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7 2 mergeback may 10 v2 (#5928)
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* 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 hapifhir/hapi-fhir-jpaserver-starter#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 hapifhir/hapi-fhir-jpaserver-starter#675 (#5892)

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

* Enhance mdm interceptor (#5899)

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

* Added javadoc

* Cahngelog

* spotless

---------

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

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

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

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

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

* Add changelog.

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

Commit code reviewer suggestion.

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

---------

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

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

* Failing test.

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

* Implement fix.

* Spotless.

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

* Fix changelog file.

* Apply suggestions from code review

Apply code review suggestions.

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

* Spotless

---------

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

* cve fix (#5906)

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

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

* Fixing issues with postgres LOB migration.

* addressing code review comments for audit/transaction logs.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for BinaryStorageEntity migration post code review.

* test and implementation for TermConcept
 migration post code review.

* applying spotless

* test and implementation for TermConceptProperty
 migration post code review.

* test and implementation for TermValueSetConcept
 migration post code review.

* fixing migration version

* fixing migration task

* changelog

* fixing changelog

* Minor renames

* addressing comments and suggestions from second code review.

* passing tests

* fixing more tests

---------

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

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

* spotless

* Cahgnelog, tests

* more tests

* refactor style checks

---------

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

* Convert a few nulls to aggressive denies

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

* Change sort type on chains

* Change sort type on chains

* Test for MS SQL

* Comments

* Version bump

* version bump to 7.3.1-SNAPSHOT

---------

Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
Co-authored-by: Michael Buckley <michaelabuckley@gmail.com>
Co-authored-by: Long Ma <long@smilecdr.com>
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@longma1 @lukedegruchy
@epeartree @nathandoef @TipzCM @dotasek @jkiddo @tadgh @michaelabuckley
11 people authored May 13, 2024
1 parent 3572d59 commit 078e87a
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Showing 145 changed files with 1,713 additions and 521 deletions.
2 changes: 1 addition & 1 deletion hapi-deployable-pom/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-android/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-base/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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8 changes: 7 additions & 1 deletion hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java
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Expand Up @@ -2387,13 +2387,19 @@ public enum Pointcut implements IPointcut {
* <li>
* ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent - Contains information about the from and to resources.
* </li>
* <li>
* ca.uhn.fhir.mdm.model.mdmevents.MdmTransactionContext - Contains information about the Transaction context, e.g. merge or link.
* </li>
* </ul>
* <p>
* Hooks should return <code>void</code>.
* </p>
*/
MDM_POST_MERGE_GOLDEN_RESOURCES(
void.class, "ca.uhn.fhir.rest.api.server.RequestDetails", "ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent"),
void.class,
"ca.uhn.fhir.rest.api.server.RequestDetails",
"ca.uhn.fhir.mdm.model.mdmevents.MdmMergeEvent",
"ca.uhn.fhir.mdm.model.MdmTransactionContext"),

/**
* <b>MDM Link History Hook:</b>
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4 changes: 2 additions & 2 deletions hapi-fhir-bom/pom.xml
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Expand Up @@ -4,15 +4,15 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>

<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-checkstyle/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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11 changes: 9 additions & 2 deletions hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
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Expand Up @@ -19,6 +19,7 @@
*/
package ca.uhn.fhir.cli;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
Expand All @@ -31,6 +32,7 @@
import ca.uhn.fhir.util.AttachmentUtil;
import ca.uhn.fhir.util.FileUtil;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
Expand Down Expand Up @@ -265,7 +267,7 @@ private void invokeOperation(
"Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
}

private void addFileToRequestBundle(IBaseParameters theInputParameters, String theFileName, byte[] theBytes) {
protected void addFileToRequestBundle(IBaseParameters theInputParameters, String theFileName, byte[] theBytes) {

byte[] bytes = theBytes;
String fileName = theFileName;
Expand All @@ -277,7 +279,7 @@ private void addFileToRequestBundle(IBaseParameters theInputParameters, String t
FileUtil.formatFileSize(ourTransferSizeLimit));

try {
File tempFile = File.createTempFile("hapi-fhir-cli", suffix);
File tempFile = File.createTempFile("hapi-fhir-cli", "." + suffix);
tempFile.deleteOnExit();
try (OutputStream fileOutputStream = new FileOutputStream(tempFile, false)) {
fileOutputStream.write(bytes);
Expand Down Expand Up @@ -363,4 +365,9 @@ static String stripPath(String thePath) {
}
return retVal;
}

@VisibleForTesting
void setFhirContext(FhirContext theFhirContext) {
myFhirCtx = theFhirContext;
}
}
87 changes: 87 additions & 0 deletions ...hir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,10 @@
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.r4.model.Attachment;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Type;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
Expand All @@ -43,6 +47,7 @@
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
Expand All @@ -54,6 +59,8 @@
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertInstanceOf;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyList;
Expand Down Expand Up @@ -479,6 +486,86 @@ public void testUploadTerminologyWithEndpointValidation(String theFhirVersion, b
uploadICD10UsingCompressedFile(theFhirVersion, theIncludeTls);
}

@ParameterizedTest
@MethodSource("paramsProvider")
@SuppressWarnings("unused") // Both params for @BeforeEach
void testZipFileInParameters(String theFhirVersion, boolean theIncludeTls) {
final IBaseParameters inputParameters = switch (myCtx.getVersion().getVersion()) {
case DSTU2, DSTU2_HL7ORG, DSTU2_1 -> new org.hl7.fhir.dstu2.model.Parameters();
case DSTU3 -> new org.hl7.fhir.dstu3.model.Parameters();
case R4 -> new Parameters();
case R4B -> new org.hl7.fhir.r4b.model.Parameters();
case R5 -> new org.hl7.fhir.r5.model.Parameters();
};

final UploadTerminologyCommand uploadTerminologyCommand = new UploadTerminologyCommand();
uploadTerminologyCommand.setFhirContext(myCtx);
uploadTerminologyCommand.setTransferSizeBytes(1);

uploadTerminologyCommand.addFileToRequestBundle(inputParameters, "something.zip", new byte[] {1,2});

final String actualAttachmentUrl = getAttachmentUrl(inputParameters, myCtx);
assertTrue(actualAttachmentUrl.endsWith(".zip"));
}

private static String getAttachmentUrl(IBaseParameters theInputParameters, FhirContext theCtx) {
switch (theCtx.getVersion().getVersion()) {
case DSTU2:
case DSTU2_HL7ORG:
case DSTU2_1: {
assertInstanceOf(org.hl7.fhir.dstu2.model.Parameters.class, theInputParameters);
final org.hl7.fhir.dstu2.model.Parameters dstu2Parameters = (org.hl7.fhir.dstu2.model.Parameters) theInputParameters;
final List<org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent> dstu2ParametersList = dstu2Parameters.getParameter();
final Optional<org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent> optDstu2FileParam = dstu2ParametersList.stream().filter(param -> TerminologyUploaderProvider.PARAM_FILE.equals(param.getName())).findFirst();
assertTrue(optDstu2FileParam.isPresent());
final org.hl7.fhir.dstu2.model.Type dstu2Value = optDstu2FileParam.get().getValue();
assertInstanceOf(org.hl7.fhir.dstu2.model.Attachment.class, dstu2Value);
final org.hl7.fhir.dstu2.model.Attachment dstu2Attachment = (org.hl7.fhir.dstu2.model.Attachment) dstu2Value;
return dstu2Attachment.getUrl();
}
case DSTU3: {
assertInstanceOf(org.hl7.fhir.dstu3.model.Parameters.class, theInputParameters);
final org.hl7.fhir.dstu3.model.Parameters dstu3Parameters = (org.hl7.fhir.dstu3.model.Parameters) theInputParameters;
final List<org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent> dstu3ParametersList = dstu3Parameters.getParameter();
final Optional<org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent> optDstu3FileParam = dstu3ParametersList.stream().filter(param -> TerminologyUploaderProvider.PARAM_FILE.equals(param.getName())).findFirst();
assertTrue(optDstu3FileParam.isPresent());
final org.hl7.fhir.dstu3.model.Type dstu3Value = optDstu3FileParam.get().getValue();
assertInstanceOf(org.hl7.fhir.dstu3.model.Attachment.class, dstu3Value);
final org.hl7.fhir.dstu3.model.Attachment dstu3Attachment = (org.hl7.fhir.dstu3.model.Attachment) dstu3Value;
return dstu3Attachment.getUrl();
}
case R4: {
assertInstanceOf(Parameters.class, theInputParameters);
final Parameters r4Parameters = (Parameters) theInputParameters;
final Parameters.ParametersParameterComponent r4Parameter = r4Parameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
final Type r4Value = r4Parameter.getValue();
assertInstanceOf(Attachment.class, r4Value);
final Attachment r4Attachment = (Attachment) r4Value;
return r4Attachment.getUrl();
}
case R4B: {
assertInstanceOf(org.hl7.fhir.r4b.model.Parameters.class, theInputParameters);
final org.hl7.fhir.r4b.model.Parameters r4bParameters = (org.hl7.fhir.r4b.model.Parameters) theInputParameters;
final org.hl7.fhir.r4b.model.Parameters.ParametersParameterComponent r4bParameter = r4bParameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
final org.hl7.fhir.r4b.model.DataType value = r4bParameter.getValue();
assertInstanceOf(org.hl7.fhir.r4b.model.Attachment.class, value);
final org.hl7.fhir.r4b.model.Attachment r4bAttachment = (org.hl7.fhir.r4b.model.Attachment) value;
return r4bAttachment.getUrl();
}
case R5: {
assertInstanceOf(org.hl7.fhir.r5.model.Parameters.class, theInputParameters);
final org.hl7.fhir.r5.model.Parameters r4Parameters = (org.hl7.fhir.r5.model.Parameters) theInputParameters;
final org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent parameter = r4Parameters.getParameter(TerminologyUploaderProvider.PARAM_FILE);
final org.hl7.fhir.r5.model.DataType value = parameter.getValue();
assertInstanceOf(org.hl7.fhir.r5.model.Attachment.class, value);
final org.hl7.fhir.r5.model.Attachment attachment = (org.hl7.fhir.r5.model.Attachment) value;
return attachment.getUrl();
}
default:
throw new IllegalStateException("Unknown FHIR version: " + theCtx.getVersion().getVersion());
}
}

private void uploadICD10UsingCompressedFile(String theFhirVersion, boolean theIncludeTls) throws IOException {
if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
Expand Down
2 changes: 1 addition & 1 deletion hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-cli/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-client-okhttp/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-client/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-converter/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-dist/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-docs/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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4 changes: 4 additions & 0 deletions ...ca/uhn/hapi/fhir/changelog/7_2_0/5861-enhance-rule-builder-code-support-multiple-ids.yaml
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---
type: add
issue: 5861
title: "Enhance RuleBuilder code to support multiple instance IDs."
5 changes: 5 additions & 0 deletions ...ources/ca/uhn/hapi/fhir/changelog/7_2_0/5865-updating-name-of-full-text-field-search.yaml
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---
type: fix
issue: 5865
title: "Moving the Hibernate.Search annotation for text indexing from the lob column to the column added as part of the
PostgreSql LOB migration."
5 changes: 5 additions & 0 deletions .../hapi/fhir/changelog/7_2_0/5877-exception-when-updating-token-param-with-large-value.yaml
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---
type: fix
issue: 5877
title: "Previously, updating a tokenParam with a value greater than 200 characters would raise a SQLException.
This issue has been fixed."
6 changes: 6 additions & 0 deletions ...ca/uhn/hapi/fhir/changelog/7_2_0/5886-mdm-apply-survivorship-number-format-exception.yaml
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---
type: fix
issue: 5886
title: "Previously, either updating links on, or deleting one of two patients with non-numeric IDs linked to a golden
patient would result in a HAPI-0389 if there were survivorship rules.
This issue has been fixed for both the update links and delete cases."
7 changes: 7 additions & 0 deletions .../uhn/hapi/fhir/changelog/7_2_0/5888-update-binary-security-interceptor-documentation.yaml
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---
type: fix
issue: 5888
title: "Updated documentation on binary_security_interceptor to specify using
`STORAGE_PRE_INITIATE_BULK_EXPORT` not `STORAGE_INITIATE_BULK_EXPORT` pointcut
to change bulk export parameters.
"
5 changes: 5 additions & 0 deletions ...ca/uhn/hapi/fhir/changelog/7_2_0/5890-add-possibility-to-persist-data-to-lob-columns.yaml
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---
type: add
issue: 5890
title: "As part of the migration from LOB, provided the capability to force persisting data to LOB columns. The default
behavior is to not persist in lob columns."
6 changes: 6 additions & 0 deletions ...ca/uhn/hapi/fhir/changelog/7_2_0/5893-hapi-fhir-cli-upload-terminology-zip-hapi-0862.yaml
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---
type: fix
issue: 5893
title: "Previously, hapi-fhir-cli: upload-terminology failed with a HAPI-0862 error when uploading LOINC.
This has been fixed."

5 changes: 5 additions & 0 deletions ...es/ca/uhn/hapi/fhir/changelog/7_2_0/5898-ld-megascale-meta-operation-fails-hapi-0389.yaml
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---
type: fix
issue: 5898
title: "Previously, triggering a `$meta` via GET on a new patient with Megascale configured resulted in error HAPI-0389. This has been corrected
This has been fixed."
4 changes: 4 additions & 0 deletions ...ocs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5899-enhance-mdm-interceptor.yaml
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---
type: add
issue: 5899
title: "The `MDM_POST_MERGE_GOLDEN_RESOURCES` now supports an additional parameter, of type `ca.uhn.fhir.mdm.model.MdmTransactionContext`. Thanks to Jens Villadsen for the contribution."
4 changes: 4 additions & 0 deletions ...ources/ca/uhn/hapi/fhir/changelog/7_2_0/5904-query-chained-sort-returns-less-results.yaml
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---
type: fix
issue: 5904
title: "Chained sort would exclude results that did not have resources matching the sort chain. These are now included, and sorted at the end."
4 changes: 4 additions & 0 deletions ...s/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5915-bulk-export-security-woes.yaml
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---
type: fix
issue: 5915
title: "Previously, in some edge case scenarios the Bulk Export Rule Applier could accidentally permit a Patient type level bulk export request, even if the calling user only had permissions to a subset of patients. This has been corrected."
4 changes: 4 additions & 0 deletions ...-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5917-chain-sort-mssql.yaml
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---
type: fix
issue: 5917
title: "Fix chained sorts on strings when using MS Sql"
7 changes: 6 additions & 1 deletion ...rc/main/resources/ca/uhn/hapi/fhir/docs/security/binary_security_interceptor.md
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Expand Up @@ -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.
2 changes: 1 addition & 1 deletion hapi-fhir-jacoco/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.3.1-SNAPSHOT</version>
<version>7.3.2-SNAPSHOT</version>

<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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