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Merge branch 'master' into jd-20240905-add-batch-and-chunk-ids-to-logging-context

This commit is contained in:
jdar 2024-09-25 16:20:32 -07:00
parent 9f4630db06 377e44b6ca
commit e148c76a09
118 changed files with 1399 additions and 1043 deletions
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2
hapi-deployable-pom/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
View File

@ -136,6 +136,7 @@ public enum VersionEnum {
V6_8_5,
V6_8_6,
V6_8_7,
V6_8_8,
V6_9_0,

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

@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
@ -12,7 +12,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../pom.xml</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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6218-fix-ref-integrity-on-write-disabled-still-checks-refs.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 6218
jira: SMILE-8370
title: "Previously, when disabling the 'Enforce Referential Integrity on Write' setting, referential integrity was still
partially enforced when posting a resource with an invalid reference. This has now been fixed."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6262-fix-cds-hooks-invocation-when-extension-passed-in-request.yaml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 6262
title: "Previously, when a `extension` was passed in as a part of the CDS hooks request, it would result in a `400 service not found`. This behaviour has now been fixed."

10
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6283-remove-unneeded-fields-from-resource-table.yaml Normal file
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@ -0,0 +1,10 @@
---
type: remove
issue: 6283
title: "Hibernate Search Fulltext fields which were unused
have been removed from indexing.
This will reduce storage usage in Lucene and Elasticsearch.
The fields that were removed are: `myNarrativeTextEdgeNGram`,
`myNarrativeTextNGram`, `myNarrativeTextPhonetic`, `myContentTextEdgeNGram`,
`myContentTextNGram`, `myContentTextPhonetic`.
"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6290-mssql-migration-trim-fix.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 6290
title: "Previously, a specific migration task was using the `TRIM()` function, which does not exist in MSSQL 2012. This was causing migrations targeting MSSQL 2012 to fail.
This has been corrected and replaced with usage of a combination of LTRIM() and RTRIM(). Thanks to Primož Delopst at Better for the contribution!"

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6305-search-missing-qualifier-does-not-work-reference-parameters.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 6305
title: "Previously, when having StorageSettings#getIndexMissingFields() == IndexEnabledEnum.DISABLED (default value)
and attempting to search with the missing qualifier against a resource type with multiple search parameters of type reference,
the returned results would be incorrect. This has been fixed."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/changes.yaml
View File

@ -4,6 +4,7 @@
title: "The version of a few dependencies have been bumped to more recent versions
(dependent HAPI modules listed in brackets):
<ul>
<li>org.hl7.fhir.core (Base): 6.3.18 -&gt; 6.3.23</li>
<li>Bower/Moment.js (hapi-fhir-testpage-overlay): 2.27.0 -&gt; 2.29.4</li>
<li>htmlunit (Base): 3.9.0 -&gt; 3.11.0</li>
<li>Elasticsearch (Base): 8.11.1 -&gt; 8.14.3</li>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -588,8 +588,8 @@ public class PackageInstallerSvcImpl implements IPackageInstallerSvc {
if (statusTypes.isEmpty()) {
return true;
}
// Resource has a null status field
if (statusTypes.get(0).getValue() == null) {
// Resource has no status field, or an explicitly null one
if (!statusTypes.get(0).hasValue() || statusTypes.get(0).getValue() == null) {
return false;
}
// Resource has a status, and we need to check based on type

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

@ -800,14 +800,19 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
subquery.addCustomColumns(1);
subquery.addFromTable(getTable());
String resourceType = theParams.getResourceTablePredicateBuilder().getResourceType();
RuntimeSearchParam paramDefinition =
mySearchParamRegistry.getRuntimeSearchParam(resourceType, theParams.getParamName());
List<String> pathList = paramDefinition.getPathsSplitForResourceType(resourceType);
Condition subQueryCondition = ComboCondition.and(
BinaryCondition.equalTo(
getResourceIdColumn(),
theParams.getResourceTablePredicateBuilder().getResourceIdColumn()),
BinaryCondition.equalTo(
getResourceTypeColumn(),
generatePlaceholder(
theParams.getResourceTablePredicateBuilder().getResourceType())));
BinaryCondition.equalTo(getResourceTypeColumn(), generatePlaceholder(resourceType)),
ComboCondition.or(pathList.stream()
.map(path -> BinaryCondition.equalTo(getColumnSourcePath(), generatePlaceholder(path)))
.toArray(BinaryCondition[]::new)));
subquery.addCondition(subQueryCondition);

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -3,7 +3,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -3,7 +3,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

1
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/config/PartitionSettings.java
View File

@ -34,6 +34,7 @@ public class PartitionSettings {
private boolean myAlwaysOpenNewTransactionForDifferentPartition;
private boolean myConditionalCreateDuplicateIdentifiersEnabled = false;
public PartitionSettings() {}
/**
* Should we always open a new database transaction if the partition context changes
*

30
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java
View File

@ -119,21 +119,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
searchable = Searchable.YES,
projectable = Projectable.YES,
analyzer = "standardAnalyzer")
@FullTextField(
name = "myContentTextEdgeNGram",
searchable = Searchable.YES,
projectable = Projectable.NO,
analyzer = "autocompleteEdgeAnalyzer")
@FullTextField(
name = "myContentTextNGram",
searchable = Searchable.YES,
projectable = Projectable.NO,
analyzer = "autocompleteNGramAnalyzer")
@FullTextField(
name = "myContentTextPhonetic",
searchable = Searchable.YES,
projectable = Projectable.NO,
analyzer = "autocompletePhoneticAnalyzer")
@OptimisticLock(excluded = true)
@IndexingDependency(derivedFrom = @ObjectPath(@PropertyValue(propertyName = "myVersion")))
private String myContentText;
@ -171,21 +156,6 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
searchable = Searchable.YES,
projectable = Projectable.YES,
analyzer = "standardAnalyzer")
@FullTextField(
name = "myNarrativeTextEdgeNGram",
searchable = Searchable.YES,
projectable = Projectable.NO,
analyzer = "autocompleteEdgeAnalyzer")
@FullTextField(
name = "myNarrativeTextNGram",
searchable = Searchable.YES,
projectable = Projectable.NO,
analyzer = "autocompleteNGramAnalyzer")
@FullTextField(
name = "myNarrativeTextPhonetic",
searchable = Searchable.YES,
projectable = Projectable.NO,
analyzer = "autocompletePhoneticAnalyzer")
@OptimisticLock(excluded = true)
@IndexingDependency(derivedFrom = @ObjectPath(@PropertyValue(propertyName = "myVersion")))
private String myNarrativeText;

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

6
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamExtractor.java
View File

@ -44,13 +44,13 @@ public interface ISearchParamExtractor {
/**
* Constant for the {@literal theSearchParamFilter} parameters on this interface
* indicating that all search parameters should be indexed.
* indicating that all search parameters should be extracted.
*/
ISearchParamFilter ALL_PARAMS = t -> t;
/**
* Constant for the {@literal theSearchParamFilter} parameters on this interface
* indicating that no search parameters should be indexed.
* indicating that no search parameters should be extracted.
*/
ISearchParamFilter NO_PARAMS = t -> Collections.emptyList();
@ -155,7 +155,7 @@ public interface ISearchParamExtractor {
interface ISearchParamFilter {
/**
* Given the list of search parameters for indexing, an implementation of this
* Given the list of search parameters for extracting, an implementation of this
* interface may selectively remove any that it wants to remove (or can add if desired).
* <p>
* Implementations must not modify the list that is passed in. If changes are

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu2/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-dstu3/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-r4/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

168
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ReferentialIntegrityTest.java
View File

@ -1,19 +1,26 @@
package ca.uhn.fhir.jpa.dao.r4;
import static org.junit.jupiter.api.Assertions.assertEquals;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.IdType;
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.Reference;
import org.junit.jupiter.api.AfterEach;
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 static org.assertj.core.api.Assertions.assertThat;
import java.util.stream.Stream;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
public class FhirResourceDaoR4ReferentialIntegrityTest extends BaseJpaR4Test {
@ -23,51 +30,168 @@ public class FhirResourceDaoR4ReferentialIntegrityTest extends BaseJpaR4Test {
myStorageSettings.setEnforceReferentialIntegrityOnWrite(new JpaStorageSettings().isEnforceReferentialIntegrityOnWrite());
myStorageSettings.setEnforceReferentialIntegrityOnDelete(new JpaStorageSettings().isEnforceReferentialIntegrityOnDelete());
myStorageSettings.setEnforceReferenceTargetTypes(new JpaStorageSettings().isEnforceReferenceTargetTypes());
myStorageSettings.setResourceClientIdStrategy(new JpaStorageSettings().getResourceClientIdStrategy());
}
@ParameterizedTest
@MethodSource("paramsProvider_withResourceType")
public void referentialIntegrityOnWriteSetting_unknownIds_fullScopeTest(boolean theIsEnforceRefIntegrityEnabled,
JpaStorageSettings.ClientIdStrategyEnum theClientIdStrategy,
String theReferenceId) {
// Given
myStorageSettings.setEnforceReferentialIntegrityOnWrite(theIsEnforceRefIntegrityEnabled);
myStorageSettings.setEnforceReferenceTargetTypes(theIsEnforceRefIntegrityEnabled);
myStorageSettings.setResourceClientIdStrategy(theClientIdStrategy);
Patient p = new Patient();
p.setManagingOrganization(new Reference(theReferenceId));
if (theIsEnforceRefIntegrityEnabled) {
try {
// When
myPatientDao.create(p);
fail();
} catch (InvalidRequestException e) {
// Then
assertEquals(Msg.code(1094) + "Resource " + theReferenceId + " not found, specified in path: Patient.managingOrganization", e.getMessage());
}
} else {
// Disabled ref integrity on write case: all POSTs should succeed
// When
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
// Then
p = myPatientDao.read(id);
assertEquals(theReferenceId, p.getManagingOrganization().getReference());
}
}
private static Stream<Arguments> paramsProvider_withResourceType() {
// theIsEnforceRefIntegrityEnabled, theClientIdStrategy, theReferenceId
// note: client ID is tested since resolving the resource reference is different depending on the strategy
return Stream.of(
Arguments.of(true, JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC, "Organization/123"),
Arguments.of(true, JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC, "Organization/A123"),
Arguments.of(true, JpaStorageSettings.ClientIdStrategyEnum.ANY, "Organization/123"),
Arguments.of(true, JpaStorageSettings.ClientIdStrategyEnum.ANY, "Organization/A123"),
Arguments.of(false, JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC, "Organization/123"),
Arguments.of(false, JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC, "Organization/A123"),
Arguments.of(false, JpaStorageSettings.ClientIdStrategyEnum.ANY, "Organization/123"),
Arguments.of(false, JpaStorageSettings.ClientIdStrategyEnum.ANY, "Organization/A123")
);
}
@Test
public void testCreateUnknownReferenceFail() throws Exception {
public void testRefIntegrityOnWrite_withReferenceIdOfAnotherResourceType() {
// Given
myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC);
// Create Observation with some ID...
Observation obs = new Observation();
IIdType obsId = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
// And reference a non-existing Organization resource with the same ID as the Observation
Patient p = new Patient();
p.setManagingOrganization(new Reference("Organization/AAA"));
p.setManagingOrganization(new Reference(new IdType("Organization", obsId.getIdPart())));
try {
// When
myPatientDao.create(p);
fail();
} catch (InvalidRequestException e) {
assertEquals(Msg.code(1094) + "Resource Organization/AAA not found, specified in path: Patient.managingOrganization", e.getMessage());
} catch (UnprocessableEntityException e) {
// Then: identify that it is the wrong resource type, since ref integrity is enabled
assertEquals(Msg.code(1095) + "Resource contains reference to unknown resource ID Organization/" + obsId.getIdPart(), e.getMessage());
}
// Given: now disable referential integrity on write
myStorageSettings.setEnforceReferentialIntegrityOnWrite(false);
// When
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
// Then: this should now succeed
p = myPatientDao.read(id);
assertEquals("Organization/" + obsId.getIdPart(), p.getManagingOrganization().getReference());
}
@Test
public void testCreateUnknownReferenceAllowed() {
myStorageSettings.setEnforceReferentialIntegrityOnWrite(false);
@ParameterizedTest
@MethodSource("paramsProvider_noResourceType")
public void testRefIntegrityOnWrite_withValidReferenceId_shouldAlwaysSucceed(boolean theIsEnforceRefIntegrityEnabled,
JpaStorageSettings.ClientIdStrategyEnum theClientIdStrategy,
String theReferenceId) {
// Given
myStorageSettings.setEnforceReferentialIntegrityOnWrite(theIsEnforceRefIntegrityEnabled);
myStorageSettings.setEnforceReferenceTargetTypes(theIsEnforceRefIntegrityEnabled);
myStorageSettings.setResourceClientIdStrategy(theClientIdStrategy);
Organization obs = new Organization();
obs.setId(theReferenceId);
myOrganizationDao.update(obs, mySrd);
String qualifiedReferenceId = "Organization/" + theReferenceId;
Patient p = new Patient();
p.setManagingOrganization(new Reference("Organization/AAA"));
p.setManagingOrganization(new Reference(qualifiedReferenceId));
// When
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
// Then
p = myPatientDao.read(id);
assertEquals("Organization/AAA", p.getManagingOrganization().getReference());
assertEquals(qualifiedReferenceId, p.getManagingOrganization().getReference());
}
@Test
public void testCreateUnknownReferenceAllowed_NumericId() {
myStorageSettings.setEnforceReferentialIntegrityOnWrite(false);
myStorageSettings.setEnforceReferenceTargetTypes(false);
private static Stream<Arguments> paramsProvider_noResourceType() {
// theIsEnforceRefIntegrityEnabled, theClientIdStrategy, theReferenceId
// note: client ID is tested since resolving the resource reference is different depending on the strategy
return Stream.of(
Arguments.of(true, JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC, "A123"),
Arguments.of(true, JpaStorageSettings.ClientIdStrategyEnum.ANY, "123"),
Arguments.of(true, JpaStorageSettings.ClientIdStrategyEnum.ANY, "A123"),
Arguments.of(false, JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC, "A123"),
Arguments.of(false, JpaStorageSettings.ClientIdStrategyEnum.ANY, "123"),
Arguments.of(false, JpaStorageSettings.ClientIdStrategyEnum.ANY, "A123")
);
}
@ParameterizedTest
@MethodSource("paramsProvider_noResourceType")
public void testRefIntegrityOnWrite_withReferenceIdOfDeletedResource(boolean theIsEnforceRefIntegrityEnabled,
JpaStorageSettings.ClientIdStrategyEnum theClientIdStrategy,
String theReferenceId) {
// Given
myStorageSettings.setEnforceReferentialIntegrityOnWrite(theIsEnforceRefIntegrityEnabled);
myStorageSettings.setEnforceReferenceTargetTypes(theIsEnforceRefIntegrityEnabled);
myStorageSettings.setResourceClientIdStrategy(theClientIdStrategy);
Organization obs = new Organization();
obs.setId(theReferenceId);
IIdType obsId = myOrganizationDao.update(obs, mySrd).getId();
String qualifiedReferenceId = "Organization/" + theReferenceId;
myOrganizationDao.delete(obsId, mySrd);
Patient p = new Patient();
p.setManagingOrganization(new Reference("Organization/123"));
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
p.setManagingOrganization(new Reference(qualifiedReferenceId));
p = myPatientDao.read(id);
assertEquals("Organization/123", p.getManagingOrganization().getReference());
if (theIsEnforceRefIntegrityEnabled) {
try {
// When
myPatientDao.create(p);
fail();
} catch (InvalidRequestException e) {
// Then
assertEquals(Msg.code(1096) + "Resource " + qualifiedReferenceId + " is deleted, specified in path: Patient.managingOrganization", e.getMessage());
}
} else {
// Disabled ref integrity on write case: all POSTs should succeed
// When
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
// Then
p = myPatientDao.read(id);
assertEquals(qualifiedReferenceId, p.getManagingOrganization().getReference());
}
}
@Test
public void testDeleteFail() throws Exception {
public void testDeleteFail() {
Organization o = new Organization();
o.setName("FOO");
IIdType oid = myOrganizationDao.create(o).getId().toUnqualifiedVersionless();
@ -89,7 +213,7 @@ public class FhirResourceDaoR4ReferentialIntegrityTest extends BaseJpaR4Test {
}
@Test
public void testDeleteAllow() throws Exception {
public void testDeleteAllow() {
myStorageSettings.setEnforceReferentialIntegrityOnDelete(false);
Organization o = new Organization();

963
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchMissingTest.java
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292
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
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@ -217,7 +217,7 @@ import static org.mockito.Mockito.when;
public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4Test.class);
private SearchCoordinatorSvcImpl mySearchCoordinatorSvcRaw;
private CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
@Autowired
private ISearchDao mySearchEntityDao;
@ -413,15 +413,15 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient pt1 = new Patient();
pt1.addName().setFamily("Elizabeth");
String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
String pt1id = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
Patient pt2 = new Patient();
pt2.addName().setFamily("fghijk");
String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
String pt2id = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless().getValue();
Patient pt3 = new Patient();
pt3.addName().setFamily("zzzzz");
myPatientDao.create(pt3).getId().toUnqualifiedVersionless().getValue();
myPatientDao.create(pt3, mySrd).getId().toUnqualifiedVersionless().getValue();
Bundle output = myClient
@ -450,7 +450,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient pt1 = new Patient();
pt1.addName().setFamily("Smith%");
String pt1id = myPatientDao.create(pt1).getId().toUnqualifiedVersionless().getValue();
String pt1id = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
Bundle output = myClient
.search()
@ -463,7 +463,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient pt2 = new Patient();
pt2.addName().setFamily("Sm%ith");
String pt2id = myPatientDao.create(pt2).getId().toUnqualifiedVersionless().getValue();
String pt2id = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless().getValue();
output = myClient
.search()
@ -740,7 +740,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient p = new Patient();
p.addName().setFamily("FAM").addGiven("GIV");
IIdType id = myPatientDao.create(p).getId();
IIdType id = myPatientDao.create(p, mySrd).getId();
myClient.read().resource("Patient").withId(id.toUnqualifiedVersionless()).execute();
@ -763,7 +763,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient p = new Patient();
p.addName().setFamily("FAM").addGiven("GIV");
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
myClient
.delete()
@ -1025,57 +1025,58 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
public void testCreateAndReadBackResourceWithContainedReferenceToContainer() {
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
String input = "{\n" +
" \"resourceType\": \"Organization\",\n" +
" \"id\": \"1\",\n" +
" \"meta\": {\n" +
" \"tag\": [\n" +
" {\n" +
" \"system\": \"https://blah.org/deployment\",\n" +
" \"code\": \"e69414dd-b5c2-462d-bcfd-9d04d6b16596\",\n" +
" \"display\": \"DEPLOYMENT\"\n" +
" },\n" +
" {\n" +
" \"system\": \"https://blah.org/region\",\n" +
" \"code\": \"b47d7a5b-b159-4bed-a8f8-3258e6603adb\",\n" +
" \"display\": \"REGION\"\n" +
" },\n" +
" {\n" +
" \"system\": \"https://blah.org/provider\",\n" +
" \"code\": \"28c30004-0333-40cf-9e7f-3f9e080930bd\",\n" +
" \"display\": \"PROVIDER\"\n" +
" }\n" +
" ]\n" +
" },\n" +
" \"contained\": [\n" +
" {\n" +
" \"resourceType\": \"Location\",\n" +
" \"id\": \"2\",\n" +
" \"position\": {\n" +
" \"longitude\": 51.443238301454289,\n" +
" \"latitude\": 7.34196905697293\n" +
" },\n" +
" \"managingOrganization\": {\n" +
" \"reference\": \"#\"\n" +
" }\n" +
" }\n" +
" ],\n" +
" \"type\": [\n" +
" {\n" +
" \"coding\": [\n" +
" {\n" +
" \"system\": \"https://blah.org/fmc/OrganizationType\",\n" +
" \"code\": \"CLINIC\",\n" +
" \"display\": \"Clinic\"\n" +
" }\n" +
" ]\n" +
" }\n" +
" ],\n" +
" \"name\": \"testOrg\"\n" +
"}";
String input = """
{
"resourceType": "Organization",
"id": "1",
"meta": {
"tag": [
{
"system": "https://blah.org/deployment",
"code": "e69414dd-b5c2-462d-bcfd-9d04d6b16596",
"display": "DEPLOYMENT"
},
{
"system": "https://blah.org/region",
"code": "b47d7a5b-b159-4bed-a8f8-3258e6603adb",
"display": "REGION"
},
{
"system": "https://blah.org/provider",
"code": "28c30004-0333-40cf-9e7f-3f9e080930bd",
"display": "PROVIDER"
}
]
},
"contained": [
{
"resourceType": "Location",
"id": "2",
"position": {
"longitude": 51.443238301454289,
"latitude": 7.34196905697293
},
"managingOrganization": {
"reference": "#"
}
}
],
"type": [
{
"coding": [
{
"system": "https://blah.org/fmc/OrganizationType",
"code": "CLINIC",
"display": "Clinic"
}
]
}
],
"name": "testOrg"
}""";
Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, input);
IIdType id = myOrganizationDao.create(org).getId();
IIdType id = myOrganizationDao.create(org, mySrd).getId();
org = myOrganizationDao.read(id);
String output = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(org);
@ -1095,9 +1096,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
List<IBaseResource> outcome = myClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
runInTransaction(() -> {
assertEquals(100, myResourceTableDao.count());
});
runInTransaction(() -> assertEquals(100, myResourceTableDao.count()));
Bundle found = myClient
.search()
@ -1306,7 +1305,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
@Test
public void testCreateQuestionnaireResponseWithValidation() throws IOException {
public void testCreateQuestionnaireResponseWithValidation() {
CodeSystem cs = new CodeSystem();
cs.setUrl("http://cs");
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
@ -1906,8 +1905,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
* Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL but we want to make sure that works too..
*/
Socket sock = new Socket();
sock.setSoTimeout(3000);
try {
try (sock) {
sock.setSoTimeout(3000);
sock.connect(new InetSocketAddress("localhost", myPort));
sock.getOutputStream().write(("DELETE /fhir/context/Patient?identifier=http://ghh.org/patient|" + methodName + " HTTP/1.1\n").getBytes(StandardCharsets.UTF_8));
sock.getOutputStream().write("Host: localhost\n".getBytes(StandardCharsets.UTF_8));
@ -1915,7 +1914,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
BufferedReader socketInput = new BufferedReader(new InputStreamReader(sock.getInputStream()));
// String response = "";
StringBuilder b = new StringBuilder();
char[] buf = new char[1000];
while (socketInput.read(buf) != -1) {
@ -1925,9 +1923,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
ourLog.debug("Resp: {}", resp);
} catch (SocketTimeoutException e) {
e.printStackTrace();
} finally {
sock.close();
ourLog.debug(e.getMessage(), e);
}
Thread.sleep(1000);
@ -2398,7 +2394,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
assertThat(idValues).as(idValues.toString()).hasSize(10);
idValues = searchAndReturnUnqualifiedIdValues(myServerBase + "/_history?_at=gt" + InstantDt.withCurrentTime().getYear());
assertThat(idValues).hasSize(0);
assertThat(idValues).isEmpty();
}
@ -2427,7 +2423,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myMemoryCacheService.invalidateCaches(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID);
}
Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).execute();
Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).execute();
assertEquals(1, history.getEntry().size());
BundleEntryComponent historyEntry0 = history.getEntry().get(0);
// validate entry.fullUrl
@ -2476,7 +2472,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myMemoryCacheService.invalidateCaches(MemoryCacheService.CacheEnum.PID_TO_FORCED_ID);
}
Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).execute();
Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).execute();
assertEquals(1, history.getEntry().size());
BundleEntryComponent historyEntry0 = history.getEntry().get(0);
// validate entry.fullUrl
@ -2508,7 +2504,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
ourLog.info("Res ID: {}", id);
Bundle history = myClient.history().onInstance(id.getValue()).andReturnBundle(Bundle.class).prettyPrint().summaryMode(SummaryEnum.DATA).execute();
Bundle history = myClient.history().onInstance(id.getValue()).returnBundle(Bundle.class).prettyPrint().summaryMode(SummaryEnum.DATA).execute();
assertThat(history.getEntry()).hasSize(3);
assertEquals(id.withVersion("3").getValue(), history.getEntry().get(0).getResource().getId());
assertThat(((Patient) history.getEntry().get(0).getResource()).getName()).hasSize(1);
@ -2746,7 +2742,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
int total = 20;
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
Coding tagCode = new Coding();
tagCode.setCode("test");
@ -2757,7 +2753,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.addTag(tagCode);
t.setStatus(Task.TaskStatus.REQUESTED);
t.getOwner().setReference(orgId.getValue());
myTaskDao.create(t);
myTaskDao.create(t, mySrd);
}
HashSet<String> ids = new HashSet<>();
@ -2835,12 +2831,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
if (orgCount > 0) {
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
orgCount--;
t.getOwner().setReference(orgId.getValue());
}
myTaskDao.create(t);
myTaskDao.create(t, mySrd);
}
}
@ -2909,12 +2905,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
if (orgCount > 0) {
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
orgCount--;
t.getOwner().setReference(orgId.getValue());
}
myTaskDao.create(t);
myTaskDao.create(t, mySrd);
}
}
@ -2961,13 +2957,13 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
public void testIncludeCountDoesntIncludeIncludes() {
Organization org = new Organization();
org.setName("ORG");
IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
for (int i = 0; i < 10; i++) {
Patient pt = new Patient();
pt.getManagingOrganization().setReference(orgId.getValue());
pt.addName().setFamily("FAM" + i);
myPatientDao.create(pt);
myPatientDao.create(pt, mySrd);
}
Bundle bundle = myClient
@ -3168,7 +3164,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("2", newPt.getIdElement().getVersionIdPart());
assertEquals(false, newPt.getActive());
assertFalse(newPt.getActive());
}
@Test
@ -3196,7 +3192,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("1", newPt.getIdElement().getVersionIdPart());
assertEquals(true, newPt.getActive());
assertTrue(newPt.getActive());
}
@Test
@ -3226,7 +3222,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("2", newPt.getIdElement().getVersionIdPart());
assertEquals(false, newPt.getActive());
assertFalse(newPt.getActive());
}
@Test
@ -3255,7 +3251,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient newPt = myClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("2", newPt.getIdElement().getVersionIdPart());
assertEquals(false, newPt.getActive());
assertFalse(newPt.getActive());
}
@Test
@ -3323,12 +3319,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
{
Bundle returned = myClient.search().forResource(Patient.class).encodedXml().returnBundle(Bundle.class).execute();
assertThat(returned.getEntry().size()).isGreaterThan(1);
assertThat(returned.getEntry()).hasSizeGreaterThan(1);
assertEquals(BundleType.SEARCHSET, returned.getType());
}
{
Bundle returned = myClient.search().forResource(Patient.class).encodedJson().returnBundle(Bundle.class).execute();
assertThat(returned.getEntry().size()).isGreaterThan(1);
assertThat(returned.getEntry()).hasSizeGreaterThan(1);
}
}
@ -3350,7 +3346,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
});
Bundle bundle = myClient.history().onServer().andReturnBundle(Bundle.class).execute();
Bundle bundle = myClient.history().onServer().returnBundle(Bundle.class).execute();
assertEquals(1, bundle.getTotal());
assertThat(bundle.getEntry()).hasSize(1);
assertEquals(id2.getIdPart(), bundle.getEntry().get(0).getResource().getIdElement().getIdPart());
@ -3507,15 +3503,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
assertThat(text).doesNotContain("\"B\"");
assertThat(text).doesNotContain("\"B1\"");
}
// HttpGet read = new HttpGet(ourServerBase + "/Observation?patient=P5000000302&_sort:desc=code&code:in=http://fkcfhir.org/fhir/vs/ccdacapddialysisorder");
// try (CloseableHttpResponse response = ourHttpClient.execute(read)) {
// String text = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
// ourLog.info(text);
// assertEquals(Constants.STATUS_HTTP_200_OK, response.getStatusLine().getStatusCode());
// assertThat(text).doesNotContain("\"text\",\"type\"");
// }
}
@Test
@ -3873,9 +3860,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
p.addName().setFamily(methodName + "1");
IIdType pid1 = myClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
Thread.sleep(10);
long time1 = System.currentTimeMillis();
Thread.sleep(10);
Patient p2 = new Patient();
p2.addName().setFamily(methodName + "2");
@ -4064,9 +4049,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
public void testSearchLastUpdatedParamRp() throws InterruptedException {
String methodName = "testSearchLastUpdatedParamRp";
int sleep = 100;
Thread.sleep(sleep);
DateTimeType beforeAny = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
IIdType id1a;
{
@ -4083,9 +4065,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
id1b = myClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
}
Thread.sleep(1100);
DateTimeType beforeR2 = new DateTimeType(new Date(), TemporalPrecisionEnum.MILLI);
Thread.sleep(1100);
IIdType id2;
{
@ -4249,13 +4229,12 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
matches = bundle.getEntry().size();
assertThat(matches).isGreaterThan(0);
assertThat(matches).isPositive();
}
@Test
public void testSearchReturnsSearchDate() throws Exception {
Date before = new Date();
Thread.sleep(1);
//@formatter:off
Bundle found = myClient
@ -4266,7 +4245,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
.execute();
//@formatter:on
Thread.sleep(1);
Date after = new Date();
InstantType updated = found.getMeta().getLastUpdatedElement();
@ -4300,7 +4278,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4313,7 +4291,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4326,7 +4304,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4339,24 +4317,24 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
// > 1m
String uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt1|http://unitsofmeasure.org|m");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(3);
//>= 100cm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt100|http://unitsofmeasure.org|cm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(3);
//>= 10dm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt10|http://unitsofmeasure.org|dm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(3);
}
@ -4381,7 +4359,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4392,7 +4370,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4403,7 +4381,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4414,7 +4392,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
String uri;
@ -4451,7 +4429,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4462,7 +4440,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -4474,7 +4452,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
myCaptureQueriesListener.clear();
@ -4490,8 +4468,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
//-- check use normalized quantity table to search
String searchSql = myCaptureQueriesListener.getSelectQueries().get(0).getSql(true, true);
assertThat(searchSql).doesNotContain("HFJ_SPIDX_QUANTITY t0");
assertThat(searchSql).contains("HFJ_SPIDX_QUANTITY_NRML");
assertThat(searchSql).doesNotContain("HFJ_SPIDX_QUANTITY t0").contains("HFJ_SPIDX_QUANTITY_NRML");
}
@Test
@ -5044,7 +5021,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5056,7 +5033,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5068,7 +5045,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5080,7 +5057,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
String uri = myServerBase + "/Observation?_sort=code-value-quantity";
@ -5092,7 +5069,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
found = myFhirContext.newXmlParser().parseResource(Bundle.class, output);
}
ourLog.debug("Bundle: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
ourLog.debug("Bundle: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
List<IIdType> list = toUnqualifiedVersionlessIds(found);
assertThat(found.getEntry()).hasSize(4);
@ -5129,7 +5106,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5145,7 +5122,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5161,7 +5138,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -5176,7 +5153,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
comp.setValue(new Quantity().setValue(250));
oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
String uri = myServerBase + "/Observation?_sort=combo-code-value-quantity";
@ -5188,7 +5165,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
found = myFhirContext.newXmlParser().parseResource(Bundle.class, output);
}
ourLog.debug("Bundle: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
ourLog.debug("Bundle: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(found));
List<IIdType> list = toUnqualifiedVersionlessIds(found);
assertThat(found.getEntry()).hasSize(4);
@ -5264,9 +5241,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
List<IIdType> list = toUnqualifiedVersionlessIds(found);
ourLog.info(methodName + " found: " + list.toString() + " - Wanted " + orgMissing + " but not " + orgNotMissing);
assertThat(list).doesNotContain(orgNotMissing);
assertThat(list).doesNotContain(deletedIdMissingTrue);
assertThat(list).contains(orgMissing);
assertThat(list).doesNotContain(orgNotMissing).doesNotContain(deletedIdMissingTrue).contains(orgMissing);
}
@Test
@ -5927,7 +5902,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
Date before = new Date();
Thread.sleep(100);
pt = new Patient();
pt.setId(id.getIdPart());
@ -6450,7 +6424,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
obs.setValue(new Quantity().setValueElement(new DecimalType(125.12)).setUnit("CM").setSystem(UcumServiceUtil.UCUM_CODESYSTEM_URL).setCode("cm"));
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
IIdType opid1 = myObservationDao.create(obs, mySrd).getId();
@ -6463,7 +6437,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
cc.addCoding().setCode("2345-7").setSystem("http://loinc.org");
obs.setValue(new Quantity().setValueElement(new DecimalType(24.12)).setUnit("CM").setSystem(UcumServiceUtil.UCUM_CODESYSTEM_URL).setCode("cm"));
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
myObservationDao.update(obs, mySrd);
}
@ -6479,7 +6453,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -6492,7 +6466,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -6505,25 +6479,25 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
myObservationDao.create(obs, mySrd);
ourLog.debug("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.debug("Observation: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
// > 1m
String uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt1|http://unitsofmeasure.org|m");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(2);
//>= 100cm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt100|http://unitsofmeasure.org|cm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(2);
//>= 10dm
uri = myServerBase + "/Observation?code-value-quantity=http://" + UrlUtil.escapeUrlParam("loinc.org|2345-7$gt10|http://unitsofmeasure.org|dm");
ourLog.info("uri = " + uri);
ourLog.info("uri = {}", uri);
ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids).hasSize(2);
}
@ -6540,7 +6514,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setBirthDateElement(new DateType("2073"));
pid0 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info("pid0 " + pid0);
}
@ -6553,7 +6527,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
}
uri = myServerBase + "/Patient?_total=accurate&birthdate=gt2072-01-01";
@ -6564,7 +6538,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, resp);
ourLog.debug("Patient: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourLog.debug("Patient: {}\n", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
}
}
@ -6995,9 +6969,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
&& theInput.IsEnforceRefOnType
&& theInput.IsEnforceRefOnWrite).isFalse();
} catch (InvalidRequestException ex) {
assertThat(ex.getMessage().contains(
"Invalid resource reference"
)).as(ex.getMessage()).isTrue();
assertThat(ex.getMessage()).as(ex.getMessage()).contains("Invalid resource reference");
} finally {
myStorageSettings.setEnforceReferentialIntegrityOnWrite(isEnforceRefOnWrite);
myStorageSettings.setEnforceReferenceTargetTypes(isEnforceRefTargetTypes);
@ -7331,9 +7303,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setBirthDate(cal.getTime());
}
return patient;
}, (isMissing) -> {
return doSearch(Patient.class, Patient.BIRTHDATE.isMissing(isMissing));
});
}, (isMissing) -> doSearch(Patient.class, Patient.BIRTHDATE.isMissing(isMissing)));
}
@ParameterizedTest
@ -7346,9 +7316,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setGender(AdministrativeGender.FEMALE);
}
return patient;
}, isMissing -> {
return doSearch(Patient.class, Patient.GENDER.isMissing(isMissing));
});
}, isMissing -> doSearch(Patient.class, Patient.GENDER.isMissing(isMissing)));
}
@ParameterizedTest
@ -7364,9 +7332,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
patient.setGeneralPractitioner(Collections.singletonList(new Reference(practitionerId)));
}
return patient;
}, isMissing -> {
return doSearch(Patient.class, Patient.GENERAL_PRACTITIONER.isMissing(isMissing));
});
}, isMissing -> doSearch(Patient.class, Patient.GENERAL_PRACTITIONER.isMissing(isMissing)));
}
@ParameterizedTest
@ -7409,9 +7375,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
sp.setUrl("http://example.com");
}
return sp;
}, isMissing -> {
return doSearch(SearchParameter.class, SearchParameter.URL.isMissing(isMissing));
});
}, isMissing -> doSearch(SearchParameter.class, SearchParameter.URL.isMissing(isMissing)));
}
@ParameterizedTest
@ -7424,9 +7388,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
obs.setValue(new Quantity(3));
}
return obs;
}, isMissing -> {
return doSearch(Observation.class, Observation.VALUE_QUANTITY.isMissing(isMissing));
});
}, isMissing -> doSearch(Observation.class, Observation.VALUE_QUANTITY.isMissing(isMissing)));
}
@ParameterizedTest
@ -7457,7 +7419,7 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Y doTask(X theInput);
}
private static class MissingSearchTestParameters {
public static class MissingSearchTestParameters {
/**
* The setting for IndexMissingFields
*/

132
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
View File

@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.term;
import static org.junit.jupiter.api.Assertions.assertNull;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.context.support.LookupCodeRequest;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
@ -20,9 +19,10 @@ import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import jakarta.persistence.EntityManager;
import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IdType;
@ -40,8 +40,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.core.io.ClassPathResource;
import jakarta.persistence.EntityManager;
import jakarta.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
@ -82,14 +80,12 @@ import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UPLOAD_
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_XML_FILE;
import static java.util.stream.Collectors.joining;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.fail;
import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_ALL_VALUESET_ID;
import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
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.fail;
import static org.mockito.Mockito.when;
/**
@ -141,9 +137,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Autowired
private Batch2JobHelper myBatchJobHelper;
private ZipCollectionBuilder myFiles;
private ServletRequestDetails myRequestDetails = new ServletRequestDetails();
private final ServletRequestDetails myRequestDetails = new ServletRequestDetails();
private Properties uploadProperties;
private IFhirResourceDao<ValueSet> myValueSetIFhirResourceDao;
@ -182,17 +176,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private void validateValidateCode(String theCurrentVersion, Collection<String> allVersions) {
IValidationSupport.CodeValidationResult resultNoVersioned = myCodeSystemDao.validateCode(null,
new UriType(BASE_LOINC_URL), null, new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultNoVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultNoVersioned.getDisplay());
IValidationSupport.CodeValidationResult resultVersioned = myCodeSystemDao.validateCode(null,
new UriType(BASE_LOINC_URL), null, new CodeType(VS_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultVersioned.getDisplay());
validateValidateCodeForVersion(theCurrentVersion);
allVersions.forEach(this::validateValidateCodeForVersion);
}
@ -215,13 +199,15 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private void validateValueLookup(String theCurrentVersion, Collection<String> allVersions) {
IValidationSupport.LookupCodeResult resultNoVer = myValidationSupport.lookupCode(
new ValidationSupportContext(myValidationSupport), new LookupCodeRequest(BASE_LOINC_URL, VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE));
new ValidationSupportContext(myValidationSupport),
new LookupCodeRequest(BASE_LOINC_URL, VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE));
assertNotNull(resultNoVer);
String expectedNoVer = prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
assertEquals(expectedNoVer, resultNoVer.getCodeDisplay());
IValidationSupport.LookupCodeResult resultWithVer = myValidationSupport.lookupCode(
new ValidationSupportContext(myValidationSupport), new LookupCodeRequest(BASE_LOINC_URL, VS_VERSIONED_ON_UPLOAD_FIRST_CODE));
new ValidationSupportContext(myValidationSupport),
new LookupCodeRequest(BASE_LOINC_URL, VS_VERSIONED_ON_UPLOAD_FIRST_CODE));
assertNotNull(resultWithVer);
String expectedWithVer = prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
assertEquals(expectedWithVer, resultWithVer.getCodeDisplay());
@ -278,42 +264,28 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private void validateExpandedTermConcepts(String theCurrentVersion, Collection<String> theAllVersions) {
runInTransaction(() -> {
TermConcept termConceptNoVerCsvNoVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
assertNotNull(termConceptNoVerCsvNoVer);
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvNoVer.getDisplay());
TermConcept termConceptVerCsvNoVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
assertNotNull(termConceptVerCsvNoVer);
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvNoVer.getDisplay());
if (theCurrentVersion != null) {
TermConcept termConceptNoVerCsvVer = (TermConcept) myEntityManager.createQuery(
TermConcept termConceptNoVerCsvNoVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theCurrentVersion + "'").getSingleResult();
assertNotNull(termConceptNoVerCsvVer);
VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
assertNotNull(termConceptNoVerCsvNoVer);
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvVer.getDisplay());
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvNoVer.getDisplay());
TermConcept termConceptVerCsvVer = (TermConcept) myEntityManager.createQuery(
TermConcept termConceptVerCsvNoVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theCurrentVersion + "'").getSingleResult();
assertNotNull(termConceptVerCsvVer);
VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
assertNotNull(termConceptVerCsvNoVer);
// data should have version because it was loaded with a version
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvVer.getDisplay());
}
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvNoVer.getDisplay());
theAllVersions.forEach(this::validateExpandedTermConceptsForVersion);
if (theCurrentVersion != null) {
validateExpandedTermConceptsForVersion(theCurrentVersion);
}
theAllVersions.forEach(this::validateExpandedTermConceptsForVersion);
});
}
private void validateExpandedTermConceptsForVersion(String theVersion) {
TermConcept termConceptNoVer = (TermConcept) myEntityManager.createQuery(
"select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
@ -384,7 +356,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
* no the CodeSystem version.
*/
private void validateValueSetSearchForVersion(String theVersion) {
// for no versioned VS (VS version, different than CS version)
// for no versioned VS (VS version, different from CS version)
SearchParameterMap paramsUploadNoVer = new SearchParameterMap("url", new UriParam(VS_NO_VERSIONED_ON_UPLOAD));
paramsUploadNoVer.add("version", new TokenParam(theVersion));
@ -398,7 +370,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
assertEquals(expectedLoadNoVersionUnqualifiedId, loadNoVersionValueSet.getIdElement().getIdPart());
// versioned VS (VS version, different than CS version)
// versioned VS (VS version, different from CS version)
SearchParameterMap paramsUploadVer = new SearchParameterMap("url", new UriParam(VS_VERSIONED_ON_UPLOAD));
paramsUploadVer.add("version", new TokenParam(VS_ANSWER_LIST_VERSION + "-" + theVersion));
@ -437,8 +409,8 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
Set<String> theExpectedIdVersionsPlusNull = Sets.newHashSet(theExpectedIdVersions);
theExpectedIdVersionsPlusNull.add(null);
assertThat(theExpectedIdVersionsPlusNull).containsExactlyInAnyOrderElementsOf(theValueSets.stream().map(r -> ((ValueSet) r).getVersion()).toList());
List<String> valueSetVersions = theValueSets.stream().map(r -> ((ValueSet) r).getVersion()).toList();
assertThat(valueSetVersions).containsExactlyInAnyOrderElementsOf(theExpectedIdVersionsPlusNull);
}
@ -455,14 +427,13 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
// for CodeSystem:
// _ current CS is present and has no version
CodeSystem codeSystem = myCodeSystemDao.read(new IdType(LOINC_LOW));
CodeSystem codeSystem = myCodeSystemDao.read(new IdType(LOINC_LOW), myRequestDetails);
String csString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem);
ourLog.info("CodeSystem:\n" + csString);
ourLog.info("CodeSystem:\n {}", csString);
HashSet<String> shouldNotBePresentVersions = new HashSet<>(possibleVersions);
theAllVersions.forEach(shouldNotBePresentVersions::remove);
shouldNotBePresentVersions.forEach(vv -> assertFalse(csString.contains(vv),
"Found version string: '" + vv + "' in CodeSystem: " + csString));
assertThat(shouldNotBePresentVersions).noneSatisfy(vv -> assertThat(vv).isEqualTo(codeSystem.getVersion()));
// same reading it from term service
CodeSystem cs = myITermReadSvc.fetchCanonicalCodeSystemFromCompleteContext(BASE_LOINC_URL);
@ -501,7 +472,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test()
public void uploadCurrentNoVersion() throws Exception {
IIdType csId = uploadLoincCodeSystem(null, true);
uploadLoincCodeSystem(null, true);
runCommonValidations(Collections.emptyList());
@ -516,7 +487,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Test()
public void uploadWithVersion() throws Exception {
String ver = "2.67";
IIdType csId = uploadLoincCodeSystem(ver, true);
uploadLoincCodeSystem(ver, true);
runCommonValidations(Collections.singletonList(ver));
@ -637,25 +608,6 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
assertThat(vsContainsDisplay).contains(expectedDisplay);
}
private void validateValidateCodeLoincAllVS(String theCurrentVersion, Collection<String> allVersions) {
IValidationSupport.CodeValidationResult resultNoVersioned = myCodeSystemDao.validateCode(null,
new UriType(BASE_LOINC_URL), null, new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultNoVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultNoVersioned.getDisplay());
IValidationSupport.CodeValidationResult resultVersioned = myCodeSystemDao.validateCode(null,
new UriType(BASE_LOINC_URL), null, new CodeType(VS_VERSIONED_ON_UPLOAD_FIRST_CODE),
null, null, null, null);
assertNotNull(resultVersioned);
assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultVersioned.getDisplay());
allVersions.forEach(this::validateValidateCodeForVersion);
}
private void validateValueExpandLoincAllVsForVersion(String theVersion) {
ValueSet vs = myValueSetDao.expandByIdentifier(LOINC_ALL_VS_URL + "|" + theVersion, null);
assertThat(vs.getExpansion().getContains()).hasSize(ALL_VS_QTY);
@ -664,7 +616,6 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
checkContainsElementVersion(vs, theVersion);
}
/**
* Validates TermConcepts were created in the sequence indicated by the parameters
* and their displays match the expected versions
@ -735,8 +686,8 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
}
private IIdType uploadLoincCodeSystem(String theVersion, boolean theMakeItCurrent) throws Exception {
myFiles = new ZipCollectionBuilder();
private void uploadLoincCodeSystem(String theVersion, boolean theMakeItCurrent) throws Exception {
ZipCollectionBuilder files = new ZipCollectionBuilder();
myRequestDetails.getUserData().put(LOINC_CODESYSTEM_MAKE_CURRENT, theMakeItCurrent);
uploadProperties.put(LOINC_CODESYSTEM_MAKE_CURRENT.getCode(), Boolean.toString(theMakeItCurrent));
@ -749,12 +700,10 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
uploadProperties.put(LOINC_CODESYSTEM_VERSION.getCode(), theVersion);
}
addLoincMandatoryFilesToZip(myFiles, theVersion);
addLoincMandatoryFilesToZip(files, theVersion);
UploadStatistics stats = myTermLoaderSvc.loadLoinc(myFiles.getFiles(), mySrd);
myTermLoaderSvc.loadLoinc(files.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
return stats.getTarget();
}
@ -787,10 +736,12 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
private TermCodeSystemVersion fetchCurrentCodeSystemVersion() {
runInTransaction(() -> {
@SuppressWarnings("unchecked")
List<TermCodeSystem> tcsList = myEntityManager.createQuery("from TermCodeSystem").getResultList();
@SuppressWarnings("unchecked")
List<TermCodeSystemVersion> tcsvList = myEntityManager.createQuery("from TermCodeSystemVersion").getResultList();
ourLog.error("tcslist: {}", tcsList.stream().map(tcs -> tcs.toString()).collect(joining("\n", "\n", "")));
ourLog.error("tcsvlist: {}", tcsvList.stream().map(v -> v.toString()).collect(joining("\n", "\n", "")));
ourLog.error("tcslist: {}", tcsList.stream().map(TermCodeSystem::toString).collect(joining("\n", "\n", "")));
ourLog.error("tcsvlist: {}", tcsvList.stream().map(TermCodeSystemVersion::toString).collect(joining("\n", "\n", "")));
if (tcsList.size() != 1) {
throw new IllegalStateException("More than one TCS: " +
@ -807,8 +758,9 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
}
private static void addBaseLoincMandatoryFilesToZip(
ZipCollectionBuilder theFiles, Boolean theIncludeTop2000, String theClassPathPrefix) throws IOException {
private static void addBaseLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles,
@SuppressWarnings("SameParameterValue") Boolean theIncludeTop2000,
String theClassPathPrefix) throws IOException {
theFiles.addFileZip(theClassPathPrefix, LOINC_XML_FILE.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());

2
hapi-fhir-jpaserver-test-r4b/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-r5/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/api/ICdsServiceRegistry.java
View File

@ -45,7 +45,7 @@ public interface ICdsServiceRegistry {
* @param theCdsServiceRequestJson the service request
* @return the service response
*/
CdsServiceResponseJson callService(String theServiceId, CdsServiceRequestJson theCdsServiceRequestJson);
CdsServiceResponseJson callService(String theServiceId, Object theCdsServiceRequestJson);
/**
* This is the REST method available at https://example.com/cds-services/{theServiceId}/feedback

2
hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/api/json/CdsHooksExtension.java
View File

@ -20,9 +20,11 @@
package ca.uhn.hapi.fhir.cdshooks.api.json;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* Users can define CDS Hooks extensions by extending this class.
* Implementors can extend this class for defining their custom extensions.
*/
@JsonIgnoreProperties(ignoreUnknown = true)
public class CdsHooksExtension implements IModelJson {}

2
hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/api/json/CdsServiceRequestContextJson.java
View File

@ -21,6 +21,7 @@ package ca.uhn.hapi.fhir.cdshooks.api.json;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonAnyGetter;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.Collections;
@ -29,6 +30,7 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
@JsonIgnoreProperties(ignoreUnknown = true)
public class CdsServiceRequestContextJson extends BaseCdsServiceJson implements IModelJson {
@JsonAnyGetter

5
hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/config/CdsHooksConfig.java
View File

@ -31,6 +31,7 @@ import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.module.CdsHooksObjectMapperFactory;
import ca.uhn.hapi.fhir.cdshooks.serializer.CdsServiceRequestJsonDeserializer;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsConfigServiceImpl;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsServiceRegistryImpl;
@ -100,13 +101,15 @@ public class CdsHooksConfig {
ICdsCrServiceFactory theCdsCrServiceFactory,
ICrDiscoveryServiceFactory theCrDiscoveryServiceFactory,
FhirContext theFhirContext) {
final CdsServiceRequestJsonDeserializer cdsServiceRequestJsonDeserializer =
new CdsServiceRequestJsonDeserializer(theFhirContext, theObjectMapper);
return new CdsServiceRegistryImpl(
theCdsHooksContextBooter,
theCdsPrefetchSvc,
theObjectMapper,
theCdsCrServiceFactory,
theCrDiscoveryServiceFactory,
theFhirContext);
cdsServiceRequestJsonDeserializer);
}
@Bean

3
hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/controller/CdsHooksController.java
View File

@ -21,7 +21,6 @@ package ca.uhn.hapi.fhir.cdshooks.controller;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceFeedbackJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServicesJson;
import org.springframework.http.HttpStatus;
@ -73,7 +72,7 @@ public class CdsHooksController {
method = {RequestMethod.POST},
consumes = {MediaType.APPLICATION_JSON_VALUE})
public ResponseEntity<CdsServiceResponseJson> cdsServiceRequest(
@PathVariable("cds_hook") String theCdsHook, @RequestBody CdsServiceRequestJson theCdsServiceRequestJson) {
@PathVariable("cds_hook") String theCdsHook, @RequestBody Object theCdsServiceRequestJson) {
CdsServiceResponseJson response = myCdsServiceRegistry.callService(theCdsHook, theCdsServiceRequestJson);
return ResponseEntity.status(200)
.contentType(MediaType.APPLICATION_JSON)

111
hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/serializer/CdsServiceRequestJsonDeserializer.java
View File

@ -20,84 +20,60 @@
package ca.uhn.hapi.fhir.cdshooks.serializer;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.serializer.FhirResourceDeserializer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsHooksExtension;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestContextJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsServiceRegistryImpl;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
import com.fasterxml.jackson.databind.module.SimpleModule;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.io.IOException;
import java.util.LinkedHashMap;
import java.util.Map;
public class CdsServiceRequestJsonDeserializer extends StdDeserializer<CdsServiceRequestJson> {
private final CdsServiceRegistryImpl myCdsServiceRegistry;
public class CdsServiceRequestJsonDeserializer {
private final ObjectMapper myObjectMapper;
private final FhirContext myFhirContext;
private final IParser myParser;
public CdsServiceRequestJsonDeserializer(CdsServiceRegistryImpl theCdsServiceRegistry, FhirContext theFhirContext) {
super(CdsServiceRequestJson.class);
myCdsServiceRegistry = theCdsServiceRegistry;
public CdsServiceRequestJsonDeserializer(
@Nonnull FhirContext theFhirContext, @Nonnull ObjectMapper theObjectMapper) {
myFhirContext = theFhirContext;
myParser = myFhirContext.newJsonParser().setPrettyPrint(true);
// We create a new ObjectMapper instead of using the one from the ApplicationContext to avoid an infinite loop
// during deserialization.
myObjectMapper = new ObjectMapper();
configureObjectMapper(myObjectMapper);
myObjectMapper = theObjectMapper;
}
@Override
public CdsServiceRequestJson deserialize(JsonParser theJsonParser, DeserializationContext theDeserializationContext)
throws IOException {
final JsonNode cdsServiceRequestJsonNode = theJsonParser.getCodec().readTree(theJsonParser);
final JsonNode hookNode = cdsServiceRequestJsonNode.get("hook");
final JsonNode extensionNode = cdsServiceRequestJsonNode.get("extension");
final JsonNode requestContext = cdsServiceRequestJsonNode.get("context");
final CdsServiceRequestJson cdsServiceRequestJson =
myObjectMapper.treeToValue(cdsServiceRequestJsonNode, CdsServiceRequestJson.class);
if (extensionNode != null) {
CdsHooksExtension myRequestExtension = deserializeExtension(hookNode.textValue(), extensionNode.toString());
cdsServiceRequestJson.setExtension(myRequestExtension);
public CdsServiceRequestJson deserialize(
@Nonnull CdsServiceJson theCdsServiceJson, @Nonnull Object theCdsServiceRequestJson) {
final JsonNode cdsServiceRequestJsonNode =
myObjectMapper.convertValue(theCdsServiceRequestJson, JsonNode.class);
final JsonNode contextNode = cdsServiceRequestJsonNode.get("context");
validateHookInstance(cdsServiceRequestJsonNode.get("hookInstance"));
validateHook(cdsServiceRequestJsonNode.get("hook"));
validateContext(contextNode);
try {
final JsonNode extensionNode = cdsServiceRequestJsonNode.get("extension");
final CdsServiceRequestJson cdsServiceRequestJson =
myObjectMapper.convertValue(cdsServiceRequestJsonNode, CdsServiceRequestJson.class);
LinkedHashMap<String, Object> map = myObjectMapper.readValue(contextNode.toString(), LinkedHashMap.class);
cdsServiceRequestJson.setContext(deserializeContext(map));
if (extensionNode != null) {
CdsHooksExtension myRequestExtension =
deserializeExtension(theCdsServiceJson, extensionNode.toString());
cdsServiceRequestJson.setExtension(myRequestExtension);
}
return cdsServiceRequestJson;
} catch (JsonProcessingException | IllegalArgumentException theEx) {
throw new InvalidRequestException(Msg.code(2551) + "Invalid CdsServiceRequest received. " + theEx);
}
if (requestContext != null) {
LinkedHashMap<String, Object> map =
myObjectMapper.readValue(requestContext.toString(), LinkedHashMap.class);
cdsServiceRequestJson.setContext(deserializeRequestContext(map));
}
return cdsServiceRequestJson;
}
void configureObjectMapper(ObjectMapper theObjectMapper) {
SimpleModule module = new SimpleModule();
module.addDeserializer(IBaseResource.class, new FhirResourceDeserializer(myFhirContext));
theObjectMapper.registerModule(module);
// set this as we will need to ignore properties which are not defined by specific implementation.
theObjectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
}
CdsHooksExtension deserializeExtension(String theServiceId, String theExtension) throws JsonProcessingException {
final CdsServiceJson cdsServicesJson = myCdsServiceRegistry.getCdsServiceJson(theServiceId);
Class<? extends CdsHooksExtension> extensionClass = cdsServicesJson.getExtensionClass();
if (extensionClass == null) {
return null;
}
return myObjectMapper.readValue(theExtension, extensionClass);
}
CdsServiceRequestContextJson deserializeRequestContext(LinkedHashMap<String, Object> theMap)
CdsServiceRequestContextJson deserializeContext(LinkedHashMap<String, Object> theMap)
throws JsonProcessingException {
final CdsServiceRequestContextJson cdsServiceRequestContextJson = new CdsServiceRequestContextJson();
for (Map.Entry<String, Object> entry : theMap.entrySet()) {
@ -114,4 +90,31 @@ public class CdsServiceRequestJsonDeserializer extends StdDeserializer<CdsServic
}
return cdsServiceRequestContextJson;
}
private CdsHooksExtension deserializeExtension(
@Nonnull CdsServiceJson theCdsServiceJson, @Nonnull String theExtension) throws JsonProcessingException {
Class<? extends CdsHooksExtension> extensionClass = theCdsServiceJson.getExtensionClass();
if (extensionClass == null) {
return null;
}
return myObjectMapper.readValue(theExtension, extensionClass);
}
private void validateHook(JsonNode hookIdNode) {
if (hookIdNode == null) {
throw new InvalidRequestException(Msg.code(2549) + "hook cannot be null for a CdsServiceRequest.");
}
}
private void validateHookInstance(JsonNode hookInstanceNode) {
if (hookInstanceNode == null) {
throw new InvalidRequestException(Msg.code(2548) + "hookInstance cannot be null for a CdsServiceRequest.");
}
}
private void validateContext(JsonNode requestContextNode) {
if (requestContextNode == null) {
throw new InvalidRequestException(Msg.code(2550) + "context cannot be null for a CdsServiceRequest.");
}
}
}

23
hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/svc/CdsServiceRegistryImpl.java
View File

@ -20,7 +20,6 @@
package ca.uhn.hapi.fhir.cdshooks.svc;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsMethod;
@ -38,7 +37,6 @@ import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICrDiscoveryServiceFactory;
import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchSvc;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.module.SimpleModule;
import com.google.common.annotations.VisibleForTesting;
import jakarta.annotation.Nonnull;
import jakarta.annotation.PostConstruct;
@ -50,7 +48,7 @@ import java.util.function.Function;
public class CdsServiceRegistryImpl implements ICdsServiceRegistry {
private static final Logger ourLog = LoggerFactory.getLogger(CdsServiceRegistryImpl.class);
private final CdsServiceRequestJsonDeserializer myCdsServiceRequestJsonDeserializer;
private CdsServiceCache myServiceCache;
private final CdsHooksContextBooter myCdsHooksContextBooter;
@ -65,19 +63,13 @@ public class CdsServiceRegistryImpl implements ICdsServiceRegistry {
ObjectMapper theObjectMapper,
ICdsCrServiceFactory theCdsCrServiceFactory,
ICrDiscoveryServiceFactory theCrDiscoveryServiceFactory,
FhirContext theFhirContext) {
CdsServiceRequestJsonDeserializer theCdsServiceRequestJsonDeserializer) {
myCdsHooksContextBooter = theCdsHooksContextBooter;
myCdsPrefetchSvc = theCdsPrefetchSvc;
myObjectMapper = theObjectMapper;
// registering this deserializer here instead of
// CdsHooksObjectMapperFactory to avoid circular
// dependency
SimpleModule module = new SimpleModule();
module.addDeserializer(
CdsServiceRequestJson.class, new CdsServiceRequestJsonDeserializer(this, theFhirContext));
myObjectMapper.registerModule(module);
myCdsCrServiceFactory = theCdsCrServiceFactory;
myCrDiscoveryServiceFactory = theCrDiscoveryServiceFactory;
myCdsServiceRequestJsonDeserializer = theCdsServiceRequestJsonDeserializer;
}
@PostConstruct
@ -91,10 +83,13 @@ public class CdsServiceRegistryImpl implements ICdsServiceRegistry {
}
@Override
public CdsServiceResponseJson callService(String theServiceId, CdsServiceRequestJson theCdsServiceRequestJson) {
public CdsServiceResponseJson callService(String theServiceId, Object theCdsServiceRequestJson) {
final CdsServiceJson cdsServiceJson = getCdsServiceJson(theServiceId);
final CdsServiceRequestJson deserializedRequest =
myCdsServiceRequestJsonDeserializer.deserialize(cdsServiceJson, theCdsServiceRequestJson);
ICdsServiceMethod serviceMethod = (ICdsServiceMethod) getCdsServiceMethodOrThrowException(theServiceId);
myCdsPrefetchSvc.augmentRequest(theCdsServiceRequestJson, serviceMethod);
Object response = serviceMethod.invoke(myObjectMapper, theCdsServiceRequestJson, theServiceId);
myCdsPrefetchSvc.augmentRequest(deserializedRequest, serviceMethod);
Object response = serviceMethod.invoke(myObjectMapper, deserializedRequest, theServiceId);
return encodeServiceResponse(theServiceId, response);
}

15
hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/controller/CdsHooksControllerTest.java
View File

@ -5,6 +5,7 @@ import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceFeebackOutcomeEnum;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceFeedbackJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestContextJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseCardJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
@ -118,6 +119,7 @@ public class CdsHooksControllerTest {
request.setHookInstance(TEST_HOOK_INSTANCE);
request.setHook(HelloWorldService.TEST_HOOK);
request.setFhirServer(TEST_FHIR_SERVER);
request.setContext( withCdsServiceRequestContext());
String requestBody = myObjectMapper.writeValueAsString(request);
@ -142,8 +144,9 @@ public class CdsHooksControllerTest {
CdsServiceRequestJson request = new CdsServiceRequestJson();
request.setExtension(requestExtension);
request.setFhirServer(TEST_FHIR_SERVER);
request.setHook(HelloWorldService.TEST_HOOK_UNIVERSE_ID);
request.setHook(HelloWorldService.TEST_HOOK);
request.setContext(withCdsServiceRequestContext());
request.setHookInstance(UUID.randomUUID().toString());
String requestBody = myObjectMapper.writeValueAsString(request);
@ -163,6 +166,7 @@ public class CdsHooksControllerTest {
request.setHookInstance(TEST_HOOK_INSTANCE);
request.setHook(HelloWorldService.TEST_HOOK);
request.setFhirServer(TEST_FHIR_SERVER);
request.setContext(withCdsServiceRequestContext());
String requestBody = myObjectMapper.writeValueAsString(request);
@ -268,4 +272,11 @@ public class CdsHooksControllerTest {
return JsonUtil.serialize(input, true);
}
@Nonnull
private static CdsServiceRequestContextJson withCdsServiceRequestContext() {
CdsServiceRequestContextJson cdsServiceRequestContextJson = new CdsServiceRequestContextJson();
cdsServiceRequestContextJson.put("patientId", "Patient/123");
return cdsServiceRequestContextJson;
}
}

187
hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/serializer/CdsServiceRequestJsonDeserializerTest.java
View File

@ -1,106 +1,152 @@
package ca.uhn.hapi.fhir.cdshooks.serializer;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsHooksExtension;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestContextJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
import ca.uhn.hapi.fhir.cdshooks.custom.extensions.model.ExampleExtension;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsServiceRegistryImpl;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.LinkedHashMap;
import java.util.UUID;
import static org.assertj.core.api.Assertions.assertThat;
import static org.mockito.Mockito.doReturn;
import static org.assertj.core.api.Assertions.assertThatThrownBy;
@ExtendWith(MockitoExtension.class)
class CdsServiceRequestJsonDeserializerTest {
@Mock
private CdsServiceRegistryImpl myCdsServiceRegistry;
private static final String SERVICE_ID = "service-id";
private static final String EXAMPLE_PROPERTY_VALUE = "example-value";
private static final String EXAMPLE_PROPERTY_KEY = "example-property";
private static final String HOOK_ID = "hook-id";
private final FhirContext myFhirContext = FhirContext.forR4();
private final ObjectMapper myObjectMapper = new ObjectMapper();
private CdsServiceRequestJsonDeserializer myFixture;
@BeforeEach()
void setup() {
myFixture = new CdsServiceRequestJsonDeserializer(myCdsServiceRegistry, myFhirContext);
myFixture = new CdsServiceRequestJsonDeserializer(myFhirContext, myObjectMapper);
}
@Test
void configureObjectMapper() {
void deserialize_shouldDeserialize_whenValidCdsServiceRequestWithExtensionReceived() {
// setup
ObjectMapper input = new ObjectMapper();
final CdsServiceJson cdsServiceJson = withCdsServiceJsonIncludingExtensionClass();
final LinkedHashMap<String, Object> extension = withExtension();
final LinkedHashMap<String, Object> request = withRequest(extension);
request.put("context", withContext());
// execute
myFixture.configureObjectMapper(input);
final CdsServiceRequestJson actual = myFixture.deserialize(cdsServiceJson, request);
// validate
assertThat(input.getRegisteredModuleIds()).hasSize(1);
assertThat(actual.getExtension()).isInstanceOf(ExampleExtension.class);
final ExampleExtension actualExtension = (ExampleExtension) actual.getExtension();
assertThat(actualExtension.getExampleProperty()).isEqualTo(EXAMPLE_PROPERTY_VALUE);
}
@Test
void deserializeExtensionWhenClassFoundShouldDeserializeExtension() throws JsonProcessingException {
void deserialize_shouldIgnoreExtraFieldsInsideExtension_whenExtensionContainsMoreFieldsThanDefinedInClass() {
// setup
final CdsServiceJson cdsServiceJson = withCdsServiceJsonIncludingExtensionClass();
final LinkedHashMap<String, Object> extension = withExtension();
extension.put("example-extra-property", "example-extra-value");
final LinkedHashMap<String, Object> request = withRequest(extension);
request.put("context", withContext());
// execute
final CdsServiceRequestJson actual = myFixture.deserialize(cdsServiceJson, request);
// validate
assertThat(actual.getExtension()).isInstanceOf(ExampleExtension.class);
final ExampleExtension actualExtension = (ExampleExtension) actual.getExtension();
assertThat(actualExtension.getExampleProperty()).isEqualTo(EXAMPLE_PROPERTY_VALUE);
assertThat(actual.getContext().get("encounterId")).isEqualTo("Encounter/123");
}
@Nonnull
private static LinkedHashMap<String, Object> withContext() {
final LinkedHashMap<String, Object> context = new LinkedHashMap<>();
context.put("encounterId", "Encounter/123");
return context;
}
@Test
void deserialize_shouldThrow_whenCdsServiceRequestIncludesInvalidProperty() {
// setup
final CdsServiceJson cdsServiceJson = withCdsServiceJsonIncludingExtensionClass();
final LinkedHashMap<String, Object> extension = withExtension();
final LinkedHashMap<String, Object> request = withRequest(extension);
request.put("invalid-key", "some-value");
request.put("context", withContext());
// execute & validate
assertThatThrownBy(
() -> myFixture.deserialize(cdsServiceJson, request))
.isInstanceOf(InvalidRequestException.class)
.hasMessageContaining("HAPI-2551:")
.hasMessageContaining("Invalid CdsServiceRequest received.");
}
@Test
void deserialize_shouldReturnNullExtension_whenNotClassFound() {
// setup
final String serviceId = "service-id";
final String extension = """
{
"example-property": "example-value"
}
""";
final CdsServiceJson cdsServiceJson = new CdsServiceJson();
cdsServiceJson.setId(serviceId);
cdsServiceJson.setExtensionClass(ExampleExtension.class);
doReturn(cdsServiceJson).when(myCdsServiceRegistry).getCdsServiceJson(serviceId);
cdsServiceJson.setId(SERVICE_ID);
final LinkedHashMap<String, Object> extension = withExtension();
extension.put("example-extra-property", "example-extra-value");
final LinkedHashMap<String, Object> request = withRequest(extension);
request.put("context", withContext());
// execute
final ExampleExtension actual = (ExampleExtension) myFixture.deserializeExtension(serviceId, extension);
final CdsServiceRequestJson actual = myFixture.deserialize(cdsServiceJson, request);
// validate
assertThat(actual.getExampleProperty()).isEqualTo("example-value");
assertThat(actual.getExtension()).isNull();
}
@Test
void deserializeExtensionWhenClassFoundButExtensionHasExtraPropertiesShouldIgnoreExtraProperties() throws JsonProcessingException {
void deserialize_shouldThrow_whenHookNotFoundInRequest() {
// setup
final String serviceId = "service-id";
final String extension = """
{
"example-property": "example-value",
"example-extra-property": "example-extra-value"
}
""";
final CdsServiceJson cdsServiceJson = new CdsServiceJson();
cdsServiceJson.setId(serviceId);
cdsServiceJson.setExtensionClass(ExampleExtension.class);
doReturn(cdsServiceJson).when(myCdsServiceRegistry).getCdsServiceJson(serviceId);
// execute
final ExampleExtension actual = (ExampleExtension) myFixture.deserializeExtension(serviceId, extension);
// validate
assertThat(actual.getExampleProperty()).isEqualTo("example-value");
final CdsServiceJson cdsServiceJson = withCdsServiceJsonIncludingExtensionClass();
final LinkedHashMap<String, Object> request = new LinkedHashMap<>();
request.put("context", withContext());
request.put("hookInstance", UUID.randomUUID().toString());
// execute and validate
assertThatThrownBy(() -> myFixture.deserialize(cdsServiceJson, request))
.isInstanceOf(InvalidRequestException.class)
.hasMessageContaining("HAPI-2549:")
.hasMessageContaining("hook cannot be null for a CdsServiceRequest.");
}
@Test
void deserializeExtensionWhenNotClassFoundShouldReturnNull() throws JsonProcessingException {
void deserialize_shouldThrow_whenContextNotFoundInRequest() {
// setup
final String serviceId = "service-id";
final String extension = """
{
"example-property": "example-value"
}
""";
final CdsServiceJson cdsServiceJson = new CdsServiceJson();
cdsServiceJson.setId(serviceId);
doReturn(cdsServiceJson).when(myCdsServiceRegistry).getCdsServiceJson(serviceId);
// execute
final CdsHooksExtension actual = myFixture.deserializeExtension(serviceId, extension);
// validate
assertThat(actual).isNull();
final CdsServiceJson cdsServiceJson = withCdsServiceJsonIncludingExtensionClass();
final LinkedHashMap<String, Object> request = new LinkedHashMap<>();
request.put("hook", HOOK_ID);
request.put("hookInstance", UUID.randomUUID().toString());
// execute and validate
assertThatThrownBy(() -> myFixture.deserialize(cdsServiceJson, request))
.isInstanceOf(InvalidRequestException.class)
.hasMessageContaining("HAPI-2550:")
.hasMessageContaining("context cannot be null for a CdsServiceRequest.");
}
@Test
void deserializeRequestContextShouldDeserializeValidContext() throws JsonProcessingException {
void deserialize_shouldThrow_whenHookInstanceNotFoundInRequest() {
// setup
final CdsServiceJson cdsServiceJson = withCdsServiceJsonIncludingExtensionClass();
final LinkedHashMap<String, Object> request = new LinkedHashMap<>();
request.put("context", withContext());
request.put("hook", HOOK_ID);
// execute and validate
assertThatThrownBy(() -> myFixture.deserialize(cdsServiceJson, request))
.isInstanceOf(InvalidRequestException.class)
.hasMessageContaining("HAPI-2548:")
.hasMessageContaining("hookInstance cannot be null for a CdsServiceRequest.");
}
@Test
void deserializeRequestContext_shouldDeserialize_whenContextIsValid() throws JsonProcessingException {
// setup
final String encounterId = "123";
final Patient patientContext = new Patient();
@ -109,9 +155,34 @@ class CdsServiceRequestJsonDeserializerTest {
input.put("encounterId", encounterId);
input.put("patient", patientContext);
// execute
final CdsServiceRequestContextJson actual = myFixture.deserializeRequestContext(input);
final CdsServiceRequestContextJson actual = myFixture.deserializeContext(input);
// validate
assertThat(actual.get("encounterId")).isEqualTo(encounterId);
assertThat(actual.get("patient")).usingRecursiveComparison().isEqualTo(patientContext);
}
@Nonnull
private static LinkedHashMap<String, Object> withExtension() {
final LinkedHashMap<String, Object> extension = new LinkedHashMap<>();
extension.put(EXAMPLE_PROPERTY_KEY, EXAMPLE_PROPERTY_VALUE);
return extension;
}
@Nonnull
private static CdsServiceJson withCdsServiceJsonIncludingExtensionClass() {
final CdsServiceJson cdsServiceJson = new CdsServiceJson();
cdsServiceJson.setId(SERVICE_ID);
cdsServiceJson.setExtensionClass(ExampleExtension.class);
cdsServiceJson.setHook(HOOK_ID);
return cdsServiceJson;
}
@Nonnull
private static LinkedHashMap<String, Object> withRequest(@Nonnull LinkedHashMap<String, Object> theExtension) {
final LinkedHashMap<String, Object> request = new LinkedHashMap<>();
request.put("extension", theExtension);
request.put("hookInstance", UUID.randomUUID().toString());
request.put("hook", HOOK_ID);
return request;
}
}

7
hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/svc/CdsServiceRegistryImplTest.java
View File

@ -1,10 +1,10 @@
package ca.uhn.hapi.fhir.cdshooks.svc;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceFeedbackJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
import ca.uhn.hapi.fhir.cdshooks.serializer.CdsServiceRequestJsonDeserializer;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceFactory;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICrDiscoveryServiceFactory;
import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchSvc;
@ -33,13 +33,14 @@ class CdsServiceRegistryImplTest {
private ICrDiscoveryServiceFactory myCrDiscoveryServiceFactory;
@Mock
private CdsServiceCache myCdsServiceCache;
@Mock
private CdsServiceRequestJsonDeserializer myCdsServiceRequestJsonDeserializer;
private final ObjectMapper myObjectMapper = new ObjectMapper();
private final FhirContext myFhirContext = FhirContext.forR4();
private CdsServiceRegistryImpl myFixture;
@BeforeEach()
void setup() {
myFixture = new CdsServiceRegistryImpl(myCdsHooksContextBooter, myCdsPrefetchSvc, myObjectMapper, myCdsCrServiceFactory, myCrDiscoveryServiceFactory, myFhirContext);
myFixture = new CdsServiceRegistryImpl(myCdsHooksContextBooter, myCdsPrefetchSvc, myObjectMapper, myCdsCrServiceFactory, myCrDiscoveryServiceFactory, myCdsServiceRequestJsonDeserializer);
}
@Test

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-api/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

4
hapi-fhir-serviceloaders/hapi-fhir-caching-caffeine/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -21,7 +21,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
</dependency>
<dependency>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-guava/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-serviceloaders/hapi-fhir-caching-testing/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<artifactId>hapi-fhir</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<artifactId>hapi-deployable-pom</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

18
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ForceIdMigrationFixTask.java
View File

@ -89,7 +89,7 @@ public class ForceIdMigrationFixTask extends BaseTask {
" set fhir_id = coalesce( "
+
// case 5.
" trim(fhir_id), "
trimFhirId()
+
// case 3
" (select f.forced_id from hfj_forced_id f where f.resource_pid = res_id), "
@ -109,6 +109,22 @@ public class ForceIdMigrationFixTask extends BaseTask {
}
}
private String trimFhirId() {
switch (getDriverType()) {
case MSSQL_2012:
return " LTRIM(RTRIM(fhir_id)), ";
case H2_EMBEDDED:
case DERBY_EMBEDDED:
case MARIADB_10_1:
case MYSQL_5_7:
case POSTGRES_9_4:
case ORACLE_12C:
case COCKROACHDB_21_1:
default:
return " trim(fhir_id), ";
}
}
private String getWhereClauseByDBType() {
switch (getDriverType()) {
case MSSQL_2012:

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

16
hapi-fhir-storage-cr/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -145,6 +145,20 @@
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<!-- For test CR config that's exported to downstream modules -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
<exclusions>
<!-- prevent conflict with other version of this dependency sourced from elsewhere -->
<exclusion>
<groupId>org.glassfish</groupId>
<artifactId>jakarta.json</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- test -->
<dependency>
<groupId>org.testcontainers</groupId>

2
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/IRepositoryFactory.java
View File

@ -21,8 +21,10 @@ package ca.uhn.fhir.cr.common;
import ca.uhn.fhir.cr.repo.HapiFhirRepository;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import com.google.common.annotations.Beta;
@FunctionalInterface
@Beta
public interface IRepositoryFactory {
HapiFhirRepository create(RequestDetails theRequestDetails);
}

31
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/common/RepositoryFactoryForRepositoryInterface.java Normal file
View File

@ -0,0 +1,31 @@
/*-
* #%L
* HAPI FHIR - Clinical Reasoning
* %%
* Copyright (C) 2014 - 2024 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%
*/
package ca.uhn.fhir.cr.common;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.opencds.cqf.fhir.api.Repository;
/**
* Factory interface to return a {@link Repository} from a {@link RequestDetails}
*/
@FunctionalInterface
public interface RepositoryFactoryForRepositoryInterface {
Repository create(RequestDetails theRequestDetails);
}

8
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/RepositoryConfig.java
View File

@ -20,6 +20,7 @@
package ca.uhn.fhir.cr.config;
import ca.uhn.fhir.cr.common.IRepositoryFactory;
import ca.uhn.fhir.cr.common.RepositoryFactoryForRepositoryInterface;
import ca.uhn.fhir.cr.repo.HapiFhirRepository;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.rest.server.RestfulServer;
@ -28,8 +29,15 @@ import org.springframework.context.annotation.Configuration;
@Configuration
public class RepositoryConfig {
@Bean
IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
}
@Bean
RepositoryFactoryForRepositoryInterface repositoryFactoryForInterface(
DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
}
}

4
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/r4/CrR4Config.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.cr.config.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.cr.common.IRepositoryFactory;
import ca.uhn.fhir.cr.common.RepositoryFactoryForRepositoryInterface;
import ca.uhn.fhir.cr.config.ProviderLoader;
import ca.uhn.fhir.cr.config.ProviderSelector;
import ca.uhn.fhir.cr.config.RepositoryConfig;
@ -66,7 +67,8 @@ public class CrR4Config {
@Bean
IMeasureServiceFactory r4MeasureServiceFactory(
IRepositoryFactory theRepositoryFactory, MeasureEvaluationOptions theEvaluationOptions) {
RepositoryFactoryForRepositoryInterface theRepositoryFactory,
MeasureEvaluationOptions theEvaluationOptions) {
return rd -> new R4MeasureService(theRepositoryFactory.create(rd), theEvaluationOptions);
}

25
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/TestCqlProperties.java → hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/test/TestCqlProperties.java
View File

@ -1,4 +1,23 @@
package ca.uhn.fhir.cr;
/*-
* #%L
* HAPI FHIR - Clinical Reasoning
* %%
* Copyright (C) 2014 - 2024 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%
*/
package ca.uhn.fhir.cr.config.test;
import org.cqframework.cql.cql2elm.CqlCompilerException;
import org.cqframework.cql.cql2elm.CqlCompilerOptions;
@ -7,7 +26,9 @@ import org.cqframework.cql.cql2elm.LibraryBuilder;
import org.opencds.cqf.fhir.cql.CqlEngineOptions;
import org.opencds.cqf.fhir.cql.CqlOptions;
/**
* Common CQL properties shared with downstream modules.
*/
public class TestCqlProperties {
//cql settings

34
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/TestCrConfig.java → hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/test/TestCrConfig.java
View File

@ -1,4 +1,23 @@
package ca.uhn.fhir.cr;
/*-
* #%L
* HAPI FHIR - Clinical Reasoning
* %%
* Copyright (C) 2014 - 2024 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%
*/
package ca.uhn.fhir.cr.config.test;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
import ca.uhn.fhir.context.FhirContext;
@ -47,6 +66,9 @@ import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
/**
* Common hapi-fhir clinical reasoning config shared with downstream modules.
*/
@Configuration
@Import({SubscriptionSubmitterConfig.class, SubscriptionChannelConfig.class})
public class TestCrConfig {
@ -77,7 +99,9 @@ public class TestCrConfig {
}
@Bean
public TestCqlProperties testCqlProperties(){
return new TestCqlProperties();}
return new TestCqlProperties();
}
@Bean
public JpaStorageSettings storageSettings() {
JpaStorageSettings storageSettings = new JpaStorageSettings();
@ -87,12 +111,6 @@ public class TestCrConfig {
storageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
return storageSettings;
}
@Bean
public PartitionHelper partitionHelper() {
return new PartitionHelper();
}
@Bean
public ModelManager modelManager(Map<ModelIdentifier, Model> theGlobalModelCache) {
return new ModelManager(theGlobalModelCache);

28
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/TestCrR4Config.java → hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/config/test/r4/TestCrR4Config.java
View File

@ -1,9 +1,28 @@
package ca.uhn.fhir.cr.r4;
/*-
* #%L
* HAPI FHIR - Clinical Reasoning
* %%
* Copyright (C) 2014 - 2024 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%
*/
package ca.uhn.fhir.cr.config.test.r4;
import ca.uhn.fhir.cr.TestCqlProperties;
import ca.uhn.fhir.cr.TestCrConfig;
import ca.uhn.fhir.cr.common.CqlThreadFactory;
import ca.uhn.fhir.cr.config.r4.CrR4Config;
import ca.uhn.fhir.cr.config.test.TestCqlProperties;
import ca.uhn.fhir.cr.config.test.TestCrConfig;
import org.cqframework.cql.cql2elm.CqlCompilerOptions;
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
import org.cqframework.cql.cql2elm.model.Model;
@ -30,6 +49,9 @@ import java.util.Set;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
/**
* Common hapi-fhir clinical reasoning config specifically for R4 shared with downstream modules.
*/
@Configuration
@Import({TestCrConfig.class, CrR4Config.class})
public class TestCrR4Config {

10
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/TestHapiFhirCrPartitionConfig.java Normal file
View File

@ -0,0 +1,10 @@
package ca.uhn.fhir.cr;
import org.springframework.context.annotation.Bean;
public class TestHapiFhirCrPartitionConfig {
@Bean
public PartitionHelper partitionHelper() {
return new PartitionHelper();
}
}

6
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/dstu3/TestCrDstu3Config.java
View File

@ -1,8 +1,9 @@
package ca.uhn.fhir.cr.dstu3;
import ca.uhn.fhir.cr.TestCqlProperties;
import ca.uhn.fhir.cr.TestCrConfig;
import ca.uhn.fhir.cr.TestHapiFhirCrPartitionConfig;
import ca.uhn.fhir.cr.config.test.TestCqlProperties;
import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
import ca.uhn.fhir.cr.config.test.TestCrConfig;
import org.cqframework.cql.cql2elm.CqlCompilerOptions;
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
import org.cqframework.cql.cql2elm.model.Model;
@ -26,6 +27,7 @@ import java.util.Set;
@Configuration
@Import({
TestHapiFhirCrPartitionConfig.class,
TestCrConfig.class,
CrDstu3Config.class
})

3
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/BaseCrR4TestServer.java
View File

@ -2,10 +2,12 @@ package ca.uhn.fhir.cr.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cr.IResourceLoader;
import ca.uhn.fhir.cr.TestHapiFhirCrPartitionConfig;
import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
import ca.uhn.fhir.cr.config.test.r4.TestCrR4Config;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
@ -38,6 +40,7 @@ import java.util.concurrent.TimeUnit;
@ContextConfiguration(classes = {
TestHapiFhirCrPartitionConfig.class,
TestCrR4Config.class,
ApplyOperationConfig.class,
ExtractOperationConfig.class,

8
hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/CrResourceListenerTests.java → hapi-fhir-storage-cr/src/test/java/ca/uhn/fhir/cr/r4/CrResourceListenerTest.java
View File

@ -1,6 +1,6 @@
package ca.uhn.fhir.cr.r4;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheRefresherImpl;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerCacheRefresher;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryImpl;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.IdType;
@ -16,13 +16,13 @@ import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@ExtendWith(SpringExtension.class)
public class CrResourceListenerTests extends BaseCrR4TestServer {
public class CrResourceListenerTest extends BaseCrR4TestServer {
@Autowired
EvaluationSettings myEvaluationSettings;
@Autowired
ResourceChangeListenerRegistryImpl myResourceChangeListenerRegistry;
@Autowired
ResourceChangeListenerCacheRefresherImpl myResourceChangeListenerCacheRefresher;
IResourceChangeListenerCacheRefresher myResourceChangeListenerCacheRefresher;
public MeasureReport runEvaluateMeasure(String periodStart, String periodEnd, String subject, String measureId, String reportType, String practitioner){
@ -118,7 +118,7 @@ public class CrResourceListenerTests extends BaseCrR4TestServer {
myResourceChangeListenerCacheRefresher.refreshExpiredCachesAndNotifyListeners();
//cache should be invalidated for matching library name and version
assertThat(myEvaluationSettings.getLibraryCache()).hasSize(6);
assertThat(myEvaluationSettings.getLibraryCache()).hasSize(7);
}
@Test

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

57
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
View File

@ -134,7 +134,7 @@ public class DaoResourceLinkResolver<T extends IResourcePersistentId> implements
type, targetReference, idPart, theRequest, theTransactionDetails);
if (!createdTableOpt.isPresent()) {
if (myStorageSettings.isEnforceReferentialIntegrityOnWrite() == false) {
if (!myStorageSettings.isEnforceReferentialIntegrityOnWrite()) {
return null;
}
@ -150,20 +150,8 @@ public class DaoResourceLinkResolver<T extends IResourcePersistentId> implements
"Resolved resource of type {} as PID: {}",
resolvedResource.getResourceType(),
resolvedResource.getPersistentId());
if (!resourceType.equals(resolvedResource.getResourceType())) {
ourLog.error(
"Resource with PID {} was of type {} and wanted {}",
resolvedResource.getPersistentId(),
resourceType,
resolvedResource.getResourceType());
throw new UnprocessableEntityException(Msg.code(1095)
+ "Resource contains reference to unknown resource ID " + targetResourceId.getValue());
}
if (resolvedResource.getDeleted() != null) {
String resName = resolvedResource.getResourceType();
throw new InvalidRequestException(Msg.code(1096) + "Resource " + resName + "/" + idPart
+ " is deleted, specified in path: " + sourcePath);
if (!validateResolvedResourceOrThrow(resourceType, resolvedResource, targetResourceId, idPart, sourcePath)) {
return null;
}
if (persistentId == null) {
@ -182,6 +170,45 @@ public class DaoResourceLinkResolver<T extends IResourcePersistentId> implements
return resolvedResource;
}
/**
* Validates the resolved resource.
* If 'Enforce Referential Integrity on Write' is enabled:
* Throws <code>UnprocessableEntityException</code> when resource types do not match
* Throws <code>InvalidRequestException</code> when the resolved resource was deleted
* <p>
* Otherwise, return false when resource types do not match or resource was deleted
* and return true if the resolved resource is valid.
*/
private boolean validateResolvedResourceOrThrow(
String resourceType,
IResourceLookup resolvedResource,
IIdType targetResourceId,
String idPart,
String sourcePath) {
if (!resourceType.equals(resolvedResource.getResourceType())) {
ourLog.error(
"Resource with PID {} was of type {} and wanted {}",
resolvedResource.getPersistentId(),
resourceType,
resolvedResource.getResourceType());
if (!myStorageSettings.isEnforceReferentialIntegrityOnWrite()) {
return false;
}
throw new UnprocessableEntityException(Msg.code(1095)
+ "Resource contains reference to unknown resource ID " + targetResourceId.getValue());
}
if (resolvedResource.getDeleted() != null) {
if (!myStorageSettings.isEnforceReferentialIntegrityOnWrite()) {
return false;
}
String resName = resolvedResource.getResourceType();
throw new InvalidRequestException(Msg.code(1096) + "Resource " + resName + "/" + idPart
+ " is deleted, specified in path: " + sourcePath);
}
return true;
}
@Nullable
@Override
public IBaseResource loadTargetResource(

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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-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>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4b/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.5.0-SNAPSHOT</version>
<version>7.5.1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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