Rel 6 0 mb 3 (#3933)

* adding version.yaml, updating version in pom.xml

* It is possible to write to a resource in a partition the user is not authorized to. (#3397)

* fixed

* remove sout

* add msg.code

* fix failed tests

* fix equal sign

* update msg code

* extract method

* Fix up code numbers

* Clean changelog

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

* Revert final artifact version

* add graphql test (#3585)

* added graphql birthdate test

* fix variable name

* typo

* 3506 mdm log enhancement (#3543)

* Providing Fixme's to be reworked at a later time.

* Adding // FIXME Anna to assist our Austrian friend.

* Adding logging test as a first step in addressing issue #2822.

* hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

hapifhir#3506 part 2: enhance logging for (un)successful MDM matching

* Update MdmMatchLinkSvc.java

#3506 move "narrowed down" log to different place

* #3506 added scores and tests

#3506 added scores and tests

* #3506 formatting

#3506 formatting

* #3506 create changelog file

#3506 create changelog file

* #3506 fix typo

#3506 fix typo

* #3506 fix part 3, minor formatting

#3506 fix part 3, minor formatting

* #3506 fix tests

#3506 fix tests

Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>

* mdm matching (#3579)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

* begin with failing test

* fixed

* changelog

* add jira tag

* Update to 6 1 (#3582)

* added changelog folder, upped version

* version enum

* add a few more unit tests to assert proper NO_MATCH exclusion

* revert merge master doh! bad reflexes

* revert merge origin master

* unrevert revert.  ugh what a pain

* merge recovery.  fix poms.

* merge recovery.  more reverting

* merge recovery.  more reverting

* merge recovery.  more reverting

* Revert "merge recovery.  fix poms."

This reverts commit ae6e0ddb06.

* more revert revert reversions

* more revert revert reversions

* pre-review cleanup

Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: Mark Iantorno <markiantorno@gmail.com>

* Fix regression of 3411 - _lastUpdated gets clobbered during $reindex job (#3586)

* When chunking for the reindex job, don't clobber the lastUpdated if provided by the caller.

* License

* Ks 20220508 log colour (#3592)

* don't use colours when output is redirected to a file

* change log

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter… (#3551) (#3594)

* Added fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

* Update HapiFhirJpaMigrationTasks.java

Corrected ordering

* Update HapiFhirJpaMigrationTasks.java

Moving index status to be last operation

* Revert "Update HapiFhirJpaMigrationTasks.java"

This reverts commit 37bfd3e66e.

* Moved to bottom

Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>

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

* 3584 case sensitive string elasticsearch (#3596)

* Fix for case-sensitive search with newer elasticsearch

* Test and fix ascii normalization too

* more test cases

* comments

* Docs update empi usecase (#3598)

* Update diagram for use case 5

* Add new page for database support

* Licnese

* Mb norm fix (#3604)

* Normalize query since wildcard searches aren't normalized in elastic

* Handle batch2 job cancellation (#3603)

* Handle batch2 job cancellation

* Add CANCELLED status

* Remove unuseful test

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* Add batch2 interfaces to obtain recent instances (#3601)

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>

* changelog folder

* Documentation change, added warning log and change log for ticket (#3609)

Co-authored-by: Steven Li <steven@smilecdr.com>

* fix ne for lastUpdated search param (#3589)

* init/wip

* add implementation, add tests

* add checks and some refactoring

* refactor and simplify tests

* refactor

* get rid of some of the warnings

* add changelog

* remove my todos

* redo ne logic to account for less precise dates

* add tests

* refactoring

* rename to follow convention

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>

* Version bump

* Add skip of checkstyle to upload

* Typo

* upping version enum, upping version number, 6.0.1

* Group Bulk Export rules exiting too early.  (#3643)

* Implementation, test, changelog

* Add jira link

* adding backport in yaml for 3642

* adding folder for 6.0.1 release

* pom changes to publish checkstyle to sonatype

* bad version in pom file

* Make FulltextSearchSvcImpl optional bean for ValuesetOperationProvider

* AUtomcplete error code

* updating comment indicating final erorr code

* Bump error code

* fixing version enum so release docs generate correctly, adding additional changelog for 3650

* 3684 subscription for delivering delete events formatted wrong (#3685)

* Fixed issue with delivering delete events Subscriptions

* Extracted deliverer class name to a constant, now shared across tests and interceptor class

* Added change log and doc changes

* moved the constant to a more appropriate place

Co-authored-by: Steven Li <steven@smilecdr.com>

* Version bump

* Add version enum

* Version enum and folder

* adding release pipeline yml file fo azure

* Adding autoclose for sonatype publishing (#3797)

* Add impl test and changelog (#3713)

* fix up changelog, new version

* Version bump

* Updating version to: 6.0.4 post release.

* reverting 6.0.4 commit

* Updating version to: 6.0.4 post release.

* removing double entry from preious release

* Add support for DSTU3 delete subscrion events, add test

* Add changelogP

* Add version enum

* Remove notnull

* Add test for DSTU2

* Updating version to: 6.0.5 post release.

* Fix up

* wip

* Adding solution and changeLog file.

* Adding failing test.

* fix up

* Version bump

Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: katiesmilecdr <88786813+katiesmilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: alackerbauer <33912849+alackerbauer@users.noreply.github.com>
Co-authored-by: Etienne Poirier <etienne.poirier@smilecdr.com>
Co-authored-by: Anna <anna@MacBook-Pro.local>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>
Co-authored-by: Jens Kristian Villadsen <jvi@trifork.com>
Co-authored-by: michaelabuckley <michael.buckley@smilecdr.com>
Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: StevenXLi <stevenli_8118@hotmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java

@@ -97,8 +97,11 @@ public enum VersionEnum {
 	V6_0_0,
 	V6_0_1,
 	V6_0_2,
+	V6_0_3,
+	V6_0_4,
+	V6_0_5,
 	V6_1_0,
-	V6_2_0,
+	V6_2_0
 	;
 
 	public static VersionEnum latestVersion() {

hapi-fhir-checkstyle/pom.xml

@@ -36,8 +36,46 @@
 		</dependency>
 	</dependencies>
 
+	<profiles>
+		<!-- For releases, we need to generate javadoc and sources JAR -->
+		<profile>
+			<id>release</id>
+			<activation>
+				<activeByDefault>false</activeByDefault>
+				<property>
+					<name>deployToSonatype</name>
+				</property>
+			</activation>
 			<build>
 				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-source-plugin</artifactId>
+						<version>3.2.1</version>
+						<executions>
+							<execution>
+								<id>attach-sources</id>
+								<goals>
+									<goal>jar-no-fork</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-javadoc-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<id>attach-javadoc</id>
+								<goals>
+									<goal>jar</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
 				</plugins>
 			</build>
+		</profile>
+	</profiles>
 </project>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_3/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2022-07-18"
+codename: "Tanuki"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_4/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2022-07-22"
+codename: "Tanuki"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_5/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2022-08-29"
+codename: "Tanuki"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3243-subscription-deletes-dstu2-dstu3.yaml

@@ -1,5 +1,6 @@
 ---
 type: add
 issue: 3243
+backport: 6.0.4
 title: "Previously, the `http://hapifhir.io/fhir/StructureDefinition/subscription-send-delete-messages` extension on REST-HOOK subscription channel element was only valid for R4. This has been expanded to support DSTU3 and DSTU2."
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3703-delete-subscription-fails.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 3703
+backport: 6.0.3
+title: "Previously, using the `http://hapifhir.io/fhir/StructureDefinition/subscription-send-delete-messages` extension on a subscription, 
+along with a subscription that used a Search Expression criteria (e.g. `Patient?gender=male`) would cause a failure during an attempt to send the delete.
+ This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3937-searching-with-target-resource-parameter-in-include-fails.yaml

@@ -1,5 +1,6 @@
 ---
 type: fix
 issue: 3937
+backport: 6.0.5
 jira: SMILE-4959
 title: "Fixing bug where searching with a target resource parameter (Coverage:payor:Patient) as value to an _include parameter would fail with a 500 response."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -164,6 +164,7 @@ import static org.apache.commons.lang3.StringUtils.left;
 import static org.apache.commons.lang3.StringUtils.trim;
 
 
+
 /*
  * #%L
  * HAPI FHIR JPA Server

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java

@@ -75,6 +75,7 @@ import org.hl7.fhir.r4.model.RiskAssessment;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Nested;

hapi-fhir-spring-boot/pom.xml

@@ -41,6 +41,47 @@
 			</plugin>
 		</plugins>
 	</build>
-
+	<profiles>
+		<!-- For releases, we need to generate javadoc and sources JAR -->
+		<profile>
+			<id>release</id>
+			<activation>
+				<activeByDefault>false</activeByDefault>
+				<property>
+					<name>deployToSonatype</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-source-plugin</artifactId>
+						<version>3.2.1</version>
+						<executions>
+							<execution>
+								<id>attach-sources</id>
+								<goals>
+									<goal>jar-no-fork</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-javadoc-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<id>attach-javadoc</id>
+								<goals>
+									<goal>jar</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
 </project>
 

hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/coordinator/JobMaintenanceServiceImplTest.java

@@ -3,9 +3,9 @@ package ca.uhn.fhir.batch2.coordinator;
 import ca.uhn.fhir.batch2.api.IJobCompletionHandler;
 import ca.uhn.fhir.batch2.api.IJobPersistence;
 import ca.uhn.fhir.batch2.api.JobCompletionDetails;
+import ca.uhn.fhir.batch2.model.JobDefinition;
 import ca.uhn.fhir.batch2.channel.BatchJobSender;
 import ca.uhn.fhir.batch2.maintenance.JobMaintenanceServiceImpl;
-import ca.uhn.fhir.batch2.model.JobDefinition;
 import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.batch2.model.JobWorkNotification;
 import ca.uhn.fhir.batch2.model.StatusEnum;

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionCanonicalizer.java

@@ -27,8 +27,10 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionMatchingStrategy;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
+import ca.uhn.fhir.model.api.BasePrimitive;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.dstu2.resource.Subscription;
+import ca.uhn.fhir.model.primitive.BooleanDt;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@@ -44,7 +46,6 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r5.model.Enumerations;
-import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -112,8 +113,8 @@ public class SubscriptionCanonicalizer {
 		return theSubscription.getChannel().getUndeclaredExtensionsByUrl(EX_SEND_DELETE_MESSAGES)
 			.stream()
 			.map(ExtensionDt::getValue)
-			.map(value -> (org.hl7.fhir.dstu2.model.BooleanType) value)
+			.map(value -> (BooleanDt) value)
-			.map(org.hl7.fhir.dstu2.model.BooleanType::booleanValue)
+			.map(BasePrimitive::getValue)
 			.findFirst()
 			.orElse(false);
 	}
@@ -189,7 +190,6 @@ public class SubscriptionCanonicalizer {
 		return retVal;
 	}
 
-	@NotNull
 	private Boolean extractSendDeletesDstu3(org.hl7.fhir.dstu3.model.Subscription subscription) {
 		return subscription.getChannel().getExtensionsByUrl(EX_SEND_DELETE_MESSAGES).stream()
 			.map(org.hl7.fhir.dstu3.model.Extension::getValue)

hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionCanonicalizerTest.java

@@ -2,6 +2,8 @@ package ca.uhn.fhir.jpa.subscription.match.registry;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
+import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.primitive.BooleanDt;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Subscription;
@@ -39,4 +41,16 @@ class SubscriptionCanonicalizerTest {
 
 		assertTrue(canonicalSubscription.getSendDeleteMessages());
 	}
+
+	@Test
+	public void testCanonicalizeDstu2SendDeleteMessages() {
+		SubscriptionCanonicalizer dstu2Canonicalizer = new SubscriptionCanonicalizer(FhirContext.forDstu2());
+		ca.uhn.fhir.model.dstu2.resource.Subscription dstu2Sub = new ca.uhn.fhir.model.dstu2.resource.Subscription();
+		ExtensionDt extensionDt = new ExtensionDt();
+		extensionDt.setUrl(EX_SEND_DELETE_MESSAGES);
+		extensionDt.setValue(new BooleanDt(true));
+		dstu2Sub.getChannel().addUndeclaredExtension(extensionDt);
+		CanonicalSubscription canonicalize = dstu2Canonicalizer.canonicalize(dstu2Sub);
+		assertTrue(canonicalize.getSendDeleteMessages());
+	}
 }

hapi-tinder-test/pom.xml

@@ -480,5 +480,46 @@
 			</resource>
 		</resources>
 	</build>
-
+	<profiles>
+		<!-- For releases, we need to generate javadoc and sources JAR -->
+		<profile>
+			<id>release</id>
+			<activation>
+				<activeByDefault>false</activeByDefault>
+				<property>
+					<name>deployToSonatype</name>
+				</property>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-source-plugin</artifactId>
+						<version>3.2.1</version>
+						<executions>
+							<execution>
+								<id>attach-sources</id>
+								<goals>
+									<goal>jar-no-fork</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-javadoc-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<id>attach-javadoc</id>
+								<goals>
+									<goal>jar</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
 </project>

pom.xml

@@ -2021,17 +2021,6 @@
 					<artifactId>spring-boot-maven-plugin</artifactId>
 					<version>${spring_boot_version}</version>
 				</plugin>
-				<plugin>
-					<groupId>org.sonatype.plugins</groupId>
-					<artifactId>nexus-staging-maven-plugin</artifactId>
-					<version>1.6.8</version>
-					<extensions>true</extensions>
-					<configuration>
-						<serverId>ossrh</serverId>
-						<nexusUrl>https://oss.sonatype.org/</nexusUrl>
-						<autoReleaseAfterClose>true</autoReleaseAfterClose>
-					</configuration>
-				</plugin>
 				<plugin>
 					<groupId>org.basepom.maven</groupId>
 					<artifactId>duplicate-finder-maven-plugin</artifactId>
@@ -2740,41 +2729,6 @@
 				</plugins>
 			</build>
 		</profile>
-		<profile>
-			<id>SIGN_ARTIFACTS</id>
-			<activation>
-				<property>
-					<name>gpg.passphrase</name>
-				</property>
-			</activation>
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.apache.maven.plugins</groupId>
-						<artifactId>maven-gpg-plugin</artifactId>
-						<executions>
-							<execution>
-								<id>sign-artifacts</id>
-								<phase>verify</phase>
-								<goals>
-									<goal>sign</goal>
-								</goals>
-								<configuration>
-									<!--
-									These arguments are needed for GPG 2.1+ per
-									https://stackoverflow.com/questions/53992950/maven-gpg-plugin-failing-with-inappropriate-ioctl-for-device-when-running-unde
-									-->
-									<gpgArguments>
-										<arg>--pinentry-mode</arg>
-										<arg>loopback</arg>
-									</gpgArguments>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
 		<profile>
 			<id>ALLMODULES</id>
 			<activation>
@@ -3031,6 +2985,61 @@
 				</plugins>
 			</build>
 		</profile>
-
+		<profile>
+			<id>ossrh-repo</id>
+			<activation>
+				<activeByDefault>false</activeByDefault>
+				<property>
+					<name>deployToSonatype</name>
+				</property>
+			</activation>
+			<distributionManagement>
+				<snapshotRepository>
+					<id>ossrh</id>
+					<url>https://oss.sonatype.org/content/repositories/snapshots</url>
+				</snapshotRepository>
+				<repository>
+					<id>ossrh</id>
+					<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
+				</repository>
+			</distributionManagement>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.sonatype.plugins</groupId>
+						<artifactId>nexus-staging-maven-plugin</artifactId>
+						<version>1.6.13</version>
+						<extensions>true</extensions>
+						<configuration>
+							<serverId>ossrh</serverId>
+							<nexusUrl>https://oss.sonatype.org/</nexusUrl>
+							<autoReleaseAfterClose>true</autoReleaseAfterClose>
+						</configuration>
+					</plugin>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-gpg-plugin</artifactId>
+						<version>1.6</version>
+						<executions>
+							<execution>
+								<id>sign-artifacts</id>
+								<phase>verify</phase>
+								<goals>
+									<goal>sign</goal>
+								</goals>
+								<configuration>
+									<keyname>${gpg.keyname}</keyname>
+									<passphraseServerId>${gpg.keyname}</passphraseServerId>
+									<gpgArguments>
+										<arg>--pinentry-mode</arg>
+										<arg>loopback</arg>
+									</gpgArguments>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
 	</profiles>
 </project>