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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>io.onfhir</groupId>
<artifactId>tofhir_2.13</artifactId>
<version>${revision}</version>
<packaging>pom</packaging>
<name>toFHIR</name>
<description>toFHIR is a high-performance and scalable data transformation suite that can read existing data from
various sources (CSV/Test/JSON/Parquet/Avro files, relational databases, Hive tables) and transform to FHIR
resources through mapping definitions.
</description>
<url>https://onfhir.io/tofhir</url>
<licenses>
<license>
<name>Apache License, Version 2.0</name>
<url>https://www.apache.org/licenses/LICENSE-2.0</url>
</license>
</licenses>
<developers>
<developer>
<id>sinaci</id>
<name>Ali Anıl Sınacı</name>
<email>[email protected]</email>
<organization>SRDC Corp.</organization>
<organizationUrl>https://www.srdc.com.tr</organizationUrl>
</developer>
<developer>
<id>tnamli</id>
<name>Tuncay Namlı</name>
<email>[email protected]</email>
<organization>SRDC Corp.</organization>
<organizationUrl>https://www.srdc.com.tr</organizationUrl>
</developer>
<developer>
<id>suatgonul</id>
<name>Suat Gönül</name>
<email>[email protected]</email>
<organization>SRDC Corp.</organization>
<organizationUrl>https://www.srdc.com.tr</organizationUrl>
</developer>
<developer>
<id>dogukan10</id>
<name>Doğukan Çavdaroğlu</name>
<email>[email protected]</email>
<organization>SRDC Corp.</organization>
<organizationUrl>https://www.srdc.com.tr</organizationUrl>
</developer>
<developer>
<id>YemreGurses</id>
<name>Yunus Emre Gürses</name>
<email>[email protected]</email>
<organization>SRDC Corp.</organization>
<organizationUrl>https://www.srdc.com.tr</organizationUrl>
</developer>
<developer>
<id>Okanmercan99</id>
<name>Okan Mercan</name>
<email>[email protected]</email>
<organization>SRDC Corp.</organization>
<organizationUrl>https://www.srdc.com.tr</organizationUrl>
</developer>
</developers>
<scm>
<connection>scm:git:git://github.com/srdc/tofhir.git</connection>
<developerConnection>scm:git:ssh://github.com:srdc/tofhir.git</developerConnection>
<url>https://github.com/srdc/tofhir/tree/main</url>
</scm>
<modules>
<module>tofhir-engine</module>
<module>tofhir-server</module>
<module>tofhir-common</module>
<module>tofhir-server-common</module>
<module>tofhir-rxnorm</module>
</modules>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<!-- This is a special placeholder to manage the version from a single property throughout the parent and child modules. No other property name can be used. -->
<!-- https://maven.apache.org/maven-ci-friendly.html -->
<revision>1.1-SNAPSHOT</revision>
<scala.version>2.13.16</scala.version>
<scala.binary.version>2.13</scala.binary.version>
<!--Dependency versions-->
<scala-logging.version>3.9.5</scala-logging.version>
<onfhir.version>3.4-SNAPSHOT</onfhir.version>
<onfhir-template-engine.version>1.1-SNAPSHOT</onfhir-template-engine.version>
<spark-on-fhir.version>1.0-SNAPSHOT</spark-on-fhir.version>
<json4s.version>3.7.0-M11</json4s.version>
<logback-more-appenders.version>1.8.8</logback-more-appenders.version>
<fluent-logger.version>0.3.4</fluent-logger.version>
<com.fasterxml.version>2.15.1</com.fasterxml.version>
<scalatest.version>3.2.17</scalatest.version>
<spark.version>3.5.4</spark.version>
<jackson.version>2.15.1</jackson.version>
<logback.version>1.2.11</logback.version>
<logstash-logback-encoder.version>7.2</logstash-logback-encoder.version>
<typesafe.config.version>1.4.3</typesafe.config.version>
<mockito.version>1.17.30</mockito.version>
<postgres.version>42.7.0</postgres.version>
<h2db.version>2.2.224</h2db.version>
<cron4j.version>2.2.5</cron4j.version>
<testcontainers>1.19.3</testcontainers>
<akka.version>2.8.5</akka.version>
<akka-http.version>10.5.3</akka-http.version>
<reflections.version>0.10.2</reflections.version>
<opencsv.version>5.8</opencsv.version>
<onfhir-definitions-microservices.version>1.0-SNAPSHOT</onfhir-definitions-microservices.version>
</properties>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.8.1</version>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
<scalaCompatVersion>${scala.binary.version}</scalaCompatVersion>
<encoding>UTF-8</encoding>
<args>
<arg>-deprecation</arg>
<arg>-feature</arg>
</args>
</configuration>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<!-- Configures the POM to include additional source directories containing Scala code.
This plugin ensures that Maven recognizes and compiles these directories along with the main source code. -->
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.2.5</version>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<version>2.2.0</version>
<configuration>
<reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>TestSuite.txt</filereports>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.5.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.4.1</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>flatten-maven-plugin</artifactId>
<version>1.6.0</version>
<configuration>
</configuration>
<executions>
<execution>
<id>flatten</id>
<phase>process-resources</phase>
<goals>
<goal>flatten</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencyManagement>
<dependencies>
<!-- Scala Library itself-->
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}</version>
</dependency>
<!-- onFHIR dependencies -->
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-expression_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-template-engine_${scala.binary.version}</artifactId>
<version>${onfhir-template-engine.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-path_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-client_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-config_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-common_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-r4_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-server-r4_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-server-r5_${scala.binary.version}</artifactId>
<version>${onfhir.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>fhir-api-spark-source_${scala.binary.version}</artifactId>
<version>${spark-on-fhir.version}</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>io.onfhir</groupId>-->
<!-- <artifactId>fhir-spark-util</artifactId>-->
<!-- <version>${spark-on-fhir.version}</version>-->
<!-- </dependency>-->
<!-- <dependency>-->
<!-- <groupId>io.onfhir</groupId>-->
<!-- <artifactId>fhir-path-spark_${scala.binary.version}</artifactId>-->
<!-- <version>${spark-on-fhir.version}</version>-->
<!-- </dependency>-->
<!-- JSON4S -->
<dependency>
<groupId>org.json4s</groupId>
<artifactId>json4s-jackson_${scala.binary.version}</artifactId>
<version>${json4s.version}</version>
<!-- <exclusions>-->
<!-- <exclusion>-->
<!-- <groupId>com.fasterxml.jackson.core</groupId>-->
<!-- <artifactId>jackson-databind</artifactId>-->
<!-- </exclusion>-->
<!-- </exclusions>-->
</dependency>
<!-- Dependency for Fluentd-Logback Integration -->
<!-- This library provides additional appenders (namely, ch.qos.logback.more.appenders.DataFluentAppender)
for Logback, extending its capabilities.-->
<dependency>
<groupId>com.sndyuk</groupId>
<artifactId>logback-more-appenders</artifactId>
<version>${logback-more-appenders.version}</version>
</dependency>
<!-- This dependency provides access to the Fluentd Logger Library, which allows the applications to easily
send logs to Fluentd-->
<dependency>
<groupId>org.fluentd</groupId>
<artifactId>fluent-logger</artifactId>
<version>${fluent-logger.version}</version>
</dependency>
<!-- The end of dependencies for Fluentd-Logback Integration-->
<!-- These are required for Spark and resolving among different versions coming from akka and json4s -->
<!-- Dependency from jackson-dataformat-csv and logstash-logback-encoder-->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.version}</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>com.fasterxml.jackson.module</groupId>-->
<!-- <artifactId>jackson-module-scala_${scala.binary.version}</artifactId>-->
<!-- <version>${com.fasterxml.version}</version>-->
<!-- </dependency>-->
<!-- Spark dependencies -->
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
<version>${spark.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
<!--
Exclude the "org.apache.commons:commons-lang3:jar:3.12.0" dependency to avoid conflicts with the version
"org.apache.commons:commons-lang3:jar:3.14.0" provided by "onfhir".
-->
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
<version>${spark.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql-kafka-0-10_${scala.binary.version}</artifactId>
<version>${spark.version}</version>
</dependency>
<!-- Scala Logging -->
<dependency>
<groupId>com.typesafe.scala-logging</groupId>
<artifactId>scala-logging_${scala.binary.version}</artifactId>
<version>${scala-logging.version}</version>
</dependency>
<!-- Logback dependencies -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback.version}</version>
</dependency>
<dependency>
<groupId>net.logstash.logback</groupId>
<artifactId>logstash-logback-encoder</artifactId>
<version>${logstash-logback-encoder.version}</version>
</dependency>
<!--
The `log4j-over-slf4j` library serves as a bridge to route logging calls from Log4j's API to SLF4J.
This allows applications originally written with Log4j to seamlessly integrate with SLF4J-compatible logging backends, such as Logback.
Here is the logging flow enabled by this library:
Application → Log4j API → log4j-over-slf4j → SLF4J → Logging Backend (e.g., Logback)
Why is this dependency needed?
- Normally, this dependency is not required.
- However, when working with a Spark Cluster, this library becomes essential because Spark uses Log4j as its default logging framework,
while our application uses Logback.
- By including `log4j-over-slf4j`, we ensure that Spark's Log4j logging is redirected to SLF4J, and ultimately handled by Logback.
-->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
<version>1.7.32</version>
</dependency>
<!-- Application Configuration -->
<dependency>
<groupId>com.typesafe</groupId>
<artifactId>config</artifactId>
<version>${typesafe.config.version}</version>
</dependency>
<!-- For CSV parsing -->
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-csv</artifactId>
<version>${jackson.version}</version>
</dependency>
<!-- Postgres driver for Spark Read JDBC -->
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgres.version}</version>
</dependency>
<!-- cron4j -->
<dependency>
<groupId>it.sauronsoftware.cron4j</groupId>
<artifactId>cron4j</artifactId>
<version>${cron4j.version}</version>
</dependency>
<!-- Akka HTTP Suite -->
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-http_${scala.binary.version}</artifactId>
<version>${akka-http.version}</version>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-http-core_${scala.binary.version}</artifactId>
<version>${akka-http.version}</version>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-http-caching_${scala.binary.version}</artifactId>
<version>${akka-http.version}</version>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-actor-typed_${scala.binary.version}</artifactId>
<version>${akka.version}</version>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-stream-typed_${scala.binary.version}</artifactId>
<version>${akka.version}</version>
</dependency>
<!-- toFHIR Dependencies -->
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>tofhir-server-common_2.13</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>tofhir-engine_2.13</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>tofhir-engine_2.13</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>tofhir-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>tofhir-server-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>tofhir-rxnorm_2.13</artifactId>
<version>${project.version}</version>
</dependency>
<!-- onFHIR Definitions Microservices -->
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-fhirpath-functions</artifactId>
<version>${onfhir-definitions-microservices.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-resource-definitions</artifactId>
<version>${onfhir-definitions-microservices.version}</version>
</dependency>
<dependency>
<groupId>io.onfhir</groupId>
<artifactId>onfhir-definition-commons</artifactId>
<version>${onfhir-definitions-microservices.version}</version>
</dependency>
<!-- Testkit for Akka Http-->
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-http-testkit_${scala.binary.version}</artifactId>
<version>${akka.http.version}</version>
<scope>test</scope>
</dependency>
<!-- For Unit testing -->
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.binary.version}</artifactId>
<version>${scalatest.version}</version>
<scope>test</scope>
</dependency>
<!-- For mocking -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-scala_2.13</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
<!-- For database testing -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>${h2db.version}</version>
<scope>test</scope>
</dependency>
<!-- Test containers to initialize Docker containers during tests -->
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers-bom</artifactId>
<version>${testcontainers}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<!-- Reflections -->
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>${reflections.version}</version>
</dependency>
<!-- For CSV reading -->
<dependency>
<groupId>com.opencsv</groupId>
<artifactId>opencsv</artifactId>
<version>${opencsv.version}</version>
</dependency>
<!-- For integrating Delta Lake with Spark in a Scala project -->
<dependency>
<groupId>io.delta</groupId>
<artifactId>delta-spark_${scala.binary.version}</artifactId>
<version>3.0.0</version>
</dependency>
</dependencies>
</dependencyManagement>
<profiles>
<profile>
<id>release</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-source</id>
<phase>compile</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>doc-jar</goal>
</goals>
</execution>
</executions>
</plugin>
<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>
<gpgArguments>
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>false</autoReleaseAfterClose>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile><!-- to run: mvn compile -P sources -->
<id>sources</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-source</id>
<goals>
<!-- Creates a JAR file containing the source code of a Maven project
Unlike the regular jar goal, jar-no-fork does not fork a new JVM (Java Virtual Machine) process to execute the goal.
This means it runs within the same JVM as the Maven build process, which can have implications for performance and memory usage.-->
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<!-- Generates Javadoc documentation and packages it into a JAR file containing HTML files. -->
<goal>doc-jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>xtest</id>
<properties>
<maven.test.skip>true</maven.test.skip>
</properties>
</profile>
</profiles>
<repositories>
<repository>
<id>oss-snapshots</id>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
<snapshots>
<enabled>true</enabled>
<updatePolicy>always</updatePolicy>
</snapshots>
</repository>
</repositories>
<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<name>Sonatype Nexus Snapshots</name>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<name>Nexus Release Repository</name>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url>
</repository>
</distributionManagement>
</project>