk(new ArrayList<>(expandedMemberResourceIds), QUERY_CHUNK_SIZE, (idChunk) -> {
queryResourceTypeWithReferencesToPatients(myReadPids, idChunk);
queryResourceTypeWithReferencesToPatients(myExpandedMemberPids, idChunk);
});
if (ourLog.isDebugEnabled()) {
ourLog.debug("Resource PIDs to be Bulk Exported: [{}]", myReadPids.stream().map(ResourcePersistentId::toString).collect(Collectors.joining(",")));
ourLog.debug("Resource PIDs to be Bulk Exported: {}", myExpandedMemberPids);
}
return myReadPids.iterator();
return myExpandedMemberPids.iterator();
}
/**
@ -243,6 +249,7 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
}
private void queryResourceTypeWithReferencesToPatients(Set<ResourcePersistentId> myReadPids, List<String> idChunk) {
//Build SP map
//First, inject the _typeFilters and _since from the export job
List<SearchParameterMap> expandedSpMaps = createSearchParameterMapsForResourceType();
@ -251,12 +258,16 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
//Since we are in a bulk job, we have to ensure the user didn't jam in a patient search param, since we need to manually set that.
validateSearchParameters(expandedSpMap);
// Now, further filter the query with patient references defined by the chunk of IDs we have.
filterSearchByResourceIds(idChunk, expandedSpMap);
// Fetch and cache a search builder for this resource type
ISearchBuilder searchBuilder = getSearchBuilderForLocalResourceType();
// Now, further filter the query with patient references defined by the chunk of IDs we have.
if (PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(myResourceType)) {
filterSearchByHasParam(idChunk, expandedSpMap);
} else {
filterSearchByResourceIds(idChunk, expandedSpMap);
}
//Execute query and all found pids to our local iterator.
IResultIterator resultIterator = searchBuilder.createQuery(expandedSpMap, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
while (resultIterator.hasNext()) {
@ -265,17 +276,41 @@ public class GroupBulkItemReader extends BaseJpaBulkItemReader implements ItemRe
}
}
/**
*
* @param idChunk
* @param expandedSpMap
*/
private void filterSearchByHasParam(List<String> idChunk, SearchParameterMap expandedSpMap) {
HasOrListParam hasOrListParam = new HasOrListParam();
idChunk.stream().forEach(id -> hasOrListParam.addOr(buildHasParam(id)));
expandedSpMap.add("_has", hasOrListParam);
}
private HasParam buildHasParam(String theId) {
if ("Practitioner".equalsIgnoreCase(myResourceType)) {
return new HasParam("Patient", "general-practitioner", "_id", theId);
} else if ("Organization".equalsIgnoreCase(myResourceType)) {
return new HasParam("Patient", "organization", "_id", theId);
} else {
throw new IllegalArgumentException(Msg.code(2077) + " We can't handle forward references onto type " + myResourceType);
}
}
private void filterSearchByResourceIds(List<String> idChunk, SearchParameterMap expandedSpMap) {
ReferenceOrListParam orList = new ReferenceOrListParam();
idChunk.forEach(id -> orList.add(new ReferenceParam(id)));
expandedSpMap.add(getPatientSearchParamForCurrentResourceType().getName(), orList);
}
private RuntimeSearchParam validateSearchParameters(SearchParameterMap expandedSpMap) {
RuntimeSearchParam runtimeSearchParam = getPatientSearchParamForCurrentResourceType();
if (expandedSpMap.get(runtimeSearchParam.getName()) != null) {
throw new IllegalArgumentException(Msg.code(792) + String.format("Group Bulk Export manually modifies the Search Parameter called [%s], so you may not include this search parameter in your _typeFilter!", runtimeSearchParam.getName()));
private void validateSearchParameters(SearchParameterMap expandedSpMap) {
if (PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(myResourceType)) {
return;
} else {
RuntimeSearchParam runtimeSearchParam = getPatientSearchParamForCurrentResourceType();
if (expandedSpMap.get(runtimeSearchParam.getName()) != null) {
throw new IllegalArgumentException(Msg.code(792) + String.format("Group Bulk Export manually modifies the Search Parameter called [%s], so you may not include this search parameter in your _typeFilter!", runtimeSearchParam.getName()));
}
}
return runtimeSearchParam;
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportJobSchedulingHelperImpl.java
View File

@ -200,7 +200,7 @@ public class BulkDataExportJobSchedulingHelperImpl implements IBulkDataExportJob
Optional<BulkExportJobEntity> jobToDelete = myTxTemplate.execute(t -> {
Pageable page = PageRequest.of(0, 1);
Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByExpiry(page, new Date());
Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findNotRunningByExpiry(page, new Date());
if (submittedJobs.isEmpty()) {
return Optional.empty();
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportSvcImpl.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.i18n.Msg;
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.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
@ -78,10 +79,11 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
private DaoRegistry myDaoRegistry;
@Autowired
private FhirContext myContext;
@Autowired
private DaoConfig myDaoConfig;
private Set<String> myCompartmentResources;
private final int myRetentionPeriod = (int) (2 * DateUtils.MILLIS_PER_HOUR);
@Transactional
@Override
@ -233,8 +235,18 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
.setStatus(theJob.getStatus());
}
/**
* If the retention period is set to <= 0, set it to null, which prevents it from getting expired, otherwise, set
* the retention period.
*
* @param theJob the job to update the expiry for.
*/
private void updateExpiry(BulkExportJobEntity theJob) {
theJob.setExpiry(DateUtils.addMilliseconds(new Date(), myRetentionPeriod));
if (myDaoConfig.getBulkExportFileRetentionPeriodHours() > 0) {
theJob.setExpiry(DateUtils.addHours(new Date(), myDaoConfig.getBulkExportFileRetentionPeriodHours()));
} else {
theJob.setExpiry(null);
}
}
@Transactional

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -139,6 +139,7 @@ import ca.uhn.fhir.jpa.validation.ValidationSettings;
import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IDeleteExpungeJobSubmitter;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.interceptor.ResponseTerminologyTranslationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
@ -261,8 +262,11 @@ public class JpaConfig {
@Bean(name = "myBinaryStorageInterceptor")
@Lazy
public BinaryStorageInterceptor binaryStorageInterceptor() {
return new BinaryStorageInterceptor();
public BinaryStorageInterceptor binaryStorageInterceptor(DaoConfig theDaoConfig) {
BinaryStorageInterceptor interceptor = new BinaryStorageInterceptor();
interceptor.setAllowAutoInflateBinaries(theDaoConfig.isAllowAutoInflateBinaries());
interceptor.setAutoInflateBinariesMaximumSize(theDaoConfig.getAutoInflateBinariesMaximumBytes());
return interceptor;
}
@Bean
@ -754,8 +758,8 @@ public class JpaConfig {
@Bean
@Scope("prototype")
public ExpungeOperation expungeOperation(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
return new ExpungeOperation(theResourceName, theResourceId, theVersion, theExpungeOptions, theRequestDetails);
public ExpungeOperation expungeOperation(String theResourceName, ResourcePersistentId theResourceId, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
return new ExpungeOperation(theResourceName, theResourceId, theExpungeOptions, theRequestDetails);
}
@Bean

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -77,6 +77,7 @@ import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -1422,7 +1423,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
*/
if (thePerformIndexing) {
if (newParams == null) {
myExpungeService.deleteAllSearchParams(entity.getId());
myExpungeService.deleteAllSearchParams(new ResourcePersistentId(entity.getId()));
} else {
// Synchronize search param indexes

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -70,6 +70,7 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
@ -310,17 +311,28 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
notifyInterceptors(RestOperationTypeEnum.CREATE, requestDetails);
}
String resourceIdBeforeStorage = theResource.getIdElement().getIdPart();
boolean resourceHadIdBeforeStorage = isNotBlank(resourceIdBeforeStorage);
boolean resourceIdWasServerAssigned = theResource.getUserData(JpaConstants.RESOURCE_ID_SERVER_ASSIGNED) == Boolean.TRUE;
HookParams hookParams;
// Notify interceptor for accepting/rejecting client assigned ids
if (!resourceIdWasServerAssigned && resourceHadIdBeforeStorage) {
hookParams = new HookParams()
.add(IBaseResource.class, theResource)
.add(RequestDetails.class, theRequest);
doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRESTORAGE_CLIENT_ASSIGNED_ID, hookParams);
}
// Interceptor call: STORAGE_PRESTORAGE_RESOURCE_CREATED
HookParams hookParams = new HookParams()
hookParams = new HookParams()
.add(IBaseResource.class, theResource)
.add(RequestDetails.class, theRequest)
.addIfMatchesType(ServletRequestDetails.class, theRequest)
.add(TransactionDetails.class, theTransactionDetails);
doCallHooks(theTransactionDetails, theRequest, Pointcut.STORAGE_PRESTORAGE_RESOURCE_CREATED, hookParams);
String resourceIdBeforeStorage = theResource.getIdElement().getIdPart();
boolean resourceHadIdBeforeStorage = isNotBlank(resourceIdBeforeStorage);
boolean resourceIdWasServerAssigned = theResource.getUserData(JpaConstants.RESOURCE_ID_SERVER_ASSIGNED) == Boolean.TRUE;
if (resourceHadIdBeforeStorage && !resourceIdWasServerAssigned) {
validateResourceIdCreation(theResource, theRequest);
}
@ -887,10 +899,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
throw new PreconditionFailedException(Msg.code(969) + "Can not perform version-specific expunge of resource " + theId.toUnqualified().getValue() + " as this is the current version");
}
return myExpungeService.expunge(getResourceName(), entity.getResourceId(), entity.getVersion(), theExpungeOptions, theRequest);
return myExpungeService.expunge(getResourceName(), new ResourcePersistentId(entity.getResourceId(), entity.getVersion()), theExpungeOptions, theRequest);
}
return myExpungeService.expunge(getResourceName(), entity.getResourceId(), null, theExpungeOptions, theRequest);
return myExpungeService.expunge(getResourceName(), new ResourcePersistentId(entity.getResourceId()), theExpungeOptions, theRequest);
}
@Override
@ -898,7 +910,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
public ExpungeOutcome expunge(ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
ourLog.info("Beginning TYPE[{}] expunge operation", getResourceName());
return myExpungeService.expunge(getResourceName(), null, null, theExpungeOptions, theRequestDetails);
return myExpungeService.expunge(getResourceName(), null, theExpungeOptions, theRequestDetails);
}
@Override

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -83,7 +83,7 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
@Override
@Transactional(propagation = Propagation.NEVER)
public ExpungeOutcome expunge(ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
return myExpungeService.expunge(null, null, null, theExpungeOptions, theRequestDetails);
return myExpungeService.expunge(null, null, theExpungeOptions, theRequestDetails);
}
@Transactional(propagation = Propagation.REQUIRED)

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBulkExportJobDao.java
View File

@ -43,6 +43,9 @@ public interface IBulkExportJobDao extends JpaRepository<BulkExportJobEntity, Lo
@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myExpiry < :cutoff")
Slice<BulkExportJobEntity> findByExpiry(Pageable thePage, @Param("cutoff") Date theCutoff);
@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myExpiry IS NOT NULL and j.myExpiry < :cutoff AND j.myStatus <> 'BUILDING'")
Slice<BulkExportJobEntity> findNotRunningByExpiry(Pageable thePage, @Param("cutoff") Date theCutoff);
@Query("SELECT j FROM BulkExportJobEntity j WHERE j.myRequest = :request AND j.myCreated > :createdAfter AND j.myStatus <> :status ORDER BY j.myCreated DESC")
Slice<BulkExportJobEntity> findExistingJob(Pageable thePage, @Param("request") String theRequest, @Param("createdAfter") Date theCreatedAfter, @Param("status") BulkExportJobStatusEnum theNotStatus);

69
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ResourceExpungeService.java
View File

@ -48,6 +48,7 @@ import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.model.primitive.IdDt;
@ -125,15 +126,15 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public List<Long> findHistoricalVersionsOfNonDeletedResources(String theResourceName, Long theResourceId, Long theVersion, int theRemainingCount) {
public List<ResourcePersistentId> findHistoricalVersionsOfNonDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theRemainingCount) {
Pageable page = PageRequest.of(0, theRemainingCount);
Slice<Long> ids;
if (theResourceId != null) {
if (theVersion != null) {
ids = toSlice(myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theResourceId, theVersion));
if (theResourceId != null && theResourceId.getId() != null) {
if (theResourceId.getVersion() != null) {
ids = toSlice(myResourceHistoryTableDao.findForIdAndVersionAndFetchProvenance(theResourceId.getIdAsLong(), theResourceId.getVersion()));
} else {
ids = myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResourceId(page, theResourceId);
ids = myResourceHistoryTableDao.findIdsOfPreviousVersionsOfResourceId(page, theResourceId.getIdAsLong());
}
} else {
if (theResourceName != null) {
@ -143,16 +144,16 @@ public class ResourceExpungeService implements IResourceExpungeService {
}
}
return ids.getContent();
return ResourcePersistentId.fromLongList(ids.getContent());
}
@Override
@Transactional
public List<Long> findHistoricalVersionsOfDeletedResources(String theResourceName, Long theResourceId, int theRemainingCount) {
public List<ResourcePersistentId> findHistoricalVersionsOfDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theRemainingCount) {
Pageable page = PageRequest.of(0, theRemainingCount);
Slice<Long> ids;
if (theResourceId != null) {
ids = myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceId, theResourceName);
ids = myResourceTableDao.findIdsOfDeletedResourcesOfType(page, theResourceId.getIdAsLong(), theResourceName);
ourLog.info("Expunging {} deleted resources of type[{}] and ID[{}]", ids.getNumberOfElements(), theResourceName, theResourceId);
} else {
if (theResourceName != null) {
@ -163,14 +164,14 @@ public class ResourceExpungeService implements IResourceExpungeService {
ourLog.info("Expunging {} deleted resources (all types)", ids.getNumberOfElements());
}
}
return ids.getContent();
return ResourcePersistentId.fromLongList(ids.getContent());
}
@Override
@Transactional
public void expungeCurrentVersionOfResources(RequestDetails theRequestDetails, List<Long> theResourceIds, AtomicInteger theRemainingCount) {
for (Long next : theResourceIds) {
expungeCurrentVersionOfResource(theRequestDetails, next, theRemainingCount);
public void expungeCurrentVersionOfResources(RequestDetails theRequestDetails, List<ResourcePersistentId> theResourceIds, AtomicInteger theRemainingCount) {
for (ResourcePersistentId next : theResourceIds) {
expungeCurrentVersionOfResource(theRequestDetails, next.getIdAsLong(), theRemainingCount);
if (theRemainingCount.get() <= 0) {
return;
}
@ -226,9 +227,9 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public void expungeHistoricalVersionsOfIds(RequestDetails theRequestDetails, List<Long> theResourceIds, AtomicInteger theRemainingCount) {
for (Long next : theResourceIds) {
expungeHistoricalVersionsOfId(theRequestDetails, next, theRemainingCount);
public void expungeHistoricalVersionsOfIds(RequestDetails theRequestDetails, List<ResourcePersistentId> theResourceIds, AtomicInteger theRemainingCount) {
for (ResourcePersistentId next : theResourceIds) {
expungeHistoricalVersionsOfId(theRequestDetails, next.getIdAsLong(), theRemainingCount);
if (theRemainingCount.get() <= 0) {
return;
}
@ -237,9 +238,9 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public void expungeHistoricalVersions(RequestDetails theRequestDetails, List<Long> theHistoricalIds, AtomicInteger theRemainingCount) {
for (Long next : theHistoricalIds) {
expungeHistoricalVersion(theRequestDetails, next, theRemainingCount);
public void expungeHistoricalVersions(RequestDetails theRequestDetails, List<ResourcePersistentId> theHistoricalIds, AtomicInteger theRemainingCount) {
for (ResourcePersistentId next : theHistoricalIds) {
expungeHistoricalVersion(theRequestDetails, next.getIdAsLong(), theRemainingCount);
if (theRemainingCount.get() <= 0) {
return;
}
@ -256,7 +257,7 @@ public class ResourceExpungeService implements IResourceExpungeService {
ourLog.info("Expunging current version of resource {}", resource.getIdDt().getValue());
deleteAllSearchParams(resource.getResourceId());
deleteAllSearchParams(new ResourcePersistentId(resource.getResourceId()));
resource.getTags().clear();
if (resource.getForcedId() != null) {
@ -271,48 +272,48 @@ public class ResourceExpungeService implements IResourceExpungeService {
@Override
@Transactional
public void deleteAllSearchParams(Long theResourceId) {
ResourceTable resource = myResourceTableDao.findById(theResourceId).orElse(null);
public void deleteAllSearchParams(ResourcePersistentId theResourceId) {
ResourceTable resource = myResourceTableDao.findById(theResourceId.getIdAsLong()).orElse(null);
if (resource == null || resource.isParamsUriPopulated()) {
myResourceIndexedSearchParamUriDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamUriDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsCoordsPopulated()) {
myResourceIndexedSearchParamCoordsDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamCoordsDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsDatePopulated()) {
myResourceIndexedSearchParamDateDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamDateDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsNumberPopulated()) {
myResourceIndexedSearchParamNumberDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamNumberDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsQuantityPopulated()) {
myResourceIndexedSearchParamQuantityDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamQuantityDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsQuantityNormalizedPopulated()) {
myResourceIndexedSearchParamQuantityNormalizedDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamQuantityNormalizedDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsStringPopulated()) {
myResourceIndexedSearchParamStringDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamStringDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsTokenPopulated()) {
myResourceIndexedSearchParamTokenDao.deleteByResourceId(theResourceId);
myResourceIndexedSearchParamTokenDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsComboStringUniquePresent()) {
myResourceIndexedCompositeStringUniqueDao.deleteByResourceId(theResourceId);
myResourceIndexedCompositeStringUniqueDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isParamsComboTokensNonUniquePresent()) {
myResourceIndexedComboTokensNonUniqueDao.deleteByResourceId(theResourceId);
myResourceIndexedComboTokensNonUniqueDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
mySearchParamPresentDao.deleteByResourceId(theResourceId);
mySearchParamPresentDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isHasLinks()) {
myResourceLinkDao.deleteByResourceId(theResourceId);
myResourceLinkDao.deleteByResourceId(theResourceId.getIdAsLong());
}
if (resource == null || resource.isHasTags()) {
myResourceTagDao.deleteByResourceId(theResourceId);
myResourceTagDao.deleteByResourceId(theResourceId.getIdAsLong());
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/SearchScrollQueryExecutorAdaptor.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao.search;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.search.builder.ISearchQueryExecutor;
import org.hibernate.search.engine.backend.common.DocumentReference;
import org.hibernate.search.engine.search.query.SearchScroll;

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/job/DeleteExpungeProcessor.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.dao.expunge.ResourceForeignKey;
import ca.uhn.fhir.jpa.dao.expunge.ResourceTableFKProvider;
import ca.uhn.fhir.jpa.dao.index.IJpaIdHelperService;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -84,10 +85,11 @@ public class DeleteExpungeProcessor implements ItemProcessor<List<Long>, List<St
return;
}
List<ResourcePersistentId> targetPidsAsResourceIds = ResourcePersistentId.fromLongList(thePids);
List<ResourceLink> conflictResourceLinks = Collections.synchronizedList(new ArrayList<>());
PartitionRunner partitionRunner = new PartitionRunner(PROCESS_NAME, THREAD_PREFIX, myDaoConfig.getExpungeBatchSize(), myDaoConfig.getExpungeThreadCount());
Consumer<List<Long>> listConsumer = someTargetPids -> findResourceLinksWithTargetPidIn(thePids, someTargetPids, conflictResourceLinks);
partitionRunner.runInPartitionedThreads(thePids, listConsumer);
Consumer<List<ResourcePersistentId>> listConsumer = someTargetPids -> findResourceLinksWithTargetPidIn(targetPidsAsResourceIds, someTargetPids, conflictResourceLinks);
partitionRunner.runInPartitionedThreads(targetPidsAsResourceIds, listConsumer);
if (conflictResourceLinks.isEmpty()) {
return;
@ -105,14 +107,16 @@ public class DeleteExpungeProcessor implements ItemProcessor<List<Long>, List<St
targetResourceId + " because " + sourceResourceId + " refers to it via the path " + firstConflict.getSourcePath());
}
public void findResourceLinksWithTargetPidIn(List<Long> theAllTargetPids, List<Long> theSomeTargetPids, List<ResourceLink> theConflictResourceLinks) {
public void findResourceLinksWithTargetPidIn(List<ResourcePersistentId> theAllTargetPids, List<ResourcePersistentId> theSomeTargetPids, List<ResourceLink> theConflictResourceLinks) {
List<Long> allTargetPidsAsLongs = ResourcePersistentId.toLongList(theAllTargetPids);
List<Long> someTargetPidsAsLongs = ResourcePersistentId.toLongList(theSomeTargetPids);
// We only need to find one conflict, so if we found one already in an earlier partition run, we can skip the rest of the searches
if (theConflictResourceLinks.isEmpty()) {
List<ResourceLink> conflictResourceLinks = myResourceLinkDao.findWithTargetPidIn(theSomeTargetPids).stream()
List<ResourceLink> conflictResourceLinks = myResourceLinkDao.findWithTargetPidIn(someTargetPidsAsLongs).stream()
// Filter out resource links for which we are planning to delete the source.
// theAllTargetPids contains a list of all the pids we are planning to delete. So we only want
// to consider a link to be a conflict if the source of that link is not in theAllTargetPids.
.filter(link -> !theAllTargetPids.contains(link.getSourceResourcePid()))
.filter(link -> !allTargetPidsAsLongs.contains(link.getSourceResourcePid()))
.collect(Collectors.toList());
// We do this in two steps to avoid lock contention on this synchronized list

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BulkExportJobEntity.java
View File

@ -78,7 +78,7 @@ public class BulkExportJobEntity implements Serializable {
@Column(name = "STATUS_TIME", nullable = false)
private Date myStatusTime;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "EXP_TIME", nullable = false)
@Column(name = "EXP_TIME", nullable = true)
private Date myExpiry;
@Column(name = "REQUEST", nullable = false, length = REQUEST_LENGTH)
private String myRequest;
@ -146,7 +146,7 @@ public class BulkExportJobEntity implements Serializable {
if (myStatus != null) {
b.append("status", myStatus + " " + new InstantType(myStatusTime).getValueAsString());
}
b.append("created", new InstantType(myExpiry).getValueAsString());
b.append("created", new InstantType(myCreated).getValueAsString());
b.append("expiry", new InstantType(myExpiry).getValueAsString());
b.append("request", myRequest);
b.append("since", mySince);

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -289,6 +289,11 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.addColumn("20220416.1", "CUR_GATED_STEP_ID")
.nullable()
.type(ColumnTypeEnum.STRING, 100);
//Make Job expiry nullable so that we can prevent job expiry by using a null value.
version
.onTable("HFJ_BLK_EXPORT_JOB").modifyColumn("20220423.1", "EXP_TIME").nullable().withType(ColumnTypeEnum.DATE_TIMESTAMP);
}
/**

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
View File

@ -546,17 +546,12 @@ public class QueryStack {
//Ensure that the name of the search param
// (e.g. the `code` in Patient?_has:Observation:subject:code=sys|val)
// exists on the target resource type.
RuntimeSearchParam owningParameterDef = mySearchParamRegistry.getActiveSearchParam(targetResourceType, paramName);
if (owningParameterDef == null) {
throw new InvalidRequestException(Msg.code(1209) + "Unknown parameter name: " + targetResourceType + ':' + parameterName);
}
RuntimeSearchParam owningParameterDef = mySearchParamRegistry.getRuntimeSearchParam(targetResourceType, paramName);
//Ensure that the name of the back-referenced search param on the target (e.g. the `subject` in Patient?_has:Observation:subject:code=sys|val)
//exists on the target resource.
RuntimeSearchParam joiningParameterDef = mySearchParamRegistry.getActiveSearchParam(targetResourceType, paramReference);
if (joiningParameterDef == null) {
throw new InvalidRequestException(Msg.code(1210) + "Unknown parameter name: " + targetResourceType + ':' + paramReference);
}
//exists on the target resource, or in the top-level Resource resource.
mySearchParamRegistry.getRuntimeSearchParam(targetResourceType, paramReference);
IQueryParameterAnd<?> parsedParam = JpaParamUtil.parseQueryParams(mySearchParamRegistry, myFhirContext, owningParameterDef, paramName, parameters);

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchQueryExecutors.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.search.builder;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.apache.commons.lang3.Validate;

2
hapi-fhir-jpaserver-cql/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-model/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/HibernateSearchIndexWriter.java
View File

@ -131,12 +131,12 @@ public class HibernateSearchIndexWriter {
nestedQtyNode.addValue(QTY_SYSTEM, theValue.getSystem());
nestedQtyNode.addValue(QTY_VALUE, theValue.getValue());
if ( ! myModelConfig.getNormalizedQuantitySearchLevel().storageOrSearchSupported()) { return; }
if ( ! myModelConfig.getNormalizedQuantitySearchLevel().storageOrSearchSupported()) { continue; }
//-- convert the value/unit to the canonical form if any
Pair canonicalForm = UcumServiceUtil.getCanonicalForm(theValue.getSystem(),
BigDecimal.valueOf(theValue.getValue()), theValue.getCode());
if (canonicalForm == null) { return; }
if (canonicalForm == null) { continue; }
double canonicalValue = Double.parseDouble(canonicalForm.getValue().asDecimal());
String canonicalUnits = canonicalForm.getCode();

2
hapi-fhir-jpaserver-searchparam/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

173
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
View File

@ -49,9 +49,14 @@ import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.mockito.ArgumentCaptor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -63,6 +68,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
@ -74,6 +80,7 @@ import java.util.stream.Stream;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -127,10 +134,40 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
}
@Test
public void testPurgeExpiredJobs() {
// Create an expired job
/**
* Returns parameters in format of:
*
* 1. Bulk Job status
* 2. Expiry Date that should be set on the job
* 3. How many jobs should be left after running a purge pass.
*/
static Stream<Arguments> bulkExpiryStatusProvider() {
Date previousTime = DateUtils.addHours(new Date(), -1);
Date futureTime = DateUtils.addHours(new Date(), 50);
return Stream.of(
//Finished jobs with standard expiries.
Arguments.of(BulkExportJobStatusEnum.COMPLETE, previousTime, 0),
Arguments.of(BulkExportJobStatusEnum.COMPLETE, futureTime, 1),
//Finished job with null expiry
Arguments.of(BulkExportJobStatusEnum.COMPLETE, null, 1),
//Expired errored job.
Arguments.of(BulkExportJobStatusEnum.ERROR, previousTime, 0),
//Unexpired errored job.
Arguments.of(BulkExportJobStatusEnum.ERROR, futureTime, 1),
//Expired job but currently still running.
Arguments.of(BulkExportJobStatusEnum.BUILDING, previousTime, 1)
);
}
@ParameterizedTest
@MethodSource("bulkExpiryStatusProvider")
public void testBulkExportExpiryRules(BulkExportJobStatusEnum theStatus, Date theExpiry, int theExpectedCountAfterPurge) {
runInTransaction(() -> {
Binary b = new Binary();
@ -138,8 +175,8 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
String binaryId = myBinaryDao.create(b, new SystemRequestDetails()).getId().toUnqualifiedVersionless().getValue();
BulkExportJobEntity job = new BulkExportJobEntity();
job.setStatus(BulkExportJobStatusEnum.COMPLETE);
job.setExpiry(DateUtils.addHours(new Date(), -1));
job.setStatus(theStatus);
job.setExpiry(theExpiry);
job.setJobId(UUID.randomUUID().toString());
job.setCreated(new Date());
job.setRequest("$export");
@ -156,7 +193,6 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
file.setCollection(collection);
file.setResource(binaryId);
myBulkExportCollectionFileDao.save(file);
});
// Check that things were created
@ -170,14 +206,13 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
// Run a purge pass
myBulkDataExportJobSchedulingHelper.purgeExpiredFiles();
// Check that things were deleted
// Check for correct remaining resources based on inputted rules from method provider.
runInTransaction(() -> {
assertEquals(0, myResourceTableDao.count());
assertThat(myBulkExportJobDao.findAll(), Matchers.empty());
assertEquals(0, myBulkExportCollectionDao.count());
assertEquals(0, myBulkExportCollectionFileDao.count());
assertEquals(theExpectedCountAfterPurge, myResourceTableDao.count());
assertEquals(theExpectedCountAfterPurge, myBulkExportJobDao.findAll().size());
assertEquals(theExpectedCountAfterPurge, myBulkExportCollectionDao.count());
assertEquals(theExpectedCountAfterPurge, myBulkExportCollectionFileDao.count());
});
}
@Test
@ -423,7 +458,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
// Fetch the job again
status = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
assertEquals(BulkExportJobStatusEnum.COMPLETE, status.getStatus());
assertEquals(5, status.getFiles().size());
assertEquals(7, status.getFiles().size());
// Iterate over the files
for (IBulkDataExportSvc.FileEntry next : status.getFiles()) {
@ -443,6 +478,12 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
} else if ("CareTeam".equals(next.getResourceType())) {
assertThat(nextContents, containsString("\"id\":\"CT0\""));
assertEquals(16, nextContents.split("\n").length);
} else if ("Practitioner".equals(next.getResourceType())) {
assertThat(nextContents, containsString("\"id\":\"PRACT0\""));
assertEquals(11, nextContents.split("\n").length);
} else if ("Organization".equals(next.getResourceType())) {
assertThat(nextContents, containsString("\"id\":\"ORG0\""));
assertEquals(11, nextContents.split("\n").length);
} else if ("Group".equals(next.getResourceType())) {
assertThat(nextContents, containsString("\"id\":\"G0\""));
assertEquals(1, nextContents.split("\n").length);
@ -702,7 +743,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
bulkDataExportOptions.setSince(null);
bulkDataExportOptions.setFilters(null);
bulkDataExportOptions.setGroupId(myPatientGroupId);
bulkDataExportOptions.setExpandMdm(true);
bulkDataExportOptions.setExpandMdm(false);
bulkDataExportOptions.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(bulkDataExportOptions);
@ -727,6 +768,58 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
assertThat(nextContents, is(containsString("IMM8")));
}
@Test
public void testGroupBatchJobFindsForwardReferencesIfNeeded() {
createResources();
// Create a bulk job
BulkDataExportOptions bulkDataExportOptions = new BulkDataExportOptions();
bulkDataExportOptions.setOutputFormat(null);
bulkDataExportOptions.setResourceTypes(Sets.newHashSet("Practitioner","Organization", "Observation"));
bulkDataExportOptions.setSince(null);
bulkDataExportOptions.setFilters(null);
bulkDataExportOptions.setGroupId(myPatientGroupId);
bulkDataExportOptions.setExpandMdm(false);
//FIXME GGG Make sure this works with MDM Enabled as well.
bulkDataExportOptions.setExportStyle(BulkDataExportOptions.ExportStyle.GROUP);
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(bulkDataExportOptions);
myBulkDataExportJobSchedulingHelper.startSubmittedJobs();
awaitAllBulkJobCompletions();
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
assertThat(jobInfo.getStatus(), equalTo(BulkExportJobStatusEnum.COMPLETE));
assertThat(jobInfo.getFiles().size(), equalTo(3));
// Iterate over the files
String nextContents = getBinaryContents(jobInfo, 0);
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Practitioner")));
assertThat(nextContents, is(containsString("PRACT0")));
assertThat(nextContents, is(containsString("PRACT2")));
assertThat(nextContents, is(containsString("PRACT4")));
assertThat(nextContents, is(containsString("PRACT6")));
assertThat(nextContents, is(containsString("PRACT8")));
nextContents = getBinaryContents(jobInfo, 1);
assertThat(jobInfo.getFiles().get(1).getResourceType(), is(equalTo("Organization")));
assertThat(nextContents, is(containsString("ORG0")));
assertThat(nextContents, is(containsString("ORG2")));
assertThat(nextContents, is(containsString("ORG4")));
assertThat(nextContents, is(containsString("ORG6")));
assertThat(nextContents, is(containsString("ORG8")));
//Ensure _backwards_ references still work
nextContents = getBinaryContents(jobInfo, 2);
assertThat(jobInfo.getFiles().get(2).getResourceType(), is(equalTo("Observation")));
assertThat(nextContents, is(containsString("OBS0")));
assertThat(nextContents, is(containsString("OBS2")));
assertThat(nextContents, is(containsString("OBS4")));
assertThat(nextContents, is(containsString("OBS6")));
assertThat(nextContents, is(containsString("OBS8")));
}
@Test
public void testGroupBatchJobMdmExpansionIdentifiesGoldenResources() {
createResources();
@ -867,6 +960,14 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
assertThat(nextContents, is(containsString("CT4")));
assertThat(nextContents, is(containsString("CT6")));
assertThat(nextContents, is(containsString("CT8")));
//These should be brought in via MDM.
assertThat(nextContents, is(containsString("CT1")));
assertThat(nextContents, is(containsString("CT3")));
assertThat(nextContents, is(containsString("CT5")));
assertThat(nextContents, is(containsString("CT7")));
assertThat(nextContents, is(containsString("CT9")));
}
@ -1209,13 +1310,23 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
}
private void createResources() {
SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
Group group = new Group();
group.setId("G0");
//Manually create a Practitioner
IIdType goldenPractId = createPractitionerWithIndex(999);
//Manually create an Organization
IIdType goldenOrgId = createOrganizationWithIndex(999);
//Manually create a golden record
Patient goldenPatient = new Patient();
goldenPatient.setId("PAT999");
SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
goldenPatient.setGeneralPractitioner(Collections.singletonList(new Reference(goldenPractId.toVersionless())));
goldenPatient.setManagingOrganization(new Reference(goldenOrgId.toVersionless()));
DaoMethodOutcome g1Outcome = myPatientDao.update(goldenPatient, srd);
Long goldenPid = runInTransaction(() -> myIdHelperService.getPidOrNull(g1Outcome.getResource()));
@ -1225,7 +1336,9 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
createCareTeamWithIndex(999, g1Outcome.getId());
for (int i = 0; i < 10; i++) {
DaoMethodOutcome patientOutcome = createPatientWithIndex(i);
IIdType orgId = createOrganizationWithIndex(i);
IIdType practId = createPractitionerWithIndex(i);
DaoMethodOutcome patientOutcome = createPatientWithIndexAndGPAndManagingOrganization(i, practId, orgId);
IIdType patId = patientOutcome.getId().toUnqualifiedVersionless();
Long sourcePid = runInTransaction(() -> myIdHelperService.getPidOrNull(patientOutcome.getResource()));
@ -1254,7 +1367,9 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
//Create some nongroup patients MDM linked to a different golden resource. They shouldnt be included in the query.
for (int i = 0; i < 5; i++) {
int index = 1000 + i;
DaoMethodOutcome patientOutcome = createPatientWithIndex(index);
IIdType orgId = createOrganizationWithIndex(i);
IIdType practId = createPractitionerWithIndex(i);
DaoMethodOutcome patientOutcome = createPatientWithIndexAndGPAndManagingOrganization(index, practId, orgId);
IIdType patId = patientOutcome.getId().toUnqualifiedVersionless();
Long sourcePid = runInTransaction(() -> myIdHelperService.getPidOrNull(patientOutcome.getResource()));
linkToGoldenResource(goldenPid2, sourcePid);
@ -1271,12 +1386,26 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
}
}
private DaoMethodOutcome createPatientWithIndex(int i) {
private IIdType createPractitionerWithIndex(int theIndex) {
Practitioner pract = new Practitioner();
pract.setId("PRACT" + theIndex);
return myPractitionerDao.update(pract, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.defaultPartition())).getId();
}
private IIdType createOrganizationWithIndex(int theIndex) {
Organization org = new Organization();
org.setId("ORG" + theIndex);
return myOrganizationDao.update(org, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.defaultPartition())).getId();
}
private DaoMethodOutcome createPatientWithIndexAndGPAndManagingOrganization(int theIndex, IIdType thePractId, IIdType theOrgId) {
Patient patient = new Patient();
patient.setId("PAT" + i);
patient.setGender(i % 2 == 0 ? Enumerations.AdministrativeGender.MALE : Enumerations.AdministrativeGender.FEMALE);
patient.addName().setFamily("FAM" + i);
patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
patient.setId("PAT" + theIndex);
patient.setGender(theIndex % 2 == 0 ? Enumerations.AdministrativeGender.MALE : Enumerations.AdministrativeGender.FEMALE);
patient.addName().setFamily("FAM" + theIndex);
patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + theIndex);
patient.setManagingOrganization(new Reference(theOrgId.toVersionless()));
patient.setGeneralPractitioner(Collections.singletonList(new Reference(thePractId.toVersionless())));
return myPatientDao.update(patient, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.defaultPartition()));
}

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java
View File

@ -499,7 +499,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
myPatientDao.search(params);
fail();
} catch (InvalidRequestException e) {
assertEquals(Msg.code(1210) + "Unknown parameter name: Observation:soooooobject", e.getMessage());
assertEquals(Msg.code(1209) + "Unknown parameter name: Observation:soooooobject", e.getMessage());
}
}

7
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeHookTest.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.test.BaseJpaDstu3Test;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.test.concurrency.PointcutLatch;
import org.hl7.fhir.dstu3.model.Patient;
@ -61,7 +62,7 @@ public class ExpungeHookTest extends BaseJpaDstu3Test {
myEverythingLatch.setExpectedCount(1);
ExpungeOptions options = new ExpungeOptions();
options.setExpungeEverything(true);
myExpungeService.expunge(null, null, null, options, null);
myExpungeService.expunge(null, null, options, null);
myEverythingLatch.awaitExpected();
assertPatientGone(id);
@ -94,7 +95,7 @@ public class ExpungeHookTest extends BaseJpaDstu3Test {
// Expunge everything with the service.
myEverythingLatch.setExpectedCount(1);
myExpungeService.expunge(null, null, null, options, mySrd);
myExpungeService.expunge(null, null, options, mySrd);
myEverythingLatch.awaitExpected();
assertPatientGone(id);
@ -122,7 +123,7 @@ public class ExpungeHookTest extends BaseJpaDstu3Test {
options.setExpungeDeletedResources(true);
myExpungeResourceLatch.setExpectedCount(2);
myExpungeService.expunge("Patient", expungeId.getIdPartAsLong(), null, options, null);
myExpungeService.expunge("Patient", new ResourcePersistentId(expungeId.getIdPartAsLong()), options, null);
HookParams hookParams = myExpungeResourceLatch.awaitExpected().get(0);
IIdType hookId = hookParams.get(IIdType.class);

33
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/expunge/PartitionRunnerTest.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.test.concurrency.PointcutLatch;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.builder.ToStringBuilder;
@ -34,8 +35,8 @@ public class PartitionRunnerTest {
@Test
public void emptyList() {
List<Long> resourceIds = buildPidList(0);
Consumer<List<Long>> partitionConsumer = buildPartitionConsumer(myLatch);
List<ResourcePersistentId> resourceIds = buildPidList(0);
Consumer<List<ResourcePersistentId>> partitionConsumer = buildPartitionConsumer(myLatch);
myLatch.setExpectedCount(0);
getPartitionRunner().runInPartitionedThreads(resourceIds, partitionConsumer);
@ -54,19 +55,19 @@ public class PartitionRunnerTest {
return new PartitionRunner("TEST", "test", theBatchSize, theThreadCount);
}
private List<Long> buildPidList(int size) {
List<Long> list = new ArrayList<>();
private List<ResourcePersistentId> buildPidList(int size) {
List<ResourcePersistentId> list = new ArrayList<>();
for (long i = 0; i < size; ++i) {
list.add(i + 1);
list.add(new ResourcePersistentId(i + 1));
}
return list;
}
@Test
public void oneItem() throws InterruptedException {
List<Long> resourceIds = buildPidList(1);
List<ResourcePersistentId> resourceIds = buildPidList(1);
Consumer<List<Long>> partitionConsumer = buildPartitionConsumer(myLatch);
Consumer<List<ResourcePersistentId>> partitionConsumer = buildPartitionConsumer(myLatch);
myLatch.setExpectedCount(1);
getPartitionRunner().runInPartitionedThreads(resourceIds, partitionConsumer);
PartitionCall partitionCall = (PartitionCall) PointcutLatch.getLatchInvocationParameter(myLatch.awaitExpected());
@ -77,9 +78,9 @@ public class PartitionRunnerTest {
@Test
public void twoItems() throws InterruptedException {
List<Long> resourceIds = buildPidList(2);
List<ResourcePersistentId> resourceIds = buildPidList(2);
Consumer<List<Long>> partitionConsumer = buildPartitionConsumer(myLatch);
Consumer<List<ResourcePersistentId>> partitionConsumer = buildPartitionConsumer(myLatch);
myLatch.setExpectedCount(1);
getPartitionRunner().runInPartitionedThreads(resourceIds, partitionConsumer);
PartitionCall partitionCall = (PartitionCall) PointcutLatch.getLatchInvocationParameter(myLatch.awaitExpected());
@ -89,9 +90,9 @@ public class PartitionRunnerTest {
@Test
public void tenItemsBatch5() throws InterruptedException {
List<Long> resourceIds = buildPidList(10);
List<ResourcePersistentId> resourceIds = buildPidList(10);
Consumer<List<Long>> partitionConsumer = buildPartitionConsumer(myLatch);
Consumer<List<ResourcePersistentId>> partitionConsumer = buildPartitionConsumer(myLatch);
myLatch.setExpectedCount(2);
getPartitionRunner(5).runInPartitionedThreads(resourceIds, partitionConsumer);
List<HookParams> calls = myLatch.awaitExpected();
@ -106,13 +107,13 @@ public class PartitionRunnerTest {
@Test
public void nineItemsBatch5() throws InterruptedException {
List<Long> resourceIds = buildPidList(9);
List<ResourcePersistentId> resourceIds = buildPidList(9);
// We don't care in which order, but one partition size should be
// 5 and one should be 4
Set<Integer> nums = Sets.newHashSet(5, 4);
Consumer<List<Long>> partitionConsumer = buildPartitionConsumer(myLatch);
Consumer<List<ResourcePersistentId>> partitionConsumer = buildPartitionConsumer(myLatch);
myLatch.setExpectedCount(2);
getPartitionRunner(5).runInPartitionedThreads(resourceIds, partitionConsumer);
List<HookParams> calls = myLatch.awaitExpected();
@ -127,9 +128,9 @@ public class PartitionRunnerTest {
@Test
public void tenItemsOneThread() throws InterruptedException {
List<Long> resourceIds = buildPidList(10);
List<ResourcePersistentId> resourceIds = buildPidList(10);
Consumer<List<Long>> partitionConsumer = buildPartitionConsumer(myLatch);
Consumer<List<ResourcePersistentId>> partitionConsumer = buildPartitionConsumer(myLatch);
myLatch.setExpectedCount(2);
getPartitionRunner(5, 1).runInPartitionedThreads(resourceIds, partitionConsumer);
List<HookParams> calls = myLatch.awaitExpected();
@ -145,7 +146,7 @@ public class PartitionRunnerTest {
}
}
private Consumer<List<Long>> buildPartitionConsumer(PointcutLatch latch) {
private Consumer<List<ResourcePersistentId>> buildPartitionConsumer(PointcutLatch latch) {
return list -> latch.call(new PartitionCall(Thread.currentThread().getName(), list.size()));
}

34
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4InterceptorTest.java
View File

@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -32,6 +33,7 @@ import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.doAnswer;
import static org.mockito.Mockito.inOrder;
@ -511,6 +513,7 @@ public class FhirResourceDaoR4InterceptorTest extends BaseJpaR4Test {
Patient p = new Patient();
p.setActive(false);
IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
p = myPatientDao.read(id);
@ -518,6 +521,37 @@ public class FhirResourceDaoR4InterceptorTest extends BaseJpaR4Test {
}
@Test
public void testPrestorageClientAssignedIdInterceptorCanDenyClientAssignedIds() {
Object interceptor = new Object() {
@Hook(Pointcut.STORAGE_PRESTORAGE_CLIENT_ASSIGNED_ID)
public void prestorageClientAssignedId(IBaseResource theResource, RequestDetails theRequest) {
throw new ForbiddenOperationException("Client assigned id rejected.");
}
};
mySrdInterceptorService.registerInterceptor(interceptor);
{//Ensure interceptor is not invoked on create.
Patient serverAssignedPatient = new Patient();
try {
myPatientDao.create(serverAssignedPatient, mySrd);
} catch (ForbiddenOperationException e) {
fail("Interceptor was invoked, and should not have been!");
}
}
{//Ensure attempting to set a client assigned id is rejected by our interceptor.
try {
Patient clientAssignedPatient = new Patient();
clientAssignedPatient.setId("Patient/custom-id");
myPatientDao.update(clientAssignedPatient, mySrd);
fail();
} catch (ForbiddenOperationException e) {
assertEquals("Client assigned id rejected.", e.getMessage());
}
}
}
/**
* Make sure that both JPA interceptors and RestfulServer interceptors can
* get called

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -1157,7 +1157,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
myPatientDao.search(params);
fail();
} catch (InvalidRequestException e) {
assertEquals(Msg.code(1210) + "Unknown parameter name: Observation:soooooobject", e.getMessage());
assertEquals(Msg.code(1209) + "Unknown parameter name: Observation:soooooobject", e.getMessage());
}
}

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoHashesTest.java
View File

@ -639,7 +639,7 @@ public class FhirResourceDaoR4SearchNoHashesTest extends BaseJpaR4Test {
myPatientDao.search(params);
fail();
} catch (InvalidRequestException e) {
assertEquals(Msg.code(1210) + "Unknown parameter name: Observation:soooooobject", e.getMessage());
assertEquals(Msg.code(1209) + "Unknown parameter name: Observation:soooooobject", e.getMessage());
}
}

73
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java
View File

@ -92,6 +92,7 @@ import static ca.uhn.fhir.jpa.model.util.UcumServiceUtil.UCUM_CODESYSTEM_URL;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasSize;
@ -1184,6 +1185,78 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
}
@Test
void testMultipleComponentsHandlesAndOr() {
Observation obs1 = getObservation();
addComponentWithCodeAndQuantity(obs1, "8480-6", 107);
addComponentWithCodeAndQuantity(obs1, "8462-4", 60);
IIdType obs1Id = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
Observation obs2 = getObservation();
addComponentWithCodeAndQuantity(obs2, "8480-6",307);
addComponentWithCodeAndQuantity(obs2, "8462-4",260);
myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
// andClauses
{
String theUrl = "/Observation?component-value-quantity=107&component-value-quantity=60";
List<String> resourceIds = myTestDaoSearch.searchForIds(theUrl);
assertThat("when same component with qtys 107 and 60", resourceIds, hasItem(equalTo(obs1Id.getIdPart())));
}
{
String theUrl = "/Observation?component-value-quantity=107&component-value-quantity=260";
List<String> resourceIds = myTestDaoSearch.searchForIds(theUrl);
assertThat("when same component with qtys 107 and 260", resourceIds, empty());
}
//andAndOrClauses
{
String theUrl = "/Observation?component-value-quantity=107&component-value-quantity=gt50,lt70";
List<String> resourceIds = myTestDaoSearch.searchForIds(theUrl);
assertThat("when same component with qtys 107 and lt70,gt80", resourceIds, hasItem(equalTo(obs1Id.getIdPart())));
}
{
String theUrl = "/Observation?component-value-quantity=50,70&component-value-quantity=260";
List<String> resourceIds = myTestDaoSearch.searchForIds(theUrl);
assertThat("when same component with qtys 50,70 and 260", resourceIds, empty());
}
// multipleAndsWithMultipleOrsEach
{
String theUrl = "/Observation?component-value-quantity=50,60&component-value-quantity=105,107";
List<String> resourceIds = myTestDaoSearch.searchForIds(theUrl);
assertThat("when same component with qtys 50,60 and 105,107", resourceIds, hasItem(equalTo(obs1Id.getIdPart())));
}
{
String theUrl = "/Observation?component-value-quantity=50,60&component-value-quantity=250,260";
List<String> resourceIds = myTestDaoSearch.searchForIds(theUrl);
assertThat("when same component with qtys 50,60 and 250,260", resourceIds, empty());
}
}
private Observation getObservation() {
Observation obs = new Observation();
obs.getCode().addCoding().setCode("85354-9").setSystem("http://loinc.org");
obs.setStatus(Observation.ObservationStatus.FINAL);
return obs;
}
private Quantity getQuantity(double theValue) {
return new Quantity().setValue(theValue).setUnit("mmHg").setSystem("http://unitsofmeasure.org").setCode("mm[Hg]");
}
private Observation.ObservationComponentComponent addComponentWithCodeAndQuantity(Observation theObservation, String theConceptCode, double theQuantityValue) {
Observation.ObservationComponentComponent comp = theObservation.addComponent();
CodeableConcept cc1_1 = new CodeableConcept();
cc1_1.addCoding().setCode(theConceptCode).setSystem("http://loinc.org");
comp.setCode(cc1_1);
comp.setValue(getQuantity(theQuantityValue));
return comp;
}
}

601
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/HibernateSearchSandboxTest.java Normal file
View File

@ -0,0 +1,601 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHibernateSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.storage.test.DaoTestDataBuilder;
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
import ca.uhn.fhir.test.utilities.docker.RequiresDocker;
import com.google.common.collect.Lists;
import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep;
import org.hibernate.search.engine.search.predicate.dsl.MatchPredicateOptionsStep;
import org.hibernate.search.engine.search.predicate.dsl.PredicateFinalStep;
import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
import org.hibernate.search.engine.search.query.SearchResult;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Quantity;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.transaction.PlatformTransactionManager;
import javax.persistence.EntityManager;
import java.util.Collections;
import java.util.List;
import static ca.uhn.fhir.jpa.model.search.HibernateSearchIndexWriter.NESTED_SEARCH_PARAM_ROOT;
import static ca.uhn.fhir.jpa.model.search.HibernateSearchIndexWriter.QTY_CODE;
import static ca.uhn.fhir.jpa.model.search.HibernateSearchIndexWriter.QTY_PARAM_NAME;
import static ca.uhn.fhir.jpa.model.search.HibernateSearchIndexWriter.QTY_SYSTEM;
import static ca.uhn.fhir.jpa.model.search.HibernateSearchIndexWriter.QTY_VALUE;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* Just a sandbox. Never intended to run by pipes
*/
@ExtendWith(SpringExtension.class)
@RequiresDocker
@ContextConfiguration(classes = {
TestR4Config.class,
TestHibernateSearchAddInConfig.Elasticsearch.class,
DaoTestDataBuilder.Config.class,
TestDaoSearch.Config.class
})
@Disabled
public class HibernateSearchSandboxTest extends BaseJpaTest {
@Autowired
private EntityManager myEntityManager;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private ITestDataBuilder myTestDataBuilder;
@Autowired
private IResourceReindexingSvc myResourceReindexingSvc;
@Autowired
@Qualifier("mySystemDaoR4")
private IFhirSystemDao<Bundle, Meta> mySystemDao;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
@Autowired
private IBulkDataExportJobSchedulingHelper myBulkDataScheduleHelper;
@Autowired
@Qualifier("myObservationDaoR4")
private IFhirResourceDao<Observation> myObservationDao;
// @BeforeEach
// public void beforePurgeDatabase() {
// purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataScheduleHelper);
// }
@BeforeEach
public void enableContainsAndLucene() {
myDaoConfig.setAllowContainsSearches(true);
myDaoConfig.setAdvancedLuceneIndexing(true);
}
@Nested
public class NotNestedObjectQueries {
/**
* Show that when there is only one and clause with "or" entries, we can add the shoulds
* at the top level
*/
@Test
public void searchModelingMultipleAndWithOneOringClauseTest() {
String system = "http://loinc.org";
Observation obs1 = new Observation();
obs1.getCode().setText("Systolic Blood Pressure");
obs1.getCode().addCoding().setCode("obs1").setSystem(system).setDisplay("Systolic Blood Pressure");
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setValue(new Quantity(123));
obs1.getNoteFirstRep().setText("obs1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
runInTransaction(() -> {
SearchSession searchSession = Search.session(myEntityManager);
SearchResult<ResourceTable> result = searchSession.search(ResourceTable.class)
.where(f -> f.bool(b -> {
b.must(f.match().field("myResourceType").matching("Observation"));
b.must(f.match().field("sp.code.token.system").matching("http://loinc.org"));
b.should(f.match().field("sp.code.token.code").matching("obs3"));
b.should(f.match().field("sp.code.token.code").matching("obs1"));
b.minimumShouldMatchNumber(1);
}))
.fetchAll();
long totalHitCount = result.total().hitCount();
// List<ResourceTable> hits = result.hits();
});
}
/**
* Shows that when there is multiple "and" clause with "or" entries, we need to group each one in a "must" clause
* to be able to add a minimumShouldMatchNumber(1); to each group
*/
@Test
public void searchModelingMultipleAndWithMultipleOrClausesTest() {
String system = "http://loinc.org";
Observation obs1 = new Observation();
obs1.getCode().setText("Systolic Blood Pressure");
obs1.getCode().addCoding().setCode("obs1").setSystem(system).setDisplay("Systolic Blood Pressure");
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setValue(new Quantity(123));
obs1.getNoteFirstRep().setText("obs1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
runInTransaction(() -> {
SearchSession searchSession = Search.session(myEntityManager);
SearchResult<ResourceTable> result = searchSession.search(ResourceTable.class)
.where(f -> f.bool(b -> {
b.must(f.match().field("myResourceType").matching("Observation"));
b.must(f.match().field("sp.code.token.system").matching("http://loinc.org"));
b.must(f.bool(p -> {
p.should(f.match().field("sp.code.token.code").matching("obs3"));
p.should(f.match().field("sp.code.token.code").matching("obs1"));
p.minimumShouldMatchNumber(1);
}));
b.must(f.bool(p -> {
p.should(f.match().field("sp.code.token.code").matching("obs5"));
p.should(f.match().field("sp.code.token.code").matching("obs1"));
p.minimumShouldMatchNumber(1);
}));
}))
.fetchAll();
long totalHitCount = result.total().hitCount();
// List<ResourceTable> hits = result.hits();
});
}
}
@Nested
public class NestedObjectQueries {
/**
* Show that when there is only one and clause with "or" entries, we can add the shoulds
* at the top level
*/
@Test
public void searchModelingAndMultipleAndWithOneOringClauseTest() {
IIdType myResourceId = myTestDataBuilder.createObservation(myTestDataBuilder.withElementAt("valueQuantity",
myTestDataBuilder.withPrimitiveAttribute("value", 0.6)
// myTestDataBuilder.withPrimitiveAttribute("system", UCUM_CODESYSTEM_URL),
// myTestDataBuilder.withPrimitiveAttribute("code", "mm[Hg]")
));
runInTransaction(() -> {
SearchSession searchSession = Search.session(myEntityManager);
SearchResult<ResourceTable> result = searchSession.search(ResourceTable.class)
.where(f -> f.bool(b -> {
b.must(f.match().field("myResourceType").matching("Observation"));
b.must(f.nested().objectField("nsp.value-quantity")
.nest(f.bool()
.must(f.range().field("nsp.value-quantity.quantity.value").lessThan(0.7))
.should(f.range().field("nsp.value-quantity.quantity.value").between(0.475, 0.525))
.should(f.range().field("nsp.value-quantity.quantity.value").between(0.57, 0.63))
.minimumShouldMatchNumber(1)
));
}))
.fetchAll();
// long totalHitCount = result.total().hitCount();
// List<ResourceTable> hits = result.hits();
});
}
/**
* Shows that when there is multiple "and" clause with "or" entries, we need to group each one in a "must" clause
* to be able to add a minimumShouldMatchNumber(1); to each group
*/
@Test
public void searchModelingMultipleAndWithMultipleOrClausesTest() {
IIdType myResourceId = myTestDataBuilder.createObservation(myTestDataBuilder.withElementAt("valueQuantity",
myTestDataBuilder.withPrimitiveAttribute("value", 0.6)
// myTestDataBuilder.withPrimitiveAttribute("system", UCUM_CODESYSTEM_URL),
// myTestDataBuilder.withPrimitiveAttribute("code", "mm[Hg]")
));
runInTransaction(() -> {
SearchSession searchSession = Search.session(myEntityManager);
SearchResult<ResourceTable> result = searchSession.search(ResourceTable.class)
.where(f -> f.bool(b -> {
b.must(f.match().field("myResourceType").matching("Observation"));
b.must(f.nested().objectField("nsp.value-quantity")
.nest(f.bool()
.must(f.range().field("nsp.value-quantity.quantity.value").lessThan(0.7))
.must(f.bool(p -> {
p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.475, 0.525));
p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.57, 0.63));
p.minimumShouldMatchNumber(1);
}))
.must(f.bool(p -> {
p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.2, 0.8));
p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.7, 0.9));
p.minimumShouldMatchNumber(1);
}))
.minimumShouldMatchNumber(1)
));
}))
.fetchAll();
// long totalHitCount = result.total().hitCount();
// List<ResourceTable> hits = result.hits();
});
// runInTransaction(() -> {
// SearchSession searchSession = Search.session(myEntityManager);
// SearchResult<ResourceTable> result = searchSession.search(ResourceTable.class)
// .where(f -> f.bool(b -> {
// b.must(f.match().field("myResourceType").matching("Observation"));
// b.must(f.bool()
// .must(f.range().field("nsp.value-quantity.quantity.value").lessThan(0.7))
//
// .must(f.bool(p -> {
// p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.475, 0.525));
// p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.57, 0.63));
// p.minimumShouldMatchNumber(1);
// }))
//
// .must(f.bool(p -> {
// p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.2, 0.8));
// p.should(f.range().field("nsp.value-quantity.quantity.value").between(0.7, 0.9));
// p.minimumShouldMatchNumber(1);
// }))
//
// .minimumShouldMatchNumber(1)
// );
// }))
// .fetchAll();
//// long totalHitCount = result.total().hitCount();
//// List<ResourceTable> hits = result.hits();
// });
}
}
/**
* Following code is the beginning of refactoring the queries for cleaner structure, which means
* to try to achieve the clean query structure modeled by previous tests, but using generic methods
*/
@Nested
public class FragmentedCodeNotNested {
private SearchPredicateFactory fact;
@Test
public void searchModelingMultipleAndOneOrClauseTest() {
String system = "http://loinc.org";
Observation obs1 = new Observation();
obs1.getCode().setText("Systolic Blood Pressure");
obs1.getCode().addCoding().setCode("obs1").setSystem(system).setDisplay("Systolic Blood Pressure");
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setValue(new Quantity(123));
obs1.getNoteFirstRep().setText("obs1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
String paramName = "value-quantity";
List<List<IQueryParameterType>> theQuantityAndOrTerms = Lists.newArrayList();
theQuantityAndOrTerms.add(Collections.singletonList(
new QuantityParam().setValue(0.7)));
theQuantityAndOrTerms.add(Lists.newArrayList(
new QuantityParam().setValue(0.5),
new QuantityParam().setValue(0.6)
));
runInTransaction(() -> {
SearchSession searchSession = Search.session(myEntityManager);
SearchResult<ResourceTable> result = searchSession.search(ResourceTable.class)
.where(f -> {
TestPredBuilder builder = new TestPredBuilder(f);
return builder.buildAndOrPredicates(paramName, theQuantityAndOrTerms);
})
.fetchAll();
long totalHitCount = result.total().hitCount();
// List<ResourceTable> hits = result.hits();
});
}
@Test
public void searchModelingMultipleAndMultipleOrClauseTest() {
String system = "http://loinc.org";
Observation obs1 = new Observation();
obs1.getCode().setText("Systolic Blood Pressure");
obs1.getCode().addCoding().setCode("obs1").setSystem(system).setDisplay("Systolic Blood Pressure");
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setValue(new Quantity(123));
obs1.getNoteFirstRep().setText("obs1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
String paramName = "value-quantity";
List<List<IQueryParameterType>> theQuantityAndOrTerms = Lists.newArrayList();
theQuantityAndOrTerms.add(Collections.singletonList(
new QuantityParam().setValue(0.7)));
theQuantityAndOrTerms.add(Lists.newArrayList(
new QuantityParam().setValue(0.5),
new QuantityParam().setValue(0.6)
));
theQuantityAndOrTerms.add(Lists.newArrayList(
new QuantityParam().setValue(0.9),
new QuantityParam().setValue(0.6)
));
runInTransaction(() -> {
SearchSession searchSession = Search.session(myEntityManager);
SearchResult<ResourceTable> result = searchSession.search(ResourceTable.class)
.where(f -> {
TestPredBuilder builder = new TestPredBuilder(f);
return builder.buildAndOrPredicates(paramName, theQuantityAndOrTerms);
})
.fetchAll();
long totalHitCount = result.total().hitCount();
// List<ResourceTable> hits = result.hits();
});
}
}
private static class TestPredBuilder {
private static final double QTY_APPROX_TOLERANCE_PERCENT = .10;
private static final double QTY_TOLERANCE_PERCENT = .05;
SearchPredicateFactory myPredicateFactory;
public TestPredBuilder(SearchPredicateFactory theF) { myPredicateFactory = theF; }
public PredicateFinalStep buildAndOrPredicates(
String theSearchParamName, List<List<IQueryParameterType>> theAndOrTerms) {
boolean isNested = isNested(theSearchParamName);
// we need to know if there is more than one "and" predicate (outer list) with more than one "or" predicate (inner list)
long maxOrPredicateSize = theAndOrTerms.stream().map(List::size).filter(s -> s > 1).count();
BooleanPredicateClausesStep<?> topBool = myPredicateFactory.bool();
topBool.must(myPredicateFactory.match().field("myResourceType").matching("Observation"));
BooleanPredicateClausesStep<?> activeBool = topBool;
if (isNested) {
BooleanPredicateClausesStep<?> nestedBool = myPredicateFactory.bool();
activeBool = nestedBool;
}
for (List<IQueryParameterType> andTerm : theAndOrTerms) {
if (andTerm.size() == 1) {
// buildSinglePredicate
// activeBool.must(myPredicateFactory.match().field("nsp.value-quantity.quantity.value").matching(0.7));
addOnePredicate(activeBool, true, theSearchParamName, andTerm.get(0));
continue;
}
if (maxOrPredicateSize <= 1) {
// this is the only list of or predicates with more than 1 entry so
// no need to separate it in a group. Can be part of main and clauses
for (IQueryParameterType orTerm : andTerm) {
addOnePredicate(activeBool, false, theSearchParamName, orTerm);
}
activeBool.minimumShouldMatchNumber(1);
} else {
// this is not the only list of or predicates with more than 1 entry
// so all of them need to be separated in groups with a minimumShouldMatchNumber(1)
activeBool.must(myPredicateFactory.bool(p -> {
for (IQueryParameterType orTerm : andTerm) {
addOnePredicate(p, false, theSearchParamName, orTerm);
}
p.minimumShouldMatchNumber(1);
}));
}
}
if (isNested) {
topBool.must(myPredicateFactory.nested().objectField("nsp.value-quantity").nest(activeBool));
}
return topBool;
}
private boolean isNested(String theSearchParamName) {
if (theSearchParamName.equals("value-quantity")) {
return true;
}
return false;
}
private void addOnePredicate(BooleanPredicateClausesStep<?> theTopBool, boolean theIsMust,
String theParamName, IQueryParameterType theParameterType) {
if (theParameterType instanceof QuantityParam) {
addQuantityOrClauses(theTopBool, theIsMust, theParamName, theParameterType);
return;
}
throw new IllegalStateException("Shouldn't reach this code");
}
private void addQuantityOrClauses(BooleanPredicateClausesStep<?> theTopBool, boolean theIsMust,
String theSearchParamName, IQueryParameterType theParamType) {
String fieldPath = NESTED_SEARCH_PARAM_ROOT + "." + theSearchParamName + "." + QTY_PARAM_NAME;
QuantityParam qtyParam = QuantityParam.toQuantityParam(theParamType);
ParamPrefixEnum activePrefix = qtyParam.getPrefix() == null ? ParamPrefixEnum.EQUAL : qtyParam.getPrefix();
// if (myModelConfig.getNormalizedQuantitySearchLevel() == NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED) {
// QuantityParam canonicalQty = UcumServiceUtil.toCanonicalQuantityOrNull(qtyParam);
// if (canonicalQty != null) {
// String valueFieldPath = fieldPath + "." + QTY_VALUE_NORM;
// setPrefixedQuantityPredicate(orQuantityTerms, activePrefix, canonicalQty, valueFieldPath);
// orQuantityTerms.must(myPredicateFactory.match()
// .field(fieldPath + "." + QTY_CODE_NORM)
// .matching(canonicalQty.getUnits()));
// return orQuantityTerms;
// }
// }
// not NORMALIZED_QUANTITY_SEARCH_SUPPORTED or non-canonicalizable parameter
addQuantityTerms(theTopBool, theIsMust, activePrefix, qtyParam, fieldPath);
}
private void addQuantityTerms(BooleanPredicateClausesStep<?> theTopBool, boolean theIsMust,
ParamPrefixEnum theActivePrefix, QuantityParam theQtyParam, String theFieldPath) {
String valueFieldPath = theFieldPath + "." + QTY_VALUE;
PredicateFinalStep rangePred = getPrefixedRangePredicate(theActivePrefix, theQtyParam, valueFieldPath);
addMustOrShould(theIsMust, theTopBool, rangePred);
if (isNotBlank(theQtyParam.getSystem())) {
addFieldPredicate(theIsMust, theTopBool, theFieldPath + "." + QTY_SYSTEM, theQtyParam.getSystem());
}
if (isNotBlank(theQtyParam.getUnits())) {
addFieldPredicate(theIsMust, theTopBool, theFieldPath + "." + QTY_CODE, theQtyParam.getUnits());
}
}
private void addFieldPredicate(boolean theIsMust, BooleanPredicateClausesStep<?> theTopBool, String theFieldPath, String theValue) {
MatchPredicateOptionsStep<?> pred = myPredicateFactory.match().field(theFieldPath).matching(theValue);
addMustOrShould(theIsMust, theTopBool, pred);
}
private void addMustOrShould(boolean theIsMust, BooleanPredicateClausesStep<?> theTopBool, PredicateFinalStep thePredicate) {
if (theIsMust) {
theTopBool.must(thePredicate);
} else {
theTopBool.should(thePredicate);
}
}
private PredicateFinalStep getPrefixedRangePredicate(
ParamPrefixEnum thePrefix, QuantityParam theQuantity, String valueFieldPath) {
double value = theQuantity.getValue().doubleValue();
double approxTolerance = value * QTY_APPROX_TOLERANCE_PERCENT;
double defaultTolerance = value * QTY_TOLERANCE_PERCENT;
switch (thePrefix) {
// searches for resource quantity between passed param value +/- 10%
case APPROXIMATE:
return myPredicateFactory.range()
.field(valueFieldPath)
.between(value - approxTolerance, value + approxTolerance);
// searches for resource quantity between passed param value +/- 5%
case EQUAL:
return myPredicateFactory.range()
.field(valueFieldPath)
.between(value - defaultTolerance, value + defaultTolerance);
// searches for resource quantity > param value
case GREATERTHAN:
case STARTS_AFTER: // treated as GREATERTHAN because search doesn't handle ranges
return myPredicateFactory.range()
.field(valueFieldPath)
.greaterThan(value);
// searches for resource quantity not < param value
case GREATERTHAN_OR_EQUALS:
return myPredicateFactory.range()
.field(valueFieldPath)
.atLeast(value);
// searches for resource quantity < param value
case LESSTHAN:
case ENDS_BEFORE: // treated as LESSTHAN because search doesn't handle ranges
return myPredicateFactory.range()
.field(valueFieldPath)
.lessThan(value);
// searches for resource quantity not > param value
case LESSTHAN_OR_EQUALS:
return myPredicateFactory.range()
.field(valueFieldPath)
.atMost(value);
// NOT_EQUAL: searches for resource quantity not between passed param value +/- 5%
case NOT_EQUAL:
return myPredicateFactory.bool(b -> {
b.should(myPredicateFactory.range()
.field(valueFieldPath)
.between(null, value - defaultTolerance));
b.should(myPredicateFactory.range()
.field(valueFieldPath)
.between(value + defaultTolerance, null));
b.minimumShouldMatchNumber(1);
});
}
throw new IllegalStateException("Should not reach here");
}
}
@Override
protected FhirContext getFhirContext() {
return myFhirContext;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
}

111
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/graphql/DaoRegistryGraphQLStorageServicesTest.java
View File

@ -6,6 +6,10 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.BundleUtil;
import org.apache.http.NameValuePair;
import org.apache.http.client.utils.URLEncodedUtils;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Appointment;
import org.hl7.fhir.r4.model.CodeableConcept;
@ -18,22 +22,21 @@ import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.charset.StandardCharsets;
import java.util.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.SEARCH_ID_PARAM;
import static ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices.SEARCH_OFFSET_PARAM;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.when;
@ -56,16 +59,16 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
myDaoConfig.setFilterParameterEnabled(true);
}
private String createSomeAppointment() {
CodeableConcept someCodeableConcept = new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY"));
private void createSomeAppointmentWithType(String id, CodeableConcept type) {
Appointment someAppointment = new Appointment();
someAppointment.setAppointmentType(someCodeableConcept);
return myAppointmentDao.create(someAppointment).getId().getIdPart();
someAppointment.setId(id);
someAppointment.setAppointmentType(type);
myAppointmentDao.update(someAppointment);
}
@Test
public void testListResourcesGraphqlArgumentConversion() {
String appointmentId = createSomeAppointment();
createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));
Argument argument = new Argument("appointment_type", new StringValue("TEST_CODE"));
@ -73,12 +76,12 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
assertFalse(result.isEmpty());
assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
}
@Test
public void testListResourceGraphqlFilterArgument() {
String appointmentId = createSomeAppointment();
createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));
Argument argument = new Argument("_filter", new StringValue("appointment-type eq TEST_CODE"));
@ -86,12 +89,12 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
assertFalse(result.isEmpty());
assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
}
@Test
public void testListResourceGraphqlTokenArgumentWithSystem() {
String appointmentId = createSomeAppointment();
createSomeAppointmentWithType("hapi-1", new CodeableConcept(new Coding("TEST_SYSTEM", "TEST_CODE", "TEST_DISPLAY")));;
Argument argument = new Argument("appointment_type", new StringValue("TEST_SYSTEM|TEST_CODE"));
@ -99,7 +102,7 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
assertFalse(result.isEmpty());
assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals(appointmentId)));
assertTrue(result.stream().anyMatch((it) -> it.getIdElement().getIdPart().equals("hapi-1")));
}
@Test
@ -109,9 +112,9 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
List<IBaseResource> result = new ArrayList<>();
try {
mySvc.listResources(mySrd, "Appointment", Collections.singletonList(argument), result);
fail();
fail("InvalidRequestException should be thrown.");
} catch (InvalidRequestException e) {
assertEquals(Msg.code(1275) + "Unknown GraphQL argument \"test\". Value GraphQL argument for this type are: [_content, _id, _lastUpdated, _profile, _security, _source, _tag, _text, actor, appointment_type, based_on, date, identifier, location, part_status, patient, practitioner, reason_code, reason_reference, service_category, service_type, slot, specialty, status, supporting_info]", e.getMessage());
assertTrue(e.getMessage().contains("Unknown GraphQL argument \"test\"."));
}
}
@ -160,7 +163,7 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
assertFalse(result.isEmpty());
assertEquals(5, result.size());
List<String> expectedId = Arrays.asList("hapi-1", "hapi-2", "hapi-0", "hapi-3", "hapi-4");
List<String> expectedId = Arrays.asList("hapi-1", "hapi-2", "hapi-0", "hapi-3", "hapi-4");
assertTrue(result.stream().allMatch((it) -> expectedId.contains(it.getIdElement().getIdPart())));
//_offset=5
@ -173,7 +176,67 @@ public class DaoRegistryGraphQLStorageServicesTest extends BaseJpaR4Test {
assertFalse(result2.isEmpty());
assertEquals(5, result2.size());
List<String> expectedId2 = Arrays.asList("hapi-5", "hapi-6", "hapi-7", "hapi-8", "hapi-9");
List<String> expectedId2 = Arrays.asList("hapi-5", "hapi-6", "hapi-7", "hapi-8", "hapi-9");
assertTrue(result2.stream().allMatch((it) -> expectedId2.contains(it.getIdElement().getIdPart())));
}
@Test
public void testSearch() {
createSomePatientWithId("hapi-1");
List<Argument> arguments = Collections.emptyList();
IBaseBundle bundle = mySvc.search(mySrd, "Patient", arguments);
List<String> result = toUnqualifiedVersionlessIdValues(bundle);
assertEquals(1, result.size());
assertEquals("Patient/hapi-1", result.get(0));
}
@Test
public void testSearchNextPage() throws URISyntaxException {
createSomePatientWithId("hapi-1");
createSomePatientWithId("hapi-2");
createSomePatientWithId("hapi-3");
List<Argument> arguments = Collections.singletonList(new Argument("_count", new StringValue("1")));
IBaseBundle bundle = mySvc.search(mySrd, "Patient", arguments);
Optional<String> nextUrl = Optional.ofNullable(BundleUtil.getLinkUrlOfType(myFhirContext, bundle, "next"));
assertTrue(nextUrl.isPresent());
List<NameValuePair> params = URLEncodedUtils.parse(new URI(nextUrl.get()), StandardCharsets.UTF_8);
Optional<String> cursorId = params.stream()
.filter(it -> SEARCH_ID_PARAM.equals(it.getName()))
.map(NameValuePair::getValue)
.findAny();
Optional<String> cursorOffset = params.stream()
.filter(it -> SEARCH_OFFSET_PARAM.equals(it.getName()))
.map(NameValuePair::getValue)
.findAny();
assertTrue(cursorId.isPresent());
assertTrue(cursorOffset.isPresent());
List<Argument> nextArguments = Arrays.asList(
new Argument(SEARCH_ID_PARAM, new StringValue(cursorId.get())),
new Argument(SEARCH_OFFSET_PARAM, new StringValue(cursorOffset.get()))
);
Optional<IBaseBundle> nextBundle = Optional.ofNullable(mySvc.search(mySrd, "Patient", nextArguments));
assertTrue(nextBundle.isPresent());
}
@Test
public void testSearchInvalidCursor() {
try {
List<Argument> arguments = Arrays.asList(
new Argument(SEARCH_ID_PARAM, new StringValue("invalid-search-id")),
new Argument(SEARCH_OFFSET_PARAM, new StringValue("0"))
);
mySvc.search(mySrd, "Patient", arguments);
fail("InvalidRequestException should be thrown.");
} catch (InvalidRequestException e) {
assertTrue(e.getMessage().contains("GraphQL Cursor \"invalid-search-id\" does not exist and may have expired"));
}
}
}

31
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/BinaryStorageInterceptorR4Test.java
View File

@ -20,6 +20,8 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.CoreMatchers.notNullValue;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.blankOrNullString;
import static org.hamcrest.Matchers.containsString;
@ -47,6 +49,7 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
super.before();
myStorageSvc.setMinimumBinarySize(10);
myDaoConfig.setExpungeEnabled(true);
myInterceptorRegistry.registerInterceptor(myBinaryStorageInterceptor);
}
@ -56,7 +59,8 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
super.after();
myStorageSvc.setMinimumBinarySize(0);
myDaoConfig.setExpungeEnabled(new DaoConfig().isExpungeEnabled());
myBinaryStorageInterceptor.setAutoDeExternalizeMaximumBytes(new BinaryStorageInterceptor().getAutoDeExternalizeMaximumBytes());
myBinaryStorageInterceptor.setAutoInflateBinariesMaximumSize(new BinaryStorageInterceptor().getAutoInflateBinariesMaximumSize());
myBinaryStorageInterceptor.setAllowAutoInflateBinaries(new BinaryStorageInterceptor().isAllowAutoInflateBinaries());
MemoryBinaryStorageSvcImpl binaryStorageSvc = (MemoryBinaryStorageSvcImpl) myBinaryStorageSvc;
binaryStorageSvc.clear();
@ -109,6 +113,29 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
}
@Test
public void testCreateAndRetrieveBinary_ServerAssignedId_ExternalizedBinary_DoNotRehydrate() {
myBinaryStorageInterceptor.setAllowAutoInflateBinaries(false);
// Create a resource with a big enough binary
Binary binary = new Binary();
binary.setContentType("application/octet-stream");
binary.setData(SOME_BYTES);
DaoMethodOutcome outcome = myBinaryDao.create(binary);
// Make sure it was externalized
IIdType id = outcome.getId().toUnqualifiedVersionless();
String encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getResource());
ourLog.info("Encoded: {}", encoded);
assertThat(encoded, containsString(HapiExtensions.EXT_EXTERNALIZED_BINARY_ID));
assertThat(encoded, not(containsString("\"data\"")));
// Now read it back and make sure it was not de-externalized
Binary output = myBinaryDao.read(id, mySrd);
assertEquals("application/octet-stream", output.getContentType());
assertArrayEquals(null, output.getData());
assertThat(output.getDataElement().getExtensionByUrl(HapiExtensions.EXT_EXTERNALIZED_BINARY_ID), is(notNullValue()));
}
@Test
public void testCreateAndRetrieveBinary_ServerAssignedId_NonExternalizedBinary() {
@ -294,7 +321,7 @@ public class BinaryStorageInterceptorR4Test extends BaseResourceProviderR4Test {
@Test
public void testRetrieveBinaryAboveRetrievalThreshold() {
myBinaryStorageInterceptor.setAutoDeExternalizeMaximumBytes(5);
myBinaryStorageInterceptor.setAutoInflateBinariesMaximumSize(5);
// Create a resource with a big enough binary
Binary binary = new Binary();

75
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/MultitenantServerR4Test.java
View File

@ -1,15 +1,27 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson;
import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.bulk.BulkDataExportOptions;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
import ca.uhn.fhir.util.JsonUtil;
import com.google.common.collect.Sets;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
@ -18,17 +30,23 @@ import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.jetbrains.annotations.NotNull;
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.nio.charset.StandardCharsets;
import java.util.Date;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -36,6 +54,11 @@ import static org.junit.jupiter.api.Assertions.fail;
@SuppressWarnings("Duplicates")
public class MultitenantServerR4Test extends BaseMultitenantResourceProviderR4Test implements ITestDataBuilder {
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
@Autowired
private IBulkDataExportJobSchedulingHelper myBulkDataExportJobSchedulingHelper;
@Override
@AfterEach
public void after() throws Exception {
@ -370,6 +393,56 @@ public class MultitenantServerR4Test extends BaseMultitenantResourceProviderR4Te
assertThat(response.getEntry(), hasSize(2));
}
@Test
public void testBulkExportForDifferentPartitions() throws IOException {
setBulkDataExportProvider();
testBulkExport(TENANT_A);
testBulkExport(TENANT_B);
testBulkExport(JpaConstants.DEFAULT_PARTITION_NAME);
}
private void testBulkExport(String createInPartition) throws IOException {
// Create a patient
IBaseResource patientA = buildPatient(withActiveTrue());
SystemRequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setTenantId(createInPartition);
myPatientDao.create((Patient) patientA, requestDetails);
// Create a bulk job
BulkDataExportOptions options = new BulkDataExportOptions();
options.setResourceTypes(Sets.newHashSet("Patient"));
options.setExportStyle(BulkDataExportOptions.ExportStyle.SYSTEM);
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(options, false, requestDetails);
assertNotNull(jobDetails.getJobId());
// Run a scheduled pass to build the export and wait for completion
myBulkDataExportJobSchedulingHelper.startSubmittedJobs();
myBatchJobHelper.awaitAllBulkJobCompletions(
BatchConstants.BULK_EXPORT_JOB_NAME
);
//perform export-poll-status
HttpGet get = new HttpGet(buildExportUrl(createInPartition, jobDetails.getJobId()));
try (CloseableHttpResponse response = ourHttpClient.execute(get)) {
String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
BulkExportResponseJson responseJson = JsonUtil.deserialize(responseString, BulkExportResponseJson.class);
assertThat(responseJson.getOutput().get(0).getUrl(), containsString(JpaConstants.DEFAULT_PARTITION_NAME + "/Binary/"));
}
}
private void setBulkDataExportProvider() {
BulkDataExportProvider provider = new BulkDataExportProvider();
provider.setBulkDataExportSvcForUnitTests(myBulkDataExportSvc);
provider.setFhirContextForUnitTest(myFhirContext);
ourRestServer.registerProvider(provider);
}
private String buildExportUrl(String createInPartition, String jobId) {
return myClient.getServerBase() + "/" + createInPartition + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?"
+ JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + jobId;
}
private void createConditionWithAllowedUnqualified(IIdType idA) {
myPartitionSettings.setAllowReferencesAcrossPartitions(PartitionSettings.CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
IIdType idB = createResource("Condition", withTenant(TENANT_A), withObservationCode("http://cs", "A"));

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-server-mdm/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server-openapi/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

1
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServerConfiguration.java
View File

@ -54,6 +54,7 @@ import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;

22
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/util/ISearchParamRegistry.java
View File

@ -22,7 +22,9 @@ package ca.uhn.fhir.rest.server.util;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.context.phonetic.IPhoneticEncoder;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import javax.annotation.Nullable;
@ -40,6 +42,7 @@ public interface ISearchParamRegistry {
*/
RuntimeSearchParam getActiveSearchParam(String theResourceName, String theParamName);
/**
* @return Returns all active search params for the given resource
*/
@ -57,7 +60,6 @@ public interface ISearchParamRegistry {
default void requestRefresh() {
}
/**
* When indexing a HumanName, if a StringEncoder is set in the context, then the "phonetic" search parameter will normalize
* the String using this encoder.
@ -101,4 +103,22 @@ public interface ISearchParamRegistry {
@Nullable
RuntimeSearchParam getActiveSearchParamByUrl(String theUrl);
/**
* Find a search param for a resource. First, check the resource itself, then check the top-level `Resource` resource.
*
* @param theResourceType the resource type.
* @param theParamName the search parameter name.
*
* @return the {@link RuntimeSearchParam} that is found.
*/
default RuntimeSearchParam getRuntimeSearchParam(String theResourceType, String theParamName) {
RuntimeSearchParam availableSearchParamDef = getActiveSearchParam(theResourceType, theParamName);
if (availableSearchParamDef == null) {
availableSearchParamDef = getActiveSearchParam("Resource", theParamName);
}
if (availableSearchParamDef == null) {
throw new InvalidRequestException(Msg.code(1209) + "Unknown parameter name: " + theResourceType + ':' + theParamName);
}
return availableSearchParamDef;
}
}

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage-batch2-jobs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage-batch2/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

20
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobCompletionHandler.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.api;
/*-
* #%L
* HAPI FHIR JPA Server - Batch2 Task Processor
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.model.api.IModelJson;
public interface IJobCompletionHandler<PT extends IModelJson> {

2
hapi-fhir-storage-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

92
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java
View File

@ -4,11 +4,13 @@ import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
import ca.uhn.fhir.jpa.api.model.WarmCacheEntry;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.validation.FhirValidator;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.Sets;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
@ -298,6 +300,20 @@ public class DaoConfig {
*/
private boolean myConcurrentBundleValidation;
/**
* Since 6.0.0
*/
private boolean myAllowAutoInflateBinaries = true;
/**
* Since 6.0.0
*/
private long myAutoInflateBinariesMaximumBytes = 10 * FileUtils.ONE_MB;
/**
* Since 6.0.0
*/
private int myBulkExportFileRetentionPeriodHours = 2;
/**
* Constructor
*/
@ -2793,13 +2809,83 @@ public class DaoConfig {
* This setting indicates if a cross-partition subscription can be made.
*
* @see ModelConfig#setCrossPartitionSubscription(boolean)
* @since 7.5.0
* @since 5.7.0
*/
public void setCrossPartitionSubscription(boolean theAllowCrossPartitionSubscription) {
this.myModelConfig.setCrossPartitionSubscription(theAllowCrossPartitionSubscription);
}
public enum StoreMetaSourceInformationEnum {
/**
*
* This setting indicates whether binaries are allowed to be automatically inflated from external storage during requests.
* Default is true.
*
* @since 6.0.0
* @return whether binaries are allowed to be automatically inflated from external storage during requests.
*/
public boolean isAllowAutoInflateBinaries() {
return myAllowAutoInflateBinaries;
}
/**
* This setting indicates whether binaries are allowed to be automatically inflated from external storage during requests.
* Default is true.
*
* @since 6.0.0
* @param theAllowAutoDeExternalizingBinaries the value to set.
*/
public void setAllowAutoInflateBinaries(boolean theAllowAutoDeExternalizingBinaries) {
myAllowAutoInflateBinaries = theAllowAutoDeExternalizingBinaries;
}
/**
* This setting controls how many bytes of binaries will be automatically inflated from external storage during requests.
* which contain binary data.
* Default is 10MB
*
* @since 6.0.0
* @param theAutoInflateBinariesMaximumBytes the maximum number of bytes to de-externalize.
*/
public void setAutoInflateBinariesMaximumBytes(long theAutoInflateBinariesMaximumBytes) {
myAutoInflateBinariesMaximumBytes = theAutoInflateBinariesMaximumBytes;
}
/**
* This setting controls how many bytes of binaries will be automatically inflated from external storage during requests.
* which contain binary data.
* Default is 10MB
*
* @since 6.0.0
* @return the number of bytes to de-externalize during requests.
*/
public long getAutoInflateBinariesMaximumBytes() {
return myAutoInflateBinariesMaximumBytes;
}
/**
* This setting controls how long Bulk Export collection entities will be retained after job start.
* Default is 2 hours. Setting this value to 0 or less will cause Bulk Export collection entities to never be expired.
*
* @since 6.0.0
*/
public int getBulkExportFileRetentionPeriodHours() {
return myBulkExportFileRetentionPeriodHours;
}
/**
* This setting controls how long Bulk Export collection entities will be retained after job start.
* Default is 2 hours. Setting this value to 0 or less will cause Bulk Export collection entities to never be expired.
*
* @since 6.0.0
*/
public void setBulkExportFileRetentionPeriodHours(int theBulkExportFileRetentionPeriodHours) {
myBulkExportFileRetentionPeriodHours = theBulkExportFileRetentionPeriodHours;
}
public enum StoreMetaSourceInformationEnum {
NONE(false, false),
SOURCE_URI(true, false),
REQUEST_ID(false, true),
@ -2889,7 +2975,7 @@ public class DaoConfig {
NON_VERSIONED,
/**
* Tags are stored directly in the resource body (in the {@link ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable}
* Tags are stored directly in the resource body (in the {@link ResourceHistoryTable}
* entry for the resource, meaning that they are not indexed separately, and are versioned with the rest
* of the resource.
*/

25
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/binary/interceptor/BinaryStorageInterceptor.java
View File

@ -76,22 +76,23 @@ public class BinaryStorageInterceptor {
private BinaryAccessProvider myBinaryAccessProvider;
private Class<? extends IPrimitiveType<byte[]>> myBinaryType;
private String myDeferredListKey;
private long myAutoDeExternalizeMaximumBytes = 10 * FileUtils.ONE_MB;
private long myAutoInflateBinariesMaximumBytes = 10 * FileUtils.ONE_MB;
private boolean myAllowAutoInflateBinaries = true;
/**
* Any externalized binaries will be rehydrated if their size is below this thhreshold when
* reading the resource back. Default is 10MB.
*/
public long getAutoDeExternalizeMaximumBytes() {
return myAutoDeExternalizeMaximumBytes;
public long getAutoInflateBinariesMaximumSize() {
return myAutoInflateBinariesMaximumBytes;
}
/**
* Any externalized binaries will be rehydrated if their size is below this thhreshold when
* reading the resource back. Default is 10MB.
*/
public void setAutoDeExternalizeMaximumBytes(long theAutoDeExternalizeMaximumBytes) {
myAutoDeExternalizeMaximumBytes = theAutoDeExternalizeMaximumBytes;
public void setAutoInflateBinariesMaximumSize(long theAutoInflateBinariesMaximumBytes) {
myAutoInflateBinariesMaximumBytes = theAutoInflateBinariesMaximumBytes;
}
@SuppressWarnings("unchecked")
@ -248,6 +249,10 @@ public class BinaryStorageInterceptor {
@Hook(Pointcut.STORAGE_PRESHOW_RESOURCES)
public void preShow(IPreResourceShowDetails theDetails) throws IOException {
if (!isAllowAutoInflateBinaries()) {
return;
}
long unmarshalledByteCount = 0;
for (IBaseResource nextResource : theDetails) {
@ -265,7 +270,7 @@ public class BinaryStorageInterceptor {
throw new InvalidRequestException(Msg.code(1330) + msg);
}
if ((unmarshalledByteCount + blobDetails.getBytes()) < myAutoDeExternalizeMaximumBytes) {
if ((unmarshalledByteCount + blobDetails.getBytes()) < myAutoInflateBinariesMaximumBytes) {
byte[] bytes = myBinaryStorageSvc.fetchBlob(resourceId, attachmentId.get());
nextTarget.setData(bytes);
@ -295,6 +300,14 @@ public class BinaryStorageInterceptor {
return binaryTargets;
}
public void setAllowAutoInflateBinaries(boolean theAllowAutoInflateBinaries) {
myAllowAutoInflateBinaries = theAllowAutoInflateBinaries;
}
public boolean isAllowAutoInflateBinaries() {
return myAllowAutoInflateBinaries;
}
private static class DeferredBinaryTarget {
private final String myBlobId;
private final IBinaryTarget myBinaryTarget;

13
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/bulk/export/provider/BulkDataExportProvider.java
View File

@ -56,6 +56,7 @@ import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES;
import static org.slf4j.LoggerFactory.getLogger;
@ -105,6 +106,15 @@ public class BulkDataExportProvider {
return StringUtils.removeEnd(theRequestDetails.getServerBaseForRequest(), "/");
}
private String getDefaultPartitionServerBase(ServletRequestDetails theRequestDetails) {
if (theRequestDetails.getTenantId() == null || theRequestDetails.getTenantId().equals(JpaConstants.DEFAULT_PARTITION_NAME)) {
return getServerBase(theRequestDetails);
}
else {
return StringUtils.removeEnd(theRequestDetails.getServerBaseForRequest().replace(theRequestDetails.getTenantId(), JpaConstants.DEFAULT_PARTITION_NAME), "/");
}
}
/**
* Group/Id/$export
*/
@ -135,6 +145,7 @@ public class BulkDataExportProvider {
private void validateResourceTypesAllContainPatientSearchParams(Set<String> theResourceTypes) {
if (theResourceTypes != null) {
List<String> badResourceTypes = theResourceTypes.stream()
.filter(resourceType -> !PATIENT_BULK_EXPORT_FORWARD_REFERENCE_RESOURCE_TYPES.contains(resourceType))
.filter(resourceType -> !myBulkDataExportSvc.getPatientCompartmentResources().contains(resourceType))
.collect(Collectors.toList());
@ -195,7 +206,7 @@ public class BulkDataExportProvider {
bulkResponseDocument.setTransactionTime(status.getStatusTime());
bulkResponseDocument.setRequest(status.getRequest());
for (IBulkDataExportSvc.FileEntry nextFile : status.getFiles()) {
String serverBase = getServerBase(theRequestDetails);
String serverBase = getDefaultPartitionServerBase(theRequestDetails);
String nextUrl = serverBase + "/" + nextFile.getResourceId().toUnqualifiedVersionless().getValue();
bulkResponseDocument
.addOutput()

27
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeOperation.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
/*-
* #%L
* HAPI FHIR JPA Server
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -47,16 +48,14 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
private DaoConfig myDaoConfig;
private final String myResourceName;
private final Long myResourceId;
private final Long myVersion;
private final ResourcePersistentId myResourceId;
private final ExpungeOptions myExpungeOptions;
private final RequestDetails myRequestDetails;
private final AtomicInteger myRemainingCount;
public ExpungeOperation(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
public ExpungeOperation(String theResourceName, ResourcePersistentId theResourceId, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
myResourceName = theResourceName;
myResourceId = theResourceId;
myVersion = theVersion;
myExpungeOptions = theExpungeOptions;
myRequestDetails = theRequestDetails;
myRemainingCount = new AtomicInteger(myExpungeOptions.getLimit());
@ -64,7 +63,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
@Override
public ExpungeOutcome call() {
if (myExpungeOptions.isExpungeDeletedResources() && myVersion == null) {
if (myExpungeOptions.isExpungeDeletedResources() && (myResourceId == null || myResourceId.getVersion() == null)) {
expungeDeletedResources();
if (expungeLimitReached()) {
return expungeOutcome();
@ -82,7 +81,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
}
private void expungeDeletedResources() {
List<Long> resourceIds = findHistoricalVersionsOfDeletedResources();
List<ResourcePersistentId> resourceIds = findHistoricalVersionsOfDeletedResources();
deleteHistoricalVersions(resourceIds);
if (expungeLimitReached()) {
@ -92,14 +91,14 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
deleteCurrentVersionsOfDeletedResources(resourceIds);
}
private List<Long> findHistoricalVersionsOfDeletedResources() {
List<Long> retVal = myExpungeDaoService.findHistoricalVersionsOfDeletedResources(myResourceName, myResourceId, myRemainingCount.get());
private List<ResourcePersistentId> findHistoricalVersionsOfDeletedResources() {
List<ResourcePersistentId> retVal = myExpungeDaoService.findHistoricalVersionsOfDeletedResources(myResourceName, myResourceId, myRemainingCount.get());
ourLog.debug("Found {} historical versions", retVal.size());
return retVal;
}
private List<Long> findHistoricalVersionsOfNonDeletedResources() {
return myExpungeDaoService.findHistoricalVersionsOfNonDeletedResources(myResourceName, myResourceId, myVersion, myRemainingCount.get());
private List<ResourcePersistentId> findHistoricalVersionsOfNonDeletedResources() {
return myExpungeDaoService.findHistoricalVersionsOfNonDeletedResources(myResourceName, myResourceId, myRemainingCount.get());
}
private boolean expungeLimitReached() {
@ -111,7 +110,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
}
private void expungeOldVersions() {
List<Long> historicalIds = findHistoricalVersionsOfNonDeletedResources();
List<ResourcePersistentId> historicalIds = findHistoricalVersionsOfNonDeletedResources();
getPartitionRunner().runInPartitionedThreads(historicalIds, partition -> myExpungeDaoService.expungeHistoricalVersions(myRequestDetails, partition, myRemainingCount));
}
@ -120,11 +119,11 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
return new PartitionRunner(PROCESS_NAME, THREAD_PREFIX, myDaoConfig.getExpungeBatchSize(), myDaoConfig.getExpungeThreadCount());
}
private void deleteCurrentVersionsOfDeletedResources(List<Long> theResourceIds) {
private void deleteCurrentVersionsOfDeletedResources(List<ResourcePersistentId> theResourceIds) {
getPartitionRunner().runInPartitionedThreads(theResourceIds, partition -> myExpungeDaoService.expungeCurrentVersionOfResources(myRequestDetails, partition, myRemainingCount));
}
private void deleteHistoricalVersions(List<Long> theResourceIds) {
private void deleteHistoricalVersions(List<ResourcePersistentId> theResourceIds) {
getPartitionRunner().runInPartitionedThreads(theResourceIds, partition -> myExpungeDaoService.expungeHistoricalVersionsOfIds(myRequestDetails, partition, myRemainingCount));
}

17
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeService.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
/*-
* #%L
* HAPI FHIR JPA Server
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
@ -24,6 +24,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -42,28 +43,28 @@ public class ExpungeService {
@Autowired
private ApplicationContext myApplicationContext;
protected ExpungeOperation getExpungeOperation(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
return myApplicationContext.getBean(ExpungeOperation.class, theResourceName, theResourceId, theVersion, theExpungeOptions, theRequestDetails);
protected ExpungeOperation getExpungeOperation(String theResourceName, ResourcePersistentId theResourceId, ExpungeOptions theExpungeOptions, RequestDetails theRequestDetails) {
return myApplicationContext.getBean(ExpungeOperation.class, theResourceName, theResourceId, theExpungeOptions, theRequestDetails);
}
public ExpungeOutcome expunge(String theResourceName, Long theResourceId, Long theVersion, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
ourLog.info("Expunge: ResourceName[{}] Id[{}] Version[{}] Options[{}]", theResourceName, theResourceId, theVersion, theExpungeOptions);
public ExpungeOutcome expunge(String theResourceName, ResourcePersistentId theResourceId, ExpungeOptions theExpungeOptions, RequestDetails theRequest) {
ourLog.info("Expunge: ResourceName[{}] Id[{}] Version[{}] Options[{}]", theResourceName, theResourceId != null ? theResourceId.getId() : null, theResourceId != null ? theResourceId.getVersion() : null, theExpungeOptions);
if (theExpungeOptions.getLimit() < 1) {
throw new InvalidRequestException(Msg.code(1087) + "Expunge limit may not be less than 1. Received expunge limit " + theExpungeOptions.getLimit() + ".");
}
if (theResourceName == null && theResourceId == null && theVersion == null) {
if (theResourceName == null && (theResourceId == null || (theResourceId.getId() == null && theResourceId.getVersion() == null))) {
if (theExpungeOptions.isExpungeEverything()) {
myExpungeEverythingService.expungeEverything(theRequest);
}
}
ExpungeOperation expungeOperation = getExpungeOperation(theResourceName, theResourceId, theVersion, theExpungeOptions, theRequest);
ExpungeOperation expungeOperation = getExpungeOperation(theResourceName, theResourceId, theExpungeOptions, theRequest);
return expungeOperation.call();
}
public void deleteAllSearchParams(Long theResourceId) {
public void deleteAllSearchParams(ResourcePersistentId theResourceId) {
myExpungeDaoService.deleteAllSearchParams(theResourceId);
}
}

20
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/expunge/IExpungeEverythingService.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao.expunge;
/*-
* #%L
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.rest.api.server.RequestDetails;
import javax.annotation.Nullable;

15
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/expunge/IResourceExpungeService.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
/*-
* #%L
* HAPI FHIR JPA Server
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
@ -21,20 +21,21 @@ package ca.uhn.fhir.jpa.dao.expunge;
*/
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
public interface IResourceExpungeService {
List<Long> findHistoricalVersionsOfDeletedResources(String theResourceName, Long theResourceId, int theI);
List<ResourcePersistentId> findHistoricalVersionsOfDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theI);
List<Long> findHistoricalVersionsOfNonDeletedResources(String theResourceName, Long theResourceId, Long theVersion, int theI);
List<ResourcePersistentId> findHistoricalVersionsOfNonDeletedResources(String theResourceName, ResourcePersistentId theResourceId, int theI);
void expungeHistoricalVersions(RequestDetails theRequestDetails, List<Long> thePartition, AtomicInteger theRemainingCount);
void expungeHistoricalVersions(RequestDetails theRequestDetails, List<ResourcePersistentId> thePartition, AtomicInteger theRemainingCount);
void expungeCurrentVersionOfResources(RequestDetails theRequestDetails, List<Long> theResourceIds, AtomicInteger theRemainingCount);
void expungeCurrentVersionOfResources(RequestDetails theRequestDetails, List<ResourcePersistentId> theResourceIds, AtomicInteger theRemainingCount);
void expungeHistoricalVersionsOfIds(RequestDetails theRequestDetails, List<Long> theResourceIds, AtomicInteger theRemainingCount);
void expungeHistoricalVersionsOfIds(RequestDetails theRequestDetails, List<ResourcePersistentId> theResourceIds, AtomicInteger theRemainingCount);
void deleteAllSearchParams(Long theResourceId);
void deleteAllSearchParams(ResourcePersistentId theResourceId);
}

11
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/expunge/PartitionRunner.java
View File

@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
/*-
* #%L
* HAPI FHIR JPA Server
* HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.collect.Lists;
@ -57,7 +58,7 @@ public class PartitionRunner {
myThreadCount = theThreadCount;
}
public void runInPartitionedThreads(List<Long> theResourceIds, Consumer<List<Long>> partitionConsumer) {
public void runInPartitionedThreads(List<ResourcePersistentId> theResourceIds, Consumer<List<ResourcePersistentId>> partitionConsumer) {
List<Callable<Void>> callableTasks = buildCallableTasks(theResourceIds, partitionConsumer);
if (callableTasks.size() == 0) {
@ -92,7 +93,7 @@ public class PartitionRunner {
}
}
private List<Callable<Void>> buildCallableTasks(List<Long> theResourceIds, Consumer<List<Long>> partitionConsumer) {
private List<Callable<Void>> buildCallableTasks(List<ResourcePersistentId> theResourceIds, Consumer<List<ResourcePersistentId>> partitionConsumer) {
List<Callable<Void>> retval = new ArrayList<>();
if (myBatchSize > theResourceIds.size()) {
@ -100,9 +101,9 @@ public class PartitionRunner {
} else {
ourLog.info("Creating batch job of {} entries", theResourceIds.size());
}
List<List<Long>> partitions = Lists.partition(theResourceIds, myBatchSize);
List<List<ResourcePersistentId>> partitions = Lists.partition(theResourceIds, myBatchSize);
for (List<Long> nextPartition : partitions) {
for (List<ResourcePersistentId> nextPartition : partitions) {
if (nextPartition.size() > 0) {
Callable<Void> callableTask = () -> {
ourLog.info(myProcessName + " {} resources", nextPartition.size());

130
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/graphql/DaoRegistryGraphQLStorageServices.java
View File

@ -24,10 +24,18 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.i18n.Msg;
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.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.valueset.BundleTypeEnum;
import ca.uhn.fhir.rest.api.BundleLinks;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateOrListParam;
@ -44,8 +52,9 @@ import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
import org.apache.commons.lang3.Validate;
@ -57,19 +66,27 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.utilities.graphql.Argument;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.graphql.Value;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.TreeSet;
import java.util.stream.Collectors;
import static ca.uhn.fhir.rest.api.Constants.PARAM_COUNT;
import static ca.uhn.fhir.rest.api.Constants.PARAM_FILTER;
public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageServices {
// the constant hasn't already been defined in org.hl7.fhir.core so we define it here
static final String SEARCH_ID_PARAM = "search-id";
static final String SEARCH_OFFSET_PARAM = "search-offset";
private static final int MAX_SEARCH_SIZE = 500;
@Autowired
private FhirContext myContext;
@ -77,6 +94,12 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
private DaoRegistry myDaoRegistry;
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
private IRequestPartitionHelperSvc myPartitionHelperSvc;
@Autowired
private IPagingProvider myPagingProvider;
private IFhirResourceDao<? extends IBaseResource> getDao(String theResourceType) {
RuntimeResourceDefinition typeDef = myContext.getResourceDefinition(theResourceType);
@ -95,19 +118,18 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
return name.replaceAll("-", "_");
}
@Transactional(propagation = Propagation.NEVER)
@Override
public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
private SearchParameterMap buildSearchParams(String theType, List<Argument> theSearchParams) {
List<Argument> resourceSearchParam = theSearchParams.stream()
.filter(it -> !PARAM_COUNT.equals(it.getName()))
.collect(Collectors.toList());
FhirContext fhirContext = myContext;
RuntimeResourceDefinition typeDef = fhirContext.getResourceDefinition(theType);
IFhirResourceDao<? extends IBaseResource> dao = myDaoRegistry.getResourceDao(typeDef.getImplementingClass());
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(MAX_SEARCH_SIZE);
ResourceSearchParams searchParams = mySearchParamRegistry.getActiveSearchParams(typeDef.getName());
for (Argument nextArgument : theSearchParams) {
for (Argument nextArgument : resourceSearchParam) {
if (nextArgument.getName().equals(PARAM_FILTER)) {
String value = nextArgument.getValues().get(0).getValue();
@ -189,8 +211,17 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
params.add(searchParamName, queryParam);
}
return params;
}
@Transactional(propagation = Propagation.NEVER)
@Override
public void listResources(Object theAppInfo, String theType, List<Argument> theSearchParams, List<IBaseResource> theMatches) throws FHIRException {
SearchParameterMap params = buildSearchParams(theType, theSearchParams);
params.setLoadSynchronousUpTo(MAX_SEARCH_SIZE);
RequestDetails requestDetails = (RequestDetails) theAppInfo;
IBundleProvider response = dao.search(params, requestDetails);
IBundleProvider response = getDao(theType).search(params, requestDetails);
Integer size = response.size();
//We set size to null in SearchCoordinatorSvcImpl.executeQuery() if matching results exceeds count
//so don't throw here
@ -201,7 +232,6 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
Validate.notNull(size, "size is null");
theMatches.addAll(response.getResources(0, size));
}
@Transactional(propagation = Propagation.REQUIRED)
@ -228,10 +258,88 @@ public class DaoRegistryGraphQLStorageServices implements IGraphQLStorageService
return new ReferenceResolution(theContext, outcome);
}
private Optional<String> getArgument(List<Argument> params, String name) {
return params.stream()
.filter(it -> name.equals(it.getName()))
.map(it -> it.getValues().get(0).getValue())
.findAny();
}
@Transactional(propagation = Propagation.NEVER)
@Override
public IBaseBundle search(Object theAppInfo, String theType, List<Argument> theSearchParams) throws FHIRException {
throw new NotImplementedOperationException(Msg.code(1277) + "Not yet able to handle this GraphQL request");
RequestDetails requestDetails = (RequestDetails) theAppInfo;
Optional<String> searchIdArgument = getArgument(theSearchParams, SEARCH_ID_PARAM);
Optional<String> searchOffsetArgument = getArgument(theSearchParams, SEARCH_OFFSET_PARAM);
String searchId;
int searchOffset;
int pageSize;
IBundleProvider response;
if (searchIdArgument.isPresent() && searchOffsetArgument.isPresent()) {
searchId = searchIdArgument.get();
searchOffset = Integer.parseInt(searchOffsetArgument.get());
response = Optional.ofNullable(myPagingProvider.retrieveResultList(requestDetails, searchId)).orElseThrow(()->{
String msg = myContext.getLocalizer().getMessageSanitized(DaoRegistryGraphQLStorageServices.class, "invalidGraphqlCursorArgument", searchId);
return new InvalidRequestException(Msg.code(2076) + msg);
});
pageSize = Optional.ofNullable(response.preferredPageSize())
.orElseGet(myPagingProvider::getDefaultPageSize);
} else {
pageSize = getArgument(theSearchParams, "_count").map(Integer::parseInt)
.orElseGet(myPagingProvider::getDefaultPageSize);
SearchParameterMap params = buildSearchParams(theType, theSearchParams);
params.setCount(pageSize);
CacheControlDirective cacheControlDirective = new CacheControlDirective();
cacheControlDirective.parse(requestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL));
RequestPartitionId requestPartitionId = myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(requestDetails, theType, params, null);
response = mySearchCoordinatorSvc.registerSearch(getDao(theType), params, theType, cacheControlDirective, requestDetails, requestPartitionId);
searchOffset = 0;
searchId = myPagingProvider.storeResultList(requestDetails, response);
}
// response.size() may return {@literal null}, in that case use pageSize
String serverBase = requestDetails.getFhirServerBase();
Optional<Integer> numTotalResults = Optional.ofNullable(response.size());
int numToReturn = numTotalResults.map(integer -> Math.min(pageSize, integer - searchOffset)).orElse(pageSize);
BundleLinks links = new BundleLinks(requestDetails.getServerBaseForRequest(), null, RestfulServerUtils.prettyPrintResponse(requestDetails.getServer(), requestDetails), BundleTypeEnum.SEARCHSET);
// RestfulServerUtils.createLinkSelf not suitable here
String linkFormat = "%s/%s?_format=application/json&search-id=%s&search-offset=%d&_count=%d";
String linkSelf = String.format(linkFormat, serverBase, theType, searchId, searchOffset, pageSize);
links.setSelf(linkSelf);
boolean hasNext = numTotalResults.map(total -> (searchOffset + numToReturn) < total).orElse(true);
if (hasNext) {
String linkNext = String.format(linkFormat, serverBase, theType, searchId, searchOffset+numToReturn, pageSize);
links.setNext(linkNext);
}
if (searchOffset > 0) {
String linkPrev = String.format(linkFormat, serverBase, theType, searchId, Math.max(0, searchOffset-pageSize), pageSize);
links.setPrev(linkPrev);
}
List<IBaseResource> resourceList = response.getResources(searchOffset, numToReturn + searchOffset);
IVersionSpecificBundleFactory bundleFactory = myContext.newBundleFactory();
bundleFactory.addRootPropertiesToBundle(response.getUuid(), links, response.size(), response.getPublished());
bundleFactory.addResourcesToBundle(resourceList, BundleTypeEnum.SEARCHSET, serverBase, null, null);
IBaseResource result = bundleFactory.getResourceBundle();
return (IBaseBundle) result;
}
}

2
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE10-SNAPSHOT</version>
<version>6.0.0-PRE11-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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