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Maven assembly plugin is not including the project packages [duplicate]

This question already has answers here:
Building a fat jar using maven
(7 answers)
Closed 1 year ago.
I'm trying to build a fat jar with maven assembly plugin for distributing a desktop application.
My POM looks like
<build>
<!-- To parse properties files under resources folder : -->
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.3.0</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<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>
<archive>
<manifest>
<mainClass>com.acme.qpguard.editor.Application</mainClass>
</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>
</plugins>
</build>
The command mvn assembly: single is creating a fat jar with other dependencies, but fat jar does no include my classes.
So while starting the jar, I'm getting an error
Error: Could not find or load main class com.acme.qpguard.editor.Application
How can I fix my POM so that it includes my project files too
Please note that the project is running fine in Eclipse.

Thanks, #Mayur and #Randy Casburn. Your pointers definitely helped me in finding a fix using maven shaded plugin.
I'm posting the fix as someone may find this useful at a later point of time
<build>
<!-- To parse properties files under resources folder : -->
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>com.acme.qpguard.editor.Application</mainClass>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
Note: I have to apply a filter for removing signature files from some jars as it was breaking the execution.

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>

Maven corrupting binary files in src/main/resources when building jar

I've got an issue with a maven project where I am distributing dlls from the src/main/resources/lib folder.
The project is built as a single jar with dependencies using the maven-assembly-plugin.
Unfortunately, the maven process is corrupting my dll libraries during the copy process so that they are no longer useful to the application.
I've had a look at such concepts as resource filtering.
Here's my relevant pom.xml
Does anyone have any ideas?
I think I need to do something like this but so far it's not working for me.
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<resources>
<resource>
<directory>${basedir}/src/main/resources/lib</directory>
<filtering>false</filtering>
</resource>
</resources>
<archive>
<manifest>
<mainClass>de.bochumuniruhr.psy.bio.behaviourcoder.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
My final solution (based on the answers below):
Thank you for the great answers. I ended up going with the answer that doesn't require extending the configuration of the maven-resources-plugin. I placed my binary files in the src/main/resources/unfiltered-resources folder as I needed to filter my other resources.
Here is a link to the source code.
Below is my final working pom at the time of writing.
<build>
<finalName>BehaviourCoder_${git.build.time}_${git.commit.id.describe-short}</finalName>
<resources>
<resource>
<directory>${basedir}/src/main/resources</directory>
<filtering>true</filtering>
</resource>
<resource>
<directory>${basedir}/src/main/unfiltered-resources</directory>
<filtering>false</filtering>
</resource>
</resources>
<plugins>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.2.2</version>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
<configuration>
<generateGitPropertiesFile>true</generateGitPropertiesFile>
<injectAllReactorProjects>true</injectAllReactorProjects>
<dateFormat>yyyy-MM-dd_HHmmss</dateFormat>
<dateFormatTimeZone>UTC</dateFormatTimeZone>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>de.bochumuniruhr.psy.bio.behaviourcoder.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>

This part:
<resources>
<resource>
<directory>${basedir}/src/main/resources/lib</directory>
<filtering>false</filtering>
</resource>
</resources>
Should be under under the <build/> section like this:
<project>
<build>
<resources>
<resource>
<directory>${basedir}/src/main/resources/lib</directory>
<filtering>false</filtering>
</resource>
</resources>
<plugins>
...
</plugins>
</build>
</project>

When assembly plugin kicks in it is already too late, as the resources were already copied by maven resources plugin. You should exclude filtering on earlier phase (when the resources are being copied to target folder by maven resource plugin).
See maven's docs how to do this: https://maven.apache.org/plugins/maven-resources-plugin/examples/binaries-filtering.html
For your case this can be something like:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<nonFilteredFileExtensions>
<nonFilteredFileExtension>dll</nonFilteredFileExtension>
</nonFilteredFileExtensions>
</configuration>
</plugin>
</plugins>

.jar with Maven and Eclipse

I have a java project done with Eclipse and Maven with this estructure folder:
enter image description here
Ok, when i make a Maven install to create the .jar take this structure folder:
enter image description here
So that the hierarchy is not the same and links to the images and css do not work.
I show you the code of pom.xml
enter code here
http://maven.apache.org/xsd/maven-4.0.0.xsd">
4.0.0
com.wepall
palle
0.4.0
com.thoughtworks.xstream
xstream
com.thoughtworks.xstream
xstream
1.4.9
palle
<!-- download source code in Eclipse, best practice -->
<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>${jdk.version}</source>
<target>${jdk.version}</target>
</configuration>
</plugin>
<!-- Maven Assembly Plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<!-- get all project dependencies -->
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<!-- MainClass in mainfest make a executable jar -->
<archive>
<manifest>
<mainClass>com.wepall.palle.MainApp</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<!-- bind to the packaging phase -->
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Any ideas?
thanks a lot!!
Best regards

You should add a build section to your pom.xml:
<build>
<directory>${basedir}/target</directory>
<resources>
<resource>
<targetPath>${basedir}/target/resources</targetPath>
<directory>${basedir}/src/main/resources</directory>
</resource>
</resources>
</build>
Further Reference:
POM Reference (Build Section)

I think that you should create a war instead of a jar, because you are talking about css and images and jars should not contains that kind of files (see jar vs war).
In maven you only need to change the <packaging> of the project inside the POM.

how to make a executable jar pick the properties file during time time using maven

Hi i am using maven buil to create an executable jar, i have few properties file. if i place the properties file in
src/main/resources
maven packages them inside the jar itself. I dont want this to happen, instead i want to place the properties file in a folder called conf and i want these properties file to be avalable to the jar during runtime.
The reason why this is because in future the user can have the flexibility to chnage a few property values like port number etc without.
i have pasted the pom.xml below
<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>com.hp.nfv</groupId>
<artifactId>DescriptorA</artifactId>
<version>1.0.0</version>
<name>DescriptorA/name>
<dependencies>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.16</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.2</version>
</dependency>
</dependencies>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>prepare-package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3</version>
<configuration>
<excludes>
<exclude>**/*.properties</exclude>
</excludes>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>com.abc.Descripto</mainClass>
</manifest>
<manifestEntries>
<Class-Path>conf/</Class-Path>
</manifestEntries>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<id>copy-resources</id>
<phase>install</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/conf</outputDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
<includes>
<include>**/*.properties</include>
</includes>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
the property file i am using is 'utility.properties' which is present in the src/main/resources
i am using this in the java code as below
ResourceBundle locationUtilityProp = ResourceBundle.getBundle("utility", locale);
but when i execute the above pom.xml file, i get a jar file , which on running gives the below error
java.util.MissingResourceException: Can't find bundle for base name utility
when I un jarred the jar file, i found no .properties files in it.
I am completely new to maven so please can anyone help me make this jar pick the properties file from a directory structure other than src/main/resources at run time.

I got this requirement working , and below i have answered in detail so that it can help someone else someday
package structure:
you need to place .properties files inside src/main/resources when doing a maven build
src
|-main/java/com.abc/.java classes
|-main/resources/error.properties
after maven generates a jar file, then create a folder called config and copy all .properties files inside it. and place your jar file in same directory as your config folder as below
example
|-config
-error.properties
|-jar file generated by maven
code to fetch the resources files
static Locale locale = new Locale("en", "US");
static ResourceBundle locationUtilityProp =ResourceBundle.getBundle("error", locale);
pom.xml to create an executable jar file
first tell maven not to include any of properties files present inside src/main/resources
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<excludes>
<exclude>**/*.properties</exclude>
</excludes>
</resource>
</resources>
now include maven compiler plugin
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
</plugins>
</build>
now include the maven assembly plugin to create an executable jar.
in the mention the folder name where you want maven to pick the resource files( in my case error.properties)
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.abc.hello</mainClass>
</manifest>
<manifestEntries>
<Class-Path>config/</Class-Path>
</manifestEntries>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<!-- bind to the packaging phase -->
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>

If I got you right, you want to have a portable, configurable jar so you can edit the config without re-packaging. That can be achieved easily by providing the -cp (or -classpath) option with the path to the folder containing yout utility.properties. So the invocation looks like:
java -cp ./conf -jar youApp.jar
assuming that the config is in a conf sub-folder of where the main jar sits.
More on the classpath.