pom.xml

<?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>org.example</groupId>
    <artifactId>cdk-rest-template</artifactId>
    <version>1.0-SNAPSHOT</version>

    <properties>
        <cdk.version>2.9</cdk.version>
        <tomcat.version>10.1.25</tomcat.version>
        <spring.version>6.1.13</spring.version>
        <slf4j.version>2.0.9</slf4j.version>

        <maven.compiler.source>20</maven.compiler.source>
        <maven.compiler.target>20</maven.compiler.target>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-smiles</artifactId>
            <version>${cdk.version}</version>
        </dependency>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-silent</artifactId>
            <version>${cdk.version}</version>
        </dependency>

        <dependency>
            <groupId>org.apache.tomcat.embed</groupId>
            <artifactId>tomcat-embed-core</artifactId>
            <version>${tomcat.version}</version>
        </dependency>

        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-webmvc</artifactId>
            <version>${spring.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>commons-logging</groupId>
                    <artifactId>commons-logging</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-test</artifactId>
            <version>${spring.version}</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>jcl-over-slf4j</artifactId>
            <version>${slf4j.version}</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>log4j-over-slf4j</artifactId>
            <version>${slf4j.version}</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
            <version>${slf4j.version}</version>
        </dependency>
        <dependency>
            <!-- Tomcat, Liquibase, Postgres Driver, etc - they use java.util.logging (JUL). While we want to configure
            all the logging (not just JUL) using Logback. This SLF4J bridge allows forwarding JUL calls to Logback-->

            <!-- How to configure JUL->SLF4J:

                 <p>
                  <b>This memo is duplicated in all the places where the bridging is configured, keep it up-to-date in all of them!</b>
                 </p>

                 Overall there are several places that need changes to enabled java.util.logging -> SLF4j bridging
                 (see <a href="https://www.slf4j.org/legacy.html#jul-to-slf4j">official documentation</a>):
                 <ol>
                     <li>Add dependency jul-to-slf4j to pom.xml. The dependency contains the bridging code that accepts LogRecords from JUL</li>
                     <li>Update production logback.xml with 2 listeners: our own JulOverSlf4jInstaller (sets up the bridging),
                     LevelChangePropagator (passes logging levels from logback.xml to JUL)</li>
                     <li>Do the same for the test logback.xml or any other present in the project</li>
                 </ol> -->
            <groupId>org.slf4j</groupId>
            <artifactId>jul-to-slf4j</artifactId>
            <version>${slf4j.version}</version>
        </dependency>
        <dependency>
            <groupId>commons-logging</groupId>
            <artifactId>commons-logging</artifactId>
            <version>1.2</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
            <version>1.3.12</version>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-databind</artifactId>
            <version>2.15.2</version>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.datatype</groupId>
            <artifactId>jackson-datatype-jsr310</artifactId>
            <version>2.15.2</version>
        </dependency>

        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.13.1</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>io.rest-assured</groupId>
            <artifactId>spring-mock-mvc</artifactId>
            <version>5.5.0</version>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>3.6.0</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <shadedArtifactAttached>true</shadedArtifactAttached>
                            <transformers>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                    <mainClass>cdkapi.Starter</mainClass>
                                </transformer>
                                <!-- Different Spring libs may have different spring.handlers & spring.schemas.
                                     After shading they'll be overwritten with the latest version that the shade-plugin
                                     encounters. Here we concatenate all of instead of overwriting. -->
                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                    <resource>META-INF/spring.handlers</resource>
                                </transformer>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                    <resource>META-INF/spring.schemas</resource>
                                </transformer>
                            </transformers>

                            <filters>
                                <!--Because we're repacking with shade plug-in (which is questionable) the signatures inside the
                                archives are put into our main JAR which makes it seem our JAR is signed (and signed incorrectly).
                                So let's remove those signatures.-->
                                <filter>
                                    <artifact>*:*</artifact>
                                    <excludes>
                                        <exclude>META-INF/*.SF</exclude>
                                        <exclude>META-INF/*.DSA</exclude>
                                        <exclude>META-INF/*.RSA</exclude>
                                    </excludes>
                                </filter>
                            </filters>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

</project>