Develop Reference

How to exclude and include properly classes, packages and jar classes, lib from the jacoco report (Instrumentation offline)

I am using JaCoCo code coverage, but the report is including classes from jar, lib. (Offline Instrumentation, Maven)
I solved the problem with the offline configuration since "aspectj-maven-plugin" was changing the class files, and also now I successfully exclude the packages outside of target/classes -> src. thanks to this answer in stackoverflow.
But now I am getting the classes from jar, lib inside the report and I have not idea how to exclude then. I Show my configuration and examples below
I also tried this solution Exclude classes of jar files from jacoco coverage report But it doesn't work for me.
<exclude>**/lib/*</exclude>
My jacoco offline configuration:
<properties>
<jacoco.version>0.8.4</jacoco.version>
<argLine></argLine>
</properties>
<dependency>
<groupId>org.jacoco</groupId>
<artifactId>org.jacoco.agent</artifactId>
<classifier>runtime</classifier>
<version>${jacoco.version}</version>
</dependency>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<executions>
<execution>
<goals>
<goal>instrument</goal>
<goal>restore-instrumented-classes</goal>
<goal>report</goal>
</goals>
<configuration>
<!-- this configuration affects all goals -->
<excludes>
<exclude>*</exclude>
<exclude>com/company/rrPackage/**/*.class</exclude>
<exclude>org/**/*.class</exclude>
</excludes>
</configuration>
</execution>
</executions>
</plugin>
surefire-plugin
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.15</version>
<configuration>
<testNGArtifactName>...</testNGArtifactName>
<suiteXmlFiles>
<suiteXmlFile>...</suiteXmlFile>
</suiteXmlFiles>
<skip>${skip.test}</skip>
<systemPropertyVariables>
<jacoco-agent.destfile>target/jacoco.exec</jacoco-agent.destfile>
</systemPropertyVariables>
<properties>
...
</properties>
</configuration>
</plugin>
And the reason what I think that I am getting classes from jar inside de jacoco:report. In my pom.xml I have the following dependencies:
<dependency>
<groupId>org.hsqldb</groupId>
<artifactId>hsqldb</artifactId>
<version>2.2.9</version>
</dependency>
Also I have a couple of import in my classes like this
import org.hsqldb.lib.StringUtil;
for example:
This has no dependency on the pom.xml but is used in one of the project classes, and jacoco shows it in the report
import javax.mail.internet.AddressException;
I have other cases with the same behavior that result in the same problem: Jacoco show those classes from jar in the report, as shown in the images

Try includes instead of excludes. Notice that you need .class at the end.
try something like that:
<configuration>
<includes>
<include>com/company/package/**/*.class</include>
</includes>
</configuration>
Base on your example:
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<executions>
<execution>
<goals>
<goal>instrument</goal>
<goal>restore-instrumented-classes</goal>
<goal>report</goal>
</goals>
<configuration>
<!-- this configuration affects all goals -->
<includes>
<include>com/company/packageToInclude/**/*.class</include>
</includes>
</configuration>
</execution>
</executions>
</plugin>

I don't know how you generate lib directory, because you don't provide complete example.
However in case of the following example
src/main/java/Example.java
class Example {
}
src/test/java/ExampleTest.java
public class ExampleTest {
#org.junit.Test
public void test() {
new Example();
}
}
and 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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.example</groupId>
<artifactId>example</artifactId>
<version>0.1-SNAPSHOT</version>
<properties>
<jacoco.version>0.8.4</jacoco.version>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
<dependency>
<groupId>org.jacoco</groupId>
<artifactId>org.jacoco.agent</artifactId>
<classifier>runtime</classifier>
<version>${jacoco.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<phase>test-compile</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<includeArtifactIds>junit</includeArtifactIds>
<outputDirectory>${project.build.directory}/classes/lib</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<executions>
<execution>
<goals>
<goal>instrument</goal>
<goal>restore-instrumented-classes</goal>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<systemPropertyVariables>
<jacoco-agent.destfile>target/jacoco.exec</jacoco-agent.destfile>
</systemPropertyVariables>
</configuration>
</plugin>
</plugins>
</build>
</project>
execution of mvn clean verify produces
$ ls -R target/classes
target/classes:
Example.class lib
target/classes/lib:
junit-4.12.jar
and following report
And after addition of following <configuration>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<executions>
<execution>
<goals>
<goal>instrument</goal>
<goal>restore-instrumented-classes</goal>
<goal>report</goal>
</goals>
<configuration>
<excludes>
<exclude>lib/**</exclude>
</excludes>
</configuration>
</execution>
</executions>
</plugin>
execution of the same command mvn clean verify produces following report
If the above doesn't help, then please provide absolutely complete example allowing everybody else to reproduce exactly the same what you do.

Maven shade plugin relocate and bundle not working

In my POM.xml, I have used maven-shade plugin and relocated the httpClient dependency. But when I print the dependency tree using mvn dependency:tree, I still see the httpClient library in the tree as shown below. Why is this happening. Any help will be appreciated.
[INFO] +- org.apache.httpcomponents:httpclient:jar:4.3.5:provided
My POM.xml is as below.
<?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>com.example</groupId>
<version>1.0-SNAPSHOT</version>
<artifactId>parser</artifactId>
<packaging>jar</packaging>
<!-- change these to the appropriate values -->
<name>Parser Apps</name>
<description>Applications to showcase different parsers</description>
<properties>
<!-- change this if you desire to use a different version of Apex Core -->
<apex.version>3.4.0</apex.version>
<apex.apppackage.classpath>lib/*.jar</apex.apppackage.classpath>
<malhar.version>3.4.0</malhar.version>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<downloadSources>true</downloadSources>
</configuration>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<encoding>UTF-8</encoding>
<source>1.7</source>
<target>1.7</target>
<debug>true</debug>
<optimize>false</optimize>
<showDeprecation>true</showDeprecation>
<showWarnings>true</showWarnings>
</configuration>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.8</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>prepare-package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>target/deps</outputDirectory>
<includeScope>runtime</includeScope>
</configuration>
</execution>
</executions>
</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>
<artifactSet>
<includes>
<include>org.apache.httpcomponents.*</include>
</includes>
</artifactSet>
<relocations>
<relocation>
<pattern>org.apache.httpcomponents</pattern>
<shadedPattern>org.shaded.httpcomponents</shadedPattern>
</relocation>
</relocations>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>app-package-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<finalName>${project.artifactId}-${project.version}-apexapp</finalName>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>src/assemble/appPackage.xml</descriptor>
</descriptors>
<archiverConfig>
<defaultDirectoryMode>0755</defaultDirectoryMode>
</archiverConfig>
<archive>
<manifestEntries>
<Class-Path>${apex.apppackage.classpath}</Class-Path>
<DT-Engine-Version>${apex.version}</DT-Engine-Version>
<DT-App-Package-Group-Id>${project.groupId}</DT-App-Package-Group-Id>
<DT-App-Package-Name>${project.artifactId}</DT-App-Package-Name>
<DT-App-Package-Version>${project.version}</DT-App-Package-Version>
<DT-App-Package-Display-Name>${project.name}</DT-App-Package-Display-Name>
<DT-App-Package-Description>${project.description}</DT-App-Package-Description>
</manifestEntries>
</archive>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.7</version>
<executions>
<execution>
<phase>package</phase>
<configuration>
<target>
<move file="${project.build.directory}/${project.artifactId}-${project.version}-apexapp.jar"
tofile="${project.build.directory}/${project.artifactId}-${project.version}.apa" />
</target>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
<execution>
<!-- create resource directory for xml javadoc-->
<id>createJavadocDirectory</id>
<phase>generate-resources</phase>
<configuration>
<tasks>
<delete dir="${project.build.directory}/generated-resources/xml-javadoc"/>
<mkdir dir="${project.build.directory}/generated-resources/xml-javadoc"/>
</tasks>
</configuration>
<goals>
<goal>run</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.9.1</version>
<executions>
<execution>
<id>attach-artifacts</id>
<phase>package</phase>
<goals>
<goal>attach-artifact</goal>
</goals>
<configuration>
<artifacts>
<artifact>
<file>target/${project.artifactId}-${project.version}.apa</file>
<type>apa</type>
</artifact>
</artifacts>
<skipAttach>false</skipAttach>
</configuration>
</execution>
</executions>
</plugin>
<!-- generate javdoc -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<executions>
<!-- generate xml javadoc -->
<execution>
<id>xml-doclet</id>
<phase>generate-resources</phase>
<goals>
<goal>javadoc</goal>
</goals>
<configuration>
<doclet>com.github.markusbernhardt.xmldoclet.XmlDoclet</doclet>
<additionalparam>-d ${project.build.directory}/generated-resources/xml-javadoc -filename ${project.artifactId}-${project.version}-javadoc.xml</additionalparam>
<useStandardDocletOptions>false</useStandardDocletOptions>
<docletArtifact>
<groupId>com.github.markusbernhardt</groupId>
<artifactId>xml-doclet</artifactId>
<version>1.0.4</version>
</docletArtifact>
</configuration>
</execution>
</executions>
</plugin>
<!-- Transform xml javadoc to stripped down version containing only class/interface comments and tags-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>xml-maven-plugin</artifactId>
<version>1.0</version>
<executions>
<execution>
<id>transform-xmljavadoc</id>
<phase>generate-resources</phase>
<goals>
<goal>transform</goal>
</goals>
</execution>
</executions>
<configuration>
<transformationSets>
<transformationSet>
<dir>${project.build.directory}/generated-resources/xml-javadoc</dir>
<includes>
<include>${pmalhar.versioroject.artifactId}-${project.version}-javadoc.xml</include>
</includes>
<stylesheet>XmlJavadocCommentsExtractor.xsl</stylesheet>
<outputDir>${project.build.directory}/generated-resources/xml-javadoc</outputDir>
</transformationSet>
</transformationSets>
</configuration>
</plugin>
<!-- copy xml javadoc to class jar -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<id>copy-resources</id>
<phase>process-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/classes</outputDirectory>
<resources>
<resource>
<directory>${project.build.directory}/generated-resources/xml-javadoc</directory>
<includes>
<include>${project.artifactId}-${project.version}-javadoc.xml</include>
</includes>
<filtering>true</filtering>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<!-- add your dependencies here -->
<dependency>
<groupId>org.apache.apex</groupId>
<artifactId>malhar-library</artifactId>
<version>${malhar.version}</version>
<!--
If you know that your application does not need transitive dependencies pulled in by malhar-library,
uncomment the following to reduce the size of your app package.
-->
<!--
<exclusions>
<exclusion>
<groupId>*</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
-->
</dependency>
<dependency>
<groupId>org.apache.apex</groupId>
<artifactId>malhar-contrib</artifactId>
<version>${malhar.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.5.4</version>
</dependency>
<dependency>
<groupId>com.github.fge</groupId>
<artifactId>json-schema-validator</artifactId>
<version>2.0.1</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>net.sf.supercsv</groupId>
<artifactId>super-csv</artifactId>
<version>2.4.0</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.apex</groupId>
<artifactId>apex-common</artifactId>
<version>${apex.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.apex</groupId>
<artifactId>apex-engine</artifactId>
<version>${apex.version}</version>
<scope>provided</scope>
</dependency>

Two things -
You should be aware what relocation does is not "...relocated the httpClient dependency" but as the source suggests -
If the uber JAR is reused as a dependency of some other project,
directly including classes from the artifact's dependencies in the
uber JAR can cause class loading conflicts due to duplicate classes on
the class path. To address this issue, one can relocate the classes
which get included in the shaded artifact in order to create a private
copy of their bytecode
When you execute the mvn dependency:tree it would display all the dependencies(direct and transitive) included in your project. Instead, the maven shade plugin
shade:shade is bound to the package phase and is used to create a
shaded jar.
renaming or optimizing the dependencies further. Here goes the details for Maven Shade Plugin -
This plugin provides the capability to package the artifact in an
uber-jar, including its dependencies and to shade - i.e. rename - the
packages of some of the dependencies.

The dependency is not removed from original POM, so the behavior of dependency:tree is correct.
Shade plugin will also generate a new POM (dependency-reduced-pom.xml) wherein shaded dependencies are removed from the <dependencies> section. This looks like the one you are after.

Exclude generated-sources from code coverage without impacting overall code-coverage

I have a project for which the code coverage numbers are pretty low. After doing a deep-dive I found out the jacoco code-coverage stats are depending on target directoy instead of src.
target/generated-sources/delombok/com/
If I exclude the target directory the coverage goes down 0%. So isnt code-coverage supposed to be measured against the code (src) rather than the target folder. Below is the screenshot from SonarQube.
So the question is how do i make sure the code coverage is measured for src instead of target?
Following is the pom without dependencies:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<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>removed</groupId>
<artifactId>xxxx</artifactId>
<version>0.0.11-SNAPSHOT</version>
<packaging>war</packaging>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cassandra-maven-plugin</artifactId>
<version>2.1.7-1</version>
<configuration>
<script>${basedir}/src/main/cassandra/local_run.cql</script>
<cqlVersion>3.2.0</cqlVersion>
<startNativeTransport>true</startNativeTransport>
<nativeTransportPort>9142</nativeTransportPort>
<jmxPort>17199</jmxPort>
<storagePort>17000</storagePort>
<loadFailureIgnore>false</loadFailureIgnore>
<cuLoadFailureIgnore>false</cuLoadFailureIgnore>
</configuration>
<executions>
<execution>
<id>start</id>
<goals>
<goal>start</goal>
<goal>load</goal>
</goals>
<phase>process-classes</phase> <!--Bind cassandra start and load to process-classes which is the phase that is called up before tomcat is run -->
</execution>
<execution>
<id>stop</id>
<goals>
<goal>stop</goal>
</goals>
<!--Bind cassandra stop to generate-test-sources which is the phase that is called up before
tests are run. This is because our tests start their own cassandra -->
<phase>integration-test</phase>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.7.7</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.projectlombok</groupId>
<artifactId>lombok-maven-plugin</artifactId>
</plugin>
<!--Needed to add this so that src/main/java is recognized as a source folder -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
</plugin>
<!-- Unit Test -->
<!-- Integration Test -->
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.4</version>
<configuration>
<warName>activationloginedge</warName>
</configuration>
</plugin>
<!-- Tomcat Integration Test -->
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat7-maven-plugin</artifactId>
<configuration>
<path>/activationloginedge</path>
</configuration>
<executions>
<execution>
<id>tomcat-run</id>
<goals>
<goal>run</goal>
</goals>
<phase>pre-integration-test</phase>
<configuration>
<systemProperties>
<!-- We want test configuration for running integration tests. -->
<archaius.deployment.environment>test</archaius.deployment.environment>
<logback-lib.env>filesystem</logback-lib.env>
</systemProperties>
<fork>true</fork>
</configuration>
</execution>
<execution>
<id>tomcat-shutdown</id>
<goals>
<goal>shutdown</goal>
</goals>
<phase>post-integration-test</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.4.201502262128</version>
<executions>
<execution>
<id>pre-unit-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<destFile>${project.build.directory}/jacoco-ut.exec</destFile>
<!-- Sets the name of the property containing the settings for JaCoCo runtime agent.-->
<propertyName>surefireArgLine</propertyName>
</configuration>
</execution>
<!--Ensures that the code coverage report for unit tests is created after unit tests have been run.-->
<execution>
<id>post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<dataFile>${project.build.directory}/jacoco-ut.exec</dataFile>
<!-- Sets the output directory for the code coverage report. -->
<outputDirectory>${project.reporting.outputDirectory}/jacoco-ut</outputDirectory>
</configuration>
</execution> <execution>
<id>pre-integration-test</id>
<phase>pre-integration-test</phase>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<destFile>${project.build.directory}/jacoco-it.exec</destFile>
<!-- Sets the name of the property containing the settings for JaCoCo runtime agent.-->
<propertyName>failsafeArgLine</propertyName>
<
/configuration>
</execution>
<!-- Ensures that the code coverage report for integration tests after integration tests have been run.-->
<execution>
<id>post-integration-test</id>
<phase>post-integration-test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<dataFile>${project.build.directory}/coverage-reports/jacoco-it.exec</dataFile>
<!-- Sets the output directory for the code coverage report. -->
<outputDirectory>${project.reporting.outputDirectory}/jacoco-it</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.12.4</version>
<configuration>
<!-- Sets the VM argument line used when unit tests are run. -->
<argLine>${surefireArgLine}</argLine>
<!-- Skips unit tests if the value of skip.unit.tests property is true -->
<skipTests>${skip.unit.tests}</skipTests>
<!-- Excludes integration tests when unit tests are run. -->
<excludes>
<exclude>**/IT*.java</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.15</version> <executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
<configuration>
<!-- Sets the VM argument line used when integration tests are run-->
<argLine>${failsafeArgLine}</argLine>
<!-- Skips integration tests if the value of skip.integration.tests property is true-->
<skipTests>${skip.integration.tests}</skipTests> </configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

OK, the Lombok Maven plugin modifies the list of source folders during the Maven build, this is why the target/generated-sources/delombok folder is recognized by SonarQube as a source folder.
In order to force SonarQube to consider only your own source files, you should add the following property to your POM:
<properties>
<sonar.sources>src/main/java</sonar.sources>
</properties>
This will solve your problem.

Scala Eclipse IDE compiler giving errors until "clean" is run

I am writing a mixed Java/Scala project and my Eclipse compiler is giving errors for all of the Scala code. It seems to try to compile it as Java instead of Scala. However, when I run a clean, all of the errors go away. Also, building this using maven works completely fine.
I am building this project in Maven. Originally this project was only Java, so I added the necessary plugins/dependencies into my pom.xml.
Any idea why Eclipse is treating my Scala files as Java?
Here's my pom.xml:
<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.antlrfun</groupId>
<artifactId>antlrfun</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>Antlr4 Spark/Solr</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<antlr4.visitor>true</antlr4.visitor>
<antlr4.listener>true</antlr4.listener>
</properties>
<dependencies>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>antlr4-runtime</artifactId>
<version>4.5</version>
</dependency>
<dependency>
<groupId>junit</groupId> <!-- NOT org.junit here -->
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.10.5</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.10</artifactId>
<version>1.3.1</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.2.1</version>
<executions>
<execution>
<goals>
<goal>java</goal>
</goals>
</execution>
</executions>
<configuration>
<mainClass>org.antlrfun.Hello</mainClass>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.7</version>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/generated-sources</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<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>
<showWarnings>true</showWarnings>
<showDeprecation>true</showDeprecation>
<compilerArguments>
<Xlint/>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.antlr</groupId>
<artifactId>antlr4-maven-plugin</artifactId>
<version>4.1</version>
<configuration>
<sourceDirectory>src/main/java</sourceDirectory>
<outputDirectory>src/main/generated-sources</outputDirectory>
</configuration>
<executions>
<execution>
<goals>
<goal>antlr4</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.scala-tools</groupId>
<artifactId>maven-scala-plugin</artifactId>
<version>2.15.2</version>
<executions>
<!-- Run scala compiler in the process-resources phase, so that dependencies on
scala classes can be resolved later in the (Java) compile phase -->
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
<!-- Run scala compiler in the process-test-resources phase, so that dependencies on
scala classes can be resolved later in the (Java) test-compile phase -->
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<!-- Add src/main/scala to source path of Eclipse -->
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/scala</source>
</sources>
</configuration>
</execution>
<!-- Add src/test/scala to test source path of Eclipse -->
<execution>
<id>add-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>src/test/scala</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<!-- to generate Eclipse artifacts for projects mixing Scala and Java -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.8</version>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>true</downloadJavadocs>
<projectnatures>
<projectnature>org.scala-ide.sdt.core.scalanature</projectnature>
<projectnature>org.eclipse.jdt.core.javanature</projectnature>
</projectnatures>
<buildcommands>
<buildcommand>org.scala-ide.sdt.core.scalabuilder</buildcommand>
</buildcommands>
<classpathContainers>
<classpathContainer>org.scala-ide.sdt.launching.SCALA_CONTAINER</classpathContainer>
<classpathContainer>org.eclipse.jdt.launching.JRE_CONTAINER</classpathContainer>
</classpathContainers>
<excludes>
<!-- in Eclipse, use scala-library, scala-compiler from the SCALA_CONTAINER rather than POM <dependency> -->
<exclude>org.scala-lang:scala-library</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
</excludes>
<sourceIncludes>
<sourceInclude>**/*.scala</sourceInclude>
<sourceInclude>**/*.java</sourceInclude>
</sourceIncludes>
</configuration>
</plugin>
<!-- When run tests in the test phase, include .java and .scala source files -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.8.1</version>
<configuration>
<includes>
<include>**/*.java</include>
<include>**/*.scala</include>
</includes>
</configuration>
</plugin>
</plugins>
</build>
</project>

Clear the Scala IDE project settings by removing and adding back Scala Nature

Not able to bind plugin goals to maven lifecycle phases

I am using maven sql plugin. I am using the plugin to setup the my test db before executing integration tests. Here is my plugin configuration from my project pom. When I execute mvn clean install I expect the plugin goals to execute. But they are not getting executed. Any help will be appreciated. I am facing similar issue for aspectj plugin (configuration provided below).
My SQL plugin configuration:
<!-- Maven SQL Plugin for setting up test schema for integration tests -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>sql-maven-plugin</artifactId>
<version>1.5</version>
<dependencies> <!-- specify the dependent JDBC driver here -->
<dependency>
<groupId>${jdbc.groupId}</groupId>
<artifactId>${jdbc.artifactId}</artifactId>
<version>${jdbc.version}</version>
</dependency>
</dependencies>
<!-- common configuration shared by all executions -->
<configuration>
<driver>org.hsqldb.jdbcDriver</driver>
<url>jdbc:hsqldb:sample</url>
<username>sa</username>
<password></password>
</configuration>
<executions>
<execution>
<id>create_db_schema</id>
<phase>process-test-resources</phase>
<goals>
<goal>execute</goal>
</goals>
<!-- specific configuration for this execution -->
<configuration>
<srcFiles>
<srcFile>src/test/resources/test-schema.sql</srcFile>
</srcFiles>
</configuration>
</execution>
<execution>
<id>shutdown_db_instance</id>
<phase>process-test-resources</phase>
<goals>
<goal>execute</goal>
</goals>
<configuration>
<sqlCommand>SHUTDOWN IMMEDIATELY</sqlCommand>
</configuration>
</execution>
</executions>
</plugin>
My aspectj plugin configuration:
<!-- AspectJ Compile-time waving for spring cross-store. -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>aspectj-maven-plugin</artifactId>
<version>1.4</version>
<executions>
<execution>
<goals>
<goal>compile</goal>
<goal>test-compile</goal>
</goals>
</execution>
</executions>
<configuration>
<outxml>true</outxml>
<showWeaveInfo>true</showWeaveInfo>
<aspectLibraries>
<aspectLibrary>
<groupId>org.springframework</groupId>
<artifactId>spring-aspects</artifactId>
</aspectLibrary>
<aspectLibrary>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-mongodb-cross-store</artifactId>
</aspectLibrary>
</aspectLibraries>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>

Be sure that these plugins are not defined inside project/build/pluginManagement/plugins, but in project/build/plugins.
Only the latter are executed, those plugins will then will be checked with the pluginManagement for the final configuration.