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feature swap to non javax clinical reasoning (#5463)
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* Update to a version of Clinical Reasoning/CQL that no longer includes javax dependencies

* Rev to CR 3.0.0-PRE10

* version bump, pom changes for jakarta conflicts

* undo exclusions from other modules

* Rework exclusions

* Fix type in dependency

* new cr version, exclude conflicts in cr and cds-hooks

* remove exclusions

* pom update

* Redo the exclusions

* add retrieveSettings config

* new CR retrieve settings and config

* update config to new enums and parameters

* update unit tests and config for new cql and terminology properties

* bump CR to 3.0.0-PRE12

* spotless edits, update class path for CR config

* missing dependencies

* swap for jakarta

* moving conflicting dependencies

* Fix a couple code review items

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
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@Capt-Mac @JPercival
Capt-Mac and JPercival authored Nov 22, 2023
1 parent 9aa173a commit 86ea069
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2 changes: 1 addition & 1 deletion hapi-deployable-pom/pom.xml
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<parent>
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<version>6.11.1-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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<parent>
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<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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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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4 changes: 2 additions & 2 deletions hapi-fhir-bom/pom.xml
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<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.11.0-SNAPSHOT</version>
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<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>

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<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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<parent>
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<version>6.11.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
</parent>
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14 changes: 12 additions & 2 deletions hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
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<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
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<artifactId>spring-test</artifactId>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.simplejavamail</groupId>
<artifactId>simple-java-mail</artifactId>
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
<exclusions>
<exclusion>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>

<build>
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2 changes: 1 addition & 1 deletion hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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<parent>
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<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>
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<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>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion hapi-fhir-client/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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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>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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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>
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<version>6.11.0-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion hapi-fhir-docs/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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4 changes: 4 additions & 0 deletions ...resources/ca/uhn/hapi/fhir/changelog/7_0_0/5436-swap-to-non-javax-clinical-reasoning.yaml
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---
type: add
issue: 5436
title: "Moving clinical reasoning to non-javax dependency for alignment with incoming hapi-fhir changes, bumping CR version and updating impacted classes and services"
2 changes: 1 addition & 1 deletion hapi-fhir-jacoco/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jaxrsserver-base/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpa/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-base/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-hfql/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-ips/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-mdm/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-model/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-searchparam/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-subscription/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-dstu2/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-dstu3/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-r4/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-r4b/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-test-r5/pom.xml
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<parent>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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3 changes: 1 addition & 2 deletions hapi-fhir-jpaserver-test-utilities/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
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</exclusion>
</exclusions>
</dependency>

</dependencies>

<build>
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2 changes: 1 addition & 1 deletion hapi-fhir-jpaserver-uhnfhirtest/pom.xml
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<parent>
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<relativePath>../pom.xml</relativePath>
</parent>
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26 changes: 24 additions & 2 deletions hapi-fhir-server-cds-hooks/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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<artifactId>hapi-fhir-storage-cr</artifactId>
<version>${project.version}</version>
</dependency>

<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
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<version>${reflections_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.simplejavamail</groupId>
<artifactId>simple-java-mail</artifactId>
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
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<dependency>
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<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
<exclusions>
<exclusion>
<groupId>com.sun.activation</groupId>
<artifactId>jakarta.activation</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>

<build>
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2 changes: 1 addition & 1 deletion hapi-fhir-server-mdm/pom.xml
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
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<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
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<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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