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Maven - Invalid signature file digest for Manifest main attributes

New to java and Maven.
When trying to add dependancy to the package pulsar-functions-local-runner I am getting an error:
Failed to execute goal org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5:assembly (make-assembly) on project java-function: Execution make-assembly of goal org.apache.maven.plugins:maven-assembly-plugin:2.2-beta-5:assembly failed: Invalid signature file digest for Manifest main attributes
Using maven 3.6.3.
I am after 3 hours of searching the web, what am I missing?
This is my pom.xml file:
<?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>java-function</groupId>
<artifactId>java-function</artifactId>
<version>1.0-SNAPSHOT</version>
<dependencies>
<dependency>
<groupId>org.apache.pulsar</groupId>
<artifactId>pulsar-functions-api</artifactId>
<version>2.7.0</version>
</dependency>
<dependency>
<groupId>org.apache.pulsar</groupId>
<artifactId>pulsar-functions-local-runner</artifactId>
<version>2.7.0</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>src/</sourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.example.test.ExclamationFunction</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>assembly</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

Well i guess they made some change in the jar of 2.7.0 because changing to pulsar-functions-local-runner 2.6.0 solve the issue

Remove pulsar-client from maven, and add pulsar-common. pulsar-common has the pulsar-client-api. There is a serious conflict between pulsar-client and pulsar-common.
<dependency>
<groupId>org.apache.pulsar</groupId>
<artifactId>pulsar-common</artifactId>
<version>${pulsar.version}</version>
</dependency>
<dependency>
<groupId>org.apache.pulsar</groupId>
<artifactId>pulsar-functions-api</artifactId>
<version>${pulsar.version}</version>
</dependency>
<dependency>
<groupId>org.apache.pulsar</groupId>
<artifactId>pulsar-functions-local-runner</artifactId>
<version>${pulsar.version}</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>org.apache.pulsar</groupId>-->
<!-- <artifactId>pulsar-client</artifactId>-->
<!-- <version>${pulsar.version}</version>-->
<!-- </dependency>-->

java.lang.NoClassDefFoundError while using maven eclipse AsciidoctorJ

I'm trying to use Asciidoctor to generate an html file using the method built in asciidocj (convertFile)
I'm getting java.lang.NoClassDefFoundError:org/asciidoctor/OptionsBuilder
I'm working on eclipse ; maven and
I added the Asciidoctor dependency in the pom.xml file.
public void view(String document) {
OptionsBuilder op = OptionsBuilder.options().toFile(false);
Asciidoctor asciidoctor = create();
String html = asciidoctor.convertFile(new File(this.path + "/" + document + ".adoc"), op.asMap());
System.out.println(html);
}
<?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>ProgGl</groupId>
<artifactId>PriseDeNotes</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>PriseDeNotes</name>
<description>Projet de Prog Gl</description>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<main-class>ProgGl.PriseDeNote.App</main-class>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<mainClass>${main-class}</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.asciidoctor</groupId>
<artifactId>asciidoctor-maven-plugin</artifactId>
<version>1.5.6</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.3</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.7</version>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>${main-class}</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.1</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>package</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.0-M1</version>
<executions>
<execution>
<id>attach-javadocs</id>
<phase>package</phase>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.github.spotbugs</groupId>
<artifactId>spotbugs-maven-plugin</artifactId>
<version>3.1.7</version>
<dependencies>
<!-- overwrite dependency on spotbugs if you want to specify the version of spotbugs -->
<dependency>
<groupId>com.github.spotbugs</groupId>
<artifactId>spotbugs</artifactId>
<version>3.1.8</version>
</dependency>
</dependencies>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>3.0.0</version>
<reportSets>
<reportSet>
<reports>
<report>checkstyle</report>
</reports>
</reportSet>
</reportSets>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jxr-plugin</artifactId>
<version>2.3</version>
</plugin>
</plugins>
</reporting>
<dependencies>
<dependency>
<groupId>org.asciidoctor</groupId>
<artifactId>asciidoctorj</artifactId>
<version>2.0.0</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
mvn install, package everything is working fine,
when I execute the program I'm getting this error.
I read that it's about class path etc... but I don't understand how to do otherwise
Exception in thread "main" java.lang.NoClassDefFoundError: org/asciidoctor/OptionsBuilder
at ProgGl.PriseDeNote.Application.view(Application.java:171)
at ProgGl.PriseDeNote.Commands.ViewCommand.execute(ViewCommand.java:22)
at ProgGl.PriseDeNote.App.main(App.java:66)
Caused by: java.lang.ClassNotFoundException: org.asciidoctor.OptionsBuilder
at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 3 more
Thank you.

General, the maven assembly plugin generates another .jar called target/PriseDeNotes-0.0.1-SNAPSHOT-jar-with-dependencies.jar.
You can try java -jar target/PriseDeNotes-0.0.1-SNAPSHOT-jar-with-dependencies.jar to run the application.

I see you have the maven-assembly-plugin already. Compile with mvn clean compile assembly:single then run with java -jar target/PriseDeNotes-0.0.1-SNAPSHOT-jar-with-dependencies.jar.

I think the problem is, that maven doesn't copy the dependencies into the jar. Try to copy the dependencies in the target with the related plugin you can find here:
https://maven.apache.org/plugins/maven-dependency-plugin/examples/copying-project-dependencies.html
With this, it should copy the needed dependencies to the target folder.

Error: Could not find or load main class while executing jar file

I have created two java file my maven project one is POJO class and another one is java main class file. I want to make my project as an executable jar file which i want to run externally using java -jar command.
Please find my pom.xml file
<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>ElasticSearchUtility</groupId>
<artifactId>ElasticSearchUtility</artifactId>
<version>1.0.0-SNAPSHOT</version>
<dependencies>
<dependency>
<groupId>org.elasticsearch</groupId>
<artifactId>elasticsearch</artifactId>
<version>6.1.2</version>
</dependency>
<dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>elasticsearch-rest-high-level-client</artifactId>
<version>6.1.2</version>
</dependency>
<dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>rest</artifactId>
<version>5.1.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>false</downloadJavadocs>
</configuration>
</plugin>
<!-- Set a compiler level -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<!-- Make this jar executable -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<excludes>
<exclude>**/log4j.properties</exclude>
</excludes>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>com.es.utility.DocumentIndex</mainClass>
<classpathPrefix>dependency-jars/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
<!-- Copy project dependency -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.5.1</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<!-- exclude junit, we need runtime dependency only -->
<includeScope>runtime</includeScope>
<outputDirectory>${project.build.directory}/dependency-jars/</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
While am executing my jar file using java -jar command. Am getting the error
Error: Could not find or load main class com.es.utility.DocumentIndex
Please find my project structure also :

If there are no classes in the .jar it's probably because maven can't find them. The default path for java classes in Maven is src/main/java, try moving them there and run Maven again.

To add to #kshetline's comment, make sure com.es.utility.DocumentIndex is the correct path to your main class. When you unzip the generated jar, DocumentIndex.class should be in the com/es/utility folder.

How to create a fat jar?

With SpringBoot, you have the #SpringBootApplication annotation, but what is the equivalent with the neat Java Spark framework?
IntelliJ creates a Maven project and I added the spark dependency, but running the install goal, I get a 5 KB jar with no manifest. Not an executable jar.
The pom.xml created thus far is as follows:
<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>sparkdemo</groupId>
<artifactId>sparkdemo</artifactId>
<version>1.0 </version>
<packaging>jar</packaging>
<name>sparkdemo</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sparkjava</groupId>
<artifactId>spark-core</artifactId>
<version>2.5.4</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
<optimize>true</optimize>
<debug>true</debug>
</configuration>
</plugin>
</plugins>
</build>
</project>
Would appreciate any suggestions....Thanks!

What you need here is an executable jar that will not only contain your classes, but also classes from all your dependencies.
For that you can use the Maven Assembly Plugin.
See the sample code below.
<project>
[...]
<build>
[...]
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.sample.App</mainClass> // specify your main class here
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
[...]
</project>
Then, run mvn package and the executable jar should be located in the folder target (with a name like ProjectName-1.0-SNAPSHOT-jar-with-dependencies.jar).

Looks like you are looking for maven assembly plugin
Add this in the plugin section and run mvn package
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>assemble-all</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>

creating a jar-with-dependencies

I am creating a jar-with-dependencies in mvn 3.0.3. I have successfully done this in one project (using just mvn install) and created a complete jar-wth-dependencies. I copied the relevant chunk of POM code (<plugins>...</plugins>, which someone else wrote!) to the current project (which differs in that it has assemblies). It creates the normal snapshot jar (jumbo-converters-compchem-gaussian-0.3-SNAPSHOT.jar) but no jar-with-dependencies. How should I amend the POM?
<?xml version="1.0" encoding="UTF-8"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://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>
<parent>
<groupId>cml</groupId>
<artifactId>jumbo-converters</artifactId>
<version>0.3-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<artifactId>jumbo-converters-compchem-gaussian</artifactId>
<name>jumbo-converters-compchem-gaussian</name>
<dependencies>
<dependency>
<groupId>${jumbo.groupId}</groupId>
<artifactId>jumbo</artifactId>
</dependency>
<dependency>
<groupId>cml</groupId>
<artifactId>jumbo-converters-core</artifactId>
</dependency>
<dependency>
<groupId>cml</groupId>
<artifactId>jumbo-converters-compchem-common</artifactId>
<version>0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>cml</groupId>
<artifactId>jumbo-converters-templates</artifactId>
<version>0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>cml</groupId>
<artifactId>jumbo-converters-testutils</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>cml</groupId>
<artifactId>jumbo-converters-compchem-testutils</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>org.xmlcml.cml.converters.compchem.gaussian.GaussianLogXML2CompchemConverter</mainClass>
</manifest>
</archive>
<excludes>
<exclude>.hgsub</exclude>
<exclude>**/.hg/</exclude>
<exclude>**/.project</exclude>
<exclude>**/external/</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.xmlcml.cml.converters.compchem.gaussian.GaussianLogXML2CompchemConverter</mainClass>
</manifest>
</archive>
<excludes>
<exclude>.hgsub</exclude>
<exclude>**/.hg/</exclude>
<exclude>**/.project</exclude>
<exclude>**/external/</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>

First,
Use maven dependency plugin to retrieve/store the dependencies (more info here) to your project folder.
Ex: Say lib folder.
Now mark this lib folder as a "Resources" folder.
Like,
<resources>
<resource>
<directory>lib</directory>
<targetPath>lib</targetPath>
</resource>
</resources>
Now mvn install should include the dependencies in your final artifact.
(copying Shinchan's comment to here so it can be formatted:
Simple add this to ur pom.
<build>
<resources>
<resource>
<directory>lib</directory>
<targetPath>lib</targetPath>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.8</version>
<executions>
<execution>
<phase>install</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>lib</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>