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Question

I need to implement a Hapi-Fhir server in Quarkus. For this purpose i created a ResourceProvider with the CRUD-Operation @Create. Now I want to save the data in a custom format with JPA in an Oracle-database. Unfortunatly I am not able to Inject the EntityManager or anything else. It only works with JAX-RS annotated Resources (@Path, @GET, @POST, …)

The problematic class

import at.co.svc.emed.fhir.hibernate.FhirRepository;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.IResourceProvider;
import jakarta.enterprise.context.ApplicationScoped;
import jakarta.inject.Inject;
import jakarta.persistence.EntityManager;
import jakarta.transaction.Transactional;
import org.hl7.fhir.r5.model.MedicationRequest;

@ApplicationScoped
public class MedicationRequestResourceProvider implements IResourceProvider {
    @Inject
    EntityManager entityManager;

    @Override
    public Class<MedicationRequest> getResourceType() {
        return MedicationRequest.class;
    }

    /**
     * Create a new MedicationRequest
     * @param medicationRequest the medication request to create
     * @return MethodOutcome
     */
    @Create
    @Transactional
    public MethodOutcome createMedicationRequest(@ResourceParam MedicationRequest medicationRequest) {
        FhirRepository fhirRepository = new FhirRepository();
        fhirRepository.setDocumentId(medicationRequest.getId());
        fhirRepository.setDocument(FhirContext.forR5().newJsonParser().encodeResourceToString(medicationRequest));
        fhirRepository.setPatientReference(medicationRequest.getSubject().getReference());
        entityManager.persist(fhirRepository);

        MethodOutcome outcome = new MethodOutcome();
        outcome.setId(medicationRequest.getIdElement());
        outcome.setResource(medicationRequest);
        return outcome;
    }
}

pom.xml (censored)

<?xml version="1.0" encoding="UTF-8"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <modelVersion>4.0.0</modelVersion>
  <groupId>**.**.**.**</groupId>
  <artifactId>**-**-fhir</artifactId>
  <version>1.0.0-SNAPSHOT</version>
  <packaging>jar</packaging>
  <name>${project.artifactId}</name>

  <properties>
    <compiler-plugin.version>3.12.1</compiler-plugin.version>
    <maven.compiler.release>21</maven.compiler.release>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
    <quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
    <quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
    <quarkus.platform.version>3.9.4</quarkus.platform.version>
    <quarkus.package.type>uber-jar</quarkus.package.type>
    <quarkus.package.add-runner-suffix>false</quarkus.package.add-runner-suffix>
    <skipITs>true</skipITs>
    <surefire-plugin.version>3.2.5</surefire-plugin.version>
    <hapifhir.version>7.0.2</hapifhir.version>
    <deliver_to_biss>true</deliver_to_biss>
    <leaf_extention>jar</leaf_extention>
    <leaf_type>WebApps</leaf_type>
  </properties>
  <dependencyManagement>
    <dependencies>
      <dependency>
        <groupId>${quarkus.platform.group-id}</groupId>
        <artifactId>${quarkus.platform.artifact-id}</artifactId>
        <version>${quarkus.platform.version}</version>
        <type>pom</type>
        <scope>import</scope>
      </dependency>
      <dependency>
        <groupId>${quarkus.platform.group-id}</groupId>
        <artifactId>quarkus-camel-bom</artifactId>
        <version>${quarkus.platform.version}</version>
        <type>pom</type>
        <scope>import</scope>
      </dependency>
    </dependencies>
  </dependencyManagement>
  <dependencies>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-resteasy</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-resteasy-jsonb</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-undertow</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-smallrye-health</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-hibernate-orm</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-jdbc-oracle</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-arc</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-liquibase</artifactId>
    </dependency>
    <dependency>
      <groupId>io.quarkus</groupId>
      <artifactId>quarkus-junit5</artifactId>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>io.rest-assured</groupId>
      <artifactId>rest-assured</artifactId>
      <scope>test</scope>
    </dependency>

    <!-- This dependency includes the core HAPI-FHIR classes -->
    <dependency>
      <groupId>ca.uhn.hapi.fhir</groupId>
      <artifactId>hapi-fhir-base</artifactId>
      <version>${hapifhir.version}</version>
    </dependency>

    <!-- This dependency includes the HAPI FHIR Server Framework -->
    <dependency>
      <groupId>ca.uhn.hapi.fhir</groupId>
      <artifactId>hapi-fhir-server</artifactId>
      <version>${hapifhir.version}</version>
    </dependency>

    <!-- At least one "structures" JAR must also be included -->
    <dependency>
      <groupId>ca.uhn.hapi.fhir</groupId>
      <artifactId>hapi-fhir-structures-r5</artifactId>
      <version>${hapifhir.version}</version>
    </dependency>

    <!-- Used for validation  -->
    <dependency>
      <groupId>ca.uhn.hapi.fhir</groupId>
      <artifactId>hapi-fhir-validation-resources-r5</artifactId>
      <version>${hapifhir.version}</version>
    </dependency>
    <dependency>
      <groupId>ca.uhn.hapi.fhir</groupId>
      <artifactId>hapi-fhir-validation</artifactId>
      <version>${hapifhir.version}</version>
      <exclusions>
        <exclusion>
          <groupId>ca.uhn.hapi.fhir</groupId>
          <artifactId>org.hl7.fhir.validation</artifactId>
        </exclusion>
        <exclusion>
          <groupId>ca.uhn.hapi.fhir</groupId>
          <artifactId>org.hl7.fhir.dstu2</artifactId>
        </exclusion>
        <exclusion>
          <groupId>ca.uhn.hapi.fhir</groupId>
          <artifactId>org.hl7.fhir.dstu2016may</artifactId>
        </exclusion>
        <exclusion>
          <groupId>ca.uhn.hapi.fhir</groupId>
          <artifactId>org.hl7.fhir.dstu3</artifactId>
        </exclusion>
        <exclusion>
          <groupId>ca.uhn.hapi.fhir</groupId>
          <artifactId>org.hl7.fhir.r4</artifactId>
        </exclusion>
        <exclusion>
          <groupId>ca.uhn.hapi.fhir</groupId>
          <artifactId>org.hl7.fhir.r4b</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
  </dependencies>

  <build>
    <finalName>${project.artifactId}</finalName>
    <plugins>
      <plugin>
        <groupId>${quarkus.platform.group-id}</groupId>
        <artifactId>quarkus-maven-plugin</artifactId>
        <version>${quarkus.platform.version}</version>
        <extensions>true</extensions>
        <executions>
          <execution>
            <goals>
              <goal>build</goal>
              <goal>generate-code</goal>
              <goal>generate-code-tests</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>${compiler-plugin.version}</version>
        <configuration>
          <compilerArgs>
            <arg>-parameters</arg>
          </compilerArgs>
        </configuration>
      </plugin>
      <plugin>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>${surefire-plugin.version}</version>
        <configuration>
          <systemPropertyVariables>
            <java.util.logging.manager>org.jboss.logmanager.LogManager</java.util.logging.manager>
            <maven.home>${maven.home}</maven.home>
          </systemPropertyVariables>
        </configuration>
      </plugin>
      <plugin>
        <artifactId>maven-failsafe-plugin</artifactId>
        <version>${surefire-plugin.version}</version>
        <executions>
          <execution>
            <goals>
              <goal>integration-test</goal>
              <goal>verify</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <systemPropertyVariables>
            <native.image.path>${project.build.directory}/${project.build.finalName}-runner</native.image.path>
            <java.util.logging.manager>org.jboss.logmanager.LogManager</java.util.logging.manager>
            <maven.home>${maven.home}</maven.home>
          </systemPropertyVariables>
        </configuration>
      </plugin>
      <plugin>
        <groupId>io.smallrye</groupId>
        <artifactId>jandex-maven-plugin</artifactId>
        <version>3.1.8</version>
        <executions>
          <execution>
            <id>make-index</id>
            <goals>
              <goal>jandex</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>
  <profiles>
    <profile>
      <id>native</id>
      <activation>
        <property>
          <name>native</name>
        </property>
      </activation>
      <properties>
        <skipITs>false</skipITs>
        <quarkus.package.type>native</quarkus.package.type>
      </properties>
    </profile>
  </profiles>
</project>

application.properties (censored)

quarkus.devservices.enabled=false

# datasource configuration
quarkus.datasource.db-kind = oracle
quarkus.datasource.username = ***
quarkus.datasource.password = ***
quarkus.datasource.jdbc.url = ***

quarkus.hibernate-orm.database.generation=none
quarkus.hibernate-orm.packages = ***

# Liquibase config properties
quarkus.liquibase.enabled=false

#quarkus.liquibase.migrate-at-start=true
%dev.quarkus.log.category."***".level=DEBUG

quarkus.index-dependency.persistence.group-id = jakarta.persistence

I would like to be able to inject the EntityManager properly without the need to use jax-rs.

Thiết kế website giá rẻ

Danh mục

Injections fail in Quarkus with Hapi-Fhir