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hapi-fhir/hapi-fhir-jpaserver-base/pom.xml
Justin McKelvy 8c48a6fb91
Clinical reasoning module (#4347) 
* Add new Clinical Reasoning module

* Add config to get test up and running

* Removed FhirClient from tests

* First passing test

* Remove unused utilities

* Build updates

* exclude xxp3 and substitute with unbundled version

* Refactor to use provider factory and loader pattern

* First passing dstu3 test

* CR r4 test config and immunization tests

* Add base test classes

* Exclude transitive dependency xmlpull

* More dependency cleanup

* Refactor to remove JPA dependencies, rename module to hapi-fhir-storage-cr

* Fixes for duplicate xpp3 classes

* Remove more references to jpa

* Add mock FHIR server for terminology endpoint tests

* fix cql file for making providerr4 tests pass

* fix pom

* fix generic

* Adding r4 test cases for measure operations.

* Fix endpoint tests

* javadoc comment, temporarily comment out test results for practitioner sync

* javadoc typo fix

* adding java docs for cr module WIP

* Updates to clinical reasoning documentation

* More documentation updates

* docs now compile

* fix test

* DqmR4IT now successfully starts up, but the test does not pass

* Fix additionalData test

* Make measure service bean overridable

* adding clinical reasoning javadoc information

* Rename interfaces to start with I

* More styleguide updates

* Reformat all code in the storage-cr module

* More coding convention updates

* Remove bunches of unused code, reogranize so that fhir version in package name is consistent

* Clean up some static array initializations

* add practitioner patient list

* refactor product-line constant

* test dependency update

* add change log for cr module

* Add hapi-validation to the pom

* Exclude dependencies that are causing duplicates

* More dependencies and exclusions

* Make some base MeasureService components protected

* Update to latest cql compiler release

* fix measure service for null subject & practitioner and open up practitioner test

* Rev to release versions

* Add remaining Dstu3 tests

* update hedis bundle from policyHolder to beneficiary

* update snapshot

* Delete old CQL module

* Post-master-merge recovery

* Fix Java 17 feature usage issue

* update changelog with more information about new functionality

* Remove support chain wrapper usage

* Add javadocs to IResourceLoader

* added the property versioning for antlr jar.

* addressing code review comments.

* addressing code review comments.

* Fix typos in changelog

* Remove azure pipeline for cql module, add it for cr module

* Address exception comments, add Msg.code calls to exceptions

* Fix self-assignment bug

* Add storage-cr module to bom

* addressing coding comments.

* Addressed the variable naming convention to camelCase.

* Snapshot version bump

Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: justin.mckelvy <justin.mckelvy@smilecdr.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: Chalma Maadaadi <chalma@alphora.com>
Co-authored-by: mdnazmulkarim <nazmul.karim@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>
2023-01-10 19:49:57 +00:00

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<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.3.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR JPA Server</name>
<dependencies>
<dependency>
<groupId>com.fasterxml.woodstox</groupId>
<artifactId>woodstox-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
</dependency>
<dependency>
<groupId>co.elastic.apm</groupId>
<artifactId>apm-agent-api</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server-mdm</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-storage</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-sql-migrate</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-model</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4b</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r5</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-storage-batch2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-storage-batch2-jobs</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.ttddyy</groupId>
<artifactId>datasource-proxy</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
</dependency>
<!-- GraphQL -->
<dependency>
<groupId>com.graphql-java</groupId>
<artifactId>graphql-java</artifactId>
</dependency>
<!-- SQL Builder -->
<dependency>
<groupId>com.healthmarketscience.sqlbuilder</groupId>
<artifactId>sqlbuilder</artifactId>
</dependency>
<!-- Jackson -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.springdoc</groupId>
<artifactId>springdoc-openapi-ui</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring5</artifactId>
</dependency>
<!-- For UCUM: TODO we should replace this with org.fhir UCUM -->
<dependency>
<groupId>org.jscience</groupId>
<artifactId>jscience</artifactId>
<exclusions>
<exclusion>
<groupId>org.javolution</groupId>
<artifactId>javolution</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- Patch Dependencies -->
<dependency>
<groupId>io.dogote</groupId>
<artifactId>json-patch</artifactId>
</dependency>
<dependency>
<groupId>com.github.dnault</groupId>
<artifactId>xml-patch</artifactId>
</dependency>
<!-- FHIR RI is pulled in for UCUM support, but we don't want any of its dependencies. -->
<!--
For some reason JavaDoc crashed during site generation unless we have this dependency
-->
<dependency>
<groupId>javax.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId>
<scope>provided</scope>
</dependency>
<!--
Dependencies that need to be added since JDK9
-->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<!-- Spring -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-jpa</artifactId>
<exclusions>
<exclusion>
<artifactId>spring-aop</artifactId>
<groupId>org.springframework</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-commons</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-messaging</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-websocket</artifactId>
</dependency>
<dependency>
<groupId>javax.el</groupId>
<artifactId>javax.el-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.el</artifactId>
</dependency>
<!-- Note that we need this dependency to send log4j logging requests to slf4j -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-to-slf4j</artifactId>
</dependency>
<!-- Hibernate Search -->
<dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>elasticsearch-rest-high-level-client</artifactId>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-lucene</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate.search</groupId>
<artifactId>hibernate-search-backend-elasticsearch-aws</artifactId>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-phonetic</artifactId>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-backward-codecs</artifactId>
</dependency>
<!-- Misc -->
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server-openapi</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-caffeine</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-testing</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jetbrains</groupId>
<artifactId>annotations</artifactId>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<scope>compile</scope>
<exclusions>
<exclusion>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path-assert</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
</dependencies>
<properties>
<jackson.version>2.7.1</jackson.version>
</properties>
<build>
<plugins>
<plugin>
<groupId>de.jpdigital</groupId>
<artifactId>hibernate56-ddl-maven-plugin</artifactId>
<configuration>
<dialects>
<param>h2</param>
<param>derby_10_7</param>
<param>mysql57</param>
<param>mariadb</param>
<param>oracle12c</param>
<param>sqlserver2012</param>
</dialects>
<customDialects>
<customDialect>ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect</customDialect>
<customDialect>org.hibernate.dialect.CockroachDB201Dialect</customDialect>
</customDialects>
<outputDirectory>${project.build.directory}/classes/ca/uhn/hapi/fhir/jpa/docs/database</outputDirectory>
<packages>
<param>ca.uhn.fhir.jpa.entity</param>
<param>ca.uhn.fhir.jpa.model.entity</param>
</packages>
</configuration>
<executions>
<execution>
<phase>process-classes</phase>
<goals>
<goal>gen-ddl</goal>
</goals>
</execution>
</executions>
<dependencies>
<!--
These have been added as explicit dependencies
as JDK9 no longer includes them by default
-->
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>${jaxb_runtime_version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-model</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate_version}</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-tinder-plugin</artifactId>
<version>${project.version}</version>
<executions>
<execution>
<id>build_dstu2</id>
<goals>
<goal>generate-jparest-server</goal>
</goals>
<configuration>
<version>dstu2</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.dstu2</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu2.xml
</targetResourceSpringBeansFile>
<baseResourceNames/>
<excludeResourceNames>
<!-- <excludeResourceName>OperationDefinition</excludeResourceName> <excludeResourceName>OperationOutcome</excludeResourceName> -->
</excludeResourceNames>
</configuration>
</execution>
<execution>
<id>build_dstu3</id>
<goals>
<goal>generate-jparest-server</goal>
</goals>
<configuration>
<version>dstu3</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.dstu3</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu3.xml
</targetResourceSpringBeansFile>
<baseResourceNames></baseResourceNames>
<excludeResourceNames>
</excludeResourceNames>
</configuration>
</execution>
<execution>
<id>build_r4</id>
<goals>
<goal>generate-jparest-server</goal>
</goals>
<configuration>
<version>r4</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.r4</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r4.xml
</targetResourceSpringBeansFile>
<baseResourceNames></baseResourceNames>
<excludeResourceNames>
</excludeResourceNames>
</configuration>
</execution>
<execution>
<id>build_r4b</id>
<goals>
<goal>generate-jparest-server</goal>
</goals>
<configuration>
<version>r4b</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.r4b</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r4b.xml
</targetResourceSpringBeansFile>
<baseResourceNames></baseResourceNames>
<excludeResourceNames>
</excludeResourceNames>
</configuration>
</execution>
<execution>
<id>build_r5</id>
<goals>
<goal>generate-jparest-server</goal>
</goals>
<configuration>
<version>r5</version>
<configPackageBase>ca.uhn.fhir.jpa.config</configPackageBase>
<packageBase>ca.uhn.fhir.jpa.rp.r5</packageBase>
<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-r5.xml
</targetResourceSpringBeansFile>
<baseResourceNames></baseResourceNames>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>target/generated-sources/tinder</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
<resources>
<resource>
<directory>${project.basedir}/src/main/resources</directory>
</resource>
<resource>
<directory>${project.basedir}/target/generated-resources/tinder</directory>
</resource>
</resources>
</build>
</project>
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