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code coverage for component test not showing in multi-module project

I am using jacoco-maven-plugin to generate coverage report and using sonar-maven-plugin plugin to upload the report to SonarQube.
I am having below multi-module structure. BitBucket Project
mmproject
|
|---department-service
|
|---employee-service
|
|---component-test(This is for both the above services, code coverage for Controller)
I am using report-aggregate goal in pom.xml of component-test to merge the coverage report of employee-service, department-service and component-test module.
From component-test module.
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.6</version>
<configuration>
<excludes>
<exclude>com/jigarnaik/mmproject/*/model/*/**</exclude>
<exclude>com/jigarnaik/mmproject/*/config/*/**</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>report</id>
<phase>verify</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
<execution>
<id>report-aggregate</id>
<goals>
<goal>report-aggregate</goal>
</goals>
<phase>verify</phase>
</execution>
</executions>
</plugin>
And below is the content of parent pom.
<properties>
<java.version>11</java.version>
<swagger.version>2.9.2</swagger.version>
<sonar.language>java</sonar.language>
<sonar.java.coveragePlugin>jacoco</sonar.java.coveragePlugin>
<sonar.coverage.jacoco.xmlReportPaths>${project.basedir}/component-test/target/site/jacoco-aggregate/jacoco.xml
</sonar.coverage.jacoco.xmlReportPaths>
<sonar.java.binaries>${project.basedir}/target/classes</sonar.java.binaries>
<sonar.java.test.binaries>${project.basedir}/target/test-classes</sonar.java.test.binaries>
<sonar.exclusions>**/Application.java,**/model/*</sonar.exclusions>
</properties>
...
...
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.6</version>
<configuration>
<excludes>
<exclude>com/jigarnaik/mmproject/*/model/*/**</exclude>
<exclude>com/jigarnaik/mmproject/*/config/*/**</exclude>
<exclude>com/jigarnaik/mmproject/**/Application.java</exclude>
</excludes>
</configuration>
<executions>
<execution>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
Jacoco coverage report which is more then 80% however when I see it on SonarQube the coverage is less then 50%. It's basically not showing coverage for any of the controller which is in my component-test module.
Am I missing something over here?

How to exclude generated code from a code coverage report?

I've got the following jacoco-maven-plugin configuration:
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<configuration>
<excludes>
<exclude>**/Header*.java</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
Which should exclude from a code coverage report all generated java files that begin with Header. Unfortunately, I still see these classes in my code coverage report which makes the coveralls-maven-plugin fail when I call the coveralls:report. The error I get when I call coveralls:report is:
: No source found for HeaderMyClass.java ->
Which makes me think that the JaCoCo coverage report still contains the data for this class which was automatically generated.

Just add exclusions for report goal in jacoco-maven-plugin configuration
<execution>
<id>coverage-report</id>
<phase>post-integration-test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<excludes>
<exclude>**/*Dto.class</exclude>
<exclude>com/foo/config/*</exclude>
</excludes>
</configuration>
</execution>

Changing the pattern to:
<excludes>
<exclude>**/Header*.*</exclude>
</excludes>
did the trick

How to make PMD run at the start of the maven build rather than at the end of it?

I have the following configuration within my pom.xml that checks for PMD violations:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>${pmd.version}</version>
<configuration>
<linkXRef>true</linkXRef>
<sourceEncoding>UTF-8</sourceEncoding>
<minimumTokens>100</minimumTokens>
<targetJdk>1.7</targetJdk>
</configuration>
<executions>
<execution>
<goals>
<goal>check</goal>
<goal>cpd-check</goal>
</goals>
</execution>
</executions>
</plugin>
When I run a build using the command mvn clean install, the PMD checks are run as last step of the build process. Rather, I would want the PMD checks to run as the first step of the build.
Does anybody know how could I achieve this?

Add the phase element to your POM.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>${pmd.version}</version>
<configuration>
<linkXRef>true</linkXRef>
<sourceEncoding>UTF-8</sourceEncoding>
<minimumTokens>100</minimumTokens>
<targetJdk>1.7</targetJdk>
</configuration>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>check</goal>
<goal>cpd-check</goal>
</goals>
</execution>
</executions>
</plugin>
The validate phase is the first phase of the maven lifecycle: http://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.html

Thanks for your answers #JamesB and #PetrMensik for letting me know about the phase element within the POM. It helped me solve my problem. I finally settled for this:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>${pmd.version}</version>
<configuration>
<linkXRef>true</linkXRef>
<sourceEncoding>UTF-8</sourceEncoding>
<minimumTokens>100</minimumTokens>
<targetJdk>1.7</targetJdk>
</configuration>
<executions>
<execution>
<phase>compile</phase>
<goals>
<goal>check</goal>
<goal>cpd-check</goal>
</goals>
</execution>
</executions>
</plugin>
I used the phase:compile, the reason being I have plenty of tests in my project which take up a lot of time to execute. And, its quite irritating to wait for those tests to finish and be notified about a PMD violation at the end of all the tests. I needed something just before the tests. Hence, I settled for compile.
Further suggestions are welcome. :)

You need to hook execution of this plugin to a different Maven lifecycle phase (validation comes as the first one in default lifecycle).
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>check</goal>
<goal>cpd-check</goal>
</goals>
</execution>
</executions>
See this the list of the available Maven phases for reference.

I set build configuration
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>${pmd.plugin.version}</version>
<configuration>
<failOnViolation>true</failOnViolation>
<printFailingErrors>true</printFailingErrors>
</configuration>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>

Tomcat7 Maven Plugin and JaCoCo

Is there any way to get code coverage using JaCoCo with the tomcat7-maven-plugin embedded instance?
The jacoco-maven-plugin is configured in my WAR's POM to instrument my unit tests, but I'm not sure how to attach the jacoco agent to the embedded Tomcat instance to instrument my integration tests that run against Tomcat. Given that the Tomcat instance is embedded, I'm not sure if this approach is possible. Is there any other way to accomplish this? I can probably switch from using the Tomcat Maven Plugin to using Cargo to get coverage, but I'd prefer to stick with the Tomcat plugin if possible.
Here are a few relevant snippets from my POM:
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.6.2.201302030002</version>
<executions>
<execution>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.14</version>
<executions>
<execution>
<id>integration-tests</id>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat7-maven-plugin</artifactId>
<version>2.1</version>
<configuration>
<systemProperties>
<!-- as expected, this system property doesn't work since Tomcat is embedded, but this is the type of config I'm looking for -->
<JAVA_OPTS>-javaagent:${project.build.directory}/${jacoco.jar}=destfile=${project.build.directory}/jacoco.exec,append=true</JAVA_OPTS>
</systemProperties>
</configuration>
<executions>
<execution>
<id>tomcat-startup</id>
<goals>
<goal>run-war-only</goal>
</goals>
<phase>pre-integration-test</phase>
<configuration>
<fork>true</fork>
</configuration>
</execution>
<execution>
<id>tomcat-shutdown</id>
<goals>
<goal>shutdown</goal>
</goals>
<phase>post-integration-test</phase>
</execution>
</executions>
</plugin>
Versions: Maven 3.0.4, Tomcat Maven Plugin 2.1, Jacoco 0.6.2.201302030002, Java 7

I know its been awhile since the question was posted but I don't feel the answer really addressed the root of the problem. Code coverage may work with failsafe or surefire if you are running tests within those plugins. However, if you just want to monitor tomcat with jacoco to get a coverage report current information doesn't provide that. I found that the tomcat7-maven-plugin doesn't allow you to inject the -javaagent for jacoco by simply providing JAVA_OPTS. Switching to cargo I was able to do that like so.
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.2.201409121644</version>
<configuration>
<destFile>${sonar.jacoco.reportPath}</destFile>
<dataFile>${sonar.jacoco.reportPath}</dataFile>
<outputDirectory>${project.reporting.outputDirectory}/jacoco-it</outputDirectory>
<classDumpDir>${project.reporting.outputDirectory}/jacoco-it/classes</classDumpDir>
<skip>${skipITs}</skip>
</configuration>
<executions>
<execution>
<id>jacoco-agent</id>
<phase>pre-integration-test</phase>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<destFile>${sonar.jacoco.reportPath}</destFile>
<propertyName>jacoco.agent.itArgLine</propertyName>
</configuration>
</execution>
<execution>
<id>jacoco-report</id>
<phase>post-integration-test</phase>
<goals>
<goal>dump</goal>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.cargo</groupId>
<artifactId>cargo-maven2-plugin</artifactId>
<version>1.4.11</version>
<configuration>
<skip>${skipITs}</skip>
<container>
<containerId>tomcat7x</containerId>
<zipUrlInstaller>
<url>http://archive.apache.org/dist/tomcat/tomcat-7/v7.0.16/bin/apache-tomcat-7.0.16.zip
</url>
<downloadDir>${project.build.directory}/downloads</downloadDir>
<extractDir>${project.build.directory}/extracts</extractDir>
</zipUrlInstaller>
<dependencies>
<dependency>
<groupId>ojdbc</groupId>
<artifactId>ojdbc6</artifactId>
</dependency>
</dependencies>
</container>
<configuration>
<home>${project.build.directory}/catalina-base</home>
<properties>
<cargo.jvmargs>${jacoco.agent.itArgLine},output=tcpserver,port=6300 -Drunmode=TEST</cargo.jvmargs>
<cargo.servlet.port>9090</cargo.servlet.port>
</properties>
<configfiles>
<configfile>
<file>${basedir}/src/test/conf/context.xml</file>
<todir>conf/Catalina/localhost/</todir>
<tofile>context.xml.default</tofile>
</configfile>
</configfiles>
</configuration>
</configuration>
<executions>
<execution>
<id>start-tomcat</id>
<phase>pre-integration-test</phase>
<goals>
<goal>start</goal>
</goals>
</execution>
<execution>
<id>stop-tomcat</id>
<phase>post-integration-test</phase>
<goals>
<goal>stop</goal>
</goals>
</execution>
</executions>
</plugin>
the important parts are:
<plugin><groupId>org.jacoco</groupId> ...<propertyName>jacoco.agent.itArgLine</propertyName>
<cargo.jvmargs>${jacoco.agent.itArgLine},output=tcpserver,port=6300 </cargo.jvmargs>
When report target is run on the jacoco plugin it will create a directory in ${projectbase}/target/site/jacoco-it/index.html with your coverage report. I use this with the soapui-maven-plugin but it could be used with selenium-maven-plugin also.

You don't need pass JAVA_OPTS to tomcat embedded if you use maven-failsafe-plugin (or maven-surefire-plugin) to run yours integration test. It is because tomcat embedded run in the same process of maven-failsafe-plugin.
So when jacoco-maven-plugin execute prepare-agent it sets argLine that maven-failsafe-plugin uses too.
I created a project to test this, below part of pom:
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.6.2.201302030002</version>
<executions>
<execution>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<includes>
<include>my.project.package.only.*</include>
</includes>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat7-maven-plugin</artifactId>
<version>2.1</version>
<executions>
<execution>
<id>tomcat-startup</id>
<goals>
<goal>run-war-only</goal>
</goals>
<phase>pre-integration-test</phase>
<configuration>
<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.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<executions>
<execution>
<id>integration-tests</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>selenium-maven-plugin</artifactId>
<version>2.3</version>
<executions>
<execution>
<id>start</id>
<phase>pre-integration-test</phase>
<goals>
<goal>start-server</goal>
</goals>
<configuration>
<background>true</background>
<logOutput>true</logOutput>
<multiWindow>true</multiWindow>
</configuration>
</execution>
<execution>
<id>stop</id>
<phase>post-integration-test</phase>
<goals>
<goal>stop-server</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>

you can try to take a look at a workaround at this post: http://dougonjava.blogspot.co.il/2013/07/integration-testing-using-maven-tomcat.html

I resolved problems when setting up JaCoCo agent with embedded Tomcat by instrumenting classes offline and then just placing JaCoCo agent on Tomcat classpath (plugin dependency) and adding file jacoco-agent.properties.
I put the working configuration on my blog:
http://burkond.blogspot.de/2014/05/selenium-in-sonar-code-coverage-metrics.html

I had the exact same problem and the only solution I found was to set the MAVEN_OPTS previously to the Maven build (for example on the command line or in the configuration of a Jenkins job):
export MAVEN_OPTS=-javaagent:~/.m2/repository/org/jacoco/org.jacoco.agent/0.7.4.201502262128/org.jacoco.agent-0.7.4.201502262128-runtime.jar=destfile=./target/jacoco.exec,append=true
This will attach the jacoco agent to the embedded tomcat instance, which will report back the coverage results into the given destfile.
First, it is important that the path to the jacoco runtime JAR is correct. You can manually download and refer to it or use another Maven command to download it into your local .m2 repository:
mvn org.apache.maven.plugins:maven-dependency-plugin:2.8:get -Dartifact=org.jacoco:org.jacoco.agent:0.7.4.201502262128:jar:runtime
Second, make sure that the path to the jacoco.exec file is correct. In my case, I already have an existing jacoco.exec file in the target folder, which contains unit test results. The append=true makes sure that unit and integration tests are combined.

I managed to do it and it involves some tinkering with finicky stuff:
server/container needs to be on a separate jvm that can receive arguments (jacoco-agent). Cargo using embedded containers did not seem to work and was a pain to debug...
jvm with jacoco-it needs to stop before the jacoco analysis (duh!) but registering container-stop and jacoco-report on post-integration-test does not guarantee this... (the tcpdump, etc option in a previous answer had this problem)
defining random ports for the server/container makes this easy to integrate with continuous integration
phantomjs is an extra ;)
jacoco should be used as prepare-agent-integration and report-integration for integration-test (does not really make a difference)
Should be run as 'mvn clean verify'
Pom:
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.4.201502262128</version>
<executions>
<!-- unit test coverage -->
<execution>
<id>jacoco-pre-unit-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<destFile>${project.build.directory}/coverage-reports/jacoco-ut.exec</destFile>
<propertyName>jacoco.ut.argLine</propertyName>
</configuration>
</execution>
<execution>
<id>jacoco-post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<dataFile>${project.build.directory}/coverage-reports/jacoco-ut.exec</dataFile>
<outputDirectory>${project.reporting.outputDirectory}/jacoco-ut</outputDirectory>
</configuration>
</execution>
<!-- integration test coverage -->
<execution>
<id>jacoco-pre-integration-test</id>
<phase>pre-integration-test</phase>
<goals>
<goal>prepare-agent-integration</goal>
</goals>
<configuration>
<destFile>${project.build.directory}/coverage-reports/jacoco-it.exec</destFile>
<propertyName>jacoco.it.argLine</propertyName>
</configuration>
</execution>
<execution>
<id>jacoco-post-integration-test</id>
<phase>post-integration-test</phase>
<goals>
<goal>report-integration</goal>
</goals>
<configuration>
<dataFile>${project.build.directory}/coverage-reports/jacoco-it.exec</dataFile>
<outputDirectory>${project.reporting.outputDirectory}/jacoco-it</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>sonar-maven-plugin</artifactId>
<version>2.6</version>
</plugin>
<!-- Installs PhantomJS so it doesn't have to be pre-installed -->
<plugin>
<groupId>com.github.klieber</groupId>
<artifactId>phantomjs-maven-plugin</artifactId>
<version>0.4</version>
<executions>
<execution>
<!-- should be post-integration-test ? -->
<phase>test</phase>
<goals>
<goal>install</goal>
</goals>
</execution>
</executions>
<configuration>
<version>1.9.7</version>
</configuration>
</plugin>
<!-- Get two free ports for our test server to use -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.6</version>
<configuration>
<portNames>
<portName>jetty.port</portName>
<portName>jetty.port.stop</portName>
</portNames>
</configuration>
<executions>
<execution>
<id>reserve-port</id>
<phase>test</phase>
<goals>
<goal>reserve-network-port</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Run tests (UT) -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<argLine>${jacoco.ut.argLine}</argLine>
<skipTests>${skip.unit.tests}</skipTests>
<testFailureIgnore>true</testFailureIgnore>
<excludes>
<!-- no UT execution, to test only IT
<exclude>**/<remove this>*Test.java</exclude> -->
</excludes>
</configuration>
</plugin>
<!-- Use failsafe to run our integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.17</version>
<configuration>
<systemPropertyVariables>
<!-- pass these values to the test classes -->
<phantomjs.binary>${phantomjs.binary}</phantomjs.binary>
<jetty.port>${jetty.port}</jetty.port>
</systemPropertyVariables>
</configuration>
<executions>
<execution>
<id>integration-test</id>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.cargo</groupId>
<artifactId>cargo-maven2-plugin</artifactId>
<version>1.4.16</version>
<configuration>
<skip>${skipITs}</skip>
<container>
<containerId>tomcat8x</containerId>
<zipUrlInstaller>
<!-- did not work with 'https'. Certificate problem? -->
<url>http://archive.apache.org/dist/tomcat/tomcat-8/v8.0.26/bin/apache-tomcat-8.0.26.zip</url>
<downloadDir>${project.build.directory}/downloads</downloadDir>
<extractDir>${project.build.directory}/extracts</extractDir>
</zipUrlInstaller>
</container>
<configuration>
<home>${project.build.directory}/catalina-base</home>
<properties>
<cargo.jvmargs>${jacoco.it.argLine}</cargo.jvmargs>
<cargo.servlet.port>${jetty.port}</cargo.servlet.port>
<!-- <cargo.logging>high</cargo.logging> -->
</properties>
</configuration>
</configuration>
<executions>
<execution>
<id>cargo-start-tomcat</id>
<phase>pre-integration-test</phase>
<goals>
<goal>start</goal>
</goals>
</execution>
<execution>
<id>cargo-stop-tomcat</id>
<phase>integration-test</phase>
<goals>
<goal>stop</goal>
</goals>
</execution>
</executions>
</plugin>

Jetty sealed javax.naming

I have a legacy application using struts 1 and torque. I have made an effort last week to refactor it a bit and tried to decouple some groups of classes and introduced unit tests. As I can not test all areas of the application through unit tests, I wanted to add HtmlUnit tests.
To to this, I added the maven-failsafe-plugin and jetty to my project, like so:
<build>
...
<plugins>
...
<plugin>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.mortbay.jetty</groupId>
<artifactId>maven-jetty-plugin</artifactId>
<version>6.1.16</version>
<configuration>
<scanIntervalSeconds>10</scanIntervalSeconds>
<stopPort>8005</stopPort>
<stopKey>STOP</stopKey>
<contextPath>/</contextPath>
</configuration>
<executions>
<execution>
<id>start-jetty</id>
<phase>pre-integration-test</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<scanIntervalSeconds>0</scanIntervalSeconds>
<daemon>true</daemon>
</configuration>
</execution>
<execution>
<id>stop-jetty</id>
<phase>post-integration-test</phase>
<goals>
<goal>stop</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
The problem is, that when I run mvn verify, I get the following exception:
java.lang.SecurityException: sealing violation: can't seal package javax.naming: already loaded
I am using javax.naming in some classes, but can't find any dependency that overrides javax.naming!
Does anybody have a clue about how to figure this problem out?