7_2 branch mergeback (#5922)
* 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 --------- 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
GitHub
parent
c87b5b1d2a
commit
125513a100
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@ -2387,13 +2387,19 @@ public enum Pointcut implements IPointcut {
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* <li>
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* ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent - Contains information about the from and to resources.
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* </li>
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* <li>
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* ca.uhn.fhir.mdm.model.mdmevents.MdmTransactionContext - Contains information about the Transaction context, e.g. merge or link.
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* </li>
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* </ul>
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* <p>
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* Hooks should return <code>void</code>.
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* </p>
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*/
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MDM_POST_MERGE_GOLDEN_RESOURCES(
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void.class, "ca.uhn.fhir.rest.api.server.RequestDetails", "ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent"),
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void.class,
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"ca.uhn.fhir.rest.api.server.RequestDetails",
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"ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent",
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"ca.uhn.fhir.mdm.model.MdmTransactionContext"),
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/**
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* <b>MDM Link History Hook:</b>
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@ -19,6 +19,7 @@
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*/
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package ca.uhn.fhir.cli;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.jpa.model.util.JpaConstants;
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import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
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@ -31,6 +32,7 @@ import ca.uhn.fhir.system.HapiSystemProperties;
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import ca.uhn.fhir.util.AttachmentUtil;
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import ca.uhn.fhir.util.FileUtil;
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import ca.uhn.fhir.util.ParametersUtil;
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import com.google.common.annotations.VisibleForTesting;
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import com.google.common.base.Charsets;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.Options;
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@ -265,7 +267,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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"Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
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}
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private void addFileToRequestBundle(IBaseParameters theInputParameters, String theFileName, byte[] theBytes) {
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protected void addFileToRequestBundle(IBaseParameters theInputParameters, String theFileName, byte[] theBytes) {
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byte[] bytes = theBytes;
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String fileName = theFileName;
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@ -277,7 +279,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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FileUtil.formatFileSize(ourTransferSizeLimit));
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try {
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File tempFile = File.createTempFile("hapi-fhir-cli", suffix);
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File tempFile = File.createTempFile("hapi-fhir-cli", "." + suffix);
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tempFile.deleteOnExit();
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try (OutputStream fileOutputStream = new FileOutputStream(tempFile, false)) {
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fileOutputStream.write(bytes);
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@ -363,4 +365,9 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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}
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return retVal;
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}
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@VisibleForTesting
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void setFhirContext(FhirContext theFhirContext) {
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myFhirCtx = theFhirContext;
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}
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}
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@ -22,6 +22,10 @@ import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyS
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import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
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import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.r4.model.Attachment;
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import org.hl7.fhir.r4.model.Parameters;
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import org.hl7.fhir.r4.model.Type;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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@ -43,6 +47,7 @@ import java.io.FileOutputStream;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Stream;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipOutputStream;
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@ -54,6 +59,8 @@ import static org.hamcrest.Matchers.greaterThan;
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import static org.hamcrest.Matchers.is;
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import static org.hamcrest.Matchers.matchesPattern;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertInstanceOf;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.ArgumentMatchers.anyList;
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@ -479,6 +486,86 @@ public class UploadTerminologyCommandTest {
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uploadICD10UsingCompressedFile(theFhirVersion, theIncludeTls);
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}
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@ParameterizedTest
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@MethodSource("paramsProvider")
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@SuppressWarnings("unused") // Both params for @BeforeEach
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void testZipFileInParameters(String theFhirVersion, boolean theIncludeTls) {
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final IBaseParameters inputParameters = switch (myCtx.getVersion().getVersion()) {
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case DSTU2, DSTU2_HL7ORG, DSTU2_1 -> new org.hl7.fhir.dstu2.model.Parameters();
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case DSTU3 -> new org.hl7.fhir.dstu3.model.Parameters();
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case R4 -> new Parameters();
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case R4B -> new org.hl7.fhir.r4b.model.Parameters();
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case R5 -> new org.hl7.fhir.r5.model.Parameters();
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};
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final UploadTerminologyCommand uploadTerminologyCommand = new UploadTerminologyCommand();
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uploadTerminologyCommand.setFhirContext(myCtx);
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uploadTerminologyCommand.setTransferSizeBytes(1);
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uploadTerminologyCommand.addFileToRequestBundle(inputParameters, "something.zip", new byte[] {1,2});
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final String actualAttachmentUrl = getAttachmentUrl(inputParameters, myCtx);
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assertTrue(actualAttachmentUrl.endsWith(".zip"));
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}
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private static String getAttachmentUrl(IBaseParameters theInputParameters, FhirContext theCtx) {
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switch (theCtx.getVersion().getVersion()) {
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case DSTU2:
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case DSTU2_HL7ORG:
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case DSTU2_1: {
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assertInstanceOf(org.hl7.fhir.dstu2.model.Parameters.class, theInputParameters);
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final org.hl7.fhir.dstu2.model.Parameters dstu2Parameters = (org.hl7.fhir.dstu2.model.Parameters) theInputParameters;
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final List<org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent> dstu2ParametersList = dstu2Parameters.getParameter();
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final Optional<org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent> optDstu2FileParam = dstu2ParametersList.stream().filter(param -> TerminologyUploaderProvider.PARAM_FILE.equals(param.getName())).findFirst();
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assertTrue(optDstu2FileParam.isPresent());
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final org.hl7.fhir.dstu2.model.Type dstu2Value = optDstu2FileParam.get().getValue();
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assertInstanceOf(org.hl7.fhir.dstu2.model.Attachment.class, dstu2Value);
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final org.hl7.fhir.dstu2.model.Attachment dstu2Attachment = (org.hl7.fhir.dstu2.model.Attachment) dstu2Value;
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return dstu2Attachment.getUrl();
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}
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case DSTU3: {
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assertInstanceOf(org.hl7.fhir.dstu3.model.Parameters.class, theInputParameters);
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final org.hl7.fhir.dstu3.model.Parameters dstu3Parameters = (org.hl7.fhir.dstu3.model.Parameters) theInputParameters;
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final List<org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent> dstu3ParametersList = dstu3Parameters.getParameter();
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final Optional<org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent> optDstu3FileParam = dstu3ParametersList.stream().filter(param -> TerminologyUploaderProvider.PARAM_FILE.equals(param.getName())).findFirst();
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assertTrue(optDstu3FileParam.isPresent());
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final org.hl7.fhir.dstu3.model.Type dstu3Value = optDstu3FileParam.get().getValue();
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assertInstanceOf(org.hl7.fhir.dstu3.model.Attachment.class, dstu3Value);
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final org.hl7.fhir.dstu3.model.Attachment dstu3Attachment = (org.hl7.fhir.dstu3.model.Attachment) dstu3Value;
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return dstu3Attachment.getUrl();
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}
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case R4: {
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assertInstanceOf(Parameters.class, theInputParameters);
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final Parameters r4Parameters = (Parameters) theInputParameters;
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final Parameters.ParametersParameterComponent r4Parameter = r4Parameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
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final Type r4Value = r4Parameter.getValue();
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assertInstanceOf(Attachment.class, r4Value);
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final Attachment r4Attachment = (Attachment) r4Value;
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return r4Attachment.getUrl();
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}
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case R4B: {
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assertInstanceOf(org.hl7.fhir.r4b.model.Parameters.class, theInputParameters);
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final org.hl7.fhir.r4b.model.Parameters r4bParameters = (org.hl7.fhir.r4b.model.Parameters) theInputParameters;
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final org.hl7.fhir.r4b.model.Parameters.ParametersParameterComponent r4bParameter = r4bParameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
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final org.hl7.fhir.r4b.model.DataType value = r4bParameter.getValue();
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assertInstanceOf(org.hl7.fhir.r4b.model.Attachment.class, value);
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final org.hl7.fhir.r4b.model.Attachment r4bAttachment = (org.hl7.fhir.r4b.model.Attachment) value;
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return r4bAttachment.getUrl();
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}
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case R5: {
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assertInstanceOf(org.hl7.fhir.r5.model.Parameters.class, theInputParameters);
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final org.hl7.fhir.r5.model.Parameters r4Parameters = (org.hl7.fhir.r5.model.Parameters) theInputParameters;
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final org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent parameter = r4Parameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
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final org.hl7.fhir.r5.model.DataType value = parameter.getValue();
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assertInstanceOf(org.hl7.fhir.r5.model.Attachment.class, value);
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final org.hl7.fhir.r5.model.Attachment attachment = (org.hl7.fhir.r5.model.Attachment) value;
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return attachment.getUrl();
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}
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default:
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throw new IllegalStateException("Unknown FHIR version: " + theCtx.getVersion().getVersion());
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}
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}
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private void uploadICD10UsingCompressedFile(String theFhirVersion, boolean theIncludeTls) throws IOException {
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if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
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when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
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@ -0,0 +1,4 @@
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---
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type: add
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issue: 5861
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title: "Enhance RuleBuilder code to support multiple instance IDs."
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 5865
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title: "Moving the Hibernate.Search annotation for text indexing from the lob column to the column added as part of the
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PostgreSql LOB migration."
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 5877
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title: "Previously, updating a tokenParam with a value greater than 200 characters would raise a SQLException.
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This issue has been fixed."
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@ -0,0 +1,6 @@
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---
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type: fix
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issue: 5886
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title: "Previously, either updating links on, or deleting one of two patients with non-numeric IDs linked to a golden
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patient would result in a HAPI-0389 if there were survivorship rules.
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This issue has been fixed for both the update links and delete cases."
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@ -0,0 +1,7 @@
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---
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type: fix
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issue: 5888
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title: "Updated documentation on binary_security_interceptor to specify using
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`STORAGE_PRE_INITIATE_BULK_EXPORT` not `STORAGE_INITIATE_BULK_EXPORT` pointcut
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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."
|
||||
|
|
@ -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."
|
||||
|
||||
|
|
@ -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."
|
||||
|
|
@ -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."
|
||||
|
|
@ -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."
|
||||
|
|
@ -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."
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
---
|
||||
type: fix
|
||||
issue: 5917
|
||||
title: "Fix chained sorts on strings when using MS Sql"
|
||||
|
|
@ -14,4 +14,9 @@ This interceptor is intended to be subclassed. A simple example is shown below:
|
|||
|
||||
## Combining with Bulk Export
|
||||
|
||||
The `setBinarySecurityContextIdentifierSystem(..)` and `setBinarySecurityContextIdentifierValue(..)` properties on the `BulkExportJobParameters` object can be used to automatically populate the security context on Binary resources created by Bulk Export jobs with values that can be verified by this interceptor. An interceptor on the `STORAGE_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.
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.IBinaryStorageEntityDao;
|
|||
import ca.uhn.fhir.jpa.model.entity.BinaryStorageEntity;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import com.google.common.hash.HashingInputStream;
|
||||
import com.google.common.io.ByteStreams;
|
||||
import jakarta.annotation.Nonnull;
|
||||
|
|
@ -59,6 +60,8 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
|
|||
@Autowired
|
||||
private IBinaryStorageEntityDao myBinaryStorageEntityDao;
|
||||
|
||||
private boolean mySupportLegacyLobServer = false;
|
||||
|
||||
@Nonnull
|
||||
@Override
|
||||
@Transactional(propagation = Propagation.REQUIRED)
|
||||
|
|
@ -96,9 +99,10 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
|
|||
entity.setContentId(id);
|
||||
entity.setStorageContentBin(loadedStream);
|
||||
|
||||
// TODO: remove writing Blob in a future release
|
||||
Blob dataBlob = lobHelper.createBlob(loadedStream);
|
||||
entity.setBlob(dataBlob);
|
||||
if (mySupportLegacyLobServer) {
|
||||
Blob dataBlob = lobHelper.createBlob(loadedStream);
|
||||
entity.setBlob(dataBlob);
|
||||
}
|
||||
|
||||
// Update the entity with the final byte count and hash
|
||||
long bytes = countingInputStream.getByteCount();
|
||||
|
|
@ -169,6 +173,11 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
|
|||
return copyBinaryContentToByteArray(entityOpt);
|
||||
}
|
||||
|
||||
public DatabaseBinaryContentStorageSvcImpl setSupportLegacyLobServer(boolean theSupportLegacyLobServer) {
|
||||
mySupportLegacyLobServer = theSupportLegacyLobServer;
|
||||
return this;
|
||||
}
|
||||
|
||||
void copyBinaryContentToOutputStream(OutputStream theOutputStream, BinaryStorageEntity theEntity)
|
||||
throws IOException {
|
||||
|
||||
|
|
@ -212,4 +221,10 @@ public class DatabaseBinaryContentStorageSvcImpl extends BaseBinaryStorageSvcImp
|
|||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
public DatabaseBinaryContentStorageSvcImpl setEntityManagerForTesting(EntityManager theEntityManager) {
|
||||
myEntityManager = theEntityManager;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -73,6 +73,7 @@ import ca.uhn.fhir.jpa.delete.DeleteConflictFinderService;
|
|||
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
|
||||
import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
|
||||
import ca.uhn.fhir.jpa.entity.Search;
|
||||
import ca.uhn.fhir.jpa.entity.TermValueSet;
|
||||
import ca.uhn.fhir.jpa.esr.ExternallyStoredResourceServiceRegistry;
|
||||
import ca.uhn.fhir.jpa.graphql.DaoRegistryGraphQLStorageServices;
|
||||
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
|
||||
|
|
@ -154,6 +155,8 @@ import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
|
|||
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.TermReadSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.ValueSetConceptAccumulator;
|
||||
import ca.uhn.fhir.jpa.term.ValueSetConceptAccumulatorFactory;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
|
|
@ -822,6 +825,17 @@ public class JpaConfig {
|
|||
return new TermReadSvcImpl();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public ValueSetConceptAccumulatorFactory valueSetConceptAccumulatorFactory() {
|
||||
return new ValueSetConceptAccumulatorFactory();
|
||||
}
|
||||
|
||||
@Bean
|
||||
@Scope("prototype")
|
||||
public ValueSetConceptAccumulator valueSetConceptAccumulator(TermValueSet theTermValueSet) {
|
||||
return valueSetConceptAccumulatorFactory().create(theTermValueSet);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
|
||||
return new TermCodeSystemStorageSvcImpl();
|
||||
|
|
|
|||
|
|
@ -1410,19 +1410,20 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
|
|||
}
|
||||
|
||||
@Override
|
||||
@Transactional
|
||||
public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequest) {
|
||||
Set<TagDefinition> tagDefs = new HashSet<>();
|
||||
BaseHasResource entity = readEntity(theId, theRequest);
|
||||
for (BaseTag next : entity.getTags()) {
|
||||
tagDefs.add(next.getTag());
|
||||
}
|
||||
MT retVal = toMetaDt(theType, tagDefs);
|
||||
return myTransactionService.withRequest(theRequest).execute(() -> {
|
||||
Set<TagDefinition> tagDefs = new HashSet<>();
|
||||
BaseHasResource entity = readEntity(theId, theRequest);
|
||||
for (BaseTag next : entity.getTags()) {
|
||||
tagDefs.add(next.getTag());
|
||||
}
|
||||
MT retVal = toMetaDt(theType, tagDefs);
|
||||
|
||||
retVal.setLastUpdated(entity.getUpdatedDate());
|
||||
retVal.setVersionId(Long.toString(entity.getVersion()));
|
||||
retVal.setLastUpdated(entity.getUpdatedDate());
|
||||
retVal.setVersionId(Long.toString(entity.getVersion()));
|
||||
|
||||
return retVal;
|
||||
return retVal;
|
||||
});
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
|
|||
|
|
@ -24,6 +24,7 @@ import ca.uhn.fhir.i18n.Msg;
|
|||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
|
||||
import ca.uhn.fhir.jpa.search.DeferConceptIndexingRoutingBinder;
|
||||
import ca.uhn.fhir.util.ValidateUtil;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import jakarta.annotation.Nonnull;
|
||||
import jakarta.persistence.Column;
|
||||
import jakarta.persistence.Entity;
|
||||
|
|
@ -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.GenericField;
|
||||
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
|
||||
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
|
||||
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.ObjectPath;
|
||||
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyBinding;
|
||||
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.PropertyValue;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
|
@ -177,6 +175,11 @@ public class TermConcept implements Serializable {
|
|||
@Column(name = "PARENT_PIDS", nullable = true)
|
||||
private String myParentPids;
|
||||
|
||||
@FullTextField(
|
||||
name = "myParentPids",
|
||||
searchable = Searchable.YES,
|
||||
projectable = Projectable.YES,
|
||||
analyzer = "conceptParentPidsAnalyzer")
|
||||
@Column(name = "PARENT_PIDS_VC", nullable = true, length = Length.LONG32)
|
||||
private String myParentPidsVc;
|
||||
|
||||
|
|
@ -189,6 +192,9 @@ public class TermConcept implements Serializable {
|
|||
@Column(name = "CODE_SEQUENCE", nullable = true)
|
||||
private Integer mySequence;
|
||||
|
||||
@Transient
|
||||
private boolean mySupportLegacyLob = false;
|
||||
|
||||
public TermConcept() {
|
||||
super();
|
||||
}
|
||||
|
|
@ -362,13 +368,6 @@ public class TermConcept implements Serializable {
|
|||
return this;
|
||||
}
|
||||
|
||||
@Transient
|
||||
@FullTextField(
|
||||
name = "myParentPids",
|
||||
searchable = Searchable.YES,
|
||||
projectable = Projectable.YES,
|
||||
analyzer = "conceptParentPidsAnalyzer")
|
||||
@IndexingDependency(derivedFrom = @ObjectPath({@PropertyValue(propertyName = "myParentPidsVc")}))
|
||||
public String getParentPidsAsString() {
|
||||
return nonNull(myParentPidsVc) ? myParentPidsVc : myParentPids;
|
||||
}
|
||||
|
|
@ -458,6 +457,10 @@ public class TermConcept implements Serializable {
|
|||
|
||||
ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
|
||||
}
|
||||
|
||||
if (!mySupportLegacyLob) {
|
||||
clearParentPidsLob();
|
||||
}
|
||||
}
|
||||
|
||||
private void setParentPids(Set<Long> theParentPids) {
|
||||
|
|
@ -519,4 +522,17 @@ public class TermConcept implements Serializable {
|
|||
public List<TermConcept> getChildCodes() {
|
||||
return getChildren().stream().map(TermConceptParentChildLink::getChild).collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public void flagForLegacyLobSupport(boolean theSupportLegacyLob) {
|
||||
mySupportLegacyLob = theSupportLegacyLob;
|
||||
}
|
||||
|
||||
private void clearParentPidsLob() {
|
||||
myParentPids = null;
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
public boolean hasParentPidsLobForTesting() {
|
||||
return nonNull(myParentPids);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -54,6 +54,7 @@ import org.hibernate.validator.constraints.NotBlank;
|
|||
import java.io.Serializable;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
||||
import static java.util.Objects.nonNull;
|
||||
import static org.apache.commons.lang3.StringUtils.left;
|
||||
import static org.apache.commons.lang3.StringUtils.length;
|
||||
|
||||
|
|
@ -307,9 +308,15 @@ public class TermConceptProperty implements Serializable {
|
|||
return myId;
|
||||
}
|
||||
|
||||
public void performLegacyLobSupport(boolean theSupportLegacyLob) {
|
||||
if (!theSupportLegacyLob) {
|
||||
myValueLob = null;
|
||||
}
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
public byte[] getValueBlobForTesting() {
|
||||
return myValueLob;
|
||||
public boolean hasValueBlobForTesting() {
|
||||
return nonNull(myValueLob);
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
|
|
@ -318,8 +325,8 @@ public class TermConceptProperty implements Serializable {
|
|||
}
|
||||
|
||||
@VisibleForTesting
|
||||
public byte[] getValueBinForTesting() {
|
||||
return myValueBin;
|
||||
public boolean hasValueBinForTesting() {
|
||||
return nonNull(myValueBin);
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
|
|
|
|||
|
|
@ -20,6 +20,7 @@
|
|||
package ca.uhn.fhir.jpa.entity;
|
||||
|
||||
import ca.uhn.fhir.util.ValidateUtil;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import jakarta.annotation.Nonnull;
|
||||
import jakarta.persistence.Column;
|
||||
import jakarta.persistence.Entity;
|
||||
|
|
@ -46,6 +47,7 @@ import java.io.Serializable;
|
|||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import static java.util.Objects.nonNull;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotEmpty;
|
||||
import static org.apache.commons.lang3.StringUtils.left;
|
||||
import static org.apache.commons.lang3.StringUtils.length;
|
||||
|
|
@ -296,4 +298,13 @@ public class TermValueSetConcept implements Serializable {
|
|||
? mySourceConceptDirectParentPidsVc
|
||||
: mySourceConceptDirectParentPids;
|
||||
}
|
||||
|
||||
public void clearSourceConceptDirectParentPidsLob() {
|
||||
mySourceConceptDirectParentPids = null;
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
public boolean hasSourceConceptDirectParentPidsLob() {
|
||||
return nonNull(mySourceConceptDirectParentPids);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -43,20 +43,21 @@ import java.sql.SQLException;
|
|||
* because hibernate won't allow the view the function without it, but
|
||||
*/
|
||||
"SELECT CONCAT_WS(' ', vsc.PID, vscd.PID) AS PID, " + " vsc.PID AS CONCEPT_PID, "
|
||||
+ " vsc.VALUESET_PID AS CONCEPT_VALUESET_PID, "
|
||||
+ " vsc.VALUESET_ORDER AS CONCEPT_VALUESET_ORDER, "
|
||||
+ " vsc.SYSTEM_URL AS CONCEPT_SYSTEM_URL, "
|
||||
+ " vsc.CODEVAL AS CONCEPT_CODEVAL, "
|
||||
+ " vsc.DISPLAY AS CONCEPT_DISPLAY, "
|
||||
+ " vsc.SYSTEM_VER AS SYSTEM_VER, "
|
||||
+ " vsc.SOURCE_PID AS SOURCE_PID, "
|
||||
+ " vsc.SOURCE_DIRECT_PARENT_PIDS AS SOURCE_DIRECT_PARENT_PIDS, "
|
||||
+ " vscd.PID AS DESIGNATION_PID, "
|
||||
+ " vscd.LANG AS DESIGNATION_LANG, "
|
||||
+ " vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, "
|
||||
+ " vscd.USE_CODE AS DESIGNATION_USE_CODE, "
|
||||
+ " vscd.USE_DISPLAY AS DESIGNATION_USE_DISPLAY, "
|
||||
+ " vscd.VAL AS DESIGNATION_VAL "
|
||||
+ " vsc.VALUESET_PID AS CONCEPT_VALUESET_PID, "
|
||||
+ " vsc.VALUESET_ORDER AS CONCEPT_VALUESET_ORDER, "
|
||||
+ " vsc.SYSTEM_URL AS CONCEPT_SYSTEM_URL, "
|
||||
+ " vsc.CODEVAL AS CONCEPT_CODEVAL, "
|
||||
+ " vsc.DISPLAY AS CONCEPT_DISPLAY, "
|
||||
+ " vsc.SYSTEM_VER AS SYSTEM_VER, "
|
||||
+ " vsc.SOURCE_PID AS SOURCE_PID, "
|
||||
+ " vsc.SOURCE_DIRECT_PARENT_PIDS AS SOURCE_DIRECT_PARENT_PIDS, "
|
||||
+ " vsc.SOURCE_DIRECT_PARENT_PIDS_VC AS SOURCE_DIRECT_PARENT_PIDS_VC, "
|
||||
+ " vscd.PID AS DESIGNATION_PID, "
|
||||
+ " vscd.LANG AS DESIGNATION_LANG, "
|
||||
+ " vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, "
|
||||
+ " vscd.USE_CODE AS DESIGNATION_USE_CODE, "
|
||||
+ " vscd.USE_DISPLAY AS DESIGNATION_USE_DISPLAY, "
|
||||
+ " vscd.VAL AS DESIGNATION_VAL "
|
||||
+ "FROM TRM_VALUESET_CONCEPT vsc "
|
||||
+ "LEFT OUTER JOIN TRM_VALUESET_C_DESIGNATION vscd ON vsc.PID = vscd.VALUESET_CONCEPT_PID")
|
||||
public class TermValueSetConceptView implements Serializable, ITermValueSetConceptView {
|
||||
|
|
@ -112,6 +113,9 @@ public class TermValueSetConceptView implements Serializable, ITermValueSetConce
|
|||
@Column(name = "SOURCE_DIRECT_PARENT_PIDS", nullable = true)
|
||||
private Clob mySourceConceptDirectParentPids;
|
||||
|
||||
@Column(name = "SOURCE_DIRECT_PARENT_PIDS_VC", nullable = true)
|
||||
private String mySourceConceptDirectParentPidsVc;
|
||||
|
||||
@Override
|
||||
public Long getSourceConceptPid() {
|
||||
return mySourceConceptPid;
|
||||
|
|
@ -119,14 +123,19 @@ public class TermValueSetConceptView implements Serializable, ITermValueSetConce
|
|||
|
||||
@Override
|
||||
public String getSourceConceptDirectParentPids() {
|
||||
String retVal = null;
|
||||
|
||||
if (mySourceConceptDirectParentPids != null) {
|
||||
try (Reader characterStream = mySourceConceptDirectParentPids.getCharacterStream()) {
|
||||
return IOUtils.toString(characterStream);
|
||||
retVal = IOUtils.toString(characterStream);
|
||||
} catch (IOException | SQLException e) {
|
||||
throw new InternalErrorException(Msg.code(828) + e);
|
||||
}
|
||||
} else if (mySourceConceptDirectParentPidsVc != null) {
|
||||
retVal = mySourceConceptDirectParentPidsVc;
|
||||
}
|
||||
return null;
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.entity.BulkImportJobEntity;
|
|||
import ca.uhn.fhir.jpa.entity.Search;
|
||||
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.CalculateHashesTask;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.CalculateOrdinalDatesTask;
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.ColumnTypeEnum;
|
||||
|
|
@ -146,8 +147,16 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
|
|||
|
||||
binaryStorageBlobTable
|
||||
.renameColumn("20240404.1", "BLOB_ID", "CONTENT_ID")
|
||||
.getLastAddedTask()
|
||||
.ifPresent(BaseTask::doNothing);
|
||||
binaryStorageBlobTable
|
||||
.renameColumn("20240404.2", "BLOB_SIZE", "CONTENT_SIZE")
|
||||
.renameColumn("20240404.3", "BLOB_HASH", "CONTENT_HASH");
|
||||
.getLastAddedTask()
|
||||
.ifPresent(BaseTask::doNothing);
|
||||
binaryStorageBlobTable
|
||||
.renameColumn("20240404.3", "BLOB_HASH", "CONTENT_HASH")
|
||||
.getLastAddedTask()
|
||||
.ifPresent(BaseTask::doNothing);
|
||||
|
||||
binaryStorageBlobTable
|
||||
.modifyColumn("20240404.4", "BLOB_DATA")
|
||||
|
|
@ -159,9 +168,23 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
|
|||
.nullable()
|
||||
.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()
|
||||
.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()
|
||||
.type(ColumnTypeEnum.TEXT);
|
||||
|
||||
termValueSetConceptTable.migrateClobToText(
|
||||
"20240409.4", "SOURCE_DIRECT_PARENT_PIDS", "SOURCE_DIRECT_PARENT_PIDS_VC");
|
||||
termValueSetConceptTable
|
||||
.migrateClobToText("20240409.4", "SOURCE_DIRECT_PARENT_PIDS", "SOURCE_DIRECT_PARENT_PIDS_VC")
|
||||
.doNothing();
|
||||
}
|
||||
|
||||
{
|
||||
|
|
@ -193,7 +219,9 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
|
|||
.nullable()
|
||||
.type(ColumnTypeEnum.TEXT);
|
||||
|
||||
termConceptTable.migrateClobToText("20240410.2", "PARENT_PIDS", "PARENT_PIDS_VC");
|
||||
termConceptTable
|
||||
.migrateClobToText("20240410.2", "PARENT_PIDS", "PARENT_PIDS_VC")
|
||||
.doNothing();
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
|
|||
IPartitionLookupSvc myPartitionConfigSvc;
|
||||
|
||||
@Override
|
||||
protected RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
|
||||
public RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
|
||||
List<String> names = null;
|
||||
for (int i = 0; i < theRequestPartitionId.getPartitionIds().size(); i++) {
|
||||
|
||||
|
|
@ -59,7 +59,7 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
|
|||
}
|
||||
}
|
||||
|
||||
if (theRequestPartitionId.getPartitionNames() != null) {
|
||||
if (theRequestPartitionId.hasPartitionNames()) {
|
||||
if (partition == null) {
|
||||
Validate.isTrue(
|
||||
theRequestPartitionId.getPartitionIds().get(i) == null,
|
||||
|
|
@ -68,8 +68,8 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
|
|||
} else {
|
||||
Validate.isTrue(
|
||||
Objects.equals(
|
||||
theRequestPartitionId.getPartitionIds().get(i), partition.getId()),
|
||||
"Partition name %s does not match ID %n",
|
||||
theRequestPartitionId.getPartitionNames().get(i), partition.getName()),
|
||||
"Partition name %s does not match ID %s",
|
||||
theRequestPartitionId.getPartitionNames().get(i),
|
||||
theRequestPartitionId.getPartitionIds().get(i));
|
||||
}
|
||||
|
|
@ -94,7 +94,7 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
|
|||
}
|
||||
|
||||
@Override
|
||||
protected RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
|
||||
public RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
|
||||
List<Integer> ids = null;
|
||||
for (int i = 0; i < theRequestPartitionId.getPartitionNames().size(); i++) {
|
||||
|
||||
|
|
@ -122,9 +122,9 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
|
|||
Validate.isTrue(
|
||||
Objects.equals(
|
||||
theRequestPartitionId.getPartitionIds().get(i), partition.getId()),
|
||||
"Partition name %s does not match ID %n",
|
||||
theRequestPartitionId.getPartitionNames().get(i),
|
||||
theRequestPartitionId.getPartitionIds().get(i));
|
||||
"Partition ID %s does not match name %s",
|
||||
theRequestPartitionId.getPartitionIds().get(i),
|
||||
theRequestPartitionId.getPartitionNames().get(i));
|
||||
}
|
||||
} else {
|
||||
if (ids == null) {
|
||||
|
|
|
|||
|
|
@ -353,26 +353,39 @@ public class QueryStack {
|
|||
throw new InvalidRequestException(Msg.code(2289) + msg);
|
||||
}
|
||||
|
||||
BaseSearchParamPredicateBuilder chainedPredicateBuilder;
|
||||
DbColumn[] sortColumn;
|
||||
// add a left-outer join to a predicate for the target type, then sort on value columns(s).
|
||||
switch (targetSearchParameter.getParamType()) {
|
||||
case STRING:
|
||||
StringPredicateBuilder stringPredicateBuilder = mySqlBuilder.createStringPredicateBuilder();
|
||||
sortColumn = new DbColumn[] {stringPredicateBuilder.getColumnValueNormalized()};
|
||||
chainedPredicateBuilder = stringPredicateBuilder;
|
||||
break;
|
||||
addSortCustomJoin(
|
||||
resourceLinkPredicateBuilder.getColumnTargetResourceId(),
|
||||
stringPredicateBuilder,
|
||||
stringPredicateBuilder.createHashIdentityPredicate(targetType, theChain));
|
||||
|
||||
mySqlBuilder.addSortString(
|
||||
stringPredicateBuilder.getColumnValueNormalized(), theAscending, myUseAggregate);
|
||||
return;
|
||||
|
||||
case TOKEN:
|
||||
TokenPredicateBuilder tokenPredicateBuilder = mySqlBuilder.createTokenPredicateBuilder();
|
||||
sortColumn =
|
||||
new DbColumn[] {tokenPredicateBuilder.getColumnSystem(), tokenPredicateBuilder.getColumnValue()
|
||||
};
|
||||
chainedPredicateBuilder = tokenPredicateBuilder;
|
||||
break;
|
||||
addSortCustomJoin(
|
||||
resourceLinkPredicateBuilder.getColumnTargetResourceId(),
|
||||
tokenPredicateBuilder,
|
||||
tokenPredicateBuilder.createHashIdentityPredicate(targetType, theChain));
|
||||
|
||||
mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnSystem(), theAscending, myUseAggregate);
|
||||
mySqlBuilder.addSortString(tokenPredicateBuilder.getColumnValue(), theAscending, myUseAggregate);
|
||||
return;
|
||||
|
||||
case DATE:
|
||||
DatePredicateBuilder datePredicateBuilder = mySqlBuilder.createDatePredicateBuilder();
|
||||
sortColumn = new DbColumn[] {datePredicateBuilder.getColumnValueLow()};
|
||||
chainedPredicateBuilder = datePredicateBuilder;
|
||||
break;
|
||||
addSortCustomJoin(
|
||||
resourceLinkPredicateBuilder.getColumnTargetResourceId(),
|
||||
datePredicateBuilder,
|
||||
datePredicateBuilder.createHashIdentityPredicate(targetType, theChain));
|
||||
|
||||
mySqlBuilder.addSortDate(datePredicateBuilder.getColumnValueLow(), theAscending, myUseAggregate);
|
||||
return;
|
||||
|
||||
/*
|
||||
* 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: "
|
||||
+ 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) {
|
||||
|
|
|
|||
|
|
@ -73,7 +73,6 @@ import java.util.ArrayList;
|
|||
import java.util.Arrays;
|
||||
import java.util.Collection;
|
||||
import java.util.Collections;
|
||||
import java.util.Date;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.IdentityHashMap;
|
||||
|
|
@ -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
|
||||
private TermCodeSystem getOrCreateDistinctTermCodeSystem(
|
||||
IResourcePersistentId theCodeSystemResourcePid,
|
||||
|
|
|
|||
|
|
@ -46,6 +46,8 @@ public class TermConceptDaoSvc {
|
|||
@Autowired
|
||||
protected ITermConceptDesignationDao myConceptDesignationDao;
|
||||
|
||||
private boolean mySupportLegacyLob = false;
|
||||
|
||||
public int saveConcept(TermConcept theConcept) {
|
||||
int retVal = 0;
|
||||
|
||||
|
|
@ -70,9 +72,11 @@ public class TermConceptDaoSvc {
|
|||
retVal++;
|
||||
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
|
||||
theConcept.setUpdated(new Date());
|
||||
theConcept.flagForLegacyLobSupport(mySupportLegacyLob);
|
||||
myConceptDao.save(theConcept);
|
||||
|
||||
for (TermConceptProperty next : theConcept.getProperties()) {
|
||||
next.performLegacyLobSupport(mySupportLegacyLob);
|
||||
myConceptPropertyDao.save(next);
|
||||
}
|
||||
|
||||
|
|
@ -85,6 +89,11 @@ public class TermConceptDaoSvc {
|
|||
return retVal;
|
||||
}
|
||||
|
||||
public TermConceptDaoSvc setSupportLegacyLob(boolean theSupportLegacyLob) {
|
||||
mySupportLegacyLob = theSupportLegacyLob;
|
||||
return this;
|
||||
}
|
||||
|
||||
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
|
||||
ourLog.trace("Checking {} parents", theParents.size());
|
||||
int retVal = 0;
|
||||
|
|
@ -95,6 +104,7 @@ public class TermConceptDaoSvc {
|
|||
retVal += ensureParentsSaved(nextParent.getParents());
|
||||
if (nextParent.getId() == null) {
|
||||
nextParent.setUpdated(new Date());
|
||||
nextParent.flagForLegacyLobSupport(mySupportLegacyLob);
|
||||
myConceptDao.saveAndFlush(nextParent);
|
||||
retVal++;
|
||||
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
|
||||
|
|
|
|||
|
|
@ -293,6 +293,9 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
|
|||
@Autowired
|
||||
private InMemoryTerminologyServerValidationSupport myInMemoryTerminologyServerValidationSupport;
|
||||
|
||||
@Autowired
|
||||
private ValueSetConceptAccumulatorFactory myValueSetConceptAccumulatorFactory;
|
||||
|
||||
@Override
|
||||
public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
|
||||
TermCodeSystemVersionDetails cs = getCurrentCodeSystemVersion(theSystem);
|
||||
|
|
@ -2393,11 +2396,11 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
|
|||
});
|
||||
assert valueSet != null;
|
||||
|
||||
ValueSetConceptAccumulator accumulator = new ValueSetConceptAccumulator(
|
||||
valueSetToExpand, myTermValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao);
|
||||
ValueSetConceptAccumulator valueSetConceptAccumulator =
|
||||
myValueSetConceptAccumulatorFactory.create(valueSetToExpand);
|
||||
ValueSetExpansionOptions options = new ValueSetExpansionOptions();
|
||||
options.setIncludeHierarchy(true);
|
||||
expandValueSet(options, valueSet, accumulator);
|
||||
expandValueSet(options, valueSet, valueSetConceptAccumulator);
|
||||
|
||||
// We are done with this ValueSet.
|
||||
txTemplate.executeWithoutResult(t -> {
|
||||
|
|
@ -2412,7 +2415,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
|
|||
"Pre-expanded ValueSet[{}] with URL[{}] - Saved {} concepts in {}",
|
||||
valueSet.getId(),
|
||||
valueSet.getUrl(),
|
||||
accumulator.getConceptsSaved(),
|
||||
valueSetConceptAccumulator.getConceptsSaved(),
|
||||
sw);
|
||||
|
||||
} catch (Exception e) {
|
||||
|
|
|
|||
|
|
@ -48,6 +48,8 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
private int myDesignationsSaved;
|
||||
private int myConceptsExcluded;
|
||||
|
||||
private boolean mySupportLegacyLob = false;
|
||||
|
||||
public ValueSetConceptAccumulator(
|
||||
@Nonnull TermValueSet theTermValueSet,
|
||||
@Nonnull ITermValueSetDao theValueSetDao,
|
||||
|
|
@ -184,6 +186,10 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
concept.setSourceConceptPid(theSourceConceptPid);
|
||||
concept.setSourceConceptDirectParentPids(theSourceConceptDirectParentPids);
|
||||
|
||||
if (!mySupportLegacyLob) {
|
||||
concept.clearSourceConceptDirectParentPidsLob();
|
||||
}
|
||||
|
||||
myValueSetConceptDao.save(concept);
|
||||
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 2019-07-30 - Expansions don't include the properties themselves; they may be needed to facilitate
|
||||
// filters and parameterized expansions.
|
||||
|
||||
public ValueSetConceptAccumulator setSupportLegacyLob(boolean theSupportLegacyLob) {
|
||||
mySupportLegacyLob = theSupportLegacyLob;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
|
@ -19,6 +19,7 @@
|
|||
*/
|
||||
package ca.uhn.fhir.jpa.term.config;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
|
||||
import ca.uhn.fhir.jpa.term.TermConceptDaoSvc;
|
||||
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemDeleteJobSvc;
|
||||
|
|
@ -41,7 +42,7 @@ public class TermCodeSystemConfig {
|
|||
}
|
||||
|
||||
@Bean
|
||||
public TermConceptDaoSvc termConceptDaoSvc() {
|
||||
return new TermConceptDaoSvc();
|
||||
public TermConceptDaoSvc termConceptDaoSvc(JpaStorageSettings theJpaStorageSettings) {
|
||||
return new TermConceptDaoSvc().setSupportLegacyLob(theJpaStorageSettings.isWriteToLegacyLobColumns());
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,8 +2,11 @@ package ca.uhn.fhir.jpa.entity;
|
|||
|
||||
import com.google.common.base.Strings;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.ValueSource;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.equalTo;
|
||||
import static org.hamcrest.Matchers.is;
|
||||
import static org.hamcrest.Matchers.notNullValue;
|
||||
import static org.hamcrest.Matchers.startsWith;
|
||||
|
|
@ -21,8 +24,8 @@ public class TermConceptPropertyTest {
|
|||
termConceptProperty.setValue(ourVeryLongString);
|
||||
|
||||
// then
|
||||
assertThat(termConceptProperty.getValueBlobForTesting(), notNullValue());
|
||||
assertThat(termConceptProperty.getValueBinForTesting(), notNullValue());
|
||||
assertThat(termConceptProperty.hasValueBlobForTesting(), equalTo(true));
|
||||
assertThat(termConceptProperty.hasValueBinForTesting(), equalTo(true));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -78,4 +81,19 @@ public class TermConceptPropertyTest {
|
|||
assertThat(value, startsWith("a"));
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(booleans = {false, true})
|
||||
public void testSetValue_withSupportLegacyLob(boolean theSupportLegacyLob){
|
||||
// given
|
||||
TermConceptProperty termConceptProperty = new TermConceptProperty();
|
||||
|
||||
// when
|
||||
termConceptProperty.setValue(ourVeryLongString);
|
||||
termConceptProperty.performLegacyLobSupport(theSupportLegacyLob);
|
||||
|
||||
// then
|
||||
assertThat(termConceptProperty.hasValueBinForTesting(), equalTo(true));
|
||||
assertThat(termConceptProperty.hasValueBlobForTesting(), equalTo(theSupportLegacyLob));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -166,6 +166,7 @@ public class GoldenResourceMergerSvcImpl implements IGoldenResourceMergerSvc {
|
|||
HookParams params = new HookParams();
|
||||
params.add(MdmMergeEvent.class, event);
|
||||
params.add(RequestDetails.class, theParams.getRequestDetails());
|
||||
params.add(MdmTransactionContext.class, theParams.getMdmTransactionContext());
|
||||
myInterceptorBroadcaster.callHooks(Pointcut.MDM_POST_MERGE_GOLDEN_RESOURCES, params);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,11 +2,16 @@ package ca.uhn.fhir.jpa.mdm.svc;
|
|||
|
||||
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
|
||||
import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
|
||||
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
|
||||
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
|
||||
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNull;
|
||||
|
|
@ -55,4 +60,21 @@ class MdmSurvivorshipSvcImplIT extends BaseMdmR4Test {
|
|||
assertEquals(p1.getTelecom().size(), p1.getTelecom().size());
|
||||
assertTrue(p2.getTelecomFirstRep().equalsDeep(p1.getTelecomFirstRep()));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void matchingPatientsWith_NON_Numeric_Ids_matches_doesNotThrow_NumberFormatException() {
|
||||
final Patient frankPatient1 = buildFrankPatient();
|
||||
frankPatient1.setId("patA");
|
||||
myPatientDao.update(frankPatient1, new SystemRequestDetails());
|
||||
final Patient frankPatient2 = buildFrankPatient();
|
||||
frankPatient2.setId("patB");
|
||||
myPatientDao.update(frankPatient2, new SystemRequestDetails());
|
||||
final Patient goldenPatient = buildFrankPatient();
|
||||
myPatientDao.create(goldenPatient, new SystemRequestDetails());
|
||||
|
||||
myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, frankPatient1, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
|
||||
myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, frankPatient2, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
|
||||
|
||||
myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(goldenPatient, new MdmTransactionContext(MdmTransactionContext.OperationType.UPDATE_LINK));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -25,8 +25,9 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
|
|||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.ValueSource;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.Spy;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
|
@ -96,8 +97,9 @@ public class MdmSurvivorshipSvcImplTest {
|
|||
}
|
||||
|
||||
@SuppressWarnings({"rawtypes", "unchecked"})
|
||||
@Test
|
||||
public void rebuildGoldenResourceCurrentLinksUsingSurvivorshipRules_withManyLinks_rebuildsInUpdateOrder() {
|
||||
@ParameterizedTest
|
||||
@ValueSource(booleans = {true,false})
|
||||
public void rebuildGoldenResourceCurrentLinksUsingSurvivorshipRules_withManyLinks_rebuildsInUpdateOrder(boolean theIsUseNonNumericId) {
|
||||
// setup
|
||||
// create resources
|
||||
Patient goldenPatient = new Patient();
|
||||
|
|
@ -126,7 +128,7 @@ public class MdmSurvivorshipSvcImplTest {
|
|||
patient.addIdentifier()
|
||||
.setSystem("http://example.com")
|
||||
.setValue("Value" + i);
|
||||
patient.setId("Patient/" + i);
|
||||
patient.setId("Patient/" + (theIsUseNonNumericId ? "pat"+i : Integer.toString(i)));
|
||||
resources.add(patient);
|
||||
|
||||
MdmLinkJson link = createLinkJson(
|
||||
|
|
@ -149,8 +151,13 @@ public class MdmSurvivorshipSvcImplTest {
|
|||
when(myDaoRegistry.getResourceDao(eq("Patient")))
|
||||
.thenReturn(resourceDao);
|
||||
AtomicInteger counter = new AtomicInteger();
|
||||
when(resourceDao.readByPid(any()))
|
||||
.thenAnswer(params -> resources.get(counter.getAndIncrement()));
|
||||
if (theIsUseNonNumericId) {
|
||||
when(resourceDao.read(any(), any()))
|
||||
.thenAnswer(params -> resources.get(counter.getAndIncrement()));
|
||||
} else {
|
||||
when(resourceDao.readByPid(any()))
|
||||
.thenAnswer(params -> resources.get(counter.getAndIncrement()));
|
||||
}
|
||||
Page<MdmLinkJson> linkPage = mock(Page.class);
|
||||
when(myMdmLinkQuerySvc.queryLinks(any(), any()))
|
||||
.thenReturn(linkPage);
|
||||
|
|
|
|||
|
|
@ -34,23 +34,26 @@ import java.util.Date;
|
|||
import static java.util.Objects.nonNull;
|
||||
|
||||
@Entity
|
||||
@Table(name = "HFJ_BINARY_STORAGE")
|
||||
@Table(name = "HFJ_BINARY_STORAGE_BLOB")
|
||||
public class BinaryStorageEntity {
|
||||
|
||||
@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`.
|
||||
private String myContentId;
|
||||
|
||||
@Column(name = "RESOURCE_ID", length = 100, nullable = false)
|
||||
private String myResourceId;
|
||||
|
||||
@Column(name = "CONTENT_SIZE", nullable = true)
|
||||
@Column(name = "BLOB_SIZE", nullable = true)
|
||||
private long mySize;
|
||||
|
||||
@Column(name = "CONTENT_TYPE", nullable = false, length = 100)
|
||||
private String myContentType;
|
||||
|
||||
/**
|
||||
* @deprecated
|
||||
*/
|
||||
@Deprecated(since = "7.2.0")
|
||||
@Lob // TODO: VC column added in 7.2.0 - Remove non-VC column later
|
||||
@Column(name = "BLOB_DATA", nullable = true, insertable = true, updatable = false)
|
||||
|
|
@ -63,7 +66,7 @@ public class BinaryStorageEntity {
|
|||
@Column(name = "PUBLISHED_DATE", nullable = false)
|
||||
private Date myPublished;
|
||||
|
||||
@Column(name = "CONTENT_HASH", length = 128, nullable = true)
|
||||
@Column(name = "BLOB_HASH", length = 128, nullable = true)
|
||||
private String myHash;
|
||||
|
||||
public Date getPublished() {
|
||||
|
|
|
|||
|
|
@ -156,4 +156,30 @@ public interface IRequestPartitionHelperSvc {
|
|||
Set<Integer> toReadPartitions(@Nonnull RequestPartitionId theRequestPartitionId);
|
||||
|
||||
boolean isResourcePartitionable(String theResourceType);
|
||||
|
||||
/**
|
||||
* <b>No interceptors should be invoked by this method. It should ONLY be used when partition ids are
|
||||
* known, but partition names are not.</b>
|
||||
* <br/><br/>
|
||||
* Ensures the list of partition ids inside the given {@link RequestPartitionId} correctly map to the
|
||||
* list of partition names. If the list of partition names is empty, this method will map the correct
|
||||
* partition names and return a normalized {@link RequestPartitionId}.
|
||||
* <br/><br/>
|
||||
* @param theRequestPartitionId - An unvalidated and unnormalized {@link RequestPartitionId}.
|
||||
* @return - A {@link RequestPartitionId} with a normalized list of partition ids and partition names.
|
||||
*/
|
||||
RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId);
|
||||
|
||||
/**
|
||||
* <b>No interceptors should be invoked by this method. It should ONLY be used when partition names are
|
||||
* known, but partition ids are not.</b>
|
||||
* <br/><br/>
|
||||
* Ensures the list of partition names inside the given {@link RequestPartitionId} correctly map to the
|
||||
* list of partition ids. If the list of partition ids is empty, this method will map the correct
|
||||
* partition ids and return a normalized {@link RequestPartitionId}.
|
||||
* <br/><br/>
|
||||
* @param theRequestPartitionId - An unvalidated and unnormalized {@link RequestPartitionId}.
|
||||
* @return - A {@link RequestPartitionId} with a normalized list of partition ids and partition names.
|
||||
*/
|
||||
RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
|
@ -19,15 +19,13 @@
|
|||
*/
|
||||
package ca.uhn.fhir.jpa.subscription.submit.config;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
|
||||
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
|
||||
import ca.uhn.fhir.jpa.subscription.async.AsyncResourceModifiedProcessingSchedulerSvc;
|
||||
import ca.uhn.fhir.jpa.subscription.async.AsyncResourceModifiedSubmitterSvc;
|
||||
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelFactory;
|
||||
import ca.uhn.fhir.jpa.subscription.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.submit.interceptor.SubscriptionQueryValidator;
|
||||
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionSubmitInterceptorLoader;
|
||||
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionValidatingInterceptor;
|
||||
import ca.uhn.fhir.jpa.subscription.submit.svc.ResourceModifiedSubmitterSvc;
|
||||
|
|
@ -45,7 +43,7 @@ import org.springframework.context.annotation.Lazy;
|
|||
* matching queue for processing
|
||||
*/
|
||||
@Configuration
|
||||
@Import({SubscriptionModelConfig.class, SubscriptionMatcherInterceptorConfig.class})
|
||||
@Import({SubscriptionModelConfig.class, SubscriptionMatcherInterceptorConfig.class, SubscriptionConfig.class})
|
||||
public class SubscriptionSubmitterConfig {
|
||||
|
||||
@Bean
|
||||
|
|
@ -53,12 +51,6 @@ public class SubscriptionSubmitterConfig {
|
|||
return new SubscriptionValidatingInterceptor();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public SubscriptionQueryValidator subscriptionQueryValidator(
|
||||
DaoRegistry theDaoRegistry, SubscriptionStrategyEvaluator theSubscriptionStrategyEvaluator) {
|
||||
return new SubscriptionQueryValidator(theDaoRegistry, theSubscriptionStrategyEvaluator);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public SubscriptionSubmitInterceptorLoader subscriptionMatcherInterceptorLoader() {
|
||||
return new SubscriptionSubmitInterceptorLoader();
|
||||
|
|
|
|||
|
|
@ -22,13 +22,15 @@ package ca.uhn.fhir.jpa.topic;
|
|||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
|
||||
import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
|
||||
import ca.uhn.fhir.jpa.subscription.config.SubscriptionConfig;
|
||||
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionQueryValidator;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.context.annotation.Import;
|
||||
import org.springframework.context.annotation.Lazy;
|
||||
|
||||
@Configuration
|
||||
@Import(SubscriptionConfig.class)
|
||||
public class SubscriptionTopicConfig {
|
||||
@Bean
|
||||
SubscriptionTopicMatchingSubscriber subscriptionTopicMatchingSubscriber(FhirContext theFhirContext) {
|
||||
|
|
@ -76,13 +78,6 @@ public class SubscriptionTopicConfig {
|
|||
}
|
||||
}
|
||||
|
||||
@Bean
|
||||
@Lazy
|
||||
public SubscriptionQueryValidator subscriptionQueryValidator(
|
||||
DaoRegistry theDaoRegistry, SubscriptionStrategyEvaluator theSubscriptionStrategyEvaluator) {
|
||||
return new SubscriptionQueryValidator(theDaoRegistry, theSubscriptionStrategyEvaluator);
|
||||
}
|
||||
|
||||
@Bean
|
||||
SubscriptionTopicValidatingInterceptor subscriptionTopicValidatingInterceptor(
|
||||
FhirContext theFhirContext, SubscriptionQueryValidator theSubscriptionQueryValidator) {
|
||||
|
|
|
|||
|
|
@ -7,8 +7,12 @@ import ca.uhn.fhir.jpa.model.entity.BinaryStorageEntity;
|
|||
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import jakarta.persistence.EntityManager;
|
||||
import org.hibernate.LobHelper;
|
||||
import org.hibernate.Session;
|
||||
import org.hl7.fhir.r4.model.IdType;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.mockito.ArgumentCaptor;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
|
@ -24,6 +28,7 @@ import java.sql.SQLException;
|
|||
import java.util.Optional;
|
||||
|
||||
import static org.hamcrest.CoreMatchers.containsString;
|
||||
import static org.hamcrest.CoreMatchers.equalTo;
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.is;
|
||||
import static org.hamcrest.Matchers.matchesPattern;
|
||||
|
|
@ -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.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
import static org.mockito.ArgumentMatchers.any;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.times;
|
||||
import static org.mockito.Mockito.verify;
|
||||
|
|
@ -281,7 +287,7 @@ public class DatabaseBinaryContentStorageSvcImplTest extends BaseJpaR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testStoreBinaryContent_writesBlobAndByteArray() throws IOException {
|
||||
public void testStoreBinaryContent_byDefault_writesByteArrayOnly() throws IOException {
|
||||
// given
|
||||
ByteArrayInputStream inputStream = new ByteArrayInputStream(SOME_BYTES);
|
||||
String contentType = "image/png";
|
||||
|
|
@ -296,11 +302,41 @@ public class DatabaseBinaryContentStorageSvcImplTest extends BaseJpaR4Test {
|
|||
|
||||
// then
|
||||
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
|
||||
public static class MyConfig {
|
||||
|
||||
|
|
|
|||
|
|
@ -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.util.SqlQuery;
|
||||
import ca.uhn.fhir.jpa.util.SqlQueryList;
|
||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.storage.test.DaoTestDataBuilder;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
|
|
@ -33,6 +36,8 @@ import java.util.List;
|
|||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.empty;
|
||||
import static org.hamcrest.Matchers.not;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
/**
|
||||
* Sandbox for implementing queries.
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
||||
@Test
|
||||
void testChainedSort() {
|
||||
final IIdType practitionerId = myDataBuilder.createPractitioner(myDataBuilder.withFamily("Jones"));
|
||||
|
||||
final String id1 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithy")).getIdPart();
|
||||
final String id2 = myDataBuilder.createPatient(myDataBuilder.withFamily("Smithwick")).getIdPart();
|
||||
final String id3 = myDataBuilder.createPatient(
|
||||
myDataBuilder.withFamily("Smith"),
|
||||
myDataBuilder.withReference("generalPractitioner", practitionerId)).getIdPart();
|
||||
|
||||
|
||||
final IBundleProvider iBundleProvider = myTestDaoSearch.searchForBundleProvider("Patient?_total=ACCURATE&_sort=Practitioner:general-practitioner.family");
|
||||
assertEquals(3, iBundleProvider.size());
|
||||
|
||||
final List<IBaseResource> allResources = iBundleProvider.getAllResources();
|
||||
assertEquals(3, iBundleProvider.size());
|
||||
assertEquals(3, allResources.size());
|
||||
|
||||
final List<String> actualIds = allResources.stream().map(IBaseResource::getIdElement).map(IIdType::getIdPart).toList();
|
||||
assertTrue(actualIds.containsAll(List.of(id1, id2, id3)));
|
||||
}
|
||||
|
||||
public static final class TestDirtiesContextTestExecutionListener extends DirtiesContextTestExecutionListener {
|
||||
|
||||
@Override
|
||||
|
|
|
|||
|
|
@ -1,74 +1,189 @@
|
|||
package ca.uhn.fhir.jpa.partition;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
|
||||
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
|
||||
import ca.uhn.fhir.jpa.dao.data.IPartitionDao;
|
||||
import ca.uhn.fhir.jpa.entity.PartitionEntity;
|
||||
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
|
||||
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import org.hl7.fhir.r4.model.IdType;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.InjectMocks;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import java.util.Set;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.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)
|
||||
class RequestPartitionHelperSvcTest {
|
||||
static final Integer PARTITION_ID = 2401;
|
||||
static final String PARTITION_NAME = "JIMMY";
|
||||
static final PartitionEntity ourPartitionEntity = new PartitionEntity().setName(PARTITION_NAME);
|
||||
class RequestPartitionHelperSvcTest extends BaseJpaR4Test {
|
||||
|
||||
@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;
|
||||
@Mock
|
||||
IPartitionLookupSvc myPartitionLookupSvc;
|
||||
@Mock
|
||||
FhirContext myFhirContext;
|
||||
@Mock
|
||||
IInterceptorBroadcaster myInterceptorBroadcaster;
|
||||
@Autowired
|
||||
RequestPartitionHelperSvc mySvc;
|
||||
|
||||
@InjectMocks
|
||||
RequestPartitionHelperSvc mySvc = new RequestPartitionHelperSvc();
|
||||
Patient myPatient;
|
||||
|
||||
@Test
|
||||
public void determineReadPartitionForSystemRequest() {
|
||||
// setup
|
||||
SystemRequestDetails srd = new SystemRequestDetails();
|
||||
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionId(PARTITION_ID);
|
||||
srd.setRequestPartitionId(requestPartitionId);
|
||||
when(myPartitionSettings.isPartitioningEnabled()).thenReturn(true);
|
||||
when(myPartitionLookupSvc.getPartitionById(PARTITION_ID)).thenReturn(ourPartitionEntity);
|
||||
@BeforeEach
|
||||
public void before(){
|
||||
myPartitionDao.deleteAll();
|
||||
myPartitionSettings.setPartitioningEnabled(true);
|
||||
|
||||
// execute
|
||||
RequestPartitionId result = mySvc.determineReadPartitionForRequestForRead(srd, "Patient", new IdType("Patient/123"));
|
||||
|
||||
// verify
|
||||
assertEquals(PARTITION_ID, result.getFirstPartitionIdOrNull());
|
||||
assertEquals(PARTITION_NAME, result.getFirstPartitionNameOrNull());
|
||||
myPatient = new Patient();
|
||||
myPatient.setId(new IdType("Patient", "123", "1"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void determineCreatePartitionForSystemRequest() {
|
||||
public void testDetermineReadPartitionForSystemRequest_withPartitionIdOnly_returnsCorrectPartition() {
|
||||
// setup
|
||||
PartitionEntity partitionEntity = createPartition1();
|
||||
SystemRequestDetails srd = new SystemRequestDetails();
|
||||
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionId(PARTITION_ID);
|
||||
srd.setRequestPartitionId(requestPartitionId);
|
||||
when(myPartitionSettings.isPartitioningEnabled()).thenReturn(true);
|
||||
when(myPartitionLookupSvc.getPartitionById(PARTITION_ID)).thenReturn(ourPartitionEntity);
|
||||
Patient resource = new Patient();
|
||||
when(myFhirContext.getResourceType(resource)).thenReturn("Patient");
|
||||
srd.setRequestPartitionId(RequestPartitionId.fromPartitionId(partitionEntity.getId()));
|
||||
|
||||
// execute
|
||||
RequestPartitionId result = mySvc.determineCreatePartitionForRequest(srd, resource, "Patient");
|
||||
RequestPartitionId result = mySvc.determineReadPartitionForRequestForRead(srd, myPatient.fhirType(), myPatient.getIdElement());
|
||||
|
||||
// verify
|
||||
assertEquals(PARTITION_ID, result.getFirstPartitionIdOrNull());
|
||||
assertEquals(PARTITION_NAME, result.getFirstPartitionNameOrNull());
|
||||
assertEquals(PARTITION_ID_1, result.getFirstPartitionIdOrNull());
|
||||
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));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -884,6 +884,16 @@ public class GiantTransactionPerfTest {
|
|||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
|
||||
return RequestPartitionId.defaultPartition();
|
||||
}
|
||||
|
||||
@Override
|
||||
public RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
|
||||
return RequestPartitionId.defaultPartition();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r5;
|
|||
|
||||
import ca.uhn.fhir.context.RuntimeSearchParam;
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
|
||||
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
|
||||
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
|
||||
|
|
@ -12,6 +13,8 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
|||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.util.BundleBuilder;
|
||||
import ca.uhn.fhir.util.HapiExtensions;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r5.model.Composition;
|
||||
import org.hl7.fhir.r5.model.IdType;
|
||||
import org.hl7.fhir.r5.model.Bundle;
|
||||
|
|
@ -29,6 +32,7 @@ import org.hl7.fhir.r5.model.SearchParameter;
|
|||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
|
||||
import jakarta.annotation.Nonnull;
|
||||
|
|
@ -41,9 +45,10 @@ import static org.hamcrest.Matchers.containsInAnyOrder;
|
|||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.empty;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
|
||||
@ContextConfiguration(classes = TestHSearchAddInConfig.NoFT.class)
|
||||
@ContextConfiguration(classes = { TestHSearchAddInConfig.NoFT.class, TestDaoSearch.Config.class })
|
||||
@SuppressWarnings({"Duplicates"})
|
||||
public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
|
||||
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_E3 = "Encounter/E3";
|
||||
public static final String ORGANIZATION_O1 = "Organization/O1";
|
||||
@Autowired
|
||||
protected TestDaoSearch myTestDaoSearch;
|
||||
|
||||
@Override
|
||||
@BeforeEach
|
||||
|
|
@ -867,6 +874,47 @@ public class UpliftedRefchainsAndChainedSortingR5Test extends BaseJpaR5Test {
|
|||
assertEquals(1, countMatches(querySql, "HFJ_RES_LINK"), querySql);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void testChainedSortWithNulls() {
|
||||
final IIdType practitionerId1 = createPractitioner(withFamily("Chan"));
|
||||
final IIdType practitionerId2 = createPractitioner(withFamily("Jones"));
|
||||
|
||||
final String id1 = createPatient(withFamily("Smithy")).getIdPart();
|
||||
final String id2 = createPatient(withFamily("Smithwick"),
|
||||
withReference("generalPractitioner", practitionerId2)).getIdPart();
|
||||
final String id3 = createPatient(
|
||||
withFamily("Smith"),
|
||||
withReference("generalPractitioner", practitionerId1)).getIdPart();
|
||||
|
||||
|
||||
final IBundleProvider iBundleProvider = myTestDaoSearch.searchForBundleProvider("Patient?_total=ACCURATE&_sort=Practitioner:general-practitioner.family");
|
||||
final List<IBaseResource> allResources = iBundleProvider.getAllResources();
|
||||
assertEquals(3, iBundleProvider.size());
|
||||
assertEquals(3, allResources.size());
|
||||
|
||||
final List<String> actualIds = allResources.stream().map(IBaseResource::getIdElement).map(IIdType::getIdPart).toList();
|
||||
assertTrue(actualIds.containsAll(List.of(id1, id2, id3)));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testChainedReverseStringSort() {
|
||||
final IIdType practitionerId = createPractitioner(withFamily("Jones"));
|
||||
|
||||
final String id1 = createPatient(withFamily("Smithy")).getIdPart();
|
||||
final String id2 = createPatient(withFamily("Smithwick")).getIdPart();
|
||||
final String id3 = createPatient(
|
||||
withFamily("Smith"),
|
||||
withReference("generalPractitioner", practitionerId)).getIdPart();
|
||||
|
||||
final IBundleProvider iBundleProvider = myTestDaoSearch.searchForBundleProvider("Patient?_total=ACCURATE&_sort=-Practitioner:general-practitioner.family");
|
||||
assertEquals(3, iBundleProvider.size());
|
||||
|
||||
final List<IBaseResource> allResources = iBundleProvider.getAllResources();
|
||||
final List<String> actualIds = allResources.stream().map(IBaseResource::getIdElement).map(IIdType::getIdPart).toList();
|
||||
assertTrue(actualIds.containsAll(List.of(id3, id2, id1)));
|
||||
}
|
||||
|
||||
/**
|
||||
* Observation:focus is a Reference(Any) so it can't be used in a sort chain because
|
||||
* this would be horribly, horribly inefficient.
|
||||
|
|
|
|||
|
|
@ -1,38 +1,24 @@
|
|||
package ca.uhn.fhir.jpa.dao.r5.database;
|
||||
|
||||
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
|
||||
import ca.uhn.fhir.batch2.jobs.expunge.DeleteExpungeProvider;
|
||||
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
|
||||
import ca.uhn.fhir.jpa.api.dao.PatientEverythingParameters;
|
||||
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
|
||||
import ca.uhn.fhir.jpa.embedded.JpaEmbeddedDatabase;
|
||||
import ca.uhn.fhir.jpa.fql.provider.HfqlRestProvider;
|
||||
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
|
||||
import ca.uhn.fhir.jpa.migrate.HapiMigrationStorageSvc;
|
||||
import ca.uhn.fhir.jpa.migrate.MigrationTaskList;
|
||||
import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
|
||||
import ca.uhn.fhir.jpa.migrate.dao.HapiMigrationDao;
|
||||
import ca.uhn.fhir.jpa.migrate.tasks.HapiFhirJpaMigrationTasks;
|
||||
import ca.uhn.fhir.jpa.provider.DiffProvider;
|
||||
import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
|
||||
import ca.uhn.fhir.jpa.provider.ProcessMessageProvider;
|
||||
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
|
||||
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
|
||||
import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
|
||||
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.jpa.test.BaseJpaTest;
|
||||
import ca.uhn.fhir.jpa.test.config.TestR5Config;
|
||||
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.api.SortSpec;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.client.api.IGenericClient;
|
||||
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
|
||||
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
|
||||
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
|
||||
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
|
||||
import ca.uhn.fhir.test.utilities.server.RestfulServerConfigurerExtension;
|
||||
|
|
@ -44,7 +30,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
|
|||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r5.model.Bundle;
|
||||
import org.hl7.fhir.r5.model.IdType;
|
||||
import org.hl7.fhir.r5.model.IntegerType;
|
||||
import org.hl7.fhir.r5.model.Parameters;
|
||||
import org.hl7.fhir.r5.model.Patient;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
|
@ -55,7 +40,6 @@ import org.junit.jupiter.params.provider.ValueSource;
|
|||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.data.envers.repository.support.EnversRevisionRepositoryFactoryBean;
|
||||
|
|
@ -63,10 +47,8 @@ import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
|
|||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||
import org.springframework.transaction.PlatformTransactionManager;
|
||||
import org.springframework.web.cors.CorsConfiguration;
|
||||
|
||||
import javax.sql.DataSource;
|
||||
import java.util.Arrays;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Properties;
|
||||
|
|
@ -80,7 +62,7 @@ import static org.junit.jupiter.api.Assertions.assertThrows;
|
|||
|
||||
@ExtendWith(SpringExtension.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 {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(BaseDatabaseVerificationIT.class);
|
||||
private static final String MIGRATION_TABLENAME = "MIGRATIONS";
|
||||
|
|
@ -109,6 +91,9 @@ public abstract class BaseDatabaseVerificationIT extends BaseJpaTest implements
|
|||
@Autowired
|
||||
private DatabaseBackedPagingProvider myPagingProvider;
|
||||
|
||||
@Autowired
|
||||
TestDaoSearch myTestDaoSearch;
|
||||
|
||||
@RegisterExtension
|
||||
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])));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testChainedSort() {
|
||||
// given
|
||||
|
||||
// when
|
||||
SearchParameterMap map = SearchParameterMap
|
||||
.newSynchronous()
|
||||
.setSort(new SortSpec("Practitioner:general-practitioner.family"));
|
||||
myCaptureQueriesListener.clear();
|
||||
myPatientDao.search(map, mySrd);
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@Configuration
|
||||
|
|
@ -222,8 +221,8 @@ public abstract class BaseDatabaseVerificationIT extends BaseJpaTest implements
|
|||
}
|
||||
|
||||
public static class JpaDatabaseContextConfigParamObject {
|
||||
private JpaEmbeddedDatabase myJpaEmbeddedDatabase;
|
||||
private String myDialect;
|
||||
final JpaEmbeddedDatabase myJpaEmbeddedDatabase;
|
||||
final String myDialect;
|
||||
|
||||
public JpaDatabaseContextConfigParamObject(JpaEmbeddedDatabase theJpaEmbeddedDatabase, String theDialect) {
|
||||
myJpaEmbeddedDatabase = theJpaEmbeddedDatabase;
|
||||
|
|
|
|||
|
|
@ -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));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -9,11 +9,16 @@ import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
|
|||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.ValueSource;
|
||||
import org.mockito.ArgumentCaptor;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.equalTo;
|
||||
import static org.mockito.ArgumentMatchers.any;
|
||||
import static org.mockito.Mockito.eq;
|
||||
import static org.mockito.Mockito.times;
|
||||
|
|
@ -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));
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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.mdmevents.MdmLinkJson;
|
||||
import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
|
||||
import ca.uhn.fhir.model.primitive.IdDt;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
|
||||
import ca.uhn.fhir.util.TerserUtil;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.instance.model.api.IAnyResource;
|
||||
import org.hl7.fhir.instance.model.api.IBase;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.springframework.data.domain.Page;
|
||||
|
||||
import java.util.regex.Pattern;
|
||||
import java.util.stream.Stream;
|
||||
|
||||
public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
|
||||
private static final Pattern IS_UUID =
|
||||
Pattern.compile("[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}");
|
||||
|
||||
protected final FhirContext myFhirContext;
|
||||
|
||||
|
|
@ -133,16 +138,30 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
|
|||
String sourceId = link.getSourceId();
|
||||
|
||||
// +1 because of "/" in id: "ResourceType/Id"
|
||||
IResourcePersistentId<?> pid = getResourcePID(sourceId.substring(resourceType.length() + 1), resourceType);
|
||||
final String sourceIdUnqualified = sourceId.substring(resourceType.length() + 1);
|
||||
|
||||
// this might be a bit unperformant
|
||||
// but it depends how many links there are
|
||||
// per golden resource (unlikely to be thousands)
|
||||
return dao.readByPid(pid);
|
||||
// myMdmLinkQuerySvc.queryLinks populates sourceId with the FHIR_ID, not the RES_ID, so if we don't
|
||||
// add this conditional logic, on JPA, myIIdHelperService.newPidFromStringIdAndResourceName will fail with
|
||||
// NumberFormatException
|
||||
if (isNumericOrUuid(sourceIdUnqualified)) {
|
||||
IResourcePersistentId<?> pid = getResourcePID(sourceIdUnqualified, resourceType);
|
||||
|
||||
// this might be a bit unperformant
|
||||
// but it depends how many links there are
|
||||
// per golden resource (unlikely to be thousands)
|
||||
return dao.readByPid(pid);
|
||||
} else {
|
||||
return dao.read(new IdDt(sourceId), new SystemRequestDetails());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
private IResourcePersistentId<?> getResourcePID(String theId, String theResourceType) {
|
||||
return myIIdHelperService.newPidFromStringIdAndResourceName(theId, theResourceType);
|
||||
}
|
||||
|
||||
private boolean isNumericOrUuid(String theLongCandidate) {
|
||||
return StringUtils.isNumeric(theLongCandidate)
|
||||
|| IS_UUID.matcher(theLongCandidate).matches();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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.IIdType;
|
||||
|
||||
import java.util.Collection;
|
||||
|
||||
public interface IAuthRuleBuilderOperationNamed {
|
||||
|
||||
/**
|
||||
|
|
@ -44,6 +46,8 @@ public interface IAuthRuleBuilderOperationNamed {
|
|||
*/
|
||||
IAuthRuleBuilderOperationNamedAndScoped onInstance(IIdType theInstanceId);
|
||||
|
||||
IAuthRuleBuilderOperationNamedAndScoped onInstances(Collection<IIdType> theInstanceIds);
|
||||
|
||||
/**
|
||||
* Rule applies to invocations of this operation at the <code>instance</code> level on any instance of the given type
|
||||
*/
|
||||
|
|
|
|||
|
|
@ -22,6 +22,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
|
|||
import jakarta.annotation.Nonnull;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
/**
|
||||
* @since 5.5.0
|
||||
*/
|
||||
|
|
@ -54,10 +57,20 @@ public interface IAuthRuleBuilderRuleBulkExport {
|
|||
|
||||
IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull String theFocusResourceId);
|
||||
|
||||
IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnAllPatients();
|
||||
|
||||
default IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull IIdType theFocusResourceId) {
|
||||
return patientExportOnPatient(theFocusResourceId.getValue());
|
||||
}
|
||||
|
||||
default IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatients(
|
||||
@Nonnull Collection<IIdType> theFocusResourceIds) {
|
||||
return patientExportOnPatientStrings(
|
||||
theFocusResourceIds.stream().map(IIdType::getValue).collect(Collectors.toList()));
|
||||
}
|
||||
|
||||
IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatientStrings(Collection<String> theFocusResourceIds);
|
||||
|
||||
/**
|
||||
* Allow/deny <b>patient-level</b> export rule applies to the Group with the given resource ID, e.g. <code>Group/123</code>
|
||||
*
|
||||
|
|
|
|||
|
|
@ -736,6 +736,20 @@ public class RuleBuilder implements IAuthRuleBuilder {
|
|||
return new RuleBuilderOperationNamedAndScoped(rule);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IAuthRuleBuilderOperationNamedAndScoped onInstances(Collection<IIdType> theInstanceIds) {
|
||||
Validate.notNull(theInstanceIds, "theInstanceIds must not be null");
|
||||
theInstanceIds.forEach(instanceId -> Validate.notBlank(
|
||||
instanceId.getResourceType(),
|
||||
"at least one of theInstanceIds does not have a resource type"));
|
||||
theInstanceIds.forEach(instanceId -> Validate.notBlank(
|
||||
instanceId.getIdPart(), "at least one of theInstanceIds does not have an ID part"));
|
||||
|
||||
final OperationRule rule = createRule();
|
||||
rule.appliesToInstances(new ArrayList<>(theInstanceIds));
|
||||
return new RuleBuilderOperationNamedAndScoped(rule);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IAuthRuleBuilderOperationNamedAndScoped onInstancesOfType(
|
||||
Class<? extends IBaseResource> theType) {
|
||||
|
|
@ -869,7 +883,7 @@ public class RuleBuilder implements IAuthRuleBuilder {
|
|||
}
|
||||
|
||||
private class RuleBuilderBulkExport implements IAuthRuleBuilderRuleBulkExport {
|
||||
private RuleBulkExportImpl ruleBulkExport;
|
||||
private RuleBulkExportImpl myRuleBulkExport;
|
||||
|
||||
@Override
|
||||
public IAuthRuleBuilderRuleBulkExportWithTarget groupExportOnGroup(@Nonnull String theFocusResourceId) {
|
||||
|
|
@ -881,23 +895,60 @@ public class RuleBuilder implements IAuthRuleBuilder {
|
|||
return new RuleBuilderBulkExportWithTarget(rule);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnAllPatients() {
|
||||
if (myRuleBulkExport == null) {
|
||||
RuleBulkExportImpl rule = new RuleBulkExportImpl(myRuleName);
|
||||
rule.setMode(myRuleMode);
|
||||
myRuleBulkExport = rule;
|
||||
}
|
||||
myRuleBulkExport.setAppliesToPatientExportAllPatients();
|
||||
|
||||
// prevent duplicate rules being added
|
||||
if (!myRules.contains(myRuleBulkExport)) {
|
||||
myRules.add(myRuleBulkExport);
|
||||
}
|
||||
|
||||
return new RuleBuilderBulkExportWithTarget(myRuleBulkExport);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IAuthRuleBuilderRuleBulkExportWithTarget patientExportOnPatient(@Nonnull String theFocusResourceId) {
|
||||
if (ruleBulkExport == null) {
|
||||
if (myRuleBulkExport == null) {
|
||||
RuleBulkExportImpl rule = new RuleBulkExportImpl(myRuleName);
|
||||
rule.setAppliesToPatientExport(theFocusResourceId);
|
||||
rule.setMode(myRuleMode);
|
||||
ruleBulkExport = rule;
|
||||
myRuleBulkExport = rule;
|
||||
} else {
|
||||
ruleBulkExport.setAppliesToPatientExport(theFocusResourceId);
|
||||
myRuleBulkExport.setAppliesToPatientExport(theFocusResourceId);
|
||||
}
|
||||
|
||||
// prevent duplicate rules being added
|
||||
if (!myRules.contains(ruleBulkExport)) {
|
||||
myRules.add(ruleBulkExport);
|
||||
if (!myRules.contains(myRuleBulkExport)) {
|
||||
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
|
||||
|
|
|
|||
|
|
@ -24,12 +24,12 @@ import ca.uhn.fhir.model.primitive.IdDt;
|
|||
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.bulk.BulkExportJobParameters;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
|
@ -42,6 +42,7 @@ public class RuleBulkExportImpl extends BaseRule {
|
|||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RuleBulkExportImpl.class);
|
||||
private String myGroupId;
|
||||
private final Collection<String> myPatientIds;
|
||||
private boolean myAppliesToAllPatients;
|
||||
private BulkExportJobParameters.ExportStyle myWantExportStyle;
|
||||
private Collection<String> myResourceTypes;
|
||||
private boolean myWantAnyStyle;
|
||||
|
|
@ -69,115 +70,86 @@ public class RuleBulkExportImpl extends BaseRule {
|
|||
return null;
|
||||
}
|
||||
|
||||
BulkExportJobParameters options = (BulkExportJobParameters)
|
||||
BulkExportJobParameters inboundBulkExportRequestOptions = (BulkExportJobParameters)
|
||||
theRequestDetails.getAttribute(AuthorizationInterceptor.REQUEST_ATTRIBUTE_BULK_DATA_EXPORT_OPTIONS);
|
||||
|
||||
if (!myWantAnyStyle && options.getExportStyle() != myWantExportStyle) {
|
||||
// if style doesn't match - abstain
|
||||
if (!myWantAnyStyle && inboundBulkExportRequestOptions.getExportStyle() != myWantExportStyle) {
|
||||
return null;
|
||||
}
|
||||
|
||||
// Do we only authorize some types? If so, make sure requested types are a subset
|
||||
if (isNotEmpty(myResourceTypes)) {
|
||||
if (isEmpty(options.getResourceTypes())) {
|
||||
return null;
|
||||
if (isEmpty(inboundBulkExportRequestOptions.getResourceTypes())) {
|
||||
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
|
||||
}
|
||||
for (String next : options.getResourceTypes()) {
|
||||
if (!myResourceTypes.contains(next)) {
|
||||
if (!myResourceTypes.containsAll(inboundBulkExportRequestOptions.getResourceTypes())) {
|
||||
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
|
||||
}
|
||||
}
|
||||
|
||||
// system only supports filtering by resource type. So if we are system, or any(), then allow, since we have
|
||||
// done resource type checking
|
||||
// above
|
||||
AuthorizationInterceptor.Verdict allowVerdict = newVerdict(
|
||||
theOperation,
|
||||
theRequestDetails,
|
||||
theInputResource,
|
||||
theInputResourceId,
|
||||
theOutputResource,
|
||||
theRuleApplier);
|
||||
|
||||
if (myWantAnyStyle || myWantExportStyle == BulkExportJobParameters.ExportStyle.SYSTEM) {
|
||||
return allowVerdict;
|
||||
}
|
||||
|
||||
// assume myGroupId not empty->myStyle is group. If target group matches, then allow.
|
||||
if (isNotBlank(myGroupId) && inboundBulkExportRequestOptions.getGroupId() != null) {
|
||||
String expectedGroupId =
|
||||
new IdDt(myGroupId).toUnqualifiedVersionless().getValue();
|
||||
String actualGroupId = new IdDt(inboundBulkExportRequestOptions.getGroupId())
|
||||
.toUnqualifiedVersionless()
|
||||
.getValue();
|
||||
if (Objects.equals(expectedGroupId, actualGroupId)) {
|
||||
return allowVerdict;
|
||||
}
|
||||
}
|
||||
// patient export mode - instance or type. type can have 0..n patient ids.
|
||||
// myPatientIds == the rules built by the auth interceptor rule builder
|
||||
// options.getPatientIds() == the requested IDs in the export job.
|
||||
|
||||
// 1. If each of the requested resource IDs in the parameters are present in the users permissions, Approve
|
||||
// 2. If any requested ID is not present in the users permissions, Deny.
|
||||
if (myWantExportStyle == BulkExportJobParameters.ExportStyle.PATIENT)
|
||||
// Unfiltered Type Level
|
||||
if (myAppliesToAllPatients) {
|
||||
return allowVerdict;
|
||||
}
|
||||
|
||||
// Instance level, or filtered type level
|
||||
if (isNotEmpty(myPatientIds)) {
|
||||
// If bulk export options defines no patient IDs, return null.
|
||||
if (inboundBulkExportRequestOptions.getPatientIds().isEmpty()) {
|
||||
return null;
|
||||
} else {
|
||||
ourLog.debug("options.getPatientIds() != null");
|
||||
Set<String> requestedPatientIds = sanitizeIds(inboundBulkExportRequestOptions.getPatientIds());
|
||||
Set<String> permittedPatientIds = sanitizeIds(myPatientIds);
|
||||
if (permittedPatientIds.containsAll(requestedPatientIds)) {
|
||||
return allowVerdict;
|
||||
} else {
|
||||
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (myWantAnyStyle || myWantExportStyle == BulkExportJobParameters.ExportStyle.SYSTEM) {
|
||||
return newVerdict(
|
||||
theOperation,
|
||||
theRequestDetails,
|
||||
theInputResource,
|
||||
theInputResourceId,
|
||||
theOutputResource,
|
||||
theRuleApplier);
|
||||
}
|
||||
|
||||
if (isNotBlank(myGroupId) && options.getGroupId() != null) {
|
||||
String expectedGroupId =
|
||||
new IdDt(myGroupId).toUnqualifiedVersionless().getValue();
|
||||
String actualGroupId =
|
||||
new IdDt(options.getGroupId()).toUnqualifiedVersionless().getValue();
|
||||
if (Objects.equals(expectedGroupId, actualGroupId)) {
|
||||
return newVerdict(
|
||||
theOperation,
|
||||
theRequestDetails,
|
||||
theInputResource,
|
||||
theInputResourceId,
|
||||
theOutputResource,
|
||||
theRuleApplier);
|
||||
}
|
||||
}
|
||||
|
||||
// 1. If each of the requested resource IDs in the parameters are present in the users permissions, Approve
|
||||
// 2. If any requested ID is not present in the users permissions, Deny.
|
||||
if (myWantExportStyle == BulkExportJobParameters.ExportStyle.PATIENT && isNotEmpty(myPatientIds)) {
|
||||
List<String> permittedPatientIds = myPatientIds.stream()
|
||||
.map(id -> new IdDt(id).toUnqualifiedVersionless().getValue())
|
||||
.collect(Collectors.toList());
|
||||
if (!options.getPatientIds().isEmpty()) {
|
||||
ourLog.debug("options.getPatientIds() != null");
|
||||
List<String> requestedPatientIds = options.getPatientIds().stream()
|
||||
.map(t -> new IdDt(t).toUnqualifiedVersionless().getValue())
|
||||
.collect(Collectors.toList());
|
||||
boolean requestedPatientsPermitted = true;
|
||||
for (String requestedPatientId : requestedPatientIds) {
|
||||
if (!permittedPatientIds.contains(requestedPatientId)) {
|
||||
requestedPatientsPermitted = false;
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (requestedPatientsPermitted) {
|
||||
return newVerdict(
|
||||
theOperation,
|
||||
theRequestDetails,
|
||||
theInputResource,
|
||||
theInputResourceId,
|
||||
theOutputResource,
|
||||
theRuleApplier);
|
||||
}
|
||||
|
||||
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
|
||||
}
|
||||
|
||||
final List<String> filters = options.getFilters();
|
||||
|
||||
if (!filters.isEmpty()) {
|
||||
ourLog.debug("filters not empty");
|
||||
final Set<String> patientIdsInFilters = filters.stream()
|
||||
.filter(filter -> filter.startsWith("Patient?_id="))
|
||||
.map(filter -> filter.replace("?_id=", "/"))
|
||||
.collect(Collectors.toUnmodifiableSet());
|
||||
|
||||
boolean filteredPatientIdsPermitted = true;
|
||||
for (String patientIdInFilters : patientIdsInFilters) {
|
||||
if (!permittedPatientIds.contains(patientIdInFilters)) {
|
||||
filteredPatientIdsPermitted = false;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if (filteredPatientIdsPermitted) {
|
||||
return newVerdict(
|
||||
theOperation,
|
||||
theRequestDetails,
|
||||
theInputResource,
|
||||
theInputResourceId,
|
||||
theOutputResource,
|
||||
theRuleApplier);
|
||||
}
|
||||
|
||||
return new AuthorizationInterceptor.Verdict(PolicyEnum.DENY, this);
|
||||
}
|
||||
ourLog.debug("patientIds and filters both empty");
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
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) {
|
||||
myWantExportStyle = BulkExportJobParameters.ExportStyle.GROUP;
|
||||
myGroupId = theGroupId;
|
||||
|
|
@ -193,6 +165,16 @@ public class RuleBulkExportImpl extends BaseRule {
|
|||
myPatientIds.add(thePatientId);
|
||||
}
|
||||
|
||||
public void setAppliesToPatientExport(Collection<String> thePatientIds) {
|
||||
myWantExportStyle = BulkExportJobParameters.ExportStyle.PATIENT;
|
||||
myPatientIds.addAll(thePatientIds);
|
||||
}
|
||||
|
||||
public void setAppliesToPatientExportAllPatients() {
|
||||
myWantExportStyle = BulkExportJobParameters.ExportStyle.PATIENT;
|
||||
myAppliesToAllPatients = true;
|
||||
}
|
||||
|
||||
public void setAppliesToSystem() {
|
||||
myWantExportStyle = BulkExportJobParameters.ExportStyle.SYSTEM;
|
||||
}
|
||||
|
|
@ -212,4 +194,14 @@ public class RuleBulkExportImpl extends BaseRule {
|
|||
BulkExportJobParameters.ExportStyle getWantExportStyle() {
|
||||
return myWantExportStyle;
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
Collection<String> getPatientIds() {
|
||||
return myPatientIds;
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
Collection<String> getResourceTypes() {
|
||||
return myResourceTypes;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,16 +1,23 @@
|
|||
package ca.uhn.fhir.rest.server.interceptor.auth;
|
||||
|
||||
import ca.uhn.fhir.model.primitive.IdDt;
|
||||
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
|
||||
import com.google.common.collect.Lists;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.Arguments;
|
||||
import org.junit.jupiter.params.provider.MethodSource;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.stream.Stream;
|
||||
|
||||
import static org.hamcrest.Matchers.contains;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.assertInstanceOf;
|
||||
import static org.mockito.Mockito.mock;
|
||||
|
||||
public class RuleBuilderTest {
|
||||
|
|
@ -98,7 +105,72 @@ public class RuleBuilderTest {
|
|||
builder.allow().bulkExport().patientExportOnPatient("Patient/pat2").withResourceTypes(resourceTypes);
|
||||
List<IAuthRule> rules = builder.build();
|
||||
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
|
||||
|
|
|
|||
|
|
@ -4,6 +4,9 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
|
|||
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.bulk.BulkExportJobParameters;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Nested;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
|
|
@ -13,7 +16,6 @@ import java.util.HashSet;
|
|||
import java.util.Set;
|
||||
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertNull;
|
||||
import static org.mockito.ArgumentMatchers.any;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
|
|
@ -28,10 +30,11 @@ public class RuleBulkExportImplTest {
|
|||
@Mock
|
||||
private Set<AuthorizationFlagsEnum> myFlags;
|
||||
|
||||
|
||||
@Test
|
||||
public void testDenyBulkRequestWithInvalidResourcesTypes() {
|
||||
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
|
||||
|
||||
myRule.setMode(PolicyEnum.ALLOW);
|
||||
Set<String> myTypes = new HashSet<>();
|
||||
myTypes.add("Patient");
|
||||
myTypes.add("Practitioner");
|
||||
|
|
@ -42,33 +45,210 @@ public class RuleBulkExportImplTest {
|
|||
|
||||
BulkExportJobParameters options = new BulkExportJobParameters();
|
||||
options.setResourceTypes(myWantTypes);
|
||||
|
||||
|
||||
when(myRequestDetails.getAttribute(any())).thenReturn(options);
|
||||
|
||||
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
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
|
||||
public void testBulkRequestWithValidResourcesTypes() {
|
||||
public void testBulkExportSystem_ruleHasTypes_RequestWithTypes_allow() {
|
||||
RuleBulkExportImpl myRule = new RuleBulkExportImpl("a");
|
||||
|
||||
Set<String> myTypes = new HashSet<>();
|
||||
myTypes.add("Patient");
|
||||
myTypes.add("Practitioner");
|
||||
myRule.setResourceTypes(myTypes);
|
||||
|
||||
Set<String> myWantTypes = new HashSet<>();
|
||||
myWantTypes.add("Patient");
|
||||
myWantTypes.add("Practitioner");
|
||||
myRule.setMode(PolicyEnum.ALLOW);
|
||||
myRule.setAppliesToSystem();
|
||||
myRule.setResourceTypes(Set.of("Patient", "Practitioner"));
|
||||
|
||||
BulkExportJobParameters options = new BulkExportJobParameters();
|
||||
options.setResourceTypes(myWantTypes);
|
||||
options.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
|
||||
options.setResourceTypes(Set.of("Patient", "Practitioner"));
|
||||
|
||||
when(myRequestDetails.getAttribute(any())).thenReturn(options);
|
||||
|
||||
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
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
|
||||
|
|
@ -84,7 +264,7 @@ public class RuleBulkExportImplTest {
|
|||
when(myRequestDetails.getAttribute(any())).thenReturn(options);
|
||||
|
||||
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
assertEquals(null, verdict);
|
||||
assertAbstain(verdict);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -100,7 +280,7 @@ public class RuleBulkExportImplTest {
|
|||
when(myRequestDetails.getAttribute(any())).thenReturn(options);
|
||||
|
||||
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
|
||||
assertAllow(verdict);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -118,7 +298,7 @@ public class RuleBulkExportImplTest {
|
|||
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
|
||||
//Then: We permit the request, as a patient ID that was requested is honoured by this rule.
|
||||
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
|
||||
assertAllow(verdict);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -135,8 +315,8 @@ public class RuleBulkExportImplTest {
|
|||
//When
|
||||
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.
|
||||
assertEquals(PolicyEnum.DENY, verdict.getDecision());
|
||||
//Then: abstain
|
||||
assertDeny(verdict);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -153,28 +333,45 @@ public class RuleBulkExportImplTest {
|
|||
AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
|
||||
//Then: We make no claims about type-level export on Patient.
|
||||
assertEquals(null, verdict);
|
||||
assertAbstain(verdict);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypePatient() {
|
||||
public void testPatientExportRulesWithId_withRequestNoIds_abstains() {
|
||||
//Given
|
||||
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
|
||||
RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
|
||||
myRule.setAppliesToPatientExport("Patient/123");
|
||||
myRule.setMode(PolicyEnum.ALLOW);
|
||||
final BulkExportJobParameters options = new BulkExportJobParameters();
|
||||
BulkExportJobParameters options = new BulkExportJobParameters();
|
||||
|
||||
options.setExportStyle(BulkExportJobParameters.ExportStyle.PATIENT);
|
||||
options.setFilters(Set.of("Patient?_id=123"));
|
||||
options.setResourceTypes(Set.of("Patient"));
|
||||
when(myRequestDetails.getAttribute(any())).thenReturn(options);
|
||||
|
||||
//When
|
||||
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
|
||||
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
|
||||
//Then: We make no claims about type-level export on Patient.
|
||||
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
|
||||
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterResourceTypePatientAndFilterHasResources() {
|
||||
//Given
|
||||
|
|
@ -191,27 +388,9 @@ public class RuleBulkExportImplTest {
|
|||
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
|
||||
//Then: The patient IDs match so this is permitted
|
||||
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
|
||||
public void testPatientExportRulesOnTypeLevelExportWithTypeFilterNoResourceType() {
|
||||
|
|
@ -227,27 +406,8 @@ public class RuleBulkExportImplTest {
|
|||
//When
|
||||
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
|
||||
//Then: The patient IDs match so this is permitted
|
||||
assertEquals(PolicyEnum.ALLOW, verdict.getDecision());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void 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());
|
||||
//Then: Filters are ignored for auth purposes. The rule has an ID, indicating it is for instance level, but the job requested type level. Abstain
|
||||
assertAbstain(verdict);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -265,12 +425,12 @@ public class RuleBulkExportImplTest {
|
|||
//When
|
||||
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
|
||||
//Then: We do not have permissions on the requested patient so this is not permitted.
|
||||
assertEquals(PolicyEnum.DENY, verdict.getDecision());
|
||||
//Then: We do not have permissions on the requested patient so we abstain
|
||||
assertDeny(verdict);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testPatientExportRulesOnTypeLevelExportPermittedPatient() {
|
||||
public void testPatientExport_ruleAllowsId_requestsId_allow() {
|
||||
//Given
|
||||
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
|
||||
myRule.setAppliesToPatientExport("Patient/123");
|
||||
|
|
@ -289,7 +449,7 @@ public class RuleBulkExportImplTest {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testPatientExportRulesOnTypeLevelExportPermittedPatients() {
|
||||
public void testPatientExport_ruleAllowsIds_requestsIds_allow() {
|
||||
//Given
|
||||
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
|
||||
myRule.setAppliesToPatientExport("Patient/123");
|
||||
|
|
@ -309,7 +469,7 @@ public class RuleBulkExportImplTest {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testPatientExportRulesOnTypeLevelExportWithPermittedAndUnpermittedPatients() {
|
||||
public void testPatientExport_ruleAllowsId_requestsTooManyIds_abstain() {
|
||||
//Given
|
||||
final RuleBulkExportImpl myRule = new RuleBulkExportImpl("b");
|
||||
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);
|
||||
|
||||
//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
|
||||
public void testPatientExportRulesOnTypeLevelExportWithPermittedAndUnpermittedPatientFilters() {
|
||||
//Given
|
||||
|
|
@ -341,7 +554,22 @@ public class RuleBulkExportImplTest {
|
|||
//When
|
||||
final AuthorizationInterceptor.Verdict verdict = myRule.applyRule(myOperation, myRequestDetails, null, null, null, myRuleApplier, myFlags, myPointcut);
|
||||
|
||||
//Then: There are unpermitted patients in the request so this is not permitted.
|
||||
assertEquals(PolicyEnum.DENY, verdict.getDecision());
|
||||
//Then: There are unpermitted patients in the request so this is not permitted. abstain.
|
||||
assertAbstain(verdict);
|
||||
|
||||
}
|
||||
|
||||
private static void assertAbstain(AuthorizationInterceptor.Verdict verdict) {
|
||||
Assertions.assertEquals(null, verdict, "Expect abstain");
|
||||
}
|
||||
|
||||
private static void assertAllow(AuthorizationInterceptor.Verdict verdict) {
|
||||
Assertions.assertNotNull(verdict, "Expect ALLOW, got abstain");
|
||||
Assertions.assertEquals(PolicyEnum.ALLOW, verdict.getDecision(), "Expect ALLOW");
|
||||
}
|
||||
|
||||
private static void assertDeny(AuthorizationInterceptor.Verdict verdict) {
|
||||
Assertions.assertNotNull(verdict, "Expect DENY, got abstain");
|
||||
Assertions.assertEquals(PolicyEnum.DENY, verdict.getDecision(), "Expect DENY");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -308,6 +308,14 @@ public abstract class BaseTask {
|
|||
}
|
||||
}
|
||||
|
||||
public void doNothing() {
|
||||
setDoNothing(true);
|
||||
}
|
||||
|
||||
public void failureAllowed() {
|
||||
setFailureAllowed(true);
|
||||
}
|
||||
|
||||
public boolean isDoNothing() {
|
||||
return myDoNothing;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -22,11 +22,8 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
|
|||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
|
||||
import org.apache.commons.lang3.builder.HashCodeBuilder;
|
||||
import org.intellij.lang.annotations.Language;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.jdbc.core.ColumnMapRowMapper;
|
||||
import org.springframework.jdbc.core.JdbcTemplate;
|
||||
|
||||
import java.sql.SQLException;
|
||||
import java.util.Set;
|
||||
|
|
@ -51,53 +48,12 @@ public class RenameTableTask extends BaseTableTask {
|
|||
setDescription("Rename table " + getOldTableName());
|
||||
}
|
||||
|
||||
private void handleTableWithNewTableName() throws SQLException {
|
||||
|
||||
if (!myDeleteTargetColumnFirstIfExist) {
|
||||
throw new SQLException(Msg.code(2517) + "Can not rename " + getOldTableName() + " to " + getNewTableName()
|
||||
+ " because a table with name " + getNewTableName() + " already exists");
|
||||
}
|
||||
|
||||
// a table with the new tableName already exists and we can delete it. we will only do so if it is empty.
|
||||
Integer rowsWithData = getConnectionProperties().getTxTemplate().execute(t -> {
|
||||
String sql = "SELECT * FROM " + getNewTableName();
|
||||
JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
|
||||
jdbcTemplate.setMaxRows(1);
|
||||
return jdbcTemplate.query(sql, new ColumnMapRowMapper()).size();
|
||||
});
|
||||
|
||||
if (rowsWithData != null && rowsWithData > 0) {
|
||||
throw new SQLException(Msg.code(2518) + "Can not rename " + getOldTableName() + " to " + getNewTableName()
|
||||
+ " because a table with name " + getNewTableName() + " already exists and is populated.");
|
||||
}
|
||||
|
||||
logInfo(
|
||||
ourLog,
|
||||
"Table {} already exists - Going to drop it before renaming table {} to {}",
|
||||
getNewTableName(),
|
||||
getOldTableName(),
|
||||
getNewTableName());
|
||||
|
||||
@Language("SQL")
|
||||
String sql = "DROP TABLE " + getNewTableName();
|
||||
executeSql(getNewTableName(), sql);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void doExecute() throws SQLException {
|
||||
|
||||
Set<String> tableNames = JdbcUtils.getTableNames(getConnectionProperties());
|
||||
boolean hasTableWithNewTableName = tableNames.contains(getNewTableName());
|
||||
|
||||
if (!tableNames.contains(getOldTableName())) {
|
||||
throw new SQLException(Msg.code(2516) + "Can not rename " + getOldTableName() + " to " + getNewTableName()
|
||||
+ " because the original table does not exists");
|
||||
}
|
||||
|
||||
if (hasTableWithNewTableName) {
|
||||
handleTableWithNewTableName();
|
||||
}
|
||||
|
||||
String sql = buildRenameTableSqlStatement();
|
||||
logInfo(ourLog, "Renaming table: {}", getOldTableName());
|
||||
|
||||
|
|
|
|||
|
|
@ -57,6 +57,7 @@ import java.util.Collections;
|
|||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
|
|
@ -185,6 +186,7 @@ public class Builder {
|
|||
private final String myRelease;
|
||||
private final BaseMigrationTasks.IAcceptsTasks mySink;
|
||||
private final String myTableName;
|
||||
private BaseTask myLastAddedTask;
|
||||
|
||||
public BuilderWithTableName(String theRelease, BaseMigrationTasks.IAcceptsTasks theSink, String theTableName) {
|
||||
myRelease = theRelease;
|
||||
|
|
@ -274,6 +276,7 @@ public class Builder {
|
|||
@Override
|
||||
public void addTask(BaseTask theTask) {
|
||||
((BaseTableTask) theTask).setTableName(myTableName);
|
||||
myLastAddedTask = theTask;
|
||||
mySink.addTask(theTask);
|
||||
}
|
||||
|
||||
|
|
@ -311,6 +314,10 @@ public class Builder {
|
|||
return this;
|
||||
}
|
||||
|
||||
public Optional<BaseTask> getLastAddedTask() {
|
||||
return Optional.ofNullable(myLastAddedTask);
|
||||
}
|
||||
|
||||
/**
|
||||
* @param theFkName the name of the foreign key
|
||||
* @param theParentTableName the name of the table that exports the foreign key
|
||||
|
|
@ -323,31 +330,37 @@ public class Builder {
|
|||
addTask(task);
|
||||
}
|
||||
|
||||
public void renameTable(String theVersion, String theNewTableName) {
|
||||
public BuilderCompleteTask renameTable(String theVersion, String theNewTableName) {
|
||||
RenameTableTask task = new RenameTableTask(myRelease, theVersion, getTableName(), theNewTableName);
|
||||
addTask(task);
|
||||
return new BuilderCompleteTask(task);
|
||||
}
|
||||
|
||||
public void migratePostgresTextClobToBinaryClob(String theVersion, String theColumnName) {
|
||||
public BuilderCompleteTask migratePostgresTextClobToBinaryClob(String theVersion, String theColumnName) {
|
||||
MigratePostgresTextClobToBinaryClobTask task =
|
||||
new MigratePostgresTextClobToBinaryClobTask(myRelease, theVersion);
|
||||
task.setTableName(getTableName());
|
||||
task.setColumnName(theColumnName);
|
||||
addTask(task);
|
||||
return new BuilderCompleteTask(task);
|
||||
}
|
||||
|
||||
public void migrateBlobToBinary(String theVersion, String theFromColumName, String theToColumName) {
|
||||
public BuilderCompleteTask migrateBlobToBinary(
|
||||
String theVersion, String theFromColumName, String theToColumName) {
|
||||
MigrateColumBlobTypeToBinaryTypeTask task = new MigrateColumBlobTypeToBinaryTypeTask(
|
||||
myRelease, theVersion, getTableName(), theFromColumName, theToColumName);
|
||||
|
||||
addTask(task);
|
||||
return new BuilderCompleteTask(task);
|
||||
}
|
||||
|
||||
public void migrateClobToText(String theVersion, String theFromColumName, String theToColumName) {
|
||||
public BuilderCompleteTask migrateClobToText(
|
||||
String theVersion, String theFromColumName, String theToColumName) {
|
||||
MigrateColumnClobTypeToTextTypeTask task = new MigrateColumnClobTypeToTextTypeTask(
|
||||
myRelease, theVersion, getTableName(), theFromColumName, theToColumName);
|
||||
|
||||
addTask(task);
|
||||
return new BuilderCompleteTask(task);
|
||||
}
|
||||
|
||||
public class BuilderAddIndexWithName {
|
||||
|
|
|
|||
|
|
@ -41,26 +41,4 @@ public class RenameTableTaskTest extends BaseTest {
|
|||
assertThat(tableNames, not(hasItem(oldTableName)));
|
||||
}
|
||||
|
||||
@ParameterizedTest(name = "{index}: {0}")
|
||||
@MethodSource("data")
|
||||
public void testRenameTableTask_whenTableDoesNotExists_willRaiseException(Supplier<TestDatabaseDetails> theTestDatabaseDetails) throws SQLException {
|
||||
// given
|
||||
before(theTestDatabaseDetails);
|
||||
final String newTableName = "NEWTABLE";
|
||||
final String oldTableName = "SOMETABLE";
|
||||
|
||||
RenameTableTask task = new RenameTableTask("1", "1", oldTableName, newTableName);
|
||||
getMigrator().addTask(task);
|
||||
|
||||
// when
|
||||
try {
|
||||
getMigrator().migrate();
|
||||
fail();
|
||||
} catch (Exception e){
|
||||
// then
|
||||
assertThat(e.getMessage(), containsString("2516"));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -436,6 +436,16 @@ public class BulkDataImportProviderTest {
|
|||
public boolean isResourcePartitionable(String theResourceType) {
|
||||
return false;
|
||||
}
|
||||
|
||||
@Override
|
||||
public RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId) {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId) {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
private Date parseDate(String theString) {
|
||||
|
|
|
|||
|
|
@ -1,3 +1,22 @@
|
|||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Clinical Reasoning
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
package ca.uhn.fhir.cr.r4;
|
||||
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
|
|
|
|||
|
|
@ -1,3 +1,22 @@
|
|||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Clinical Reasoning
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
package ca.uhn.fhir.cr.r4;
|
||||
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
|
|
|
|||
|
|
@ -1,3 +1,22 @@
|
|||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Clinical Reasoning
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
package ca.uhn.fhir.cr.r4.measure;
|
||||
|
||||
import ca.uhn.fhir.cr.r4.ICollectDataServiceFactory;
|
||||
|
|
|
|||
|
|
@ -1,3 +1,22 @@
|
|||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Clinical Reasoning
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
package ca.uhn.fhir.cr.r4.measure;
|
||||
|
||||
import ca.uhn.fhir.cr.r4.IDataRequirementsServiceFactory;
|
||||
|
|
|
|||
|
|
@ -102,7 +102,9 @@ public class DaoTestDataBuilder implements ITestDataBuilder.WithSupport, ITestDa
|
|||
public void cleanup() {
|
||||
ourLog.info("cleanup {}", myIds);
|
||||
|
||||
myIds.keySet().forEach(nextType->{
|
||||
myIds.keySet().stream()
|
||||
.sorted() // Hack to ensure Patients are deleted before Practitioners. This may need to be refined.
|
||||
.forEach(nextType->{
|
||||
// todo do this in a bundle for perf.
|
||||
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(nextType);
|
||||
myIds.get(nextType).forEach(dao::delete);
|
||||
|
|
|
|||
|
|
@ -360,6 +360,14 @@ public class JpaStorageSettings extends StorageSettings {
|
|||
*/
|
||||
private long myRestDeleteByUrlResourceIdThreshold = DEFAULT_REST_DELETE_BY_URL_RESOURCE_ID_THRESHOLD;
|
||||
|
||||
/**
|
||||
* If enabled, this setting causes persisting data to legacy LOB columns as well as columns introduced
|
||||
* to migrate away from LOB columns which effectively duplicates stored information.
|
||||
*
|
||||
* @since 7.2.0
|
||||
*/
|
||||
private boolean myWriteToLegacyLobColumns = false;
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
|
|
@ -2423,8 +2431,8 @@ public class JpaStorageSettings extends StorageSettings {
|
|||
* This setting controls the validation issue severity to report when a code validation
|
||||
* finds that the code is present in the given CodeSystem, but the display name being
|
||||
* validated doesn't match the expected value(s). Defaults to
|
||||
* {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#WARNING}. Set this
|
||||
* value to {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#INFORMATION}
|
||||
* {@link IValidationSupport.IssueSeverity#WARNING}. Set this
|
||||
* value to {@link IValidationSupport.IssueSeverity#INFORMATION}
|
||||
* if you don't want to see display name validation issues at all in resource validation
|
||||
* outcomes.
|
||||
*
|
||||
|
|
@ -2439,8 +2447,8 @@ public class JpaStorageSettings extends StorageSettings {
|
|||
* This setting controls the validation issue severity to report when a code validation
|
||||
* finds that the code is present in the given CodeSystem, but the display name being
|
||||
* validated doesn't match the expected value(s). Defaults to
|
||||
* {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#WARNING}. Set this
|
||||
* value to {@link ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity#INFORMATION}
|
||||
* {@link IValidationSupport.IssueSeverity#WARNING}. Set this
|
||||
* value to {@link IValidationSupport.IssueSeverity#INFORMATION}
|
||||
* if you don't want to see display name validation issues at all in resource validation
|
||||
* outcomes.
|
||||
*
|
||||
|
|
@ -2454,6 +2462,33 @@ public class JpaStorageSettings extends StorageSettings {
|
|||
myIssueSeverityForCodeDisplayMismatch = theIssueSeverityForCodeDisplayMismatch;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method returns whether data will be stored in LOB columns as well as the columns
|
||||
* introduced to migrate away from LOB. Writing to LOB columns is set to false by
|
||||
* default. Enabling the setting will effectively double the persisted information.
|
||||
* If enabled, a careful monitoring of LOB table (if applicable) is required to avoid
|
||||
* exceeding the table maximum capacity.
|
||||
*
|
||||
* @since 7.2.0
|
||||
*/
|
||||
public boolean isWriteToLegacyLobColumns() {
|
||||
return myWriteToLegacyLobColumns;
|
||||
}
|
||||
|
||||
/**
|
||||
* This setting controls whether data will be stored in LOB columns as well as the columns
|
||||
* introduced to migrate away from LOB. Writing to LOB columns is set to false by
|
||||
* default. Enabling the setting will effectively double the persisted information.
|
||||
* When enabled, a careful monitoring of LOB table (if applicable) is required to avoid
|
||||
* exceeding the table maximum capacity.
|
||||
*
|
||||
* @param theWriteToLegacyLobColumns
|
||||
* @since 7.2.0
|
||||
*/
|
||||
public void setWriteToLegacyLobColumns(boolean theWriteToLegacyLobColumns) {
|
||||
myWriteToLegacyLobColumns = theWriteToLegacyLobColumns;
|
||||
}
|
||||
|
||||
/**
|
||||
* This setting controls whether MdmLink and other non-resource DB history is enabled.
|
||||
* <p/>
|
||||
|
|
|
|||
|
|
@ -333,10 +333,6 @@ public abstract class BaseRequestPartitionHelperSvc implements IRequestPartition
|
|||
return !myNonPartitionableResourceNames.contains(theResourceType);
|
||||
}
|
||||
|
||||
protected abstract RequestPartitionId validateAndNormalizePartitionIds(RequestPartitionId theRequestPartitionId);
|
||||
|
||||
protected abstract RequestPartitionId validateAndNormalizePartitionNames(RequestPartitionId theRequestPartitionId);
|
||||
|
||||
private void validateSinglePartitionForCreate(
|
||||
RequestPartitionId theRequestPartitionId, @Nonnull String theResourceName, Pointcut thePointcut) {
|
||||
validateRequestPartitionNotNull(theRequestPartitionId, thePointcut);
|
||||
|
|
|
|||
Loading…
Reference in New Issue