Mergeback 1 rel 8 6 (#7360)

* increase memory to elastic search container (#7326)

Co-authored-by: jdar <[email protected]>

* 7282 - Added the ability for an Interceptor to alter the HTTP Response Code when an Exception is thrown (#7303)

* 7282 - Added the ability for an Interceptor to alter the HTTP Response Code when an Exception is thrown.

* Enhanced the solution based on code review feedback.

* Removed a class that was being used to store the Http response Code and used the existing HttpStatus class instead.

* Enhanced the Unit Test.

* Enhanced the Javadoc for the Pointcut.SERVER_OUTGOING_FAILURE_OPERATIONOUTCOME enum.

* Changed the Interceptor Hook implementation based on Code Review feedback.

* Removed an unused variable declaration.

* Removed an unused variable declaration.

* Ran mvn spotless:apply to apply proper formatting.

* More code review feedback.

* Use ResponseDetails for exception outcome modification.

* Remove bit about "valid status" -- we allow anything

* changelog

* Replace the response object

---------

Co-authored-by: Michael Buckley <[email protected]>

* batch2 jobs that are cancelled will not be returned when requesting a… (#7321) (#7327)

* Improve URL processing for JpaPersistedResourceValidationSupport (#7330)

* Improve URL processing for JpaPersistedResourceValidationSupport

* Add changelog

* allow fetching subsequent pages when registering an allowed spec of r… (#7329)

* allow fetching subsequent pages when registering an allowed spec of resourcetype search

* 7833: add missing relationship between TermConcept and TermConceptProperty (#7346)

* 7316 do not expand chain refparams (#7350)

* Make sure refparams with chains are not expanded via MDM

* 7316: code review feedback

* [7269] bulk export history fails with client-assigned string IDs (#7300)

* fixed 7269 bulk export history failure with client-assigned string IDs

* fixed 7269 bulk export history failure with client-assigned string IDs

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7296-bulk-export-fails-with-string-resource-ids.yaml

Co-authored-by: jdar8 <[email protected]>

* changed string ids to IResourcePersistentId

* changed string ids to IResourcePersistentId

* batch2 jobs that are cancelled will not be returned when requesting a… (#7321)

* Bump to 8 7 (#7322)

* bump to 8.7, add version enums

* changelog folder for 8.8

* increase memory to elastic search container

---------

Co-authored-by: jdar <[email protected]>

* Update hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java

Co-authored-by: Michael Buckley <[email protected]>

* fixed with spotless

* Revert "Bump to 8 7 (#7322)"

This reverts commit 40f1128.

* Revert "changed string ids to IResourcePersistentId"

This reverts commit 06af86a.

* Revert "batch2 jobs that are cancelled will not be returned when requesting a… (#7321)"

This reverts commit be08680.

* changed string ids to IResourcePersistentId

* fixed with spotless

* Bumped version number

* adding missing change to fix build

---------

Co-authored-by: Rob Caruso <[email protected]>
Co-authored-by: jdar8 <[email protected]>
Co-authored-by: TipzCM <[email protected]>
Co-authored-by: jdar <[email protected]>
Co-authored-by: Michael Buckley <[email protected]>

* [7332] fix mdm-query-links (#7356)

* 7324 unable to access collection bundles when performing search requests (#7325)

* Add failing tests

* Fix

* Changelog

* Fix comment

* Fix test

* Try fixing CodeQL autobuild error

* Implement revision suggestions

* Add missed test case parameter

* PatientIdPartitionIntercepto should allow Encounter.subject parameter (#7348)

* Work on megascale enhancements part 6

* Add changelog

* Test fix

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7348-allow-patientidcompartmentmode-search-encounter-subject.yaml

Co-authored-by: Nathan Doef  <[email protected]>

* Test fixes

---------

Co-authored-by: Nathan Doef <[email protected]>

* Bump to spring62 (#7351)

* Bump spring framework version

* Replace Base64Utils with Base64.getEncoder()

* Bump spring boot test deps to match spring version 6.2

* Bump junit for spring tests

---------

Co-authored-by: Gary <[email protected]>

* 7217 with rel 8 6 (#7337)

* Automated Migration Testing (HAPI-FHIR) - updated test migration scripts for 8_6_0 (#7357)

* Remove dead autowire (#7365)

* Don't reuse TransactionDetails for partitioned TX execution (#7363)

* Fix tags on megascale

* Add test

* Test fix

* Version bump

---------

Co-authored-by: jdar <[email protected]>
Co-authored-by: Kevin Dougan <[email protected]>
Co-authored-by: Michael Buckley <[email protected]>
Co-authored-by: TipzCM <[email protected]>
Co-authored-by: James Agnew <[email protected]>
Co-authored-by: another-luis <[email protected]>
Co-authored-by: Rob Caruso <[email protected]>
Co-authored-by: Rob Caruso <[email protected]>
Co-authored-by: Yaling Pei <[email protected]>
Co-authored-by: jmarchionatto <[email protected]>
Co-authored-by: Nathan Doef <[email protected]>
Co-authored-by: tadgh <[email protected]>
Co-authored-by: Gary <[email protected]>
Co-authored-by: volodymyr-korzh <[email protected]>
Co-authored-by: Gary Graham <[email protected]>

Author: 15 people

.github/workflows/codeql-analysis.yml

@@ -39,19 +39,16 @@ jobs:
 
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
-      - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+      # - name: Autobuild
+      #   uses: github/codeql-action/autobuild@v2
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 https://git.io/JvXDl
 
-      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-      #    and modify them (or add more) to build your code if your project
-      #    uses a compiled language
-
-      #- run: |
-      #   make bootstrap
-      #   make release
+      # ✏️ Manual build to avoid Maven wrapper issues with CodeQL autobuild
+      - name: Build with Maven
+        run: |
+          mvn clean install -DskipTests -Dmaven.javadoc.skip=true -Dcheckstyle.skip=true -Dpmd.skip=true -Dspotbugs.skip=true -Denforcer.skip=true -Dlicense.skip=true -Drat.skip=true -Dspotless.check.skip=true
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v2

hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/Pointcut.java

@@ -608,8 +608,14 @@ public enum Pointcut implements IPointcut {
 	 * only be populated when operating in a RestfulServer implementation. It is provided as a convenience.
 	 * </li>
 	 * <li>
-	 * org.hl7.fhir.instance.model.api.IBaseOperationOutcome - The OperationOutcome resource that will be
-	 * returned.
+	 * org.hl7.fhir.instance.model.api.IBaseOperationOutcome - The OperationOutcome resource that will be returned.
+	 * </ul>
+	 * <li>
+	 * <code>ca.uhn.fhir.rest.api.server.ResponseDetails</code> - A wrapper around the Http Status Code
+	 * and resource that will be used in the response to the caller. The Pointcut may decide to change this value from the default
+	 * value of <b>500</b> representing an <b>Internal Server Error</b>.
+	 * The OperationOutcome is passed for modification directly, and as part of the ResponseDetails parameter.  To replace the response
+	 * resource entirely, use ResponseDetails.setResponseResource().
 	 * </ul>
 	 * <p>
 	 * Hook methods must return <code>void</code>
@@ -619,7 +625,8 @@ public enum Pointcut implements IPointcut {
 			void.class,
 			"ca.uhn.fhir.rest.api.server.RequestDetails",
 			"ca.uhn.fhir.rest.server.servlet.ServletRequestDetails",
-			"org.hl7.fhir.instance.model.api.IBaseOperationOutcome"),
+			"org.hl7.fhir.instance.model.api.IBaseOperationOutcome",
+			"ca.uhn.fhir.rest.api.server.ResponseDetails"),
 
 	/**
 	 * <b>Server Hook:</b>

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -55,7 +55,6 @@
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.util.Base64Utils;
 
 import java.io.BufferedReader;
 import java.io.Console;
@@ -68,6 +67,7 @@
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.util.Arrays;
+import java.util.Base64;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
@@ -363,7 +363,7 @@ protected String getAndParseOptionBasicAuthHeader(CommandLine theCommandLine, St
 			}
 
 			byte[] basicAuth = optionValue.getBytes();
-			String base64EncodedBasicAuth = Base64Utils.encodeToString(basicAuth);
+			String base64EncodedBasicAuth = Base64.getEncoder().encodeToString(basicAuth);
 			basicAuthHeaderValue = Constants.HEADER_AUTHORIZATION_VALPREFIX_BASIC + base64EncodedBasicAuth;
 		}
 		return basicAuthHeaderValue;

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7217-non-partitionable-resource-is-searched-on-non-default-partition.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 7217
+title: "Previously, searches for non-partitionable resources (e.g. a Library) could be executed against a partition that
+is not the default partition. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7282-allow-interceptor-to-alter-http-response-code-for-exceptions.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 7282
+title: "Added a new capability to the SERVER_OUTGOING_FAILURE_OPERATIONOUTCOME Pointcut so that an Interceptor can provide 
+   an HTTP Response Code and modify the OperationOutcome during Exception handling.
+   Use the ResponseDetails parameter to change the status code instead of the current default of 500."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7296-bulk-export-fails-with-string-resource-ids.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 7296
+title: "Fixed an issue in bulk export with _includeHistory=true where history records failed to export for resources with client-assigned string IDs. History
+   is now gathered using PIDs rather than forced IDs."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7324-fix-collection-bundle-authorization.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 7324
+title: "Previously, the AuthorizationInterceptor did not properly authorize searches and reads
+   for COLLECTION type Bundles when users had appropriate permissions. This has been fixed by
+   adding BundleTypeEnum.COLLECTION to the set of standalone bundle resource types that are
+   treated similarly to DOCUMENT and MESSAGE bundles for authorization purposes."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7328-allow-paging-if-allowed-spec-includes-searches.yaml

@@ -0,0 +1,8 @@
+---
+type: fix
+issue: 7328
+jira: SMILE-11137
+title: "Specifying an allowed spec of resourcetype:search would allow
+      fetching the first page, but subsequent pages would fail.
+      This has now been fixed.
+"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7330-handle-questionnaire-versioned-canonical-urls.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 7330
+title: "When performing validation against a JPA server, Questionnaire URLs with versions were not handled correctly and
+   couldn't be found by the validator. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/8_6_0/7348-allow-patientidcompartmentmode-search-encounter-subject.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 7348
+title: "Previously, the `PatientIdPartitionInterceptor` allowed searching for Encounters by patient but not by subject. This has been corrected."