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JAR under EAR(src/main/application/lib) are not part of ClassPath in Maven - [Resolved]

I am working on converting a J2EE application to Maven where the EAR project will contain a WAR module. I have followed the below URL to convert the project and it does work with some minor changes:
https://www.ibm.com/docs/en/wasdtfe?topic=projects-converting-existing-maven
In the current project, there are some libraries under the EAR folder which I cannot move to the local maven repository. The reason is old legacy code which expects these library names to be intact (myCommon.jar and no version to be added like myCommon-1.0.jar).
As a workaround, I placed these libs under EAR->src->main->application->lib folder. There is no build failure observed but the major problem is with the ClassPath for these EAR lib files as shown below:
[err] java.lang.ClassNotFoundException: com.myClass.classFromWAR
[err] at java.lang.Class.forNameImpl(Native Method)
[err] at java.lang.Class.forName(Class.java:332)
E.g. myCommon.jar contains code like the below:
public void EARLibFunc( string classNameFromWAR){
.........
//E.g. classNameFromWAR = "com.myClass.classFromWAR";
final Class warClass = Class.forName( classNameFromWAR );
.........
}
Calling above function from the java files inside WAR module reports ClassNotFoundException: EARLibFunc("com.myClass.classFromWAR");
The directory structure looks like the below:
WARProject
-src
----com
--------myClass
------------classFromWAR.java
EARProject
-src
----main
--------application
------------lib
----------------myCommon.jar
The jar files from EAR/src/main/application don't seem to be part of the ClassPath.
Can you please suggest the best practice to handle such an issue? What should be the correct layout of the EAR libraries to make it part of the ClassPath? Please be informed that the code from the EAR libraries cannot be changed (legacy code dependency issue).
For reference here are my pom settings:
WARProject pom.xml:
.......
.......
<groupId>MyApp</groupId>
<artifactId>MyApp</artifactId>
<version>3.5</version>
<packaging>war</packaging>
<description>MyApp Maven</description>
........
<build>
<resources>
<resource>
<directory>Java Source</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<warSourceDirectory>Web Content</warSourceDirectory>
</configuration>
</plugin>
</plugins>
</build>
......
EAR Project pom.xml (contains WAR module as dependency):
.....
<groupId>EARProject_EAR</groupId>
<artifactId>EARProject_EAR</artifactId>
<version>3.5</version>
<packaging>ear</packaging>
<description>My Project EAR</description>
<build>
<plugins>
<plugin>
<artifactId>maven-ear-plugin</artifactId>
<version>2.10</version>
<configuration>
<version>7</version>
<skinnyWars>true</skinnyWars>
<defaultLibBundleDir>lib</defaultLibBundleDir>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addClasspath>true</addClasspath>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>MyApp</groupId>
<artifactId>MyApp</artifactId>
<version>3.5</version>
<type>war</type>
</dependency>
</dependencies>
......
SOLUTION:
The crash reported for the CLASSPATH is resolved. Since I am moving an old legacy application to Maven, there were some old references to be cleaned-up. Below changes were required:
There were duplicate classpath references in the eclipse Project
(Project -> Properties -> Java Build Path). Even though I had
dependencies mentioned in the pom.xml of the WAR file, the project
properties were also having its references. This may or may not be
the real reason.
Reverted earlier workaround solution. Removed libraries from
EAR->src-main->application->lib and added those as dependency in the
WAR pom.xml reference. Though it has re-created other legacy issue
but I believe this will adhere to the best practices.

I think, it should be possible this way:
Install the jar in your local maven repository.
Configure the maven-ear-plugin to include third party libraries as shown here.
Add <bundleFileName>myCommon.jar</bundleFileName> to jarModule in order to give your JAR file the desired name within the EAR.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-ear-plugin</artifactId>
<version>3.2.0</version>
<configuration>
[...]
<modules>
<jarModule>
<groupId>artifactGroupId</groupId>
<artifactId>artifactId</artifactId>
<includeInApplicationXml>true</includeInApplicationXml>
<bundleFileName>myCommon.jar</bundleFileName>
</jarModule>
</modules>
</configuration>
</plugin>
</plugins>
</build>
More information can be found at the usage page of the plugin.

Conditional inclusion of files in maven

I have a JEE6 web application project.The project structure is according to maven convention.
Now I have introduced additional web.xml files for this project.
So they are now stored in WEB-INF as below:
WEB-INF/
|__ A/web.xml
|__ B/web.xml
What is the maven way to build a war to include proper xml depending upon the property.
I know the how to add custom properties in maven.But I cannot find how to configure the maven plugin such that during the war file building it chooses the appropriate file.
Any hints/suggestions/maven best practices in such cases are most welcome.
Thanks!!

maven war plugin could be configured to add and filter some external resources. See http://maven.apache.org/plugins/maven-war-plugin/examples/adding-filtering-webresources.html.
So I would make 2 maven profiles with 2 war plugin configuration like this :
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<webResources>
<resource>
<!-- this is relative to the pom.xml directory -->
<directory>src/main/webapp/WEB-INF/__A</directory>
<includes>
<include>web.xml</include>
</includes>
<targetPath>WEB-INF</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
<!-- repeat for your second profile -->
BUT I think a better solution (and if your project permits it) would be to keep only one web.xml file with some filtered properties inside. In this case, you should just configure your war plugin to enable some filtering like this :
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<filteringDeploymentDescriptors>true</filteringDeploymentDescriptors>
</configuration>
</plugin>

Resource files not found from JUnit test cases

Summary
My JUnit tests are not finding the files they require during execution.
I'm using Maven for dependency management and compilation.
Details
All files required by the test cases are located in: src/test/resources.
For example, src/test/resources/resourceFile.txt.
To access a resource I use the following code:
URL url = getClass().getResource("/resourceFile.txt").getFile();
File file = new File(url);
But then file.exists() returns false. And the error I get is:
Tests in error:
myJUnitTestCase(tests.MyJUnitTestClass): /home/me/workspace/Project%20Name/target/test-classes/resourceFile.txt (No such file or directory)
Note, the following gives the same error (notice the removed / prefix):
URL url = getClass().getClassLoader().getResource("resourceFile.txt").getFile();
File file = new File(url);
It seems as though the files from src/test/resources are not getting copied into target/test-classes.
Any ideas?
The following questions did not help
Why Can't I access src/test/resources in Junit test run with Maven?
Loading Properties File In JUnit #BeforeClass
How to deal with the test data in Junit?
Software Versions
Ubuntu 12.04
Apache Maven 2.2.1
Java 1.7.0
Eclipse (Java EE IDE for Web Developers) Indigo Service Release 2
(truncated) Maven POM
<?xml version="1.0" encoding="UTF-8"?>
<project>
<modelVersion>4.0.0</modelVersion>
<groupId>com.groupId</groupId>
<artifactId>artifactId</artifactId>
<packaging>jar</packaging>
<version>1.0-SNAPSHOT</version>
<name>name</name>
<build>
<finalName>name</finalName>
<directory>target</directory>
<outputDirectory>target/classes</outputDirectory>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/test/java</testSourceDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<testResources>
<testResource>
<directory>src/test/resources</directory>
</testResource>
</testResources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.6</source>
<target>1.6</target>
<encoding>UTF-8</encoding>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>

My mistake, the resource files WERE actually copied to target/test-classes. The problem seemed to be due to spaces in my project name, e.g. Project%20Name.
I'm now loading the file as follows and it works:
org.apache.commons.io.FileUtils.toFile(myClass().getResource("resourceFile.txt")‌​);
Or, (taken from Java: how to get a File from an escaped URL?) this may be better (no dependency on Apache Commons):
myClass().getResource("resourceFile.txt")‌​.toURI();

You know that Maven is based on the Convention over Configuration pardigm? so you shouldn't configure things which are the defaults.
All that stuff represents the default in Maven. So best practice is don't define it it's already done.
<directory>target</directory>
<outputDirectory>target/classes</outputDirectory>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/test/java</testSourceDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<testResources>
<testResource>
<directory>src/test/resources</directory>
</testResource>
</testResources>

This is actually redundant except in cases where you want to override the defaults. All of these settings are implied defaults.
You can verify that by checking your effective POM using this command
mvn help:effective-pom
<finalName>name</finalName>
<directory>target</directory>
<outputDirectory>target/classes</outputDirectory>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/test/java</testSourceDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<testResources>
<testResource>
<directory>src/test/resources</directory>
</testResource>
</testResources>
For example, if i want to point to a different test resource path or resource path you should use this otherwise you don't.
<resources>
<resource>
<directory>/home/josh/desktop/app_resources</directory>
</resource>
</resources>
<testResources>
<testResource>
<directory>/home/josh/desktop/test_resources</directory>
</testResource>
</testResources>

You may have defined:
<packaging>pom</packaging>
If you did this, the resources won't be present in the target directory when you will launch your tests. And mvn package won't create it either.
At the contrary, if you define:
<packaging>jar</packaging>
Or nothing as the default value is jar. As Maven is based on Convention over Configuration. You will end up with:
src/main/resources => target/classes
src/test/resources => target/test-classes

Main classes should be under src/main/java
and
test classes should be under src/test/java
If all in the correct places and still main classes are not accessible then
Right click project => Maven => Update Project
Hope so this will resolve the issue

The test Resource files(src/test/resources) are loaded to target/test-classes sub folder. So we can use the below code to load the test resource files.
String resource = "sample.txt";
File file = new File(getClass().getClassLoader().getResource(resource).getFile());
System.out.println(file.getAbsolutePath());
Note : Here the sample.txt file should be placed under src/test/resources folder.
For more details refer options_to_load_test_resources

Make 'maven.test.skip' as false in pom file, while building project test reource will come under test-classes.
<maven.test.skip>false</maven.test.skip>

Refer to Maven project paths from Java

I need to programmatically gather some paths inside a Maven project, in particular to refer to the project artifact.
Using
URL MyClass.class.getClassLoader().getResource(String name)
works for a path relative to the target/classes folder of the project, but since the artifact sits in the target folder it is not possible to reference it. A path like
System.getProperty("user.dir") + "/target"
does not convince me at all at least for the fact that the target folder name, while standard, is not safely portable.
Is there a Maven-aware library solution that exploits a relative path?

MavenProperties can be written to a manifest file using the maven archiver which is used by the maven war plugin or the maven jar plugin.
If you have a web app, then you can pass some information to the web.xml file, too.
This is an example of one of my projects:
from pom.xml:
------------------------------------------------
<properties>
<maven.build.timestamp.format>dd.MM.yyyy' 'HH:mm:ss</maven.build.timestamp.format>
<build-version>${env.SVN_REVISION}</build-version>
<build-date>${maven.build.timestamp}</build-date>
</properties>
.
.
.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<webResources>
<webResource>
<directory>${basedir}/src/main/webapp/WEB-INF</directory>
<includes>
<include>web.xml</include>
</includes>
<targetPath>WEB-INF</targetPath>
<filtering>true</filtering>
</webResource>
</webResources>
from web.xml:
------------------------------------------------
<context-param>
<param-name>BUILD_VERSION</param-name>
<param-value>${build-version}</param-value>
</context-param>
<context-param>
<param-name>BUILD_DATE</param-name>
<param-value>${build-date}</param-value>
</context-param>

If using maven, usually you put log4j.properties under java or resources?

Where should I put the log4j.properties file when using the conventional Maven directories?

src/main/resources is the "standard placement" for this.
Update: The above answers the question, but its not the best solution. Check out the other answers and the comments on this ... you would probably not shipping your own logging properties with the jar but instead leave it to the client (for example app-server, stage environment, etc) to configure the desired logging. Thus, putting it in src/test/resources is my preferred solution.
Note: Speaking of leaving the concrete log config to the client/user, you should consider replacing log4j with slf4j in your app.

Just putting it in src/main/resources will bundle it inside the artifact. E.g. if your artifact is a JAR, you will have the log4j.properties file inside it, losing its initial point of making logging configurable.
I usually put it in src/main/resources, and set it to be output to target like so:
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<targetPath>${project.build.directory}</targetPath>
<includes>
<include>log4j.properties</include>
</includes>
</resource>
</resources>
</build>
Additionally, in order for log4j to actually see it, you have to add the output directory to the class path.
If your artifact is an executable JAR, you probably used the maven-assembly-plugin to create it. Inside that plugin, you can add the current folder of the JAR to the class path by adding a Class-Path manifest entry like so:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.your-package.Main</mainClass>
</manifest>
<manifestEntries>
<Class-Path>.</Class-Path>
</manifestEntries>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</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>
Now the log4j.properties file will be right next to your JAR file, independently configurable.
To run your application directly from Eclipse, add the resources directory to your classpath in your run configuration: Run->Run Configurations...->Java Application->New select the Classpath tab, select Advanced and browse to your src/resources directory.

Some "data mining" accounts for that src/main/resources is the typical place.
Results on Google Code Search:
src/main/resources/log4j.properties: 4877
src/main/java/log4j.properties: 215

The resources used for initializing the project are preferably put in src/main/resources folder. To enable loading of these resources during the build, one can simply add entries in the pom.xml in maven project as a build resource
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
</build>
Other .properties files can also be kept in this folder used for initialization.
Filtering is set true if you want to have some variables in the properties files of resources folder and populate them from the profile filters properties files, which are kept in src/main/filters which is set as profiles but it is a different use case altogether. For now, you can ignore them.
This is a great resource maven resource plugins, it's useful, just browse through other sections too.

When putting resource files in another location is not the best solution you can use:
<build>
<resources>
<resource>
<directory>src/main/java</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<build>
For example when resources files (e.g. jaxb.properties) goes deep inside packages along with Java classes.

If your log4j.properties or log4j.xml file not found under src/main/resources use this PropertyConfigurator.configure("log4j.xml");
PropertyConfigurator.configure("log4j.xml");
Logger logger = LoggerFactory.getLogger(MyClass.class);
logger.error(message);

Add the below code from the resources tags in your pom.xml inside build tags.
so it means resources tags must be inside of build tags in your pom.xml
<build>
<resources>
<resource>
<directory>src/main/java/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
<build/>