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jar executable is dysfunctional while it is functional in Netbeans maven project

I have a maven project in Netbeans.
Running it shows a GUI in which you can select and read files using a JFileChooser.
The file chooser has the method getSelectedFiles() which returns a File[] which then I feed into fileProccesing(File[] files) to read them using PDDocument.load(file) from Apache pdfBox depedency.
Debugging has led to the conclusion bellow.
When running in Netbeans it works fine but when it's running as a jar executable it stops at the PDDocument.load(file) command. However no IOException is thrown.
Ether JFileChooser getSelectedFiles() returns some abnormal type of files or my pom.xml is problematic in some way. You can see my pom.xml bellow.
<?xml version="1.0" encoding="UTF-8"?>
4.0.0
<groupId>application</groupId>
<artifactId>toolToManagePdfs</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>toolToManagePdfs</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.pdfbox</groupId>
<artifactId>pdfbox</artifactId>
<version>2.0.22</version>
</dependency>
<dependency>
<groupId>org.apache.opennlp</groupId>
<artifactId>opennlp-tools</artifactId>
<version>1.9.3</version>
</dependency>
</dependencies>
<build>
<pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
<plugins>
<!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
<configuration>
<argLine>-Dfile.encoding=UTF-8</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>
application.App
</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>

A normal JAR does not contain or reference its dependencies at runtime. If you want to run a JAR, you need to either
build an executable JAR with the maven assembly plugin or maven shade plugin.
list the classpath explictly when running the JAR.

Here's what I use to have the jar files in the lib subdir:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>application.App</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.2</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
</configuration>
</execution>
</executions>
</plugin>

The problem stemmed from having all plugins inside <pluginManagement></pluginManagement>.
Moreover the configuration was incomplete and didn't include the dependencies inside the jar.Using maven-assembly-plugin fixed that.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<archive>
<manifest>
<mainClass>
application.App
</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
</plugin>

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>

maven user library not packaged in my runnable jar

I'm now programming Java for a year and had to take over several projects from a previous programmer. I'm not a programming newby since I started with .NET programming in 1998. Now for a Java project, I need to support 24 versions (and rising) of a base library (all the same structure but they are specific for a version of the 3th party application).
I started with Maven two days ago and tried this on a small demo workspace in order to learn Maven and get the required things working.
Each supported version has several jars which I encapsulated in a user library.
To make a build, I would need to modify this library to the correct version and do an export of the project as a Runnable-Jar (everything include in the jar due to license requirements).
So I created my first POM and here it is:
<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>PPC</groupId>
<artifactId>PPC</artifactId>
<version>1.0.0</version>
<packaging>jar</packaging>
<name>PPC</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>LibraryProject</groupId>
<artifactId>LibraryProject</artifactId>
<version>1.0.0</version>
<scope>compile</scope>
</dependency>
</dependencies> <profiles>
<profile>
<id>PPC_8.1</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<finalName>PPC_8.1</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<compilerVersion>1.7</compilerVersion>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<inherited>true</inherited>
<version>2.10</version>
<configuration>
<classpathContainers>
<classpathContainer>org.eclipse.jdt.launching.JRE_CONTAINER</classpathContainer>
<classpathContainer>org.eclipse.jdt.USER_LIBRARY/Primavera-P6-8.1</classpathContainer>
</classpathContainers>
</configuration>
</plugin>
<plugin>
<groupId>org.dstovall</groupId>
<artifactId>onejar-maven-plugin</artifactId>
<version>1.4.4</version>
<executions>
<execution>
<configuration>
<mainClass>com.company.main.App</mainClass>
<onejarVersion>0.97</onejarVersion>
<attachToBuild>true</attachToBuild>
<classifier>onejar</classifier>
</configuration>
<goals>
<goal>one-jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>PPC_7.0</id>
<build>
<finalName>PPC_7.0</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<compilerVersion>1.7</compilerVersion>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.10</version>
<inherited>true</inherited>
<configuration>
<classpathContainers>
<classpathContainer>org.eclipse.jdt.launching.JRE_CONTAINER</classpathContainer>
<classpathContainer>org.eclipse.jdt.USER_LIBRARY/Primavera-P6-7.0</classpathContainer>
</classpathContainers>
</configuration>
</plugin>
<plugin>
<groupId>org.dstovall</groupId>
<artifactId>onejar-maven-plugin</artifactId>
<version>1.4.4</version>
<executions>
<execution>
<configuration>
<mainClass>com.company.main.App</mainClass>
<onejarVersion>0.97</onejarVersion>
<attachToBuild>true</attachToBuild>
<classifier>onejar</classifier>
</configuration>
<goals>
<goal>one-jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<pluginRepositories>
<pluginRepository>
<id>onejar-maven-plugin.googlecode.com</id>
<url>http://onejar-maven-plugin.googlecode.com/svn/mavenrepo</url>
</pluginRepository>
</pluginRepositories>
</project>
As you can see, I have two profiles. One for v8.1 and one for v7.0.
My 'build' flow:
I run 'mvn install' on the libraryProject first.
Then I run 'mvn package' on the main project. This one build v8.1 (Default profile) as a runnable jar with all depencies in it except the user library.
The next call is 'mvn package -PPPC_7.0' which builds v7.0 without the user library.
So my question: What can I change/doing wrong so the user library is added to the runnable jar for each profile?
Thanks in advance,
Jo
PS: I'm using Eclipse Luna (Java EE IDE)

What I use is:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.clouway.App</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-my-jar-with-dependencies</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
`
Good luck!

Robby Cornelissen commented a suggestion a while back:
Any chance of just packaging that up and using it as a dependency? That would definitely solve your problem... – Robby Cornelissen Jun 11 at 8:52
I didn't want to do that, but I did not receive new suggestions (and did not find a solution myself).
So I packaged them as suggested and added them as dependency.
This is working for me now.
Thanks and until next time
Jo