7 2 mergeback may 10 v2 (#5928)

* Enhance RuleBuilder code to support multiple instances (#5852)

* Overhaul bulk export permissions.

* Overhaul bulk export permissions.

* Small tweak to rule builder.

* Cleanup validation.

* Cleanup validation.

* Code review feedback.

* Postgres terminology service hard coded column names migration (#5866)

* updating parent pids column name

* updating name of the fullTestField Search

* updating name of the fullTestField Search

* fixing typo.

* failing test.

* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;

- reverting the name of the FullTextField entity to its previous name of 'myParentPids';

- reverting the name of the lucene index to search on in the terminology service.

- updating the changelog;

* making spotless happy

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)

* initial failing test.

* solution

* adding changelog

* spotless

* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)

* Expose BaseRequestPartitionHelperSvc validate and normalize methods

* Compilation errors

* change mock test to jpa test

* change mock test to jpa test

* validateAndNormalizePartitionIds

* validateAndNormalizePartitionNames

* validateAndNormalizePartitionIds validation + bug fix

* validateAndNormalizePartitionNames validation

* fix test

* version bump

* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)

* Add failing test as well as commented out potential solution.

* Fix for NumberFormatException.

* Add conditional test for survivorship rules.

* Spotless.

* Add changelog.

* Code review feedback.

* updating documentation (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Enhance mdm interceptor (#5899)

* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.

* Added javadoc

* Cahngelog

* spotless

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.

* Add changelog.

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

Commit code reviewer suggestion.

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Fix query chained on sort bug where we over-filter results (#5903)

* Failing test.

* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.

* Implement fix.

* Spotless.

* Clean up unit test and add changelog.  Fix unit test.

* Fix changelog file.

* Apply suggestions from code review

Apply code review suggestions.

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>

* Spotless

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>

* cve fix (#5906)

Co-authored-by: Long Ma <long@smilecdr.com>

* Fixing issues with postgres LOB migration. (#5895)

* Fixing issues with postgres LOB migration.

* addressing code review comments for audit/transaction logs.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for TermConcept
 migration post code review.

* applying spotless

* test and implementation for TermConceptProperty
 migration post code review.

* test and implementation for TermValueSetConcept
 migration post code review.

* fixing migration version

* fixing migration task

* changelog

* fixing changelog

* Minor renames

* addressing comments and suggestions from second code review.

* passing tests

* fixing more tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* 6051 bulk export security errors (#5915)

* Enhance RuleBuilder code to support multiple instances (#5852)

* Overhaul bulk export permissions.

* Overhaul bulk export permissions.

* Small tweak to rule builder.

* Cleanup validation.

* Cleanup validation.

* Code review feedback.

* Postgres terminology service hard coded column names migration (#5866)

* updating parent pids column name

* updating name of the fullTestField Search

* updating name of the fullTestField Search

* fixing typo.

* failing test.

* - Moving FullTextField annotation from getter method and adding it to the newly added VC property of the entity;

- reverting the name of the FullTextField entity to its previous name of 'myParentPids';

- reverting the name of the lucene index to search on in the terminology service.

- updating the changelog;

* making spotless happy

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5879 back porting fix for issue 5877 (attempting to update a tokenparam with a value greater than 200 characters raises an sqlexception) to release rel_7_2 (#5881)

* initial failing test.

* solution

* adding changelog

* spotless

* moving changelog from 7_4_0 to 7_2_0 and deleting 7_4_0 folder.

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Expose BaseRequestPartitionHelperSvc validateAndNormalize methods (#5811)

* Expose BaseRequestPartitionHelperSvc validate and normalize methods

* Compilation errors

* change mock test to jpa test

* change mock test to jpa test

* validateAndNormalizePartitionIds

* validateAndNormalizePartitionNames

* validateAndNormalizePartitionIds validation + bug fix

* validateAndNormalizePartitionNames validation

* fix test

* version bump

* Ensure a non-numeric FHIR ID doesn't result in a NumberFormatException when processing survivorship rules (#5883)

* Add failing test as well as commented out potential solution.

* Fix for NumberFormatException.

* Add conditional test for survivorship rules.

* Spotless.

* Add changelog.

* Code review feedback.

* updating documentation (#5889)

* Ensure temp file ends with "." and then suffix. (#5894)

* bugfix to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/675 (#5892)

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Enhance mdm interceptor (#5899)

* Add MDM Transaction Context for further downstream processing giving interceptors a better chance of figuring out what happened.

* Added javadoc

* Cahngelog

* spotless

---------

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

* Fix BaseHapiFhirResourceDao $meta method to use HapiTransactionService instead of @Transaction (#5896)

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Try making ResourceTable.myTags EAGER instead of LAZY and see if it breaks anything.

* Ensure BaseHapiFhirResourceDao#metaGetOperation uses HapiTransactionService instead of @Transactional in order to resolve megascale $meta bug.

* Add changelog.

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

Commit code reviewer suggestion.

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

---------

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Fix query chained on sort bug where we over-filter results (#5903)

* Failing test.

* Ensure test cleanup doesn't fail by deleting Patients before Practitioners.

* Implement fix.

* Spotless.

* Clean up unit test and add changelog.  Fix unit test.

* Fix changelog file.

* Apply suggestions from code review

Apply code review suggestions.

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>

* Spotless

---------

Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>

* cve fix (#5906)

Co-authored-by: Long Ma <long@smilecdr.com>

* Fixing issues with postgres LOB migration. (#5895)

* Fixing issues with postgres LOB migration.

* addressing code review comments for audit/transaction logs.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for TermConcept
 migration post code review.

* applying spotless

* test and implementation for TermConceptProperty
 migration post code review.

* test and implementation for TermValueSetConcept
 migration post code review.

* fixing migration version

* fixing migration task

* changelog

* fixing changelog

* Minor renames

* addressing comments and suggestions from second code review.

* passing tests

* fixing more tests

---------

Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* refactor bulk export rule, add concept of appliestoallpatients, fix tests

* spotless

* Cahgnelog, tests

* more tests

* refactor style checks

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>

* Convert a few nulls to aggressive denies

* Change chain sort syntax for MS SQL (#5917)

* Change sort type on chains

* Change sort type on chains

* Test for MS SQL

* Comments

* Version bump

* version bump to 7.3.1-SNAPSHOT

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
This commit is contained in:
longma1 2024-05-13 16:51:03 -06:00 committed by GitHub
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commit 078e87a4aa
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145 changed files with 1748 additions and 556 deletions

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

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

View File

@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId> <artifactId>hapi-fhir-bom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<packaging>pom</packaging> <packaging>pom</packaging>
<name>HAPI FHIR BOM</name> <name>HAPI FHIR BOM</name>
@ -12,7 +12,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

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

View File

@ -22,6 +22,10 @@ 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.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain; import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator; 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.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
@ -43,6 +47,7 @@ import java.io.FileOutputStream;
import java.io.FileWriter; import java.io.FileWriter;
import java.io.IOException; import java.io.IOException;
import java.util.List; import java.util.List;
import java.util.Optional;
import java.util.stream.Stream; import java.util.stream.Stream;
import java.util.zip.ZipEntry; import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream; import java.util.zip.ZipOutputStream;
@ -54,6 +59,8 @@ import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.is; import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.matchesPattern; import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.jupiter.api.Assertions.assertEquals; 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.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyList; import static org.mockito.ArgumentMatchers.anyList;
@ -479,6 +486,86 @@ public class UploadTerminologyCommandTest {
uploadICD10UsingCompressedFile(theFhirVersion, theIncludeTls); 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 { private void uploadICD10UsingCompressedFile(String theFhirVersion, boolean theIncludeTls) throws IOException {
if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) { if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101"))); when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));

View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId> <artifactId>hapi-fhir-cli</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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

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@ -0,0 +1,5 @@
---
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."

View File

@ -0,0 +1,5 @@
---
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."

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@ -0,0 +1,6 @@
---
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."

View File

@ -0,0 +1,7 @@
---
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.
"

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@ -0,0 +1,5 @@
---
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."

View File

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

View File

@ -0,0 +1,5 @@
---
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."

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@ -0,0 +1,4 @@
---
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."

View File

@ -0,0 +1,4 @@
---
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."

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@ -0,0 +1,4 @@
---
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."

View File

@ -0,0 +1,4 @@
---
type: fix
issue: 5917
title: "Fix chained sorts on strings when using MS Sql"

View File

@ -14,4 +14,9 @@ This interceptor is intended to be subclassed. A simple example is shown below:
## Combining with Bulk Export ## 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_INITIATE_BULK_EXPORT` pointcut is the easiest way to set these properties when a new Bulk Export job is being kicked off. 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.

View File

@ -11,7 +11,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

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

View File

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

View File

@ -1410,8 +1410,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
} }
@Override @Override
@Transactional
public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequest) { public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequest) {
return myTransactionService.withRequest(theRequest).execute(() -> {
Set<TagDefinition> tagDefs = new HashSet<>(); Set<TagDefinition> tagDefs = new HashSet<>();
BaseHasResource entity = readEntity(theId, theRequest); BaseHasResource entity = readEntity(theId, theRequest);
for (BaseTag next : entity.getTags()) { for (BaseTag next : entity.getTags()) {
@ -1423,6 +1423,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
retVal.setVersionId(Long.toString(entity.getVersion())); retVal.setVersionId(Long.toString(entity.getVersion()));
return retVal; return retVal;
});
} }
@Override @Override

View File

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

View File

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

View File

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

View File

@ -51,6 +51,7 @@ import java.sql.SQLException;
+ " vsc.SYSTEM_VER AS SYSTEM_VER, " + " vsc.SYSTEM_VER AS SYSTEM_VER, "
+ " vsc.SOURCE_PID AS SOURCE_PID, " + " vsc.SOURCE_PID AS SOURCE_PID, "
+ " vsc.SOURCE_DIRECT_PARENT_PIDS AS SOURCE_DIRECT_PARENT_PIDS, " + " 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.PID AS DESIGNATION_PID, "
+ " vscd.LANG AS DESIGNATION_LANG, " + " vscd.LANG AS DESIGNATION_LANG, "
+ " vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, " + " vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, "
@ -112,6 +113,9 @@ public class TermValueSetConceptView implements Serializable, ITermValueSetConce
@Column(name = "SOURCE_DIRECT_PARENT_PIDS", nullable = true) @Column(name = "SOURCE_DIRECT_PARENT_PIDS", nullable = true)
private Clob mySourceConceptDirectParentPids; private Clob mySourceConceptDirectParentPids;
@Column(name = "SOURCE_DIRECT_PARENT_PIDS_VC", nullable = true)
private String mySourceConceptDirectParentPidsVc;
@Override @Override
public Long getSourceConceptPid() { public Long getSourceConceptPid() {
return mySourceConceptPid; return mySourceConceptPid;
@ -119,14 +123,19 @@ public class TermValueSetConceptView implements Serializable, ITermValueSetConce
@Override @Override
public String getSourceConceptDirectParentPids() { public String getSourceConceptDirectParentPids() {
String retVal = null;
if (mySourceConceptDirectParentPids != null) { if (mySourceConceptDirectParentPids != null) {
try (Reader characterStream = mySourceConceptDirectParentPids.getCharacterStream()) { try (Reader characterStream = mySourceConceptDirectParentPids.getCharacterStream()) {
return IOUtils.toString(characterStream); retVal = IOUtils.toString(characterStream);
} catch (IOException | SQLException e) { } catch (IOException | SQLException e) {
throw new InternalErrorException(Msg.code(828) + e); throw new InternalErrorException(Msg.code(828) + e);
} }
} else if (mySourceConceptDirectParentPidsVc != null) {
retVal = mySourceConceptDirectParentPidsVc;
} }
return null;
return retVal;
} }
@Override @Override

View File

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

View File

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

View File

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

View File

@ -73,7 +73,6 @@ import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collection; import java.util.Collection;
import java.util.Collections; import java.util.Collections;
import java.util.Date;
import java.util.HashMap; import java.util.HashMap;
import java.util.HashSet; import java.util.HashSet;
import java.util.IdentityHashMap; import java.util.IdentityHashMap;
@ -685,26 +684,6 @@ 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 @Nonnull
private TermCodeSystem getOrCreateDistinctTermCodeSystem( private TermCodeSystem getOrCreateDistinctTermCodeSystem(
IResourcePersistentId theCodeSystemResourcePid, IResourcePersistentId theCodeSystemResourcePid,

View File

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

View File

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

View File

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

View File

@ -0,0 +1,51 @@
/*-
* #%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;
}
}

View File

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

View File

@ -2,8 +2,11 @@ package ca.uhn.fhir.jpa.entity;
import com.google.common.base.Strings; import com.google.common.base.Strings;
import org.junit.jupiter.api.Test; 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.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.is; import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.notNullValue; import static org.hamcrest.Matchers.notNullValue;
import static org.hamcrest.Matchers.startsWith; import static org.hamcrest.Matchers.startsWith;
@ -21,8 +24,8 @@ public class TermConceptPropertyTest {
termConceptProperty.setValue(ourVeryLongString); termConceptProperty.setValue(ourVeryLongString);
// then // then
assertThat(termConceptProperty.getValueBlobForTesting(), notNullValue()); assertThat(termConceptProperty.hasValueBlobForTesting(), equalTo(true));
assertThat(termConceptProperty.getValueBinForTesting(), notNullValue()); assertThat(termConceptProperty.hasValueBinForTesting(), equalTo(true));
} }
@Test @Test
@ -78,4 +81,19 @@ public class TermConceptPropertyTest {
assertThat(value, startsWith("a")); 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));
}
} }

View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -3,7 +3,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -3,7 +3,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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

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@ -2,11 +2,16 @@ package ca.uhn.fhir.jpa.mdm.svc;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test; import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService; 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.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired; 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.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse; import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull; import static org.junit.jupiter.api.Assertions.assertNull;
@ -55,4 +60,21 @@ class MdmSurvivorshipSvcImplIT extends BaseMdmR4Test {
assertEquals(p1.getTelecom().size(), p1.getTelecom().size()); assertEquals(p1.getTelecom().size(), p1.getTelecom().size());
assertTrue(p2.getTelecomFirstRep().equalsDeep(p1.getTelecomFirstRep())); 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));
}
} }

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@ -25,8 +25,9 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; 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.Mock;
import org.mockito.Spy; import org.mockito.Spy;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
@ -96,8 +97,9 @@ public class MdmSurvivorshipSvcImplTest {
} }
@SuppressWarnings({"rawtypes", "unchecked"}) @SuppressWarnings({"rawtypes", "unchecked"})
@Test @ParameterizedTest
public void rebuildGoldenResourceCurrentLinksUsingSurvivorshipRules_withManyLinks_rebuildsInUpdateOrder() { @ValueSource(booleans = {true,false})
public void rebuildGoldenResourceCurrentLinksUsingSurvivorshipRules_withManyLinks_rebuildsInUpdateOrder(boolean theIsUseNonNumericId) {
// setup // setup
// create resources // create resources
Patient goldenPatient = new Patient(); Patient goldenPatient = new Patient();
@ -126,7 +128,7 @@ public class MdmSurvivorshipSvcImplTest {
patient.addIdentifier() patient.addIdentifier()
.setSystem("http://example.com") .setSystem("http://example.com")
.setValue("Value" + i); .setValue("Value" + i);
patient.setId("Patient/" + i); patient.setId("Patient/" + (theIsUseNonNumericId ? "pat"+i : Integer.toString(i)));
resources.add(patient); resources.add(patient);
MdmLinkJson link = createLinkJson( MdmLinkJson link = createLinkJson(
@ -149,8 +151,13 @@ public class MdmSurvivorshipSvcImplTest {
when(myDaoRegistry.getResourceDao(eq("Patient"))) when(myDaoRegistry.getResourceDao(eq("Patient")))
.thenReturn(resourceDao); .thenReturn(resourceDao);
AtomicInteger counter = new AtomicInteger(); AtomicInteger counter = new AtomicInteger();
if (theIsUseNonNumericId) {
when(resourceDao.read(any(), any()))
.thenAnswer(params -> resources.get(counter.getAndIncrement()));
} else {
when(resourceDao.readByPid(any())) when(resourceDao.readByPid(any()))
.thenAnswer(params -> resources.get(counter.getAndIncrement())); .thenAnswer(params -> resources.get(counter.getAndIncrement()));
}
Page<MdmLinkJson> linkPage = mock(Page.class); Page<MdmLinkJson> linkPage = mock(Page.class);
when(myMdmLinkQuerySvc.queryLinks(any(), any())) when(myMdmLinkQuerySvc.queryLinks(any(), any()))
.thenReturn(linkPage); .thenReturn(linkPage);

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -156,4 +156,30 @@ public interface IRequestPartitionHelperSvc {
Set<Integer> toReadPartitions(@Nonnull RequestPartitionId theRequestPartitionId); Set<Integer> toReadPartitions(@Nonnull RequestPartitionId theRequestPartitionId);
boolean isResourcePartitionable(String theResourceType); 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);
} }

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -0,0 +1,35 @@
/*-
* #%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);
}
}

View File

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

View File

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

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -7,8 +7,12 @@ import ca.uhn.fhir.jpa.model.entity.BinaryStorageEntity;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test; import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails; 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.hl7.fhir.r4.model.IdType;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.mockito.ArgumentCaptor;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
@ -24,6 +28,7 @@ import java.sql.SQLException;
import java.util.Optional; import java.util.Optional;
import static org.hamcrest.CoreMatchers.containsString; import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.is; import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.matchesPattern; import static org.hamcrest.Matchers.matchesPattern;
@ -34,6 +39,7 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull; import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail; 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.mock;
import static org.mockito.Mockito.times; import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify; import static org.mockito.Mockito.verify;
@ -281,7 +287,7 @@ public class DatabaseBinaryContentStorageSvcImplTest extends BaseJpaR4Test {
} }
@Test @Test
public void testStoreBinaryContent_writesBlobAndByteArray() throws IOException { public void testStoreBinaryContent_byDefault_writesByteArrayOnly() throws IOException {
// given // given
ByteArrayInputStream inputStream = new ByteArrayInputStream(SOME_BYTES); ByteArrayInputStream inputStream = new ByteArrayInputStream(SOME_BYTES);
String contentType = "image/png"; String contentType = "image/png";
@ -296,11 +302,41 @@ public class DatabaseBinaryContentStorageSvcImplTest extends BaseJpaR4Test {
// then // then
assertThat(binaryStorageEntity.hasStorageContent(), is(true)); assertThat(binaryStorageEntity.hasStorageContent(), is(true));
assertThat(binaryStorageEntity.hasBlob(), is(true)); assertThat(binaryStorageEntity.hasBlob(), is(false));
}); });
} }
@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 @Configuration
public static class MyConfig { public static class MyConfig {

View File

@ -9,8 +9,11 @@ import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config; import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.util.SqlQuery; import ca.uhn.fhir.jpa.util.SqlQuery;
import ca.uhn.fhir.jpa.util.SqlQueryList; 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.rest.api.server.RequestDetails;
import ca.uhn.fhir.storage.test.DaoTestDataBuilder; 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.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
@ -33,6 +36,8 @@ import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.empty; import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.not; 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. * Sandbox for implementing queries.
@ -137,6 +142,28 @@ public class FhirResourceDaoR4QuerySandbox extends BaseJpaTest {
myTestDaoSearch.assertSearchFindsInOrder("reverse sort by server assigned id", "Patient?family=smith&_sort=-_pid", id3,id2,id1); 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 { public static final class TestDirtiesContextTestExecutionListener extends DirtiesContextTestExecutionListener {
@Override @Override

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@ -1,74 +1,189 @@
package ca.uhn.fhir.jpa.partition; 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.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.data.IPartitionDao;
import ca.uhn.fhir.jpa.entity.PartitionEntity; import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.model.config.PartitionSettings; 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.api.server.SystemRequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; 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.assertEquals;
import static org.mockito.Mockito.when; import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
class RequestPartitionHelperSvcTest { class RequestPartitionHelperSvcTest extends BaseJpaR4Test {
static final Integer PARTITION_ID = 2401;
static final String PARTITION_NAME = "JIMMY";
static final PartitionEntity ourPartitionEntity = new PartitionEntity().setName(PARTITION_NAME);
@Mock 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
PartitionSettings myPartitionSettings; PartitionSettings myPartitionSettings;
@Mock @Autowired
IPartitionLookupSvc myPartitionLookupSvc; RequestPartitionHelperSvc mySvc;
@Mock
FhirContext myFhirContext;
@Mock
IInterceptorBroadcaster myInterceptorBroadcaster;
@InjectMocks Patient myPatient;
RequestPartitionHelperSvc mySvc = new RequestPartitionHelperSvc();
@Test @BeforeEach
public void determineReadPartitionForSystemRequest() { public void before(){
// setup myPartitionDao.deleteAll();
SystemRequestDetails srd = new SystemRequestDetails(); myPartitionSettings.setPartitioningEnabled(true);
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionId(PARTITION_ID);
srd.setRequestPartitionId(requestPartitionId);
when(myPartitionSettings.isPartitioningEnabled()).thenReturn(true);
when(myPartitionLookupSvc.getPartitionById(PARTITION_ID)).thenReturn(ourPartitionEntity);
// execute myPatient = new Patient();
RequestPartitionId result = mySvc.determineReadPartitionForRequestForRead(srd, "Patient", new IdType("Patient/123")); myPatient.setId(new IdType("Patient", "123", "1"));
// verify
assertEquals(PARTITION_ID, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME, result.getFirstPartitionNameOrNull());
} }
@Test @Test
public void determineCreatePartitionForSystemRequest() { public void testDetermineReadPartitionForSystemRequest_withPartitionIdOnly_returnsCorrectPartition() {
// setup // setup
PartitionEntity partitionEntity = createPartition1();
SystemRequestDetails srd = new SystemRequestDetails(); SystemRequestDetails srd = new SystemRequestDetails();
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionId(PARTITION_ID); srd.setRequestPartitionId(RequestPartitionId.fromPartitionId(partitionEntity.getId()));
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 // execute
RequestPartitionId result = mySvc.determineCreatePartitionForRequest(srd, resource, "Patient"); RequestPartitionId result = mySvc.determineReadPartitionForRequestForRead(srd, myPatient.fhirType(), myPatient.getIdElement());
// verify // verify
assertEquals(PARTITION_ID, result.getFirstPartitionIdOrNull()); assertEquals(PARTITION_ID_1, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME, result.getFirstPartitionNameOrNull()); assertEquals(PARTITION_NAME_1, result.getFirstPartitionNameOrNull());
} }
@Test
public void testDetermineCreatePartitionForRequest_withPartitionIdOnly_returnsCorrectPartition() {
// setup
PartitionEntity partitionEntity = createPartition1();
SystemRequestDetails srd = new SystemRequestDetails();
srd.setRequestPartitionId(RequestPartitionId.fromPartitionId(partitionEntity.getId()));
// execute
Patient patient = new Patient();
RequestPartitionId result = mySvc.determineCreatePartitionForRequest(srd, patient, patient.fhirType());
// verify
assertEquals(PARTITION_ID_1, result.getFirstPartitionIdOrNull());
assertEquals(PARTITION_NAME_1, 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));
}
} }

View File

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

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.context.RuntimeSearchParam; import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings; 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.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig; import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
@ -12,6 +13,8 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.BundleBuilder; import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.HapiExtensions; 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.Composition;
import org.hl7.fhir.r5.model.IdType; import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Bundle; import org.hl7.fhir.r5.model.Bundle;
@ -29,6 +32,7 @@ import org.hl7.fhir.r5.model.SearchParameter;
import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.ContextConfiguration;
import jakarta.annotation.Nonnull; import jakarta.annotation.Nonnull;
@ -41,9 +45,10 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString; import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty; import static org.hamcrest.Matchers.empty;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail; import static org.junit.jupiter.api.Assertions.fail;
@ContextConfiguration(classes = TestHSearchAddInConfig.NoFT.class) @ContextConfiguration(classes = { TestHSearchAddInConfig.NoFT.class, TestDaoSearch.Config.class })
@SuppressWarnings({"Duplicates"}) @SuppressWarnings({"Duplicates"})
public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test { public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
public static final String PRACTITIONER_PR1 = "Practitioner/PR1"; public static final String PRACTITIONER_PR1 = "Practitioner/PR1";
@ -54,6 +59,8 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
public static final String ENCOUNTER_E2 = "Encounter/E2"; public static final String ENCOUNTER_E2 = "Encounter/E2";
public static final String ENCOUNTER_E3 = "Encounter/E3"; public static final String ENCOUNTER_E3 = "Encounter/E3";
public static final String ORGANIZATION_O1 = "Organization/O1"; public static final String ORGANIZATION_O1 = "Organization/O1";
@Autowired
protected TestDaoSearch myTestDaoSearch;
@Override @Override
@BeforeEach @BeforeEach
@ -867,6 +874,47 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
assertEquals(1, countMatches(querySql, "HFJ_RES_LINK"), querySql); 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 * Observation:focus is a Reference(Any) so it can't be used in a sort chain because
* this would be horribly, horribly inefficient. * this would be horribly, horribly inefficient.

View File

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

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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -0,0 +1,57 @@
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));
}
}

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@ -9,11 +9,16 @@ import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; 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.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import java.util.Optional; 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.ArgumentMatchers.any;
import static org.mockito.Mockito.eq; import static org.mockito.Mockito.eq;
import static org.mockito.Mockito.times; import static org.mockito.Mockito.times;
@ -74,4 +79,22 @@ 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));
}
} }

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

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@ -7,7 +7,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -7,7 +7,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -31,17 +31,22 @@ import ca.uhn.fhir.mdm.api.params.MdmQuerySearchParameters;
import ca.uhn.fhir.mdm.model.MdmTransactionContext; import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.model.mdmevents.MdmLinkJson; import ca.uhn.fhir.mdm.model.mdmevents.MdmLinkJson;
import ca.uhn.fhir.mdm.util.GoldenResourceHelper; 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.SystemRequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId; import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.util.TerserUtil; 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.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase; import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.data.domain.Page; import org.springframework.data.domain.Page;
import java.util.regex.Pattern;
import java.util.stream.Stream; import java.util.stream.Stream;
public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService { 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; protected final FhirContext myFhirContext;
@ -133,16 +138,30 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
String sourceId = link.getSourceId(); String sourceId = link.getSourceId();
// +1 because of "/" in id: "ResourceType/Id" // +1 because of "/" in id: "ResourceType/Id"
IResourcePersistentId<?> pid = getResourcePID(sourceId.substring(resourceType.length() + 1), resourceType); final String sourceIdUnqualified = sourceId.substring(resourceType.length() + 1);
// 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 // this might be a bit unperformant
// but it depends how many links there are // but it depends how many links there are
// per golden resource (unlikely to be thousands) // per golden resource (unlikely to be thousands)
return dao.readByPid(pid); return dao.readByPid(pid);
} else {
return dao.read(new IdDt(sourceId), new SystemRequestDetails());
}
}); });
} }
private IResourcePersistentId<?> getResourcePID(String theId, String theResourceType) { private IResourcePersistentId<?> getResourcePID(String theId, String theResourceType) {
return myIIdHelperService.newPidFromStringIdAndResourceName(theId, theResourceType); return myIIdHelperService.newPidFromStringIdAndResourceName(theId, theResourceType);
} }
private boolean isNumericOrUuid(String theLongCandidate) {
return StringUtils.isNumeric(theLongCandidate)
|| IS_UUID.matcher(theLongCandidate).matches();
}
} }

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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

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

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@ -736,6 +736,20 @@ public class RuleBuilder implements IAuthRuleBuilder {
return new RuleBuilderOperationNamedAndScoped(rule); 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 @Override
public IAuthRuleBuilderOperationNamedAndScoped onInstancesOfType( public IAuthRuleBuilderOperationNamedAndScoped onInstancesOfType(
Class<? extends IBaseResource> theType) { Class<? extends IBaseResource> theType) {
@ -869,7 +883,7 @@ public class RuleBuilder implements IAuthRuleBuilder {
} }
private class RuleBuilderBulkExport implements IAuthRuleBuilderRuleBulkExport { private class RuleBuilderBulkExport implements IAuthRuleBuilderRuleBulkExport {
private RuleBulkExportImpl ruleBulkExport; private RuleBulkExportImpl myRuleBulkExport;
@Override @Override
public IAuthRuleBuilderRuleBulkExportWithTarget groupExportOnGroup(@Nonnull String theFocusResourceId) { public IAuthRuleBuilderRuleBulkExportWithTarget groupExportOnGroup(@Nonnull String theFocusResourceId) {
@ -881,23 +895,60 @@ public class RuleBuilder implements IAuthRuleBuilder {
return new RuleBuilderBulkExportWithTarget(rule); 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 @Override
public IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull String theFocusResourceId) { public IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull String theFocusResourceId) {
if (ruleBulkExport == null) { if (myRuleBulkExport == null) {
RuleBulkExportImpl rule = new RuleBulkExportImpl(myRuleName); RuleBulkExportImpl rule = new RuleBulkExportImpl(myRuleName);
rule.setAppliesToPatientExport(theFocusResourceId); rule.setAppliesToPatientExport(theFocusResourceId);
rule.setMode(myRuleMode); rule.setMode(myRuleMode);
ruleBulkExport = rule; myRuleBulkExport = rule;
} else { } else {
ruleBulkExport.setAppliesToPatientExport(theFocusResourceId); myRuleBulkExport.setAppliesToPatientExport(theFocusResourceId);
} }
// prevent duplicate rules being added // prevent duplicate rules being added
if (!myRules.contains(ruleBulkExport)) { if (!myRules.contains(myRuleBulkExport)) {
myRules.add(ruleBulkExport); myRules.add(myRuleBulkExport);
} }
return new RuleBuilderBulkExportWithTarget(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);
} }
@Override @Override

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@ -24,12 +24,12 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum; import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.bulk.BulkExportJobParameters; 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.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collection; import java.util.Collection;
import java.util.List;
import java.util.Objects; import java.util.Objects;
import java.util.Set; import java.util.Set;
import java.util.stream.Collectors; import java.util.stream.Collectors;
@ -42,6 +42,7 @@ public class RuleBulkExportImpl extends BaseRule {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuleBulkExportImpl.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuleBulkExportImpl.class);
private String myGroupId; private String myGroupId;
private final Collection<String> myPatientIds; private final Collection<String> myPatientIds;
private boolean myAppliesToAllPatients;
private BulkExportJobParameters.ExportStyle myWantExportStyle; private BulkExportJobParameters.ExportStyle myWantExportStyle;
private Collection<String> myResourceTypes; private Collection<String> myResourceTypes;
private boolean myWantAnyStyle; private boolean myWantAnyStyle;
@ -69,115 +70,86 @@ public class RuleBulkExportImpl extends BaseRule {
return null; return null;
} }
BulkExportJobParameters options = (BulkExportJobParameters) BulkExportJobParameters inboundBulkExportRequestOptions = (BulkExportJobParameters)
theRequestDetails.getAttribute(AuthorizationInterceptor.REQUEST_ATTRIBUTE_BULK_DATA_EXPORT_OPTIONS); theRequestDetails.getAttribute(AuthorizationInterceptor.REQUEST_ATTRIBUTE_BULK_DATA_EXPORT_OPTIONS);
// if style doesn't match - abstain
if (!myWantAnyStyle && options.getExportStyle() != myWantExportStyle) { if (!myWantAnyStyle && inboundBulkExportRequestOptions.getExportStyle() != myWantExportStyle) {
return null; return null;
} }
// Do we only authorize some types? If so, make sure requested types are a subset
if (isNotEmpty(myResourceTypes)) { if (isNotEmpty(myResourceTypes)) {
if (isEmpty(options.getResourceTypes())) { if (isEmpty(inboundBulkExportRequestOptions.getResourceTypes())) {
return null; return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
} }
for (String next : options.getResourceTypes()) { if (!myResourceTypes.containsAll(inboundBulkExportRequestOptions.getResourceTypes())) {
if (!myResourceTypes.contains(next)) {
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this); 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) { if (myWantAnyStyle || myWantExportStyle == BulkExportJobParameters.ExportStyle.SYSTEM) {
return newVerdict( return allowVerdict;
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
} }
if (isNotBlank(myGroupId) && options.getGroupId() != null) { // assume myGroupId not empty->myStyle is group. If target group matches, then allow.
if (isNotBlank(myGroupId) && inboundBulkExportRequestOptions.getGroupId() != null) {
String expectedGroupId = String expectedGroupId =
new IdDt(myGroupId).toUnqualifiedVersionless().getValue(); new IdDt(myGroupId).toUnqualifiedVersionless().getValue();
String actualGroupId = String actualGroupId = new IdDt(inboundBulkExportRequestOptions.getGroupId())
new IdDt(options.getGroupId()).toUnqualifiedVersionless().getValue(); .toUnqualifiedVersionless()
.getValue();
if (Objects.equals(expectedGroupId, actualGroupId)) { if (Objects.equals(expectedGroupId, actualGroupId)) {
return newVerdict( return allowVerdict;
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
} }
} }
// 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 // 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. // 2. If any requested ID is not present in the users permissions, Deny.
if (myWantExportStyle == BulkExportJobParameters.ExportStyle.PATIENT && isNotEmpty(myPatientIds)) { if (myWantExportStyle == BulkExportJobParameters.ExportStyle.PATIENT)
List<String> permittedPatientIds = myPatientIds.stream() // Unfiltered Type Level
.map(id -> new IdDt(id).toUnqualifiedVersionless().getValue()) if (myAppliesToAllPatients) {
.collect(Collectors.toList()); return allowVerdict;
if (!options.getPatientIds().isEmpty()) { }
// Instance level, or filtered type level
if (isNotEmpty(myPatientIds)) {
// If bulk export options defines no patient IDs, return null.
if (inboundBulkExportRequestOptions.getPatientIds().isEmpty()) {
return null;
} else {
ourLog.debug("options.getPatientIds() != null"); ourLog.debug("options.getPatientIds() != null");
List<String> requestedPatientIds = options.getPatientIds().stream() Set<String> requestedPatientIds = sanitizeIds(inboundBulkExportRequestOptions.getPatientIds());
.map(t -> new IdDt(t).toUnqualifiedVersionless().getValue()) Set<String> permittedPatientIds = sanitizeIds(myPatientIds);
.collect(Collectors.toList()); if (permittedPatientIds.containsAll(requestedPatientIds)) {
boolean requestedPatientsPermitted = true; return allowVerdict;
for (String requestedPatientId : requestedPatientIds) { } else {
if (!permittedPatientIds.contains(requestedPatientId)) {
requestedPatientsPermitted = false;
break;
}
}
if (requestedPatientsPermitted) {
return newVerdict(
theOperation,
theRequestDetails,
theInputResource,
theInputResourceId,
theOutputResource,
theRuleApplier);
}
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this); 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; return null;
} }
private Set<String> sanitizeIds(Collection<String> myPatientIds) {
return myPatientIds.stream()
.map(id -> new IdDt(id).toUnqualifiedVersionless().getValue())
.collect(Collectors.toSet());
}
public void setAppliesToGroupExportOnGroup(String theGroupId) { public void setAppliesToGroupExportOnGroup(String theGroupId) {
myWantExportStyle = BulkExportJobParameters.ExportStyle.GROUP; myWantExportStyle = BulkExportJobParameters.ExportStyle.GROUP;
myGroupId = theGroupId; myGroupId = theGroupId;
@ -193,6 +165,16 @@ public class RuleBulkExportImpl extends BaseRule {
myPatientIds.add(thePatientId); 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() { public void setAppliesToSystem() {
myWantExportStyle = BulkExportJobParameters.ExportStyle.SYSTEM; myWantExportStyle = BulkExportJobParameters.ExportStyle.SYSTEM;
} }
@ -212,4 +194,14 @@ public class RuleBulkExportImpl extends BaseRule {
BulkExportJobParameters.ExportStyle getWantExportStyle() { BulkExportJobParameters.ExportStyle getWantExportStyle() {
return myWantExportStyle; return myWantExportStyle;
} }
@VisibleForTesting
Collection<String> getPatientIds() {
return myPatientIds;
}
@VisibleForTesting
Collection<String> getResourceTypes() {
return myResourceTypes;
}
} }

View File

@ -1,16 +1,23 @@
package ca.uhn.fhir.rest.server.interceptor.auth; package ca.uhn.fhir.rest.server.interceptor.auth;
import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.Test; 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.ArrayList;
import java.util.Collection;
import java.util.List; import java.util.List;
import java.util.stream.Stream;
import static org.hamcrest.Matchers.contains; import static org.hamcrest.Matchers.contains;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertInstanceOf;
import static org.mockito.Mockito.mock; import static org.mockito.Mockito.mock;
public class RuleBuilderTest { public class RuleBuilderTest {
@ -98,7 +105,72 @@ public class RuleBuilderTest {
builder.allow().bulkExport().patientExportOnPatient("Patient/pat2").withResourceTypes(resourceTypes); builder.allow().bulkExport().patientExportOnPatient("Patient/pat2").withResourceTypes(resourceTypes);
List<IAuthRule> rules = builder.build(); List<IAuthRule> rules = builder.build();
assertEquals(rules.size(),1); assertEquals(rules.size(),1);
assertTrue(rules.get(0) instanceof RuleBulkExportImpl); 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());
} }
@Test @Test

View File

@ -4,6 +4,9 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum; import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails; import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.bulk.BulkExportJobParameters; 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.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
@ -13,7 +16,6 @@ import java.util.HashSet;
import java.util.Set; import java.util.Set;
import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.mockito.ArgumentMatchers.any; import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.when; import static org.mockito.Mockito.when;
@ -28,10 +30,11 @@ public class RuleBulkExportImplTest {
@Mock @Mock
private Set<AuthorizationFlagsEnum> myFlags; private Set<AuthorizationFlagsEnum> myFlags;
@Test @Test
public void testDenyBulkRequestWithInvalidResourcesTypes() { public void testDenyBulkRequestWithInvalidResourcesTypes() {
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a"); RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
myRule.setMode(PolicyEnum.ALLOW);
Set<String> myTypes = new HashSet<>(); Set<String> myTypes = new HashSet<>();
myTypes.add("Patient"); myTypes.add("Patient");
myTypes.add("Practitioner"); myTypes.add("Practitioner");
@ -46,29 +49,206 @@ public class RuleBulkExportImplTest {
when(myRequestDetails.getAttribute(any())).thenReturn(options); when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertEquals(PolicyEnum.DENY, verdict.getDecision()); 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 @Test
public void testBulkRequestWithValidResourcesTypes() { public void testBulkExportSystem_ruleHasTypes_RequestWithTypes_allow() {
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a"); RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
myRule.setMode(PolicyEnum.ALLOW);
Set<String> myTypes = new HashSet<>(); myRule.setAppliesToSystem();
myTypes.add("Patient"); myRule.setResourceTypes(Set.of("Patient", "Practitioner"));
myTypes.add("Practitioner");
myRule.setResourceTypes(myTypes);
Set<String> myWantTypes = new HashSet<>();
myWantTypes.add("Patient");
myWantTypes.add("Practitioner");
BulkExportJobParameters options = new BulkExportJobParameters(); BulkExportJobParameters options = new BulkExportJobParameters();
options.setResourceTypes(myWantTypes); options.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
options.setResourceTypes(Set.of("Patient", "Practitioner"));
when(myRequestDetails.getAttribute(any())).thenReturn(options); when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertNull(verdict);
assertAllow(verdict);
}
@Test
public void testBulkExportSystem_ruleHasTypes_RequestWithTooManyTypes_abstain() {
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", "Encounter"));
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);
}
}
} }
@Test @Test
@ -84,7 +264,7 @@ public class RuleBulkExportImplTest {
when(myRequestDetails.getAttribute(any())).thenReturn(options); when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertEquals(null, verdict); assertAbstain(verdict);
} }
@Test @Test
@ -100,7 +280,7 @@ public class RuleBulkExportImplTest {
when(myRequestDetails.getAttribute(any())).thenReturn(options); when(myRequestDetails.getAttribute(any())).thenReturn(options);
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
assertEquals(PolicyEnum.ALLOW, verdict.getDecision()); assertAllow(verdict);
} }
@Test @Test
@ -118,7 +298,7 @@ public class RuleBulkExportImplTest {
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); 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. //Then: We permit the request, as a patient ID that was requested is honoured by this rule.
assertEquals(PolicyEnum.ALLOW, verdict.getDecision()); assertAllow(verdict);
} }
@Test @Test
@ -135,8 +315,8 @@ public class RuleBulkExportImplTest {
//When //When
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: we should deny the request, as the requested export does not contain the patient permitted. //Then: abstain
assertEquals(PolicyEnum.DENY, verdict.getDecision()); assertDeny(verdict);
} }
@Test @Test
@ -153,28 +333,45 @@ public class RuleBulkExportImplTest {
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: We make no claims about type-level export on Patient. //Then: We make no claims about type-level export on Patient.
assertEquals(null, verdict); assertAbstain(verdict);
} }
@Test @Test
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypePatient() { public void testPatientExportRulesWithId_withRequestNoIds_abstains() {
//Given //Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b"); RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123"); myRule.setAppliesToPatientExport("Patient/123");
myRule.setMode(PolicyEnum.ALLOW); myRule.setMode(PolicyEnum.ALLOW);
final BulkExportJobParameters options = new BulkExportJobParameters(); BulkExportJobParameters options = new BulkExportJobParameters();
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT); options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
options.setFilters(Set.of("Patient?_id=123"));
options.setResourceTypes(Set.of("Patient"));
when(myRequestDetails.getAttribute(any())).thenReturn(options); when(myRequestDetails.getAttribute(any())).thenReturn(options);
//When //When
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut); AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
//Then: The patient IDs match so this is permitted //Then: We make no claims about type-level export on Patient.
assertEquals(PolicyEnum.ALLOW, verdict.getDecision()); assertAbstain(verdict);
} }
@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 @Test
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypePatientAndFilterHasResources() { public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypePatientAndFilterHasResources() {
//Given //Given
@ -191,27 +388,9 @@ public class RuleBulkExportImplTest {
final 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: The patient IDs match so this is permitted //Then: The patient IDs match so this is permitted
assertEquals(PolicyEnum.ALLOW, verdict.getDecision()); assertAbstain(verdict);
} }
@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 @Test
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterNoResourceType() { public void testPatientExportRulesOnTypeLevelExportWithTypeFilterNoResourceType() {
@ -227,27 +406,8 @@ public class RuleBulkExportImplTest {
//When //When
final 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: The patient IDs match so this is permitted //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
assertEquals(PolicyEnum.ALLOW, verdict.getDecision()); assertAbstain(verdict);
}
@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 @Test
@ -265,12 +425,12 @@ public class RuleBulkExportImplTest {
//When //When
final 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 do not have permissions on the requested patient so this is not permitted. //Then: We do not have permissions on the requested patient so we abstain
assertEquals(PolicyEnum.DENY, verdict.getDecision()); assertDeny(verdict);
} }
@Test @Test
public void testPatientExportRulesOnTypeLevelExportPermittedPatient() { public void testPatientExport_ruleAllowsId_requestsId_allow() {
//Given //Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b"); final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123"); myRule.setAppliesToPatientExport("Patient/123");
@ -289,7 +449,7 @@ public class RuleBulkExportImplTest {
} }
@Test @Test
public void testPatientExportRulesOnTypeLevelExportPermittedPatients() { public void testPatientExport_ruleAllowsIds_requestsIds_allow() {
//Given //Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b"); final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123"); myRule.setAppliesToPatientExport("Patient/123");
@ -309,7 +469,7 @@ public class RuleBulkExportImplTest {
} }
@Test @Test
public void testPatientExportRulesOnTypeLevelExportWithPermittedAndUnpermittedPatients() { public void testPatientExport_ruleAllowsId_requestsTooManyIds_abstain() {
//Given //Given
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b"); final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
myRule.setAppliesToPatientExport("Patient/123"); myRule.setAppliesToPatientExport("Patient/123");
@ -324,8 +484,61 @@ public class RuleBulkExportImplTest {
final 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: There are unpermitted patients in the request so this is not permitted. //Then: There are unpermitted patients in the request so this is not permitted.
assertEquals(PolicyEnum.DENY, verdict.getDecision()); 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);
} }
@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 @Test
public void testPatientExportRulesOnTypeLevelExportWithPermittedAndUnpermittedPatientFilters() { public void testPatientExportRulesOnTypeLevelExportWithPermittedAndUnpermittedPatientFilters() {
//Given //Given
@ -341,7 +554,22 @@ public class RuleBulkExportImplTest {
//When //When
final 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: There are unpermitted patients in the request so this is not permitted. //Then: There are unpermitted patients in the request so this is not permitted. abstain.
assertEquals(PolicyEnum.DENY, verdict.getDecision()); 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");
} }
} }

View File

@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>
@ -21,7 +21,7 @@
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-api</artifactId> <artifactId>hapi-fhir-caching-api</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>

View File

@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir-serviceloaders</artifactId> <artifactId>hapi-fhir-serviceloaders</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

View File

@ -7,7 +7,7 @@
<parent> <parent>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId> <artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
</parent> </parent>

View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>7.3.1-SNAPSHOT</version> <version>7.3.2-SNAPSHOT</version>
</parent> </parent>

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