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Revert "7_2 branch mergeback (#5922)" (#5927) 

This reverts commit 125513a100.
This commit is contained in:
Tadgh 2024-05-12 16:04:43 -07:00 committed by GitHub
parent 125513a100
commit 3572d593c1
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GPG Key ID: B5690EEEBB952194
68 changed files with 470 additions and 1662 deletions
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8
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
View File

@ -2387,19 +2387,13 @@ public enum Pointcut implements IPointcut {
* <li>
* ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent - Contains information about the from and to resources.
* </li>
* <li>
* ca.uhn.fhir.mdm.model.mdmevents.MdmTransactionContext - Contains information about the Transaction context, e.g. merge or link.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
* </p>
*/
MDM_POST_MERGE_GOLDEN_RESOURCES(
void.class,
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent",
"ca.uhn.fhir.mdm.model.MdmTransactionContext"),
void.class, "ca.uhn.fhir.rest.api.server.RequestDetails", "ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent"),
/**
* <b>MDM Link History Hook:</b>

11
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -19,7 +19,6 @@
*/
package ca.uhn.fhir.cli;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
@ -32,7 +31,6 @@ import ca.uhn.fhir.system.HapiSystemProperties;
import ca.uhn.fhir.util.AttachmentUtil;
import ca.uhn.fhir.util.FileUtil;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
@ -267,7 +265,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
"Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
}
protected void addFileToRequestBundle(IBaseParameters theInputParameters, String theFileName, byte[] theBytes) {
private void addFileToRequestBundle(IBaseParameters theInputParameters, String theFileName, byte[] theBytes) {
byte[] bytes = theBytes;
String fileName = theFileName;
@ -279,7 +277,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
FileUtil.formatFileSize(ourTransferSizeLimit));
try {
File tempFile = File.createTempFile("hapi-fhir-cli", "." + suffix);
File tempFile = File.createTempFile("hapi-fhir-cli", suffix);
tempFile.deleteOnExit();
try (OutputStream fileOutputStream = new FileOutputStream(tempFile, false)) {
fileOutputStream.write(bytes);
@ -365,9 +363,4 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
}
return retVal;
}
@VisibleForTesting
void setFhirContext(FhirContext theFhirContext) {
myFhirCtx = theFhirContext;
}
}

87
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
View File

@ -22,10 +22,6 @@ import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyS
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.r4.model.Attachment;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Type;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -47,7 +43,6 @@ import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
@ -59,8 +54,6 @@ import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertInstanceOf;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyList;
@ -486,86 +479,6 @@ public class UploadTerminologyCommandTest {
uploadICD10UsingCompressedFile(theFhirVersion, theIncludeTls);
}
@ParameterizedTest
@MethodSource("paramsProvider")
@SuppressWarnings("unused") // Both params for @BeforeEach
void testZipFileInParameters(String theFhirVersion, boolean theIncludeTls) {
final IBaseParameters inputParameters = switch (myCtx.getVersion().getVersion()) {
case DSTU2, DSTU2_HL7ORG, DSTU2_1 -> new org.hl7.fhir.dstu2.model.Parameters();
case DSTU3 -> new org.hl7.fhir.dstu3.model.Parameters();
case R4 -> new Parameters();
case R4B -> new org.hl7.fhir.r4b.model.Parameters();
case R5 -> new org.hl7.fhir.r5.model.Parameters();
};
final UploadTerminologyCommand uploadTerminologyCommand = new UploadTerminologyCommand();
uploadTerminologyCommand.setFhirContext(myCtx);
uploadTerminologyCommand.setTransferSizeBytes(1);
uploadTerminologyCommand.addFileToRequestBundle(inputParameters, "something.zip", new byte[] {1,2});
final String actualAttachmentUrl = getAttachmentUrl(inputParameters, myCtx);
assertTrue(actualAttachmentUrl.endsWith(".zip"));
}
private static String getAttachmentUrl(IBaseParameters theInputParameters, FhirContext theCtx) {
switch (theCtx.getVersion().getVersion()) {
case DSTU2:
case DSTU2_HL7ORG:
case DSTU2_1: {
assertInstanceOf(org.hl7.fhir.dstu2.model.Parameters.class, theInputParameters);
final org.hl7.fhir.dstu2.model.Parameters dstu2Parameters = (org.hl7.fhir.dstu2.model.Parameters) theInputParameters;
final List<org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent> dstu2ParametersList = dstu2Parameters.getParameter();
final Optional<org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent> optDstu2FileParam = dstu2ParametersList.stream().filter(param -> TerminologyUploaderProvider.PARAM_FILE.equals(param.getName())).findFirst();
assertTrue(optDstu2FileParam.isPresent());
final org.hl7.fhir.dstu2.model.Type dstu2Value = optDstu2FileParam.get().getValue();
assertInstanceOf(org.hl7.fhir.dstu2.model.Attachment.class, dstu2Value);
final org.hl7.fhir.dstu2.model.Attachment dstu2Attachment = (org.hl7.fhir.dstu2.model.Attachment) dstu2Value;
return dstu2Attachment.getUrl();
}
case DSTU3: {
assertInstanceOf(org.hl7.fhir.dstu3.model.Parameters.class, theInputParameters);
final org.hl7.fhir.dstu3.model.Parameters dstu3Parameters = (org.hl7.fhir.dstu3.model.Parameters) theInputParameters;
final List<org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent> dstu3ParametersList = dstu3Parameters.getParameter();
final Optional<org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent> optDstu3FileParam = dstu3ParametersList.stream().filter(param -> TerminologyUploaderProvider.PARAM_FILE.equals(param.getName())).findFirst();
assertTrue(optDstu3FileParam.isPresent());
final org.hl7.fhir.dstu3.model.Type dstu3Value = optDstu3FileParam.get().getValue();
assertInstanceOf(org.hl7.fhir.dstu3.model.Attachment.class, dstu3Value);
final org.hl7.fhir.dstu3.model.Attachment dstu3Attachment = (org.hl7.fhir.dstu3.model.Attachment) dstu3Value;
return dstu3Attachment.getUrl();
}
case R4: {
assertInstanceOf(Parameters.class, theInputParameters);
final Parameters r4Parameters = (Parameters) theInputParameters;
final Parameters.ParametersParameterComponent r4Parameter = r4Parameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
final Type r4Value = r4Parameter.getValue();
assertInstanceOf(Attachment.class, r4Value);
final Attachment r4Attachment = (Attachment) r4Value;
return r4Attachment.getUrl();
}
case R4B: {
assertInstanceOf(org.hl7.fhir.r4b.model.Parameters.class, theInputParameters);
final org.hl7.fhir.r4b.model.Parameters r4bParameters = (org.hl7.fhir.r4b.model.Parameters) theInputParameters;
final org.hl7.fhir.r4b.model.Parameters.ParametersParameterComponent r4bParameter = r4bParameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
final org.hl7.fhir.r4b.model.DataType value = r4bParameter.getValue();
assertInstanceOf(org.hl7.fhir.r4b.model.Attachment.class, value);
final org.hl7.fhir.r4b.model.Attachment r4bAttachment = (org.hl7.fhir.r4b.model.Attachment) value;
return r4bAttachment.getUrl();
}
case R5: {
assertInstanceOf(org.hl7.fhir.r5.model.Parameters.class, theInputParameters);
final org.hl7.fhir.r5.model.Parameters r4Parameters = (org.hl7.fhir.r5.model.Parameters) theInputParameters;
final org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent parameter = r4Parameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
final org.hl7.fhir.r5.model.DataType value = parameter.getValue();
assertInstanceOf(org.hl7.fhir.r5.model.Attachment.class, value);
final org.hl7.fhir.r5.model.Attachment attachment = (org.hl7.fhir.r5.model.Attachment) value;
return attachment.getUrl();
}
default:
throw new IllegalStateException("Unknown FHIR version: " + theCtx.getVersion().getVersion());
}
}
private void uploadICD10UsingCompressedFile(String theFhirVersion, boolean theIncludeTls) throws IOException {
if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5861-enhance-rule-builder-code-support-multiple-ids.yaml
View File

@ -1,4 +0,0 @@
---
type: add
issue: 5861
title: "Enhance RuleBuilder code to support multiple instance IDs."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5865-updating-name-of-full-text-field-search.yaml
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@ -1,5 +0,0 @@
---
type: fix
issue: 5865
title: "Moving the Hibernate.Search annotation for text indexing from the lob column to the column added as part of the
PostgreSql LOB migration."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5877-exception-when-updating-token-param-with-large-value.yaml
View File

@ -1,5 +0,0 @@
---
type: fix
issue: 5877
title: "Previously, updating a tokenParam with a value greater than 200 characters would raise a SQLException.
This issue has been fixed."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5886-mdm-apply-survivorship-number-format-exception.yaml
View File

@ -1,6 +0,0 @@
---
type: fix
issue: 5886
title: "Previously, either updating links on, or deleting one of two patients with non-numeric IDs linked to a golden
patient would result in a HAPI-0389 if there were survivorship rules.
This issue has been fixed for both the update links and delete cases."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5888-update-binary-security-interceptor-documentation.yaml
View File

@ -1,7 +0,0 @@
---
type: fix
issue: 5888
title: "Updated documentation on binary_security_interceptor to specify using
`STORAGE_PRE_INITIATE_BULK_EXPORT` not `STORAGE_INITIATE_BULK_EXPORT` pointcut
to change bulk export parameters.
"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5890-add-possibility-to-persist-data-to-lob-columns.yaml
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@ -1,5 +0,0 @@
---
type: add
issue: 5890
title: "As part of the migration from LOB, provided the capability to force persisting data to LOB columns. The default
behavior is to not persist in lob columns."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5893-hapi-fhir-cli-upload-terminology-zip-hapi-0862.yaml
View File

@ -1,6 +0,0 @@
---
type: fix
issue: 5893
title: "Previously, hapi-fhir-cli: upload-terminology failed with a HAPI-0862 error when uploading LOINC.
This has been fixed."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml
View File

@ -1,5 +0,0 @@
---
type: fix
issue: 5898
title: "Previously, triggering a `$meta` via GET on a new patient with Megascale configured resulted in error HAPI-0389. This has been corrected
This has been fixed."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5899-enhance-mdm-interceptor.yaml
View File

@ -1,4 +0,0 @@
---
type: add
issue: 5899
title: "The `MDM_POST_MERGE_GOLDEN_RESOURCES` now supports an additional parameter, of type `ca.uhn.fhir.mdm.model.MdmTransactionContext`. Thanks to Jens Villadsen for the contribution."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5904-query-chained-sort-returns-less-results.yaml
View File

@ -1,4 +0,0 @@
---
type: fix
issue: 5904
title: "Chained sort would exclude results that did not have resources matching the sort chain. These are now included, and sorted at the end."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5915-bulk-export-security-woes.yaml
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@ -1,4 +0,0 @@
---
type: fix
issue: 5915
title: "Previously, in some edge case scenarios the Bulk Export Rule Applier could accidentally permit a Patient type level bulk export request, even if the calling user only had permissions to a subset of patients. This has been corrected."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5917-chain-sort-mssql.yaml
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@ -1,4 +0,0 @@
---
type: fix
issue: 5917
title: "Fix chained sorts on strings when using MS Sql"

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/security/binary_security_interceptor.md
View File

@ -14,9 +14,4 @@ This interceptor is intended to be subclassed. A simple example is shown below:
## Combining with Bulk Export
The `setBinarySecurityContextIdentifierSystem(..)` and `setBinarySecurityContextIdentifierValue(..)` properties on the `BulkExportJobParameters` object can be used to automatically populate the security context on Binary resources created by Bulk Export jobs with values that can be verified by this interceptor.
An interceptor on the `STORAGE_PRE_INITIATE_BULK_EXPORT` pointcut is the recommended way to set these properties when a new Bulk Export job is being kicked off.
NB: Previous versions recommended using the `STORAGE_INITIATE_BULK_EXPORT` pointcut, but this is no longer the recommended way.
`STORAGE_PRE_INITIATE_BULK_EXPORT` pointcut is called before `STORAGE_INITIATE_BULK_EXPORT` and is thus guaranteed to be called before
any AuthorizationInterceptors.
The `setBinarySecurityContextIdentifierSystem(..)` and `setBinarySecurityContextIdentifierValue(..)` properties on the `BulkExportJobParameters` object can be used to automatically populate the security context on Binary resources created by Bulk Export jobs with values that can be verified by this interceptor. An interceptor on the `STORAGE_INITIATE_BULK_EXPORT` pointcut is the easiest way to set these properties when a new Bulk Export job is being kicked off.

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/DatabaseBinaryContentStorageSvcImpl.java
View File

@ -26,7 +26,6 @@ import ca.uhn.fhir.jpa.dao.data.IBinaryStorageEntityDao;
import ca.uhn.fhir.jpa.model.entity.BinaryStorageEntity;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.hash.HashingInputStream;
import com.google.common.io.ByteStreams;
import jakarta.annotation.Nonnull;
@ -60,8 +59,6 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
@Autowired
private IBinaryStorageEntityDao myBinaryStorageEntityDao;
private boolean mySupportLegacyLobServer = false;
@Nonnull
@Override
@Transactional(propagation = Propagation.REQUIRED)
@ -99,10 +96,9 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
entity.setContentId(id);
entity.setStorageContentBin(loadedStream);
if (mySupportLegacyLobServer) {
Blob dataBlob = lobHelper.createBlob(loadedStream);
entity.setBlob(dataBlob);
}
// TODO: remove writing Blob in a future release
Blob dataBlob = lobHelper.createBlob(loadedStream);
entity.setBlob(dataBlob);
// Update the entity with the final byte count and hash
long bytes = countingInputStream.getByteCount();
@ -173,11 +169,6 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
return copyBinaryContentToByteArray(entityOpt);
}
public DatabaseBinaryContentStorageSvcImpl setSupportLegacyLobServer(boolean theSupportLegacyLobServer) {
mySupportLegacyLobServer = theSupportLegacyLobServer;
return this;
}
void copyBinaryContentToOutputStream(OutputStream theOutputStream, BinaryStorageEntity theEntity)
throws IOException {
@ -221,10 +212,4 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
return retVal;
}
@VisibleForTesting
public DatabaseBinaryContentStorageSvcImpl setEntityManagerForTesting(EntityManager theEntityManager) {
myEntityManager = theEntityManager;
return this;
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -73,7 +73,6 @@ import ca.uhn.fhir.jpa.delete.DeleteConflictFinderService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.esr.ExternallyStoredResourceServiceRegistry;
import ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
@ -155,8 +154,6 @@ import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
import ca.uhn.fhir.jpa.term.TermReadSvcImpl;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.jpa.term.ValueSetConceptAccumulator;
import ca.uhn.fhir.jpa.term.ValueSetConceptAccumulatorFactory;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
@ -825,17 +822,6 @@ public class JpaConfig {
return new TermReadSvcImpl();
}
@Bean
public ValueSetConceptAccumulatorFactory valueSetConceptAccumulatorFactory() {
return new ValueSetConceptAccumulatorFactory();
}
@Bean
@Scope("prototype")
public ValueSetConceptAccumulator valueSetConceptAccumulator(TermValueSet theTermValueSet) {
return valueSetConceptAccumulatorFactory().create(theTermValueSet);
}
@Bean
public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
return new TermCodeSystemStorageSvcImpl();

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -1410,20 +1410,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
@Override
@Transactional
public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequest) {
return myTransactionService.withRequest(theRequest).execute(() -> {
Set<TagDefinition> tagDefs = new HashSet<>();
BaseHasResource entity = readEntity(theId, theRequest);
for (BaseTag next : entity.getTags()) {
tagDefs.add(next.getTag());
}
MT retVal = toMetaDt(theType, tagDefs);
Set<TagDefinition> tagDefs = new HashSet<>();
BaseHasResource entity = readEntity(theId, theRequest);
for (BaseTag next : entity.getTags()) {
tagDefs.add(next.getTag());
}
MT retVal = toMetaDt(theType, tagDefs);
retVal.setLastUpdated(entity.getUpdatedDate());
retVal.setVersionId(Long.toString(entity.getVersion()));
retVal.setLastUpdated(entity.getUpdatedDate());
retVal.setVersionId(Long.toString(entity.getVersion()));
return retVal;
});
return retVal;
}
@Override

36
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -24,7 +24,6 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.search.DeferConceptIndexingRoutingBinder;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.annotations.VisibleForTesting;
import jakarta.annotation.Nonnull;
import jakarta.persistence.Column;
import jakarta.persistence.Entity;
@ -59,7 +58,10 @@ import org.hibernate.search.mapper.pojo.bridge.mapping.annotation.RoutingBinderR
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.GenericField;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.ObjectPath;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyBinding;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyValue;
import org.hl7.fhir.r4.model.Coding;
import java.io.Serializable;
@ -175,11 +177,6 @@ public class TermConcept implements Serializable {
@Column(name = "PARENT_PIDS", nullable = true)
private String myParentPids;
@FullTextField(
name = "myParentPids",
searchable = Searchable.YES,
projectable = Projectable.YES,
analyzer = "conceptParentPidsAnalyzer")
@Column(name = "PARENT_PIDS_VC", nullable = true, length = Length.LONG32)
private String myParentPidsVc;
@ -192,9 +189,6 @@ public class TermConcept implements Serializable {
@Column(name = "CODE_SEQUENCE", nullable = true)
private Integer mySequence;
@Transient
private boolean mySupportLegacyLob = false;
public TermConcept() {
super();
}
@ -368,6 +362,13 @@ public class TermConcept implements Serializable {
return this;
}
@Transient
@FullTextField(
name = "myParentPids",
searchable = Searchable.YES,
projectable = Projectable.YES,
analyzer = "conceptParentPidsAnalyzer")
@IndexingDependency(derivedFrom = @ObjectPath({@PropertyValue(propertyName = "myParentPidsVc")}))
public String getParentPidsAsString() {
return nonNull(myParentPidsVc) ? myParentPidsVc : myParentPids;
}
@ -457,10 +458,6 @@ public class TermConcept implements Serializable {
ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
}
if (!mySupportLegacyLob) {
clearParentPidsLob();
}
}
private void setParentPids(Set<Long> theParentPids) {
@ -522,17 +519,4 @@ public class TermConcept implements Serializable {
public List<TermConcept> getChildCodes() {
return getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList());
}
public void flagForLegacyLobSupport(boolean theSupportLegacyLob) {
mySupportLegacyLob = theSupportLegacyLob;
}
private void clearParentPidsLob() {
myParentPids = null;
}
@VisibleForTesting
public boolean hasParentPidsLobForTesting() {
return nonNull(myParentPids);
}
}

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
View File

@ -54,7 +54,6 @@ import org.hibernate.validator.constraints.NotBlank;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import static java.util.Objects.nonNull;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@ -308,15 +307,9 @@ public class TermConceptProperty implements Serializable {
return myId;
}
public void performLegacyLobSupport(boolean theSupportLegacyLob) {
if (!theSupportLegacyLob) {
myValueLob = null;
}
}
@VisibleForTesting
public boolean hasValueBlobForTesting() {
return nonNull(myValueLob);
public byte[] getValueBlobForTesting() {
return myValueLob;
}
@VisibleForTesting
@ -325,8 +318,8 @@ public class TermConceptProperty implements Serializable {
}
@VisibleForTesting
public boolean hasValueBinForTesting() {
return nonNull(myValueBin);
public byte[] getValueBinForTesting() {
return myValueBin;
}
@VisibleForTesting

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConcept.java
View File

@ -20,7 +20,6 @@
package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.annotations.VisibleForTesting;
import jakarta.annotation.Nonnull;
import jakarta.persistence.Column;
import jakarta.persistence.Entity;
@ -47,7 +46,6 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static java.util.Objects.nonNull;
import static org.apache.commons.lang3.StringUtils.isNotEmpty;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@ -298,13 +296,4 @@ public class TermValueSetConcept implements Serializable {
? mySourceConceptDirectParentPidsVc
: mySourceConceptDirectParentPids;
}
public void clearSourceConceptDirectParentPidsLob() {
mySourceConceptDirectParentPids = null;
}
@VisibleForTesting
public boolean hasSourceConceptDirectParentPidsLob() {
return nonNull(mySourceConceptDirectParentPids);
}
}

41
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptView.java
View File

@ -43,21 +43,20 @@ import java.sql.SQLException;
* because hibernate won't allow the view the function without it, but
*/
"SELECT CONCAT_WS(' ', vsc.PID, vscd.PID) AS PID, " + " vsc.PID AS CONCEPT_PID, "
+ " vsc.VALUESET_PID AS CONCEPT_VALUESET_PID, "
+ " vsc.VALUESET_ORDER AS CONCEPT_VALUESET_ORDER, "
+ " vsc.SYSTEM_URL AS CONCEPT_SYSTEM_URL, "
+ " vsc.CODEVAL AS CONCEPT_CODEVAL, "
+ " vsc.DISPLAY AS CONCEPT_DISPLAY, "
+ " vsc.SYSTEM_VER AS SYSTEM_VER, "
+ " vsc.SOURCE_PID AS SOURCE_PID, "
+ " vsc.SOURCE_DIRECT_PARENT_PIDS AS SOURCE_DIRECT_PARENT_PIDS, "
+ " vsc.SOURCE_DIRECT_PARENT_PIDS_VC AS SOURCE_DIRECT_PARENT_PIDS_VC, "
+ " vscd.PID AS DESIGNATION_PID, "
+ " vscd.LANG AS DESIGNATION_LANG, "
+ " vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, "
+ " vscd.USE_CODE AS DESIGNATION_USE_CODE, "
+ " vscd.USE_DISPLAY AS DESIGNATION_USE_DISPLAY, "
+ " vscd.VAL AS DESIGNATION_VAL "
+ " vsc.VALUESET_PID AS CONCEPT_VALUESET_PID, "
+ " vsc.VALUESET_ORDER AS CONCEPT_VALUESET_ORDER, "
+ " vsc.SYSTEM_URL AS CONCEPT_SYSTEM_URL, "
+ " vsc.CODEVAL AS CONCEPT_CODEVAL, "
+ " vsc.DISPLAY AS CONCEPT_DISPLAY, "
+ " vsc.SYSTEM_VER AS SYSTEM_VER, "
+ " vsc.SOURCE_PID AS SOURCE_PID, "
+ " vsc.SOURCE_DIRECT_PARENT_PIDS AS SOURCE_DIRECT_PARENT_PIDS, "
+ " vscd.PID AS DESIGNATION_PID, "
+ " vscd.LANG AS DESIGNATION_LANG, "
+ " vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, "
+ " vscd.USE_CODE AS DESIGNATION_USE_CODE, "
+ " vscd.USE_DISPLAY AS DESIGNATION_USE_DISPLAY, "
+ " vscd.VAL AS DESIGNATION_VAL "
+ "FROM TRM_VALUESET_CONCEPT vsc "
+ "LEFT OUTER JOIN TRM_VALUESET_C_DESIGNATION vscd ON vsc.PID = vscd.VALUESET_CONCEPT_PID")
public class TermValueSetConceptView implements Serializable, ITermValueSetConceptView {
@ -113,9 +112,6 @@ public class TermValueSetConceptView implements Serializable, ITermValueSetConce
@Column(name = "SOURCE_DIRECT_PARENT_PIDS", nullable = true)
private Clob mySourceConceptDirectParentPids;
@Column(name = "SOURCE_DIRECT_PARENT_PIDS_VC", nullable = true)
private String mySourceConceptDirectParentPidsVc;
@Override
public Long getSourceConceptPid() {
return mySourceConceptPid;
@ -123,19 +119,14 @@ public class TermValueSetConceptView implements Serializable, ITermValueSetConce
@Override
public String getSourceConceptDirectParentPids() {
String retVal = null;
if (mySourceConceptDirectParentPids != null) {
try (Reader characterStream = mySourceConceptDirectParentPids.getCharacterStream()) {
retVal = IOUtils.toString(characterStream);
return IOUtils.toString(characterStream);
} catch (IOException | SQLException e) {
throw new InternalErrorException(Msg.code(828) + e);
}
} else if (mySourceConceptDirectParentPidsVc != null) {
retVal = mySourceConceptDirectParentPidsVc;
}
return retVal;
return null;
}
@Override

42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.entity.BulkImportJobEntity;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
import ca.uhn.fhir.jpa.migrate.taskdef.CalculateHashesTask;
import ca.uhn.fhir.jpa.migrate.taskdef.CalculateOrdinalDatesTask;
import ca.uhn.fhir.jpa.migrate.taskdef.ColumnTypeEnum;
@ -147,16 +146,8 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
binaryStorageBlobTable
.renameColumn("20240404.1", "BLOB_ID", "CONTENT_ID")
.getLastAddedTask()
.ifPresent(BaseTask::doNothing);
binaryStorageBlobTable
.renameColumn("20240404.2", "BLOB_SIZE", "CONTENT_SIZE")
.getLastAddedTask()
.ifPresent(BaseTask::doNothing);
binaryStorageBlobTable
.renameColumn("20240404.3", "BLOB_HASH", "CONTENT_HASH")
.getLastAddedTask()
.ifPresent(BaseTask::doNothing);
.renameColumn("20240404.3", "BLOB_HASH", "CONTENT_HASH");
binaryStorageBlobTable
.modifyColumn("20240404.4", "BLOB_DATA")
@ -168,23 +159,9 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.nullable()
.type(ColumnTypeEnum.BINARY);
binaryStorageBlobTable
.migrateBlobToBinary("20240404.6", "BLOB_DATA", "STORAGE_CONTENT_BIN")
.doNothing();
binaryStorageBlobTable.migrateBlobToBinary("20240404.6", "BLOB_DATA", "STORAGE_CONTENT_BIN");
binaryStorageBlobTable
.renameTable("20240404.7", "HFJ_BINARY_STORAGE")
.doNothing();
Builder.BuilderWithTableName binaryStorageTableFix = version.onTable("HFJ_BINARY_STORAGE");
binaryStorageTableFix.renameColumn("20240404.10", "CONTENT_ID", "BLOB_ID", true, true);
binaryStorageTableFix.renameColumn("20240404.20", "CONTENT_SIZE", "BLOB_SIZE", true, true);
binaryStorageTableFix.renameColumn("20240404.30", "CONTENT_HASH", "BLOB_HASH", true, true);
binaryStorageTableFix
.renameTable("20240404.40", "HFJ_BINARY_STORAGE_BLOB")
.failureAllowed();
binaryStorageBlobTable.renameTable("20240404.7", "HFJ_BINARY_STORAGE");
}
{
@ -195,9 +172,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.nullable()
.type(ColumnTypeEnum.BINARY);
termConceptPropertyTable
.migrateBlobToBinary("20240409.2", "PROP_VAL_LOB", "PROP_VAL_BIN")
.doNothing();
termConceptPropertyTable.migrateBlobToBinary("20240409.2", "PROP_VAL_LOB", "PROP_VAL_BIN");
}
{
@ -207,9 +182,8 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.nullable()
.type(ColumnTypeEnum.TEXT);
termValueSetConceptTable
.migrateClobToText("20240409.4", "SOURCE_DIRECT_PARENT_PIDS", "SOURCE_DIRECT_PARENT_PIDS_VC")
.doNothing();
termValueSetConceptTable.migrateClobToText(
"20240409.4", "SOURCE_DIRECT_PARENT_PIDS", "SOURCE_DIRECT_PARENT_PIDS_VC");
}
{
@ -219,9 +193,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.nullable()
.type(ColumnTypeEnum.TEXT);
termConceptTable
.migrateClobToText("20240410.2", "PARENT_PIDS", "PARENT_PIDS_VC")
.doNothing();
termConceptTable.migrateClobToText("20240410.2", "PARENT_PIDS", "PARENT_PIDS_VC");
}
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvc.java
View File

@ -37,7 +37,7 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
IPartitionLookupSvc myPartitionConfigSvc;
@Override
public RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
protected RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
List<String> names = null;
for (int i = 0; i < theRequestPartitionId.getPartitionIds().size(); i++) {
@ -59,7 +59,7 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
}
}
if (theRequestPartitionId.hasPartitionNames()) {
if (theRequestPartitionId.getPartitionNames() != null) {
if (partition == null) {
Validate.isTrue(
theRequestPartitionId.getPartitionIds().get(i) == null,
@ -68,8 +68,8 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
} else {
Validate.isTrue(
Objects.equals(
theRequestPartitionId.getPartitionNames().get(i), partition.getName()),
"Partition name %s does not match ID %s",
theRequestPartitionId.getPartitionIds().get(i), partition.getId()),
"Partition name %s does not match ID %n",
theRequestPartitionId.getPartitionNames().get(i),
theRequestPartitionId.getPartitionIds().get(i));
}
@ -94,7 +94,7 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
}
@Override
public RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
protected RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
List<Integer> ids = null;
for (int i = 0; i < theRequestPartitionId.getPartitionNames().size(); i++) {
@ -122,9 +122,9 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
Validate.isTrue(
Objects.equals(
theRequestPartitionId.getPartitionIds().get(i), partition.getId()),
"Partition ID %s does not match name %s",
theRequestPartitionId.getPartitionIds().get(i),
theRequestPartitionId.getPartitionNames().get(i));
"Partition name %s does not match ID %n",
theRequestPartitionId.getPartitionNames().get(i),
theRequestPartitionId.getPartitionIds().get(i));
}
} else {
if (ids == null) {

47
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
View File

@ -353,39 +353,26 @@ public class QueryStack {
throw new InvalidRequestException(Msg.code(2289) + msg);
}
// add a left-outer join to a predicate for the target type, then sort on value columns(s).
BaseSearchParamPredicateBuilder chainedPredicateBuilder;
DbColumn[] sortColumn;
switch (targetSearchParameter.getParamType()) {
case STRING:
StringPredicateBuilder stringPredicateBuilder = mySqlBuilder.createStringPredicateBuilder();
addSortCustomJoin(
resourceLinkPredicateBuilder.getColumnTargetResourceId(),
stringPredicateBuilder,
stringPredicateBuilder.createHashIdentityPredicate(targetType, theChain));
mySqlBuilder.addSortString(
stringPredicateBuilder.getColumnValueNormalized(), theAscending, myUseAggregate);
return;
sortColumn = new DbColumn[] {stringPredicateBuilder.getColumnValueNormalized()};
chainedPredicateBuilder = stringPredicateBuilder;
break;
case TOKEN:
TokenPredicateBuilder tokenPredicateBuilder = mySqlBuilder.createTokenPredicateBuilder();
addSortCustomJoin(
resourceLinkPredicateBuilder.getColumnTargetResourceId(),
tokenPredicateBuilder,
tokenPredicateBuilder.createHashIdentityPredicate(targetType, theChain));
mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnSystem(), theAscending, myUseAggregate);
mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnValue(), theAscending, myUseAggregate);
return;
sortColumn =
new DbColumn[] {tokenPredicateBuilder.getColumnSystem(), tokenPredicateBuilder.getColumnValue()
};
chainedPredicateBuilder = tokenPredicateBuilder;
break;
case DATE:
DatePredicateBuilder datePredicateBuilder = mySqlBuilder.createDatePredicateBuilder();
addSortCustomJoin(
resourceLinkPredicateBuilder.getColumnTargetResourceId(),
datePredicateBuilder,
datePredicateBuilder.createHashIdentityPredicate(targetType, theChain));
mySqlBuilder.addSortDate(datePredicateBuilder.getColumnValueLow(), theAscending, myUseAggregate);
return;
sortColumn = new DbColumn[] {datePredicateBuilder.getColumnValueLow()};
chainedPredicateBuilder = datePredicateBuilder;
break;
/*
* Note that many of the options below aren't implemented because they
@ -430,6 +417,14 @@ public class QueryStack {
+ theParamName + "." + theChain + " as this parameter. Can not sort on chains of target type: "
+ targetSearchParameter.getParamType().name());
}
addSortCustomJoin(resourceLinkPredicateBuilder.getColumnTargetResourceId(), chainedPredicateBuilder, null);
Condition predicate = chainedPredicateBuilder.createHashIdentityPredicate(targetType, theChain);
mySqlBuilder.addPredicate(predicate);
for (DbColumn next : sortColumn) {
mySqlBuilder.addSortNumeric(next, theAscending, myUseAggregate);
}
}
public void addSortOnString(String theResourceName, String theParamName, boolean theAscending) {

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -73,6 +73,7 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
@ -684,6 +685,26 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
}
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
for (TermConceptParentChildLink nextLink : theParents) {
if (nextLink.getRelationshipType() == TermConceptParentChildLink.RelationshipTypeEnum.ISA) {
TermConcept nextParent = nextLink.getParent();
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
nextParent.setUpdated(new Date());
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
}
}
}
return retVal;
}
@Nonnull
private TermCodeSystem getOrCreateDistinctTermCodeSystem(
IResourcePersistentId theCodeSystemResourcePid,

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermConceptDaoSvc.java
View File

@ -46,8 +46,6 @@ public class TermConceptDaoSvc {
@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao;
private boolean mySupportLegacyLob = false;
public int saveConcept(TermConcept theConcept) {
int retVal = 0;
@ -72,11 +70,9 @@ public class TermConceptDaoSvc {
retVal++;
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
theConcept.setUpdated(new Date());
theConcept.flagForLegacyLobSupport(mySupportLegacyLob);
myConceptDao.save(theConcept);
for (TermConceptProperty next : theConcept.getProperties()) {
next.performLegacyLobSupport(mySupportLegacyLob);
myConceptPropertyDao.save(next);
}
@ -89,11 +85,6 @@ public class TermConceptDaoSvc {
return retVal;
}
public TermConceptDaoSvc setSupportLegacyLob(boolean theSupportLegacyLob) {
mySupportLegacyLob = theSupportLegacyLob;
return this;
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
@ -104,7 +95,6 @@ public class TermConceptDaoSvc {
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
nextParent.setUpdated(new Date());
nextParent.flagForLegacyLobSupport(mySupportLegacyLob);
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java
View File

@ -293,9 +293,6 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
@Autowired
private InMemoryTerminologyServerValidationSupport myInMemoryTerminologyServerValidationSupport;
@Autowired
private ValueSetConceptAccumulatorFactory myValueSetConceptAccumulatorFactory;
@Override
public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
TermCodeSystemVersionDetails cs = getCurrentCodeSystemVersion(theSystem);
@ -2396,11 +2393,11 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
});
assert valueSet != null;
ValueSetConceptAccumulator valueSetConceptAccumulator =
myValueSetConceptAccumulatorFactory.create(valueSetToExpand);
ValueSetConceptAccumulator accumulator = new ValueSetConceptAccumulator(
valueSetToExpand, myTermValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao);
ValueSetExpansionOptions options = new ValueSetExpansionOptions();
options.setIncludeHierarchy(true);
expandValueSet(options, valueSet, valueSetConceptAccumulator);
expandValueSet(options, valueSet, accumulator);
// We are done with this ValueSet.
txTemplate.executeWithoutResult(t -> {
@ -2415,7 +2412,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
"Pre-expanded ValueSet[{}] with URL[{}] - Saved {} concepts in {}",
valueSet.getId(),
valueSet.getUrl(),
valueSetConceptAccumulator.getConceptsSaved(),
accumulator.getConceptsSaved(),
sw);
} catch (Exception e) {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -48,8 +48,6 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
private int myDesignationsSaved;
private int myConceptsExcluded;
private boolean mySupportLegacyLob = false;
public ValueSetConceptAccumulator(
@Nonnull TermValueSet theTermValueSet,
@Nonnull ITermValueSetDao theValueSetDao,
@ -186,10 +184,6 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
concept.setSourceConceptPid(theSourceConceptPid);
concept.setSourceConceptDirectParentPids(theSourceConceptDirectParentPids);
if (!mySupportLegacyLob) {
concept.clearSourceConceptDirectParentPidsLob();
}
myValueSetConceptDao.save(concept);
myValueSetDao.save(myTermValueSet.incrementTotalConcepts());
@ -259,9 +253,4 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
// TODO: DM 2019-07-16 - If so, we should also populate TermValueSetConceptProperty entities here.
// TODO: DM 2019-07-30 - Expansions don't include the properties themselves; they may be needed to facilitate
// filters and parameterized expansions.
public ValueSetConceptAccumulator setSupportLegacyLob(boolean theSupportLegacyLob) {
mySupportLegacyLob = theSupportLegacyLob;
return this;
}
}

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulatorFactory.java
View File

@ -1,51 +0,0 @@
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* 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.jpa.term;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import org.springframework.beans.factory.annotation.Autowired;
public class ValueSetConceptAccumulatorFactory {
@Autowired
private ITermValueSetDao myValueSetDao;
@Autowired
private ITermValueSetConceptDao myValueSetConceptDao;
@Autowired
private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
@Autowired
private JpaStorageSettings myStorageSettings;
public ValueSetConceptAccumulator create(TermValueSet theTermValueSet) {
ValueSetConceptAccumulator valueSetConceptAccumulator = new ValueSetConceptAccumulator(
theTermValueSet, myValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao);
valueSetConceptAccumulator.setSupportLegacyLob(myStorageSettings.isWriteToLegacyLobColumns());
return valueSetConceptAccumulator;
}
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/config/TermCodeSystemConfig.java
View File

@ -19,7 +19,6 @@
*/
package ca.uhn.fhir.jpa.term.config;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.term.TermConceptDaoSvc;
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemDeleteJobSvc;
@ -42,7 +41,7 @@ public class TermCodeSystemConfig {
}
@Bean
public TermConceptDaoSvc termConceptDaoSvc(JpaStorageSettings theJpaStorageSettings) {
return new TermConceptDaoSvc().setSupportLegacyLob(theJpaStorageSettings.isWriteToLegacyLobColumns());
public TermConceptDaoSvc termConceptDaoSvc() {
return new TermConceptDaoSvc();
}
}

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/TermConceptPropertyTest.java
View File

@ -2,11 +2,8 @@ package ca.uhn.fhir.jpa.entity;
import com.google.common.base.Strings;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.notNullValue;
import static org.hamcrest.Matchers.startsWith;
@ -24,8 +21,8 @@ public class TermConceptPropertyTest {
termConceptProperty.setValue(ourVeryLongString);
// then
assertThat(termConceptProperty.hasValueBlobForTesting(), equalTo(true));
assertThat(termConceptProperty.hasValueBinForTesting(), equalTo(true));
assertThat(termConceptProperty.getValueBlobForTesting(), notNullValue());
assertThat(termConceptProperty.getValueBinForTesting(), notNullValue());
}
@Test
@ -81,19 +78,4 @@ public class TermConceptPropertyTest {
assertThat(value, startsWith("a"));
}
@ParameterizedTest
@ValueSource(booleans = {false, true})
public void testSetValue_withSupportLegacyLob(boolean theSupportLegacyLob){
// given
TermConceptProperty termConceptProperty = new TermConceptProperty();
// when
termConceptProperty.setValue(ourVeryLongString);
termConceptProperty.performLegacyLobSupport(theSupportLegacyLob);
// then
assertThat(termConceptProperty.hasValueBinForTesting(), equalTo(true));
assertThat(termConceptProperty.hasValueBlobForTesting(), equalTo(theSupportLegacyLob));
}
}

1
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/GoldenResourceMergerSvcImpl.java
View File

@ -166,7 +166,6 @@ public class GoldenResourceMergerSvcImpl implements IGoldenResourceMergerSvc {
HookParams params = new HookParams();
params.add(MdmMergeEvent.class, event);
params.add(RequestDetails.class, theParams.getRequestDetails());
params.add(MdmTransactionContext.class, theParams.getMdmTransactionContext());
myInterceptorBroadcaster.callHooks(Pointcut.MDM_POST_MERGE_GOLDEN_RESOURCES, params);
}
}

22
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmSurvivorshipSvcImplIT.java
View File

@ -2,16 +2,11 @@ package ca.uhn.fhir.jpa.mdm.svc;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
@ -60,21 +55,4 @@ class MdmSurvivorshipSvcImplIT extends BaseMdmR4Test {
assertEquals(p1.getTelecom().size(), p1.getTelecom().size());
assertTrue(p2.getTelecomFirstRep().equalsDeep(p1.getTelecomFirstRep()));
}
@Test
public void matchingPatientsWith_NON_Numeric_Ids_matches_doesNotThrow_NumberFormatException() {
final Patient frankPatient1 = buildFrankPatient();
frankPatient1.setId("patA");
myPatientDao.update(frankPatient1, new SystemRequestDetails());
final Patient frankPatient2 = buildFrankPatient();
frankPatient2.setId("patB");
myPatientDao.update(frankPatient2, new SystemRequestDetails());
final Patient goldenPatient = buildFrankPatient();
myPatientDao.create(goldenPatient, new SystemRequestDetails());
myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, frankPatient1, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, frankPatient2, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(goldenPatient, new MdmTransactionContext(MdmTransactionContext.OperationType.UPDATE_LINK));
}
}

19
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmSurvivorshipSvcImplTest.java
View File

@ -25,9 +25,8 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
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.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.Mock;
import org.mockito.Spy;
import org.mockito.junit.jupiter.MockitoExtension;
@ -97,9 +96,8 @@ public class MdmSurvivorshipSvcImplTest {
}
@SuppressWarnings({"rawtypes", "unchecked"})
@ParameterizedTest
@ValueSource(booleans = {true,false})
public void rebuildGoldenResourceCurrentLinksUsingSurvivorshipRules_withManyLinks_rebuildsInUpdateOrder(boolean theIsUseNonNumericId) {
@Test
public void rebuildGoldenResourceCurrentLinksUsingSurvivorshipRules_withManyLinks_rebuildsInUpdateOrder() {
// setup
// create resources
Patient goldenPatient = new Patient();
@ -128,7 +126,7 @@ public class MdmSurvivorshipSvcImplTest {
patient.addIdentifier()
.setSystem("http://example.com")
.setValue("Value" + i);
patient.setId("Patient/" + (theIsUseNonNumericId ? "pat"+i : Integer.toString(i)));
patient.setId("Patient/" + i);
resources.add(patient);
MdmLinkJson link = createLinkJson(
@ -151,13 +149,8 @@ public class MdmSurvivorshipSvcImplTest {
when(myDaoRegistry.getResourceDao(eq("Patient")))
.thenReturn(resourceDao);
AtomicInteger counter = new AtomicInteger();
if (theIsUseNonNumericId) {
when(resourceDao.read(any(), any()))
.thenAnswer(params -> resources.get(counter.getAndIncrement()));
} else {
when(resourceDao.readByPid(any()))
.thenAnswer(params -> resources.get(counter.getAndIncrement()));
}
when(resourceDao.readByPid(any()))
.thenAnswer(params -> resources.get(counter.getAndIncrement()));
Page<MdmLinkJson> linkPage = mock(Page.class);
when(myMdmLinkQuerySvc.queryLinks(any(), any()))
.thenReturn(linkPage);

11
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BinaryStorageEntity.java
View File

@ -34,26 +34,23 @@ import java.util.Date;
import static java.util.Objects.nonNull;
@Entity
@Table(name = "HFJ_BINARY_STORAGE_BLOB")
@Table(name = "HFJ_BINARY_STORAGE")
public class BinaryStorageEntity {
@Id
@Column(name = "BLOB_ID", length = 200, nullable = false)
@Column(name = "CONTENT_ID", length = 200, nullable = false)
// N.B GGG: Note that the `content id` is the same as the `externalized binary id`.
private String myContentId;
@Column(name = "RESOURCE_ID", length = 100, nullable = false)
private String myResourceId;
@Column(name = "BLOB_SIZE", nullable = true)
@Column(name = "CONTENT_SIZE", nullable = true)
private long mySize;
@Column(name = "CONTENT_TYPE", nullable = false, length = 100)
private String myContentType;
/**
* @deprecated
*/
@Deprecated(since = "7.2.0")
@Lob // TODO: VC column added in 7.2.0 - Remove non-VC column later
@Column(name = "BLOB_DATA", nullable = true, insertable = true, updatable = false)
@ -66,7 +63,7 @@ public class BinaryStorageEntity {
@Column(name = "PUBLISHED_DATE", nullable = false)
private Date myPublished;
@Column(name = "BLOB_HASH", length = 128, nullable = true)
@Column(name = "CONTENT_HASH", length = 128, nullable = true)
private String myHash;
public Date getPublished() {

26
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/partition/IRequestPartitionHelperSvc.java
View File

@ -156,30 +156,4 @@ public interface IRequestPartitionHelperSvc {
Set<Integer> toReadPartitions(@Nonnull RequestPartitionId theRequestPartitionId);
boolean isResourcePartitionable(String theResourceType);
/**
* <b>No interceptors should be invoked by this method. It should ONLY be used when partition ids are
* known, but partition names are not.</b>
* <br/><br/>
* Ensures the list of partition ids inside the given {@link RequestPartitionId} correctly map to the
* list of partition names. If the list of partition names is empty, this method will map the correct
* partition names and return a normalized {@link RequestPartitionId}.
* <br/><br/>
* @param theRequestPartitionId - An unvalidated and unnormalized {@link RequestPartitionId}.
* @return - A {@link RequestPartitionId} with a normalized list of partition ids and partition names.
*/
RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId);
/**
* <b>No interceptors should be invoked by this method. It should ONLY be used when partition names are
* known, but partition ids are not.</b>
* <br/><br/>
* Ensures the list of partition names inside the given {@link RequestPartitionId} correctly map to the
* list of partition ids. If the list of partition ids is empty, this method will map the correct
* partition ids and return a normalized {@link RequestPartitionId}.
* <br/><br/>
* @param theRequestPartitionId - An unvalidated and unnormalized {@link RequestPartitionId}.
* @return - A {@link RequestPartitionId} with a normalized list of partition ids and partition names.
*/
RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId);
}

35
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/config/SubscriptionConfig.java
View File

@ -1,35 +0,0 @@
/*-
* #%L
* HAPI FHIR Subscription Server
* %%
* 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.jpa.subscription.config;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionQueryValidator;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class SubscriptionConfig {
@Bean
public SubscriptionQueryValidator subscriptionQueryValidator(
DaoRegistry theDaoRegistry, SubscriptionStrategyEvaluator theSubscriptionStrategyEvaluator) {
return new SubscriptionQueryValidator(theDaoRegistry, theSubscriptionStrategyEvaluator);
}
}

12
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/submit/config/SubscriptionSubmitterConfig.java
View File

@ -19,13 +19,15 @@
*/
package ca.uhn.fhir.jpa.subscription.submit.config;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.subscription.async.AsyncResourceModifiedProcessingSchedulerSvc;
import ca.uhn.fhir.jpa.subscription.async.AsyncResourceModifiedSubmitterSvc;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelFactory;
import ca.uhn.fhir.jpa.subscription.config.SubscriptionConfig;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
import ca.uhn.fhir.jpa.subscription.model.config.SubscriptionModelConfig;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionQueryValidator;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionSubmitInterceptorLoader;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionValidatingInterceptor;
import ca.uhn.fhir.jpa.subscription.submit.svc.ResourceModifiedSubmitterSvc;
@ -43,7 +45,7 @@ import org.springframework.context.annotation.Lazy;
* matching queue for processing
*/
@Configuration
@Import({SubscriptionModelConfig.class, SubscriptionMatcherInterceptorConfig.class, SubscriptionConfig.class})
@Import({SubscriptionModelConfig.class, SubscriptionMatcherInterceptorConfig.class})
public class SubscriptionSubmitterConfig {
@Bean
@ -51,6 +53,12 @@ public class SubscriptionSubmitterConfig {
return new SubscriptionValidatingInterceptor();
}
@Bean
public SubscriptionQueryValidator subscriptionQueryValidator(
DaoRegistry theDaoRegistry, SubscriptionStrategyEvaluator theSubscriptionStrategyEvaluator) {
return new SubscriptionQueryValidator(theDaoRegistry, theSubscriptionStrategyEvaluator);
}
@Bean
public SubscriptionSubmitInterceptorLoader subscriptionMatcherInterceptorLoader() {
return new SubscriptionSubmitInterceptorLoader();

11
hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/topic/SubscriptionTopicConfig.java
View File

@ -22,15 +22,13 @@ package ca.uhn.fhir.jpa.topic;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
import ca.uhn.fhir.jpa.subscription.config.SubscriptionConfig;
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionQueryValidator;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
@Configuration
@Import(SubscriptionConfig.class)
public class SubscriptionTopicConfig {
@Bean
SubscriptionTopicMatchingSubscriber subscriptionTopicMatchingSubscriber(FhirContext theFhirContext) {
@ -78,6 +76,13 @@ public class SubscriptionTopicConfig {
}
}
@Bean
@Lazy
public SubscriptionQueryValidator subscriptionQueryValidator(
DaoRegistry theDaoRegistry, SubscriptionStrategyEvaluator theSubscriptionStrategyEvaluator) {
return new SubscriptionQueryValidator(theDaoRegistry, theSubscriptionStrategyEvaluator);
}
@Bean
SubscriptionTopicValidatingInterceptor subscriptionTopicValidatingInterceptor(
FhirContext theFhirContext, SubscriptionQueryValidator theSubscriptionQueryValidator) {

40
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/binstore/DatabaseBinaryContentStorageSvcImplTest.java
View File

@ -7,12 +7,8 @@ import ca.uhn.fhir.jpa.model.entity.BinaryStorageEntity;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import jakarta.persistence.EntityManager;
import org.hibernate.LobHelper;
import org.hibernate.Session;
import org.hl7.fhir.r4.model.IdType;
import org.junit.jupiter.api.Test;
import org.mockito.ArgumentCaptor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.annotation.Bean;
@ -28,7 +24,6 @@ import java.sql.SQLException;
import java.util.Optional;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.matchesPattern;
@ -39,7 +34,6 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@ -287,7 +281,7 @@ public class DatabaseBinaryContentStorageSvcImplTest extends BaseJpaR4Test {
}
@Test
public void testStoreBinaryContent_byDefault_writesByteArrayOnly() throws IOException {
public void testStoreBinaryContent_writesBlobAndByteArray() throws IOException {
// given
ByteArrayInputStream inputStream = new ByteArrayInputStream(SOME_BYTES);
String contentType = "image/png";
@ -302,41 +296,11 @@ public class DatabaseBinaryContentStorageSvcImplTest extends BaseJpaR4Test {
// then
assertThat(binaryStorageEntity.hasStorageContent(), is(true));
assertThat(binaryStorageEntity.hasBlob(), is(false));
assertThat(binaryStorageEntity.hasBlob(), is(true));
});
}
@Test
public void testStoreBinaryContent_whenSupportingLegacyBlobServer_willStoreToBlobAndBinaryArray() throws IOException {
ArgumentCaptor<BinaryStorageEntity> captor = ArgumentCaptor.forClass(BinaryStorageEntity.class);
EntityManager mockedEntityManager = mock(EntityManager.class);
Session mockedSession = mock(Session.class);
LobHelper mockedLobHelper = mock(LobHelper.class);
when(mockedEntityManager.getDelegate()).thenReturn(mockedSession);
when(mockedSession.getLobHelper()).thenReturn(mockedLobHelper);
when(mockedLobHelper.createBlob(any())).thenReturn(mock(Blob.class));
// given
DatabaseBinaryContentStorageSvcImpl svc = new DatabaseBinaryContentStorageSvcImpl()
.setSupportLegacyLobServer(true)
.setEntityManagerForTesting(mockedEntityManager);
ByteArrayInputStream inputStream = new ByteArrayInputStream(SOME_BYTES);
String contentType = "image/png";
IdType resourceId = new IdType("Binary/123");
// when
svc.storeBinaryContent(resourceId, null, contentType, inputStream, new ServletRequestDetails());
// then
verify(mockedEntityManager, times(1)).persist(captor.capture());
BinaryStorageEntity capturedBinaryStorageEntity = captor.getValue();
assertThat(capturedBinaryStorageEntity.hasBlob(), equalTo(true));
assertThat(capturedBinaryStorageEntity.hasStorageContent(), equalTo(true));
}
@Configuration
public static class MyConfig {

27
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QuerySandbox.java
View File

@ -9,11 +9,8 @@ import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.util.SqlQuery;
import ca.uhn.fhir.jpa.util.SqlQueryList;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.storage.test.DaoTestDataBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@ -36,8 +33,6 @@ import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
/**
* Sandbox for implementing queries.
@ -142,28 +137,6 @@ public class FhirResourceDaoR4QuerySandbox extends BaseJpaTest {
myTestDaoSearch.assertSearchFindsInOrder("reverse sort by server assigned id", "Patient?family=smith&_sort=-_pid", id3,id2,id1);
}
@Test
void testChainedSort() {
final IIdType practitionerId = myDataBuilder.createPractitioner(myDataBuilder.withFamily("Jones"));
final String id1 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithy")).getIdPart();
final String id2 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithwick")).getIdPart();
final String id3 = myDataBuilder.createPatient(
myDataBuilder.withFamily("Smith"),
myDataBuilder.withReference("generalPractitioner", practitionerId)).getIdPart();
final IBundleProvider iBundleProvider = myTestDaoSearch.searchForBundleProvider("Patient?_total=ACCURATE&_sort=Practitioner:general-practitioner.family");
assertEquals(3, iBundleProvider.size());
final List<IBaseResource> allResources = iBundleProvider.getAllResources();
assertEquals(3, iBundleProvider.size());
assertEquals(3, allResources.size());
final List<String> actualIds = allResources.stream().map(IBaseResource::getIdElement).map(IIdType::getIdPart).toList();
assertTrue(actualIds.containsAll(List.of(id1, id2, id3)));
}
public static final class TestDirtiesContextTestExecutionListener extends DirtiesContextTestExecutionListener {
@Override

187
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/partition/RequestPartitionHelperSvcTest.java
View File

@ -1,189 +1,74 @@
package ca.uhn.fhir.jpa.partition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.data.IPartitionDao;
import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.hl7.fhir.r4.model.IdType;
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.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Set;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
class RequestPartitionHelperSvcTest extends BaseJpaR4Test {
class RequestPartitionHelperSvcTest {
static final Integer PARTITION_ID = 2401;
static final String PARTITION_NAME = "JIMMY";
static final PartitionEntity ourPartitionEntity = new PartitionEntity().setName(PARTITION_NAME);
static final int PARTITION_ID_1 = 1;
static final String PARTITION_NAME_1 = "SOME-PARTITION-1";
static final int PARTITION_ID_2 = 2;
static final String PARTITION_NAME_2 = "SOME-PARTITION-2";
static final int UNKNOWN_PARTITION_ID = 1_000_000;
static final String UNKNOWN_PARTITION_NAME = "UNKNOWN";
@Autowired
IPartitionDao myPartitionDao;
@Autowired
@Mock
PartitionSettings myPartitionSettings;
@Autowired
RequestPartitionHelperSvc mySvc;
@Mock
IPartitionLookupSvc myPartitionLookupSvc;
@Mock
FhirContext myFhirContext;
@Mock
IInterceptorBroadcaster myInterceptorBroadcaster;
Patient myPatient;
@BeforeEach
public void before(){
myPartitionDao.deleteAll();
myPartitionSettings.setPartitioningEnabled(true);
myPatient = new Patient();
myPatient.setId(new IdType("Patient", "123", "1"));
}
@InjectMocks
RequestPartitionHelperSvc mySvc = new RequestPartitionHelperSvc();
@Test
public void testDetermineReadPartitionForSystemRequest_withPartitionIdOnly_returnsCorrectPartition() {
public void determineReadPartitionForSystemRequest() {
// setup
PartitionEntity partitionEntity = createPartition1();
SystemRequestDetails srd = new SystemRequestDetails();
srd.setRequestPartitionId(RequestPartitionId.fromPartitionId(partitionEntity.getId()));
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionId(PARTITION_ID);
srd.setRequestPartitionId(requestPartitionId);
when(myPartitionSettings.isPartitioningEnabled()).thenReturn(true);
when(myPartitionLookupSvc.getPartitionById(PARTITION_ID)).thenReturn(ourPartitionEntity);
// execute
RequestPartitionId result = mySvc.determineReadPartitionForRequestForRead(srd, myPatient.fhirType(), myPatient.getIdElement());
RequestPartitionId result = mySvc.determineReadPartitionForRequestForRead(srd, "Patient", new IdType("Patient/123"));
// verify
assertEquals(PARTITION_ID_1, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME_1, result.getFirstPartitionNameOrNull());
assertEquals(PARTITION_ID, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME, result.getFirstPartitionNameOrNull());
}
@Test
public void testDetermineCreatePartitionForRequest_withPartitionIdOnly_returnsCorrectPartition() {
public void determineCreatePartitionForSystemRequest() {
// setup
PartitionEntity partitionEntity = createPartition1();
SystemRequestDetails srd = new SystemRequestDetails();
srd.setRequestPartitionId(RequestPartitionId.fromPartitionId(partitionEntity.getId()));
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionId(PARTITION_ID);
srd.setRequestPartitionId(requestPartitionId);
when(myPartitionSettings.isPartitioningEnabled()).thenReturn(true);
when(myPartitionLookupSvc.getPartitionById(PARTITION_ID)).thenReturn(ourPartitionEntity);
Patient resource = new Patient();
when(myFhirContext.getResourceType(resource)).thenReturn("Patient");
// execute
Patient patient = new Patient();
RequestPartitionId result = mySvc.determineCreatePartitionForRequest(srd, patient, patient.fhirType());
RequestPartitionId result = mySvc.determineCreatePartitionForRequest(srd, resource, "Patient");
// verify
assertEquals(PARTITION_ID_1, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME_1, result.getFirstPartitionNameOrNull());
assertEquals(PARTITION_ID, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME, result.getFirstPartitionNameOrNull());
}
@Test
public void testValidateAndNormalizePartitionIds_withPartitionIdOnly_populatesPartitionName(){
PartitionEntity partitionEntity = createPartition1();
RequestPartitionId partitionId = RequestPartitionId.fromPartitionId(partitionEntity.getId());
RequestPartitionId result = mySvc.validateAndNormalizePartitionIds(partitionId);
assertEquals(PARTITION_ID_1, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME_1, result.getFirstPartitionNameOrNull());
}
@Test
public void testValidateAndNormalizePartitionIds_withUnknownId_throwsException(){
RequestPartitionId partitionId = RequestPartitionId.fromPartitionId(UNKNOWN_PARTITION_ID);
try{
mySvc.validateAndNormalizePartitionIds(partitionId);
fail();
} catch (ResourceNotFoundException e){
assertTrue(e.getMessage().contains("No partition exists with ID 1,000,000"));
}
}
@Test
public void testValidateAndNormalizePartitionIds_withIdAndInvalidName_throwsException(){
createPartition1();
RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(PARTITION_ID_1, UNKNOWN_PARTITION_NAME);
try{
mySvc.validateAndNormalizePartitionIds(partitionId);
fail();
} catch (IllegalArgumentException e){
assertTrue(e.getMessage().contains("Partition name UNKNOWN does not match ID 1"));
}
}
@Test
public void testValidateAndNormalizePartitionIds_withMultiplePartitionIdOnly_populatesPartitionNames(){
PartitionEntity partitionEntity1 = createPartition1();
PartitionEntity partitionEntity2 = createPartition2();
RequestPartitionId partitionId = RequestPartitionId.fromPartitionIds(partitionEntity1.getId(), partitionEntity2.getId());
RequestPartitionId result = mySvc.validateAndNormalizePartitionIds(partitionId);
assertTrue(result.getPartitionIds().containsAll(Set.of(PARTITION_ID_1, PARTITION_ID_2)));
assertNotNull(result.getPartitionNames());
assertTrue(result.getPartitionNames().containsAll(Set.of(PARTITION_NAME_1, PARTITION_NAME_2)));
}
@Test
public void testValidateAndNormalizePartitionNames_withPartitionNameOnly_populatesPartitionId(){
PartitionEntity partitionEntity = createPartition1();
RequestPartitionId partitionId = RequestPartitionId.fromPartitionName(partitionEntity.getName());
RequestPartitionId result = mySvc.validateAndNormalizePartitionNames(partitionId);
assertEquals(PARTITION_ID_1, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME_1, result.getFirstPartitionNameOrNull());
}
@Test
public void testValidateAndNormalizePartitionNames_withMultiplePartitionNamesOnly_populatesPartitionIds(){
PartitionEntity partitionEntity1 = createPartition1();
PartitionEntity partitionEntity2 = createPartition2();
RequestPartitionId partitionId = RequestPartitionId.fromPartitionNames(partitionEntity1.getName(), partitionEntity2.getName());
RequestPartitionId result = mySvc.validateAndNormalizePartitionNames(partitionId);
assertTrue(result.getPartitionIds().containsAll(Set.of(PARTITION_ID_1, PARTITION_ID_2)));
assertNotNull(result.getPartitionNames());
assertTrue(result.getPartitionNames().containsAll(Set.of(PARTITION_NAME_1, PARTITION_NAME_2)));
}
@Test
public void testValidateAndNormalizePartitionNames_withUnknownName_throwsException(){
RequestPartitionId partitionId = RequestPartitionId.fromPartitionName(UNKNOWN_PARTITION_NAME);
try{
mySvc.validateAndNormalizePartitionNames(partitionId);
fail();
} catch (ResourceNotFoundException e){
assertTrue(e.getMessage().contains("Partition name \"UNKNOWN\" is not valid"));
}
}
@Test
public void testValidateAndNormalizePartitionNames_withNameAndInvalidId_throwsException(){
createPartition1();
RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(UNKNOWN_PARTITION_ID, PARTITION_NAME_1);
try{
mySvc.validateAndNormalizePartitionNames(partitionId);
fail();
} catch (IllegalArgumentException e){
assertTrue(e.getMessage().contains("Partition ID 1000000 does not match name SOME-PARTITION-1"));
}
}
private PartitionEntity createPartition1() {
return myPartitionDao.save(new PartitionEntity().setId(PARTITION_ID_1).setName(PARTITION_NAME_1));
}
private PartitionEntity createPartition2() {
return myPartitionDao.save(new PartitionEntity().setId(PARTITION_ID_2).setName(PARTITION_NAME_2));
}
}

10
hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java
View File

@ -884,16 +884,6 @@ public class GiantTransactionPerfTest {
return true;
}
@Override
public RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
return RequestPartitionId.defaultPartition();
}
@Override
public RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
return RequestPartitionId.defaultPartition();
}
}

50
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/UpliftedRefchainsAndChainedSortingR5Test.java
View File

@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
@ -13,8 +12,6 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.HapiExtensions;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.Composition;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Bundle;
@ -32,7 +29,6 @@ import org.hl7.fhir.r5.model.SearchParameter;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
import jakarta.annotation.Nonnull;
@ -45,10 +41,9 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ContextConfiguration(classes = { TestHSearchAddInConfig.NoFT.class, TestDaoSearch.Config.class })
@ContextConfiguration(classes = TestHSearchAddInConfig.NoFT.class)
@SuppressWarnings({"Duplicates"})
public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
public static final String PRACTITIONER_PR1 = "Practitioner/PR1";
@ -59,8 +54,6 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
public static final String ENCOUNTER_E2 = "Encounter/E2";
public static final String ENCOUNTER_E3 = "Encounter/E3";
public static final String ORGANIZATION_O1 = "Organization/O1";
@Autowired
protected TestDaoSearch myTestDaoSearch;
@Override
@BeforeEach
@ -874,47 +867,6 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
assertEquals(1, countMatches(querySql, "HFJ_RES_LINK"), querySql);
}
@Test
void testChainedSortWithNulls() {
final IIdType practitionerId1 = createPractitioner(withFamily("Chan"));
final IIdType practitionerId2 = createPractitioner(withFamily("Jones"));
final String id1 = createPatient(withFamily("Smithy")).getIdPart();
final String id2 = createPatient(withFamily("Smithwick"),
withReference("generalPractitioner", practitionerId2)).getIdPart();
final String id3 = createPatient(
withFamily("Smith"),
withReference("generalPractitioner", practitionerId1)).getIdPart();
final IBundleProvider iBundleProvider = myTestDaoSearch.searchForBundleProvider("Patient?_total=ACCURATE&_sort=Practitioner:general-practitioner.family");
final List<IBaseResource> allResources = iBundleProvider.getAllResources();
assertEquals(3, iBundleProvider.size());
assertEquals(3, allResources.size());
final List<String> actualIds = allResources.stream().map(IBaseResource::getIdElement).map(IIdType::getIdPart).toList();
assertTrue(actualIds.containsAll(List.of(id1, id2, id3)));
}
@Test
void testChainedReverseStringSort() {
final IIdType practitionerId = createPractitioner(withFamily("Jones"));
final String id1 = createPatient(withFamily("Smithy")).getIdPart();
final String id2 = createPatient(withFamily("Smithwick")).getIdPart();
final String id3 = createPatient(
withFamily("Smith"),
withReference("generalPractitioner", practitionerId)).getIdPart();
final IBundleProvider iBundleProvider = myTestDaoSearch.searchForBundleProvider("Patient?_total=ACCURATE&_sort=-Practitioner:general-practitioner.family");
assertEquals(3, iBundleProvider.size());
final List<IBaseResource> allResources = iBundleProvider.getAllResources();
final List<String> actualIds = allResources.stream().map(IBaseResource::getIdElement).map(IIdType::getIdPart).toList();
assertTrue(actualIds.containsAll(List.of(id3, id2, id1)));
}
/**
* Observation:focus is a Reference(Any) so it can't be used in a sort chain because
* this would be horribly, horribly inefficient.

47
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/database/BaseDatabaseVerificationIT.java
View File

@ -1,24 +1,38 @@
package ca.uhn.fhir.jpa.dao.r5.database;
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeProvider;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.api.dao.PatientEverythingParameters;
import ca.uhn.fhir.jpa.embedded.JpaEmbeddedDatabase;
import ca.uhn.fhir.jpa.fql.provider.HfqlRestProvider;
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
import ca.uhn.fhir.jpa.migrate.HapiMigrationStorageSvc;
import ca.uhn.fhir.jpa.migrate.MigrationTaskList;
import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
import ca.uhn.fhir.jpa.migrate.dao.HapiMigrationDao;
import ca.uhn.fhir.jpa.migrate.tasks.HapiFhirJpaMigrationTasks;
import ca.uhn.fhir.jpa.provider.DiffProvider;
import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
import ca.uhn.fhir.jpa.provider.ProcessMessageProvider;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestR5Config;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
import ca.uhn.fhir.test.utilities.server.RestfulServerConfigurerExtension;
@ -30,6 +44,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Patient;
import org.junit.jupiter.api.Test;
@ -40,6 +55,7 @@ import org.junit.jupiter.params.provider.ValueSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.data.envers.repository.support.EnversRevisionRepositoryFactoryBean;
@ -47,8 +63,10 @@ import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.web.cors.CorsConfiguration;
import javax.sql.DataSource;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Properties;
@ -62,7 +80,7 @@ import static org.junit.jupiter.api.Assertions.assertThrows;
@ExtendWith(SpringExtension.class)
@EnableJpaRepositories(repositoryFactoryBeanClass = EnversRevisionRepositoryFactoryBean.class)
@ContextConfiguration(classes = {BaseDatabaseVerificationIT.TestConfig.class, TestDaoSearch.Config.class})
@ContextConfiguration(classes = {BaseDatabaseVerificationIT.TestConfig.class})
public abstract class BaseDatabaseVerificationIT extends BaseJpaTest implements ITestDataBuilder {
private static final Logger ourLog = LoggerFactory.getLogger(BaseDatabaseVerificationIT.class);
private static final String MIGRATION_TABLENAME = "MIGRATIONS";
@ -91,9 +109,6 @@ public abstract class BaseDatabaseVerificationIT extends BaseJpaTest implements
@Autowired
private DatabaseBackedPagingProvider myPagingProvider;
@Autowired
TestDaoSearch myTestDaoSearch;
@RegisterExtension
protected RestfulServerExtension myServer = new RestfulServerExtension(FhirContext.forR5Cached());
@ -160,20 +175,6 @@ public abstract class BaseDatabaseVerificationIT extends BaseJpaTest implements
assertThat(values.toString(), values, containsInAnyOrder(expectedIds.toArray(new String[0])));
}
@Test
void testChainedSort() {
// given
// when
SearchParameterMap map = SearchParameterMap
.newSynchronous()
.setSort(new SortSpec("Practitioner:general-practitioner.family"));
myCaptureQueriesListener.clear();
myPatientDao.search(map, mySrd);
}
@Configuration
@ -221,8 +222,8 @@ public abstract class BaseDatabaseVerificationIT extends BaseJpaTest implements
}
public static class JpaDatabaseContextConfigParamObject {
final JpaEmbeddedDatabase myJpaEmbeddedDatabase;
final String myDialect;
private JpaEmbeddedDatabase myJpaEmbeddedDatabase;
private String myDialect;
public JpaDatabaseContextConfigParamObject(JpaEmbeddedDatabase theJpaEmbeddedDatabase, String theDialect) {
myJpaEmbeddedDatabase = theJpaEmbeddedDatabase;

57
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/TermConceptDaoSvcTest.java
View File

@ -1,57 +0,0 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.entity.TermConcept;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.ArgumentCaptor;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class TermConceptDaoSvcTest {
@Mock
private ITermConceptDao myConceptDao;
@InjectMocks
private TermConceptDaoSvc myTermConceptDaoSvc;
@ParameterizedTest
@ValueSource(booleans = {false, true})
public void testSaveConcept_withSupportLegacyLob(boolean theSupportLegacyLob){
final String parentPids = "1 2 3 4 5 6 7 8 9";
when(myConceptDao.save(any())).thenAnswer(t ->{
TermConcept codeSystem = (TermConcept) t.getArguments()[0];
codeSystem.prePersist();
return codeSystem;
});
ArgumentCaptor<TermConcept> captor = ArgumentCaptor.forClass(TermConcept.class);
// given
TermConcept termConcept = new TermConcept().setParentPids(parentPids);
// when
myTermConceptDaoSvc.setSupportLegacyLob(theSupportLegacyLob);
myTermConceptDaoSvc.saveConcept(termConcept);
// then
verify(myConceptDao, times(1)).save(captor.capture());
TermConcept capturedTermConcept = captor.getValue();
assertThat(capturedTermConcept.hasParentPidsLobForTesting(), equalTo(theSupportLegacyLob));
assertThat(capturedTermConcept.getParentPidsAsString(), equalTo(parentPids));
}
}

23
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulatorTest.java
View File

@ -9,16 +9,11 @@ import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.ArgumentCaptor;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.Optional;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.eq;
import static org.mockito.Mockito.times;
@ -79,22 +74,4 @@ public class ValueSetConceptAccumulatorTest {
}
@ParameterizedTest
@ValueSource(booleans = {false, true})
public void testPersistValueSetConcept_whenSupportLegacyLob(boolean theSupportLegacyLob){
final String sourceConceptDirectParentPids = "1 2 3 4 5 6 7";
ArgumentCaptor<TermValueSetConcept> captor = ArgumentCaptor.forClass(TermValueSetConcept.class);
myAccumulator.setSupportLegacyLob(theSupportLegacyLob);
myAccumulator.includeConcept("sys", "code", "display", null, sourceConceptDirectParentPids, null);
verify(myValueSetConceptDao, times(1)).save(captor.capture());
TermValueSetConcept capturedTermValueSetConcept = captor.getValue();
assertThat(capturedTermValueSetConcept.hasSourceConceptDirectParentPidsLob(), equalTo(theSupportLegacyLob));
assertThat(capturedTermValueSetConcept.getSourceConceptDirectParentPids(), equalTo(sourceConceptDirectParentPids));
}
}

29
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/svc/MdmSurvivorshipSvcImpl.java
View File

@ -31,22 +31,17 @@ import ca.uhn.fhir.mdm.api.params.MdmQuerySearchParameters;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.model.mdmevents.MdmLinkJson;
import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.util.TerserUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.data.domain.Page;
import java.util.regex.Pattern;
import java.util.stream.Stream;
public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
private static final Pattern IS_UUID =
Pattern.compile("[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}");
protected final FhirContext myFhirContext;
@ -138,30 +133,16 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
String sourceId = link.getSourceId();
// +1 because of "/" in id: "ResourceType/Id"
final String sourceIdUnqualified = sourceId.substring(resourceType.length() + 1);
IResourcePersistentId<?> pid = getResourcePID(sourceId.substring(resourceType.length() + 1), resourceType);
// myMdmLinkQuerySvc.queryLinks populates sourceId with the FHIR_ID, not the RES_ID, so if we don't
// add this conditional logic, on JPA, myIIdHelperService.newPidFromStringIdAndResourceName will fail with
// NumberFormatException
if (isNumericOrUuid(sourceIdUnqualified)) {
IResourcePersistentId<?> pid = getResourcePID(sourceIdUnqualified, resourceType);
// this might be a bit unperformant
// but it depends how many links there are
// per golden resource (unlikely to be thousands)
return dao.readByPid(pid);
} else {
return dao.read(new IdDt(sourceId), new SystemRequestDetails());
}
// this might be a bit unperformant
// but it depends how many links there are
// per golden resource (unlikely to be thousands)
return dao.readByPid(pid);
});
}
private IResourcePersistentId<?> getResourcePID(String theId, String theResourceType) {
return myIIdHelperService.newPidFromStringIdAndResourceName(theId, theResourceType);
}
private boolean isNumericOrUuid(String theLongCandidate) {
return StringUtils.isNumeric(theLongCandidate)
|| IS_UUID.matcher(theLongCandidate).matches();
}
}

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderOperationNamed.java
View File

@ -22,8 +22,6 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.Collection;
public interface IAuthRuleBuilderOperationNamed {
/**
@ -46,8 +44,6 @@ public interface IAuthRuleBuilderOperationNamed {
*/
IAuthRuleBuilderOperationNamedAndScoped onInstance(IIdType theInstanceId);
IAuthRuleBuilderOperationNamedAndScoped onInstances(Collection<IIdType> theInstanceIds);
/**
* Rule applies to invocations of this operation at the <code>instance</code> level on any instance of the given type
*/

13
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderRuleBulkExport.java
View File

@ -22,9 +22,6 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.Collection;
import java.util.stream.Collectors;
/**
* @since 5.5.0
*/
@ -57,20 +54,10 @@ public interface IAuthRuleBuilderRuleBulkExport {
IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull String theFocusResourceId);
IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnAllPatients();
default IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull IIdType theFocusResourceId) {
return patientExportOnPatient(theFocusResourceId.getValue());
}
default IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatients(
@Nonnull Collection<IIdType> theFocusResourceIds) {
return patientExportOnPatientStrings(
theFocusResourceIds.stream().map(IIdType::getValue).collect(Collectors.toList()));
}
IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatientStrings(Collection<String> theFocusResourceIds);
/**
* Allow/deny <b>patient-level</b> export rule applies to the Group with the given resource ID, e.g. <code>Group/123</code>
*

65
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleBuilder.java
View File

@ -736,20 +736,6 @@ public class RuleBuilder implements IAuthRuleBuilder {
return new RuleBuilderOperationNamedAndScoped(rule);
}
@Override
public IAuthRuleBuilderOperationNamedAndScoped onInstances(Collection<IIdType> theInstanceIds) {
Validate.notNull(theInstanceIds, "theInstanceIds must not be null");
theInstanceIds.forEach(instanceId -> Validate.notBlank(
instanceId.getResourceType(),
"at least one of theInstanceIds does not have a resource type"));
theInstanceIds.forEach(instanceId -> Validate.notBlank(
instanceId.getIdPart(), "at least one of theInstanceIds does not have an ID part"));
final OperationRule rule = createRule();
rule.appliesToInstances(new ArrayList<>(theInstanceIds));
return new RuleBuilderOperationNamedAndScoped(rule);
}
@Override
public IAuthRuleBuilderOperationNamedAndScoped onInstancesOfType(
Class<? extends IBaseResource> theType) {
@ -883,7 +869,7 @@ public class RuleBuilder implements IAuthRuleBuilder {
}
private class RuleBuilderBulkExport implements IAuthRuleBuilderRuleBulkExport {
private RuleBulkExportImpl myRuleBulkExport;
private RuleBulkExportImpl ruleBulkExport;
@Override
public IAuthRuleBuilderRuleBulkExportWithTarget groupExportOnGroup(@Nonnull String theFocusResourceId) {
@ -895,60 +881,23 @@ public class RuleBuilder implements IAuthRuleBuilder {
return new RuleBuilderBulkExportWithTarget(rule);
}
@Override
public IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnAllPatients() {
if (myRuleBulkExport == null) {
RuleBulkExportImpl rule = new RuleBulkExportImpl(myRuleName);
rule.setMode(myRuleMode);
myRuleBulkExport = rule;
}
myRuleBulkExport.setAppliesToPatientExportAllPatients();
// prevent duplicate rules being added
if (!myRules.contains(myRuleBulkExport)) {
myRules.add(myRuleBulkExport);
}
return new RuleBuilderBulkExportWithTarget(myRuleBulkExport);
}
@Override
public IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull String theFocusResourceId) {
if (myRuleBulkExport == null) {
if (ruleBulkExport == null) {
RuleBulkExportImpl rule = new RuleBulkExportImpl(myRuleName);
rule.setAppliesToPatientExport(theFocusResourceId);
rule.setMode(myRuleMode);
myRuleBulkExport = rule;
ruleBulkExport = rule;
} else {
myRuleBulkExport.setAppliesToPatientExport(theFocusResourceId);
ruleBulkExport.setAppliesToPatientExport(theFocusResourceId);
}
// prevent duplicate rules being added
if (!myRules.contains(myRuleBulkExport)) {
myRules.add(myRuleBulkExport);
if (!myRules.contains(ruleBulkExport)) {
myRules.add(ruleBulkExport);
}
return new RuleBuilderBulkExportWithTarget(myRuleBulkExport);
}
@Override
public IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatientStrings(
@Nonnull Collection<String> theFocusResourceIds) {
if (myRuleBulkExport == null) {
RuleBulkExportImpl rule = new RuleBulkExportImpl(myRuleName);
rule.setAppliesToPatientExport(theFocusResourceIds);
rule.setMode(myRuleMode);
myRuleBulkExport = rule;
} else {
myRuleBulkExport.setAppliesToPatientExport(theFocusResourceIds);
}
// prevent duplicate rules being added
if (!myRules.contains(myRuleBulkExport)) {
myRules.add(myRuleBulkExport);
}
return new RuleBuilderBulkExportWithTarget(myRuleBulkExport);
return new RuleBuilderBulkExportWithTarget(ruleBulkExport);
}
@Override

186
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleBulkExportImpl.java
View File

@ -24,12 +24,12 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.bulk.BulkExportJobParameters;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
@ -42,7 +42,6 @@ public class RuleBulkExportImpl extends BaseRule {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuleBulkExportImpl.class);
private String myGroupId;
private final Collection<String> myPatientIds;
private boolean myAppliesToAllPatients;
private BulkExportJobParameters.ExportStyle myWantExportStyle;
private Collection<String> myResourceTypes;
private boolean myWantAnyStyle;
@ -70,84 +69,113 @@ public class RuleBulkExportImpl extends BaseRule {
return null;
}
BulkExportJobParameters inboundBulkExportRequestOptions = (BulkExportJobParameters)
BulkExportJobParameters options = (BulkExportJobParameters)
theRequestDetails.getAttribute(AuthorizationInterceptor.REQUEST_ATTRIBUTE_BULK_DATA_EXPORT_OPTIONS);
// if style doesn't match - abstain
if (!myWantAnyStyle && inboundBulkExportRequestOptions.getExportStyle() != myWantExportStyle) {
if (!myWantAnyStyle && options.getExportStyle() != myWantExportStyle) {
return null;
}
// Do we only authorize some types? If so, make sure requested types are a subset
if (isNotEmpty(myResourceTypes)) {
if (isEmpty(inboundBulkExportRequestOptions.getResourceTypes())) {
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
}
if (!myResourceTypes.containsAll(inboundBulkExportRequestOptions.getResourceTypes())) {
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
}
}
// system only supports filtering by resource type. So if we are system, or any(), then allow, since we have
// done resource type checking
// above
AuthorizationInterceptor.Verdict allowVerdict = newVerdict(
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
if (myWantAnyStyle || myWantExportStyle == BulkExportJobParameters.ExportStyle.SYSTEM) {
return allowVerdict;
}
// assume myGroupId not empty->myStyle is group. If target group matches, then allow.
if (isNotBlank(myGroupId) && inboundBulkExportRequestOptions.getGroupId() != null) {
String expectedGroupId =
new IdDt(myGroupId).toUnqualifiedVersionless().getValue();
String actualGroupId = new IdDt(inboundBulkExportRequestOptions.getGroupId())
.toUnqualifiedVersionless()
.getValue();
if (Objects.equals(expectedGroupId, actualGroupId)) {
return allowVerdict;
}
}
// patient export mode - instance or type. type can have 0..n patient ids.
// myPatientIds == the rules built by the auth interceptor rule builder
// options.getPatientIds() == the requested IDs in the export job.
// 1. If each of the requested resource IDs in the parameters are present in the users permissions, Approve
// 2. If any requested ID is not present in the users permissions, Deny.
if (myWantExportStyle == BulkExportJobParameters.ExportStyle.PATIENT)
// Unfiltered Type Level
if (myAppliesToAllPatients) {
return allowVerdict;
}
// Instance level, or filtered type level
if (isNotEmpty(myPatientIds)) {
// If bulk export options defines no patient IDs, return null.
if (inboundBulkExportRequestOptions.getPatientIds().isEmpty()) {
if (isEmpty(options.getResourceTypes())) {
return null;
} else {
ourLog.debug("options.getPatientIds() != null");
Set<String> requestedPatientIds = sanitizeIds(inboundBulkExportRequestOptions.getPatientIds());
Set<String> permittedPatientIds = sanitizeIds(myPatientIds);
if (permittedPatientIds.containsAll(requestedPatientIds)) {
return allowVerdict;
} else {
}
for (String next : options.getResourceTypes()) {
if (!myResourceTypes.contains(next)) {
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
}
}
}
return null;
}
private Set<String> sanitizeIds(Collection<String> myPatientIds) {
return myPatientIds.stream()
.map(id -> new IdDt(id).toUnqualifiedVersionless().getValue())
.collect(Collectors.toSet());
if (myWantAnyStyle || myWantExportStyle == BulkExportJobParameters.ExportStyle.SYSTEM) {
return newVerdict(
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
}
if (isNotBlank(myGroupId) && options.getGroupId() != null) {
String expectedGroupId =
new IdDt(myGroupId).toUnqualifiedVersionless().getValue();
String actualGroupId =
new IdDt(options.getGroupId()).toUnqualifiedVersionless().getValue();
if (Objects.equals(expectedGroupId, actualGroupId)) {
return newVerdict(
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
}
}
// 1. If each of the requested resource IDs in the parameters are present in the users permissions, Approve
// 2. If any requested ID is not present in the users permissions, Deny.
if (myWantExportStyle == BulkExportJobParameters.ExportStyle.PATIENT && isNotEmpty(myPatientIds)) {
List<String> permittedPatientIds = myPatientIds.stream()
.map(id -> new IdDt(id).toUnqualifiedVersionless().getValue())
.collect(Collectors.toList());
if (!options.getPatientIds().isEmpty()) {
ourLog.debug("options.getPatientIds() != null");
List<String> requestedPatientIds = options.getPatientIds().stream()
.map(t -> new IdDt(t).toUnqualifiedVersionless().getValue())
.collect(Collectors.toList());
boolean requestedPatientsPermitted = true;
for (String requestedPatientId : requestedPatientIds) {
if (!permittedPatientIds.contains(requestedPatientId)) {
requestedPatientsPermitted = false;
break;
}
}
if (requestedPatientsPermitted) {
return newVerdict(
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
}
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
}
final List<String> filters = options.getFilters();
if (!filters.isEmpty()) {
ourLog.debug("filters not empty");
final Set<String> patientIdsInFilters = filters.stream()
.filter(filter -> filter.startsWith("Patient?_id="))
.map(filter -> filter.replace("?_id=", "/"))
.collect(Collectors.toUnmodifiableSet());
boolean filteredPatientIdsPermitted = true;
for (String patientIdInFilters : patientIdsInFilters) {
if (!permittedPatientIds.contains(patientIdInFilters)) {
filteredPatientIdsPermitted = false;
break;
}
}
if (filteredPatientIdsPermitted) {
return newVerdict(
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
}
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
}
ourLog.debug("patientIds and filters both empty");
}
return null;
}
public void setAppliesToGroupExportOnGroup(String theGroupId) {
@ -165,16 +193,6 @@ public class RuleBulkExportImpl extends BaseRule {
myPatientIds.add(thePatientId);
}
public void setAppliesToPatientExport(Collection<String> thePatientIds) {
myWantExportStyle = BulkExportJobParameters.ExportStyle.PATIENT;
myPatientIds.addAll(thePatientIds);
}
public void setAppliesToPatientExportAllPatients() {
myWantExportStyle = BulkExportJobParameters.ExportStyle.PATIENT;
myAppliesToAllPatients = true;
}
public void setAppliesToSystem() {
myWantExportStyle = BulkExportJobParameters.ExportStyle.SYSTEM;
}
@ -194,14 +212,4 @@ public class RuleBulkExportImpl extends BaseRule {
BulkExportJobParameters.ExportStyle getWantExportStyle() {
return myWantExportStyle;
}
@VisibleForTesting
Collection<String> getPatientIds() {
return myPatientIds;
}
@VisibleForTesting
Collection<String> getResourceTypes() {
return myResourceTypes;
}
}

76
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleBuilderTest.java
View File

@ -1,23 +1,16 @@
package ca.uhn.fhir.rest.server.interceptor.auth;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IIdType;
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 java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.stream.Stream;
import static org.hamcrest.Matchers.contains;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertInstanceOf;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.mock;
public class RuleBuilderTest {
@ -105,72 +98,7 @@ public class RuleBuilderTest {
builder.allow().bulkExport().patientExportOnPatient("Patient/pat2").withResourceTypes(resourceTypes);
List<IAuthRule> rules = builder.build();
assertEquals(rules.size(),1);
assertInstanceOf(RuleBulkExportImpl.class, rules.get(0));
}
public static Stream<Arguments> multipleInstancesParams() {
return Stream.of(
Arguments.of(List.of("Patient/pat1"), List.of("Patient"), PolicyEnum.ALLOW),
Arguments.of(List.of("Patient/pat1", "Patient/pat2"), List.of("Patient"), PolicyEnum.ALLOW),
Arguments.of(List.of("Patient/pat1", "Patient/pat2"), List.of("Patient", "Observation"), PolicyEnum.ALLOW),
Arguments.of(List.of("Patient/pat1"), List.of("Patient"), PolicyEnum.DENY),
Arguments.of(List.of("Patient/pat1", "Patient/pat2"), List.of("Patient"), PolicyEnum.DENY),
Arguments.of(List.of("Patient/pat1", "Patient/pat2"), List.of("Patient", "Observation"), PolicyEnum.DENY)
);
}
@ParameterizedTest
@MethodSource("multipleInstancesParams")
public void testBulkExport_PatientExportOnPatients_MultiplePatientsSingleRule(Collection<String> theExpectedPatientIds, Collection<String> theExpectedResourceTypes, PolicyEnum thePolicyEnum) {
final RuleBuilder builder = new RuleBuilder();
final IAuthRuleBuilderRule rule = switch (thePolicyEnum) {
case ALLOW -> builder.allow();
case DENY -> builder.deny();
};
rule.bulkExport().patientExportOnPatientStrings(theExpectedPatientIds).withResourceTypes(theExpectedResourceTypes);
final List<IAuthRule> rules = builder.build();
assertEquals(rules.size(),1);
final IAuthRule authRule = rules.get(0);
assertInstanceOf(RuleBulkExportImpl.class, authRule);
final RuleBulkExportImpl ruleBulkExport = (RuleBulkExportImpl) authRule;
assertEquals(theExpectedPatientIds, ruleBulkExport.getPatientIds());
assertEquals(theExpectedResourceTypes, ruleBulkExport.getResourceTypes());
assertEquals(thePolicyEnum, ruleBulkExport.getMode());
}
public static Stream<Arguments> owners() {
return Stream.of(
Arguments.of(List.of(new IdDt("Patient/pat1")), PolicyEnum.ALLOW),
Arguments.of(List.of(new IdDt("Patient/pat1")), PolicyEnum.DENY),
Arguments.of(List.of(new IdDt("Patient/pat1"), new IdDt("Patient/pat2")), PolicyEnum.ALLOW),
Arguments.of(List.of(new IdDt("Patient/pat1"), new IdDt("Patient/pat2")), PolicyEnum.DENY)
);
}
@ParameterizedTest
@MethodSource("owners")
public void testBulkExport_PatientExportOnPatients_onInstances(List<IIdType> theExpectedOwners, PolicyEnum thePolicyEnum) {
final RuleBuilder builder = new RuleBuilder();
final IAuthRuleBuilderRule rule = switch (thePolicyEnum) {
case ALLOW -> builder.allow();
case DENY -> builder.deny();
};
final List<IAuthRule> rules = rule
.operation()
.named(ProviderConstants.OPERATION_EXPORT)
.onInstances(theExpectedOwners)
.andAllowAllResponses()
.andThen()
.build();
assertEquals(rules.size(),1);
final IAuthRule authRule = rules.get(0);
assertInstanceOf(OperationRule.class, authRule);
final OperationRule operationRule = (OperationRule) authRule;
assertEquals(theExpectedOwners, operationRule.getAppliesToIds());
assertEquals(ProviderConstants.OPERATION_EXPORT, operationRule.getOperationName());
assertEquals(thePolicyEnum, operationRule.getMode());
assertTrue(rules.get(0) instanceof RuleBulkExportImpl);
}
@Test

382
hapi-fhir-server/src/test/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleBulkExportImplTest.java
View File

@ -4,9 +4,6 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.bulk.BulkExportJobParameters;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
@ -16,6 +13,7 @@ import java.util.HashSet;
import java.util.Set;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.when;
@ -30,11 +28,10 @@ public class RuleBulkExportImplTest {
@Mock
private Set<AuthorizationFlagsEnum> myFlags;
@Test
public void testDenyBulkRequestWithInvalidResourcesTypes() {
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
myRule.setMode(PolicyEnum.ALLOW);
Set<String> myTypes = new HashSet<>();
myTypes.add("Patient");
myTypes.add("Practitioner");
@ -45,210 +42,33 @@ public class RuleBulkExportImplTest {
BulkExportJobParameters options = new BulkExportJobParameters();
options.setResourceTypes(myWantTypes);
when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertDeny(verdict);
}
@Test
public void test_RuleSpecifiesResourceTypes_RequestDoesNot_Abstains() {
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
myRule.setAppliesToPatientExportAllPatients();
myRule.setMode(PolicyEnum.ALLOW);
Set<String> myTypes = new HashSet<>();
myTypes.add("Patient");
myRule.setResourceTypes(myTypes);
BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertDeny(verdict);
}
@Test
public void testBulkExportSystem_ruleHasTypes_RequestWithTypes_allow() {
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
myRule.setMode(PolicyEnum.ALLOW);
myRule.setAppliesToSystem();
myRule.setResourceTypes(Set.of("Patient", "Practitioner"));
BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
options.setResourceTypes(Set.of("Patient", "Practitioner"));
when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
assertEquals(PolicyEnum.DENY, verdict.getDecision());
}
@Test
public void testBulkExportSystem_ruleHasTypes_RequestWithTooManyTypes_abstain() {
public void testBulkRequestWithValidResourcesTypes() {
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
myRule.setMode(PolicyEnum.ALLOW);
myRule.setAppliesToSystem();
myRule.setResourceTypes(Set.of("Patient", "Practitioner"));
Set<String> myTypes = new HashSet<>();
myTypes.add("Patient");
myTypes.add("Practitioner");
myRule.setResourceTypes(myTypes);
Set<String> myWantTypes = new HashSet<>();
myWantTypes.add("Patient");
myWantTypes.add("Practitioner");
BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
options.setResourceTypes(Set.of("Patient", "Practitioner", "Encounter"));
options.setResourceTypes(myWantTypes);
when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertDeny(verdict);
}
@Nested
class StyleChecks {
BulkExportJobParameters myOptions = new BulkExportJobParameters();
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
@BeforeEach
void setUp() {
myRule.setMode(PolicyEnum.ALLOW);
when(myRequestDetails.getAttribute(any())).thenReturn(myOptions);
}
@Nested class RuleAnyStyle {
@BeforeEach
void setUp(){
myRule.setAppliesToAny();
}
@Test
public void testRuleAnyStyle_Matches_SystemStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
}
@Test
public void testRuleAnyStyle_Matches_PatientStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
}
@Test
public void testRuleAnyStyle_Matches_GroupStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.GROUP);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
}
}
@Nested
class RuleSystemStyle {
@BeforeEach
void setUp() {
myRule.setAppliesToSystem();
}
@Test
public void test_Matches_SystemStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
}
@Test
public void test_DoesntMatch_GroupStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.GROUP);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAbstain(verdict);
}
@Test
public void test_DoesntMatch_PatientStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAbstain(verdict);
}
}
@Nested
class RuleGroupStyle {
@BeforeEach
void setUp() {
myRule.setAppliesToGroupExportOnGroup("Group/123");
}
@Test
public void test_DoesntMatch_SystemStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAbstain(verdict);
}
@Test
public void test_Matches_GroupStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.GROUP);
myOptions.setGroupId("Group/123");
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
}
@Test
public void test_DoesntMatch_PatientStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAbstain(verdict);
}
}
@Nested
class RulePatientStyle {
@BeforeEach
void setUp() {
myRule.setAppliesToPatientExport("Patient/123");
}
@Test
public void test_DoesntMatch_SystemStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAbstain(verdict);
}
@Test
public void test_DoesntMatch_GroupStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.GROUP);
myOptions.setGroupId("Group/123");
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAbstain(verdict);
}
@Test
public void test_DoesntMatch_PatientStyle() {
myOptions.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
myOptions.setPatientIds(Set.of("Patient/123"));
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
}
}
assertNull(verdict);
}
@Test
@ -264,7 +84,7 @@ public class RuleBulkExportImplTest {
when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAbstain(verdict);
assertEquals(null, verdict);
}
@Test
@ -280,7 +100,7 @@ public class RuleBulkExportImplTest {
when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
}
@Test
@ -298,7 +118,7 @@ public class RuleBulkExportImplTest {
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: We permit the request, as a patient ID that was requested is honoured by this rule.
assertAllow(verdict);
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
}
@Test
@ -315,8 +135,8 @@ public class RuleBulkExportImplTest {
//When
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: abstain
assertDeny(verdict);
//Then: we should deny the request, as the requested export does not contain the patient permitted.
assertEquals(PolicyEnum.DENY, verdict.getDecision());
}
@Test
@ -333,45 +153,28 @@ public class RuleBulkExportImplTest {
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: We make no claims about type-level export on Patient.
assertAbstain(verdict);
assertEquals(null, verdict);
}
@Test
public void testPatientExportRulesWithId_withRequestNoIds_abstains() {
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypePatient() {
//Given
RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123");
myRule.setMode(PolicyEnum.ALLOW);
BulkExportJobParameters options = new BulkExportJobParameters();
final BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
options.setFilters(Set.of("Patient?_id=123"));
options.setResourceTypes(Set.of("Patient"));
when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: We make no claims about type-level export on Patient.
assertAbstain(verdict);
//Then: The patient IDs match so this is permitted
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
}
@Test
public void testPatientExportRuleWithNoIds_withRequestNoIds_allows() {
//Given
RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExportAllPatients();
myRule.setMode(PolicyEnum.ALLOW);
BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertAllow(verdict);
}
@Test
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypePatientAndFilterHasResources() {
//Given
@ -388,9 +191,27 @@ public class RuleBulkExportImplTest {
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: The patient IDs match so this is permitted
assertAbstain(verdict);
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
}
@Test
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypeObservation() {
//Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123");
myRule.setMode(PolicyEnum.ALLOW);
final BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
options.setFilters(Set.of("Patient?_id=123"));
options.setResourceTypes(Set.of("Observation"));
when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: The patient IDs match so this is permitted
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
}
@Test
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterNoResourceType() {
@ -406,8 +227,27 @@ public class RuleBulkExportImplTest {
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: Filters are ignored for auth purposes. The rule has an ID, indicating it is for instance level, but the job requested type level. Abstain
assertAbstain(verdict);
//Then: The patient IDs match so this is permitted
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
}
@Test
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterMismatch() {
//Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123");
myRule.setMode(PolicyEnum.ALLOW);
final BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
options.setFilters(Set.of("Patient?_id=456"));
options.setResourceTypes(Set.of("Patient"));
when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: The patient IDs do NOT match so this is not permitted.
assertEquals(PolicyEnum.DENY, verdict.getDecision());
}
@Test
@ -425,12 +265,12 @@ public class RuleBulkExportImplTest {
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: We do not have permissions on the requested patient so we abstain
assertDeny(verdict);
//Then: We do not have permissions on the requested patient so this is not permitted.
assertEquals(PolicyEnum.DENY, verdict.getDecision());
}
@Test
public void testPatientExport_ruleAllowsId_requestsId_allow() {
public void testPatientExportRulesOnTypeLevelExportPermittedPatient() {
//Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123");
@ -449,7 +289,7 @@ public class RuleBulkExportImplTest {
}
@Test
public void testPatientExport_ruleAllowsIds_requestsIds_allow() {
public void testPatientExportRulesOnTypeLevelExportPermittedPatients() {
//Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123");
@ -469,7 +309,7 @@ public class RuleBulkExportImplTest {
}
@Test
public void testPatientExport_ruleAllowsId_requestsTooManyIds_abstain() {
public void testPatientExportRulesOnTypeLevelExportWithPermittedAndUnpermittedPatients() {
//Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123");
@ -484,61 +324,8 @@ public class RuleBulkExportImplTest {
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: There are unpermitted patients in the request so this is not permitted.
assertDeny(verdict);
} //
@Test
public void testPatientExport_RuleAllowsAll_RequestId_allows() {
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExportAllPatients();
myRule.setMode(PolicyEnum.ALLOW);
final BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
options.setPatientIds(Set.of("Patient/123"));
when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then
assertAllow(verdict);
assertEquals(PolicyEnum.DENY, verdict.getDecision());
}
@Test
public void testPatientExport_RuleAllowsAll_RequestAll_allows() {
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExportAllPatients();
myRule.setMode(PolicyEnum.ALLOW);
final BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then
assertAllow(verdict);
}
@Test
public void testPatientExport_RuleAllowsExplicitPatient_RequestAll_abstain() {
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123");
myRule.setMode(PolicyEnum.ALLOW);
final BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then
assertAbstain(verdict);
}
@Test
public void testPatientExportRulesOnTypeLevelExportWithPermittedAndUnpermittedPatientFilters() {
//Given
@ -554,22 +341,7 @@ public class RuleBulkExportImplTest {
//When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: There are unpermitted patients in the request so this is not permitted. abstain.
assertAbstain(verdict);
}
private static void assertAbstain(AuthorizationInterceptor.Verdict verdict) {
Assertions.assertEquals(null, verdict, "Expect abstain");
}
private static void assertAllow(AuthorizationInterceptor.Verdict verdict) {
Assertions.assertNotNull(verdict, "Expect ALLOW, got abstain");
Assertions.assertEquals(PolicyEnum.ALLOW, verdict.getDecision(), "Expect ALLOW");
}
private static void assertDeny(AuthorizationInterceptor.Verdict verdict) {
Assertions.assertNotNull(verdict, "Expect DENY, got abstain");
Assertions.assertEquals(PolicyEnum.DENY, verdict.getDecision(), "Expect DENY");
//Then: There are unpermitted patients in the request so this is not permitted.
assertEquals(PolicyEnum.DENY, verdict.getDecision());
}
}

8
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTask.java
View File

@ -308,14 +308,6 @@ public abstract class BaseTask {
}
}
public void doNothing() {
setDoNothing(true);
}
public void failureAllowed() {
setFailureAllowed(true);
}
public boolean isDoNothing() {
return myDoNothing;
}

44
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/RenameTableTask.java
View File

@ -22,8 +22,11 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.intellij.lang.annotations.Language;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.jdbc.core.ColumnMapRowMapper;
import org.springframework.jdbc.core.JdbcTemplate;
import java.sql.SQLException;
import java.util.Set;
@ -48,12 +51,53 @@ public class RenameTableTask extends BaseTableTask {
setDescription("Rename table " + getOldTableName());
}
private void handleTableWithNewTableName() throws SQLException {
if (!myDeleteTargetColumnFirstIfExist) {
throw new SQLException(Msg.code(2517) + "Can not rename " + getOldTableName() + " to " + getNewTableName()
+ " because a table with name " + getNewTableName() + " already exists");
}
// a table with the new tableName already exists and we can delete it. we will only do so if it is empty.
Integer rowsWithData = getConnectionProperties().getTxTemplate().execute(t -> {
String sql = "SELECT * FROM " + getNewTableName();
JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
jdbcTemplate.setMaxRows(1);
return jdbcTemplate.query(sql, new ColumnMapRowMapper()).size();
});
if (rowsWithData != null && rowsWithData > 0) {
throw new SQLException(Msg.code(2518) + "Can not rename " + getOldTableName() + " to " + getNewTableName()
+ " because a table with name " + getNewTableName() + " already exists and is populated.");
}
logInfo(
ourLog,
"Table {} already exists - Going to drop it before renaming table {} to {}",
getNewTableName(),
getOldTableName(),
getNewTableName());
@Language("SQL")
String sql = "DROP TABLE " + getNewTableName();
executeSql(getNewTableName(), sql);
}
@Override
public void doExecute() throws SQLException {
Set<String> tableNames = JdbcUtils.getTableNames(getConnectionProperties());
boolean hasTableWithNewTableName = tableNames.contains(getNewTableName());
if (!tableNames.contains(getOldTableName())) {
throw new SQLException(Msg.code(2516) + "Can not rename " + getOldTableName() + " to " + getNewTableName()
+ " because the original table does not exists");
}
if (hasTableWithNewTableName) {
handleTableWithNewTableName();
}
String sql = buildRenameTableSqlStatement();
logInfo(ourLog, "Renaming table: {}", getOldTableName());

21
hapi-fhir-sql-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/Builder.java
View File

@ -57,7 +57,6 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
@ -186,7 +185,6 @@ public class Builder {
private final String myRelease;
private final BaseMigrationTasks.IAcceptsTasks mySink;
private final String myTableName;
private BaseTask myLastAddedTask;
public BuilderWithTableName(String theRelease, BaseMigrationTasks.IAcceptsTasks theSink, String theTableName) {
myRelease = theRelease;
@ -276,7 +274,6 @@ public class Builder {
@Override
public void addTask(BaseTask theTask) {
((BaseTableTask) theTask).setTableName(myTableName);
myLastAddedTask = theTask;
mySink.addTask(theTask);
}
@ -314,10 +311,6 @@ public class Builder {
return this;
}
public Optional<BaseTask> getLastAddedTask() {
return Optional.ofNullable(myLastAddedTask);
}
/**
* @param theFkName the name of the foreign key
* @param theParentTableName the name of the table that exports the foreign key
@ -330,37 +323,31 @@ public class Builder {
addTask(task);
}
public BuilderCompleteTask renameTable(String theVersion, String theNewTableName) {
public void renameTable(String theVersion, String theNewTableName) {
RenameTableTask task = new RenameTableTask(myRelease, theVersion, getTableName(), theNewTableName);
addTask(task);
return new BuilderCompleteTask(task);
}
public BuilderCompleteTask migratePostgresTextClobToBinaryClob(String theVersion, String theColumnName) {
public void migratePostgresTextClobToBinaryClob(String theVersion, String theColumnName) {
MigratePostgresTextClobToBinaryClobTask task =
new MigratePostgresTextClobToBinaryClobTask(myRelease, theVersion);
task.setTableName(getTableName());
task.setColumnName(theColumnName);
addTask(task);
return new BuilderCompleteTask(task);
}
public BuilderCompleteTask migrateBlobToBinary(
String theVersion, String theFromColumName, String theToColumName) {
public void migrateBlobToBinary(String theVersion, String theFromColumName, String theToColumName) {
MigrateColumBlobTypeToBinaryTypeTask task = new MigrateColumBlobTypeToBinaryTypeTask(
myRelease, theVersion, getTableName(), theFromColumName, theToColumName);
addTask(task);
return new BuilderCompleteTask(task);
}
public BuilderCompleteTask migrateClobToText(
String theVersion, String theFromColumName, String theToColumName) {
public void migrateClobToText(String theVersion, String theFromColumName, String theToColumName) {
MigrateColumnClobTypeToTextTypeTask task = new MigrateColumnClobTypeToTextTypeTask(
myRelease, theVersion, getTableName(), theFromColumName, theToColumName);
addTask(task);
return new BuilderCompleteTask(task);
}
public class BuilderAddIndexWithName {

22
hapi-fhir-sql-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/RenameTableTaskTest.java
View File

@ -41,4 +41,26 @@ public class RenameTableTaskTest extends BaseTest {
assertThat(tableNames, not(hasItem(oldTableName)));
}
@ParameterizedTest(name = "{index}: {0}")
@MethodSource("data")
public void testRenameTableTask_whenTableDoesNotExists_willRaiseException(Supplier<TestDatabaseDetails> theTestDatabaseDetails) throws SQLException {
// given
before(theTestDatabaseDetails);
final String newTableName = "NEWTABLE";
final String oldTableName = "SOMETABLE";
RenameTableTask task = new RenameTableTask("1", "1", oldTableName, newTableName);
getMigrator().addTask(task);
// when
try {
getMigrator().migrate();
fail();
} catch (Exception e){
// then
assertThat(e.getMessage(), containsString("2516"));
}
}
}

10
hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/imprt/BulkDataImportProviderTest.java
View File

@ -436,16 +436,6 @@ public class BulkDataImportProviderTest {
public boolean isResourcePartitionable(String theResourceType) {
return false;
}
@Override
public RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
return null;
}
@Override
public RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
return null;
}
}
private Date parseDate(String theString) {

19
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/ICollectDataServiceFactory.java
View File

@ -1,22 +1,3 @@
/*-
* #%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.r4;
import ca.uhn.fhir.rest.api.server.RequestDetails;

19
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/IDataRequirementsServiceFactory.java
View File

@ -1,22 +1,3 @@
/*-
* #%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.r4;
import ca.uhn.fhir.rest.api.server.RequestDetails;

19
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/CollectDataOperationProvider.java
View File

@ -1,22 +1,3 @@
/*-
* #%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.r4.measure;
import ca.uhn.fhir.cr.r4.ICollectDataServiceFactory;

19
hapi-fhir-storage-cr/src/main/java/ca/uhn/fhir/cr/r4/measure/DataRequirementsOperationProvider.java
View File

@ -1,22 +1,3 @@
/*-
* #%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.r4.measure;
import ca.uhn.fhir.cr.r4.IDataRequirementsServiceFactory;

4
hapi-fhir-storage-test-utilities/src/main/java/ca/uhn/fhir/storage/test/DaoTestDataBuilder.java
View File

@ -102,9 +102,7 @@ public class DaoTestDataBuilder implements ITestDataBuilder.WithSupport, ITestDa
public void cleanup() {
ourLog.info("cleanup {}", myIds);
myIds.keySet().stream()
.sorted() // Hack to ensure Patients are deleted before Practitioners. This may need to be refined.
.forEach(nextType->{
myIds.keySet().forEach(nextType->{
// todo do this in a bundle for perf.
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(nextType);
myIds.get(nextType).forEach(dao::delete);

43
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java
View File

@ -360,14 +360,6 @@ public class JpaStorageSettings extends StorageSettings {
*/
private long myRestDeleteByUrlResourceIdThreshold = DEFAULT_REST_DELETE_BY_URL_RESOURCE_ID_THRESHOLD;
/**
* If enabled, this setting causes persisting data to legacy LOB columns as well as columns introduced
* to migrate away from LOB columns which effectively duplicates stored information.
*
* @since 7.2.0
*/
private boolean myWriteToLegacyLobColumns = false;
/**
* Constructor
*/
@ -2431,8 +2423,8 @@ public class JpaStorageSettings extends StorageSettings {
* This setting controls the validation issue severity to report when a code validation
* finds that the code is present in the given CodeSystem, but the display name being
* validated doesn't match the expected value(s). Defaults to
* {@link IValidationSupport.IssueSeverity#WARNING}. Set this
* value to {@link IValidationSupport.IssueSeverity#INFORMATION}
* {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#WARNING}. Set this
* value to {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#INFORMATION}
* if you don't want to see display name validation issues at all in resource validation
* outcomes.
*
@ -2447,8 +2439,8 @@ public class JpaStorageSettings extends StorageSettings {
* This setting controls the validation issue severity to report when a code validation
* finds that the code is present in the given CodeSystem, but the display name being
* validated doesn't match the expected value(s). Defaults to
* {@link IValidationSupport.IssueSeverity#WARNING}. Set this
* value to {@link IValidationSupport.IssueSeverity#INFORMATION}
* {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#WARNING}. Set this
* value to {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#INFORMATION}
* if you don't want to see display name validation issues at all in resource validation
* outcomes.
*
@ -2462,33 +2454,6 @@ public class JpaStorageSettings extends StorageSettings {
myIssueSeverityForCodeDisplayMismatch = theIssueSeverityForCodeDisplayMismatch;
}
/**
* This method returns whether data will be stored in LOB columns as well as the columns
* introduced to migrate away from LOB. Writing to LOB columns is set to false by
* default. Enabling the setting will effectively double the persisted information.
* If enabled, a careful monitoring of LOB table (if applicable) is required to avoid
* exceeding the table maximum capacity.
*
* @since 7.2.0
*/
public boolean isWriteToLegacyLobColumns() {
return myWriteToLegacyLobColumns;
}
/**
* This setting controls whether data will be stored in LOB columns as well as the columns
* introduced to migrate away from LOB. Writing to LOB columns is set to false by
* default. Enabling the setting will effectively double the persisted information.
* When enabled, a careful monitoring of LOB table (if applicable) is required to avoid
* exceeding the table maximum capacity.
*
* @param theWriteToLegacyLobColumns
* @since 7.2.0
*/
public void setWriteToLegacyLobColumns(boolean theWriteToLegacyLobColumns) {
myWriteToLegacyLobColumns = theWriteToLegacyLobColumns;
}
/**
* This setting controls whether MdmLink and other non-resource DB history is enabled.
* <p/>

4
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/partition/BaseRequestPartitionHelperSvc.java
View File

@ -333,6 +333,10 @@ public abstract class BaseRequestPartitionHelperSvc implements IRequestPartition
return !myNonPartitionableResourceNames.contains(theResourceType);
}
protected abstract RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId);
protected abstract RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId);
private void validateSinglePartitionForCreate(
RequestPartitionId theRequestPartitionId, @Nonnull String theResourceName, Pointcut thePointcut) {
validateRequestPartitionNotNull(theRequestPartitionId, thePointcut);