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@nr23730
nr23730 committed Feb 20, 2024
1 parent 7aa5371 commit c31f797
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27 changes: 27 additions & 0 deletions .github/workflows/maven.yml
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# This workflow will build a Java project with Maven
# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven

name: Java CI with Maven

on:
push:

jobs:
build:
runs-on: ubuntu-latest
steps:
- name: Set up JDK 21
uses: actions/setup-java@v4
with:
distribution: 'adopt'
java-version: '21'
- name: Cache Maven packages
uses: actions/cache@v4
with:
path: ~/.m2
key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
restore-keys: ${{ runner.os }}-m2
- name: Checkout code
uses: actions/checkout@v4
- name: Build with Maven
run: mvn install
38 changes: 38 additions & 0 deletions .gitignore
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target/
!.mvn/wrapper/maven-wrapper.jar
!**/src/main/**/target/
!**/src/test/**/target/

### IntelliJ IDEA ###
.idea/*

### Eclipse ###
.apt_generated
.classpath
.factorypath
.project
.settings
.springBeans
.sts4-cache

### NetBeans ###
/nbproject/private/
/nbbuild/
/dist/
/nbdist/
/.nb-gradle/
build/
!**/src/main/**/build/
!**/src/test/**/build/

### VS Code ###
.vscode/

### Mac OS ###
.DS_Store

### local misc files ###
settings.yml

### Test data files ###
file_*.xml
8 changes: 8 additions & 0 deletions Dockerfile
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FROM docker.io/maven:3-eclipse-temurin-21 as build
COPY $PWD /openehr-obds
WORKDIR /openehr-obds
RUN mvn -DskipTests clean package

FROM gcr.io/distroless/java21-debian12
COPY --from=build /openehr-obds/target/openehr-obds-*-jar-with-dependencies.jar /app/openehr-obds.jar
ENTRYPOINT ["java", "-jar", "/app/openehr-obds.jar"]
8 changes: 8 additions & 0 deletions compose.yml
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version: "3"
services:
openehr-obds:
restart: unless-stopped
build: ./
command: "/app/settings.yml"
volumes:
- "./settings.yml:/app/settings.yml"
200 changes: 200 additions & 0 deletions pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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>

<groupId>de.uksh.medic.etl</groupId>
<artifactId>openehr-obds</artifactId>
<version>0.1-SNAPSHOT</version>

<properties>
<maven.compiler.source>21</maven.compiler.source>
<maven.compiler.target>21</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<junit.version>5.10.2</junit.version>
<maven-enforcer-plugin.version>3.4.1</maven-enforcer-plugin.version>
<maven-surefire-plugin.version>3.2.5</maven-surefire-plugin.version>
<maven-javadoc-plugin.version>3.6.3</maven-javadoc-plugin.version>
<coveralls-maven-plugin.version>4.3.0</coveralls-maven-plugin.version>
<maven-source-plugin.version>3.3.0</maven-source-plugin.version>
<exec.mainClass>de.uksh.medic.etl.OpenEhrObds</exec.mainClass>
</properties>

<dependencies>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>7.0.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>7.0.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>7.0.0</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>2.16.1</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.16.1</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
<version>2.16.1</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>6.1.3</version>
</dependency>
<dependency>
<groupId>org.tinylog</groupId>
<artifactId>tinylog-api</artifactId>
<version>2.6.2</version>
</dependency>
<dependency>
<groupId>org.tinylog</groupId>
<artifactId>tinylog-impl</artifactId>
<version>2.6.2</version>
</dependency>
<dependency>
<groupId>org.tinylog</groupId>
<artifactId>slf4j-tinylog</artifactId>
<version>2.6.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>${maven-enforcer-plugin.version}</version>
<executions>
<execution>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>3.6.3</version>
</requireMavenVersion>
</rules>
<fail>true</fail>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>${maven-javadoc-plugin.version}</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>${maven-source-plugin.version}</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>de.uksh.medic.etl.OpenEhrObds</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>3.3.1</version>
<dependencies>
<dependency>
<groupId>com.puppycrawl.tools</groupId>
<artifactId>checkstyle</artifactId>
<version>10.13.0</version>
</dependency>
<dependency>
<groupId>com.github.ngeor</groupId>
<artifactId>checkstyle-rules</artifactId>
<version>7.0.0</version>
</dependency>
</dependencies>
<configuration>
<configLocation>com/github/ngeor/checkstyle.xml</configLocation>
<skip>false</skip>
</configuration>
<executions>
<execution>
<id>checkstyle</id>
<phase>validate</phase>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
</build>
</project>
34 changes: 34 additions & 0 deletions src/main/java/de/uksh/medic/etl/OpenEhrObds.java
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package de.uksh.medic.etl;

import de.uksh.medic.etl.jobs.mdr.centraxx.CxxMdrLogin;
import de.uksh.medic.etl.settings.ConfigurationLoader;
import de.uksh.medic.etl.settings.CxxMdrSettings;
import de.uksh.medic.etl.settings.Settings;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import org.tinylog.Logger;

public final class OpenEhrObds {

private OpenEhrObds() {}

public static void main(String[] args) throws IOException {
InputStream settingsYaml = ClassLoader.getSystemClassLoader().getResourceAsStream("settings.yml");
if (args.length == 1) {
settingsYaml = new FileInputStream(args[0]);
}

ConfigurationLoader configLoader = new ConfigurationLoader();
configLoader.loadConfiguration(settingsYaml, Settings.class);

//ToDo: Replace with Kafka consumer

CxxMdrSettings mdrSettings = Settings.getCxxmdr();
if (mdrSettings != null) {
CxxMdrLogin.login(mdrSettings);
}

Logger.info("OpenEhrObds started!");
}
}
47 changes: 47 additions & 0 deletions src/main/java/de/uksh/medic/etl/jobs/mdr/centraxx/CxxMdrConvert.java
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package de.uksh.medic.etl.jobs.mdr.centraxx;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import de.uksh.medic.etl.model.mdr.centraxx.RelationConvert;
import de.uksh.medic.etl.settings.CxxMdrSettings;
import org.springframework.http.HttpEntity;
import org.springframework.http.HttpHeaders;
import org.springframework.http.MediaType;
import org.springframework.web.client.RestTemplate;

/**
* Class for data conversion using Kairos CentraXX MDR.
*/
public final class CxxMdrConvert {

private CxxMdrConvert() {
}

/**
* Converts data from a source profile to a target profile using Kairos CentraXX MDR.
* @param mdr Configuration for MDR.
* @param input Relation with input data
* @return Relation with output data
* @throws JsonProcessingException
*/
public static RelationConvert convert(CxxMdrSettings mdr, RelationConvert input) throws JsonProcessingException {

if (mdr.isTokenExpired()) {
CxxMdrLogin.login(mdr);
}

RestTemplate rt = new RestTemplate();
HttpHeaders headers = new HttpHeaders();
headers.add(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON.toString());
headers.add(HttpHeaders.ACCEPT, MediaType.APPLICATION_JSON.toString());
headers.add("Authorization", "Bearer " + mdr.getToken());
ObjectMapper om = new ObjectMapper();
om.setSerializationInclusion(com.fasterxml.jackson.annotation.JsonInclude.Include.NON_NULL)
.writeValueAsString(input);
return rt.postForObject(mdr.getUrl() + "/rest/v1/relations/convert",
new HttpEntity<>(om.writeValueAsString(input), headers),
RelationConvert.class);

}

}
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