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Maven jandex plugin does not generate index for local custom maven repositories (sometimes)

I have a multi module maven project wie quarkus modules and some custom libraries which are local maven repositories (so they can be used by the other maven projects/modules). However, so that local maven repositories are recognizable und usable by your other local maven projects, you have to manually index them for some reason. I.e. add a config like this for quarkus index to the application.properties of the project including the local maven repo dependency:
quarkus.index-dependency.<index-name>.group-id = <group-id-of-local-maven-repo>
quarkus.index-dependency.<index-name>.artifact-id = <artifact-id-of-local-maven-repo>
The problem is, this causes issues for me becausse if you have 3 layers of project dependencies, say:
Project A (custom local maven repo library)
Project B (custom local maven repo library, includes Project A dependency)
application.properties (indexing Project A library dependency)
Project C (Local maven project for an end product, includes Project B
library dependency - and through it indirectly Project A).
application.properties (indexing Project B library dependency and config for datasources or other app related things)
Then when you generate an uber-jar (fat jar) of Project C for deployment, it for some reason uses application.properties of Project B in the packaged jar, instead of from the project which im building (Project C). Thus, the app is missing key configs and does not work. Maven seems to use an inverse priority here, which i dont know if thats a bug or not. When i asked about this, i was simply told that:
"My dependencies should not have application.properties".
I tried to find a way to prevent manual indexing via application.properties and found the maven jandex plugin - which is supposed to generate an index. The next problem is, this seems to only work in some projects but not in others in the dependency hierarchy, resulting in the same situation as before, and i don't understand why. This is the pom.xml config for the plugin i have included in all 3 projects (the entire pom.xml for all is too long, so let me know if you need more info):
<properties>
...
<jandex.skip>false</jandex.skip>
...
</properties>
...
<build>
...
<plugin>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.5</version>
<inherited>true</inherited>
<executions>
<execution>
<id>make-index</id>
<goals>
<goal>jandex</goal>
</goals>
</execution>
</executions>
<configuration>
<skip>${jandex.skip}</skip>
</configuration>
</plugin>
...
The odd thing is, this works to the extend that i no longer have to index Project B library dependency in Project C application.properties, but Project B library dependency still has to manually index Project A library dependency - thus rendering the entire exercise futile. Project C having an application.properties was never the issue, and is obviously needed. Project B still requires a properties file to point to Project A now, how do i solve this?
I have a parent module POM in the root folder containing all these projects, over which this maven jandex dependency is distributed to all modules, so it looks like this:
Maven parent module (contains all dependencies and versions used by all project sub modules)
Project A (custom local maven library repo), own pom.xml with inheritance from parent module
Project B (custom local maven library repo, includes Project A library), own pom.xml with inheritance from parent module
application.properties - Indexes Project A dependency manually, this is the problematic one which needs to go!
Project C (Local maven project for REST API etc., includes Project B library), own pom.xml with inheritance from parent module
pom.xml (parent module POM, containing maven jandex dependepency among others)
Edit: One of the projects, "entity", where all the database access objects are stored, does not run the jandex plugin during mvn clean install. This is the POM of the project:
<?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.compamny.project</groupId>
<artifactId>entity</artifactId>
<version>1.0-SNAPSHOT</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-hibernate-orm</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-hibernate-validator</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-resteasy-reactive-jackson</artifactId>
<version>2.16.1.Final</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jdk8</artifactId>
<version>2.13.3</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.smallrye/jandex-maven-plugin -->
<dependency>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.0</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<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>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
<version>3.0.0</version>
<inherited>true</inherited>
<executions>
<execution>
<id>make-index</id>
<goals>
<goal>jandex</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
When i force the execution of the jandex goal with mvn io.smallrye:jandex-maven-plugin:3.0.0:jandex it creates an META-INF/jandex.jdx file, but it does not produce one when i run mvn clean install. This is not a solution since i need to build the project, run the jandex plugin and install it into my local repositories separately. Also, notice that im using the "io.smallrye" version of the jandex plugin since the "org.jboss" version seems to not work at all.

I figured it out. The jandex plugin was set in the <pluginManagement> section of the POM configuration, which made it not run on mvn clean install. I had to move it to the plugins section so it gets executed. Thanks #Ladicek for making me look closer and keep trying!

Java get version of maven dependency at runtime

Is it possible to retrieve the version of a specific maven dependency at runtime?
E.g. for the pom.xml:
<dependency>
<groupId>foo.bar</groupId>
<artifactId>foobar</artifactId>
<version>1.0</version>
</dependency>
I would like to retrieve the version 1.0 of a specific dependency with artifact ID foobar.

The most problematic part here is to find a JAR by its name. Unfortunately, there is no 100% reliable way for this in Java. To get a JAR by name, you need to scan classpath of the running application which may not always be present (e.g. because custom class loaders are used or module path is used instead of classpath).
But let's assume you are not using any fancy features like custom class loaders and you got your classpath which contains all your Maven dependencies. What do you need to do now? I'll try to describe a rough algorithm:
Retrieve paths of all JAR files from your classpath.
Scan each JAR file and find the file pom.properties. It's located in META-INF/maven/{groupId}/{artifactId}.
Find the value of the version property in pom.properties.
Again, this solution will not be completely reliable. You have to decide: do you really need the version information and for what purposes?

Are you looking at jars you created yourself? Or third-party libaries? I have published a lightweight solution for the former. So if the packaging of the jars you are looking for at runtime is in your own hands, go ahead and give it a try ;-). It may be a little more elegant than having to read XML or properties from jar files.
The idea
use a Java service loader approach to be able to add as many components/artifacts later, which can contribute their own versions at runtime. Create a very lightweight library with just a few lines of code to read, find, filter and sort all of the artifact versions on the classpath.
Create a maven source code generator plugin that generates the service implementation for each of the modules at compile time, package a very simple service in each of the jars.
The solution
Part one of the solution is the artifact-version-service library, which can be found on github and MavenCentral now. It covers the service definition and a few ways to get the artifact versions at runtime.
Part two is the artifact-version-maven-plugin, which can also be found on github and MavenCentral. It is used to have a hassle-free generator implementing the service definition for each of the artifacts.
Examples
Fetching all modules with coordinates
No more reading jar manifests, just a simple method call:
// iterate list of artifact dependencies
for (Artifact artifact : ArtifactVersionCollector.collectArtifacts()) {
// print simple artifact string example
System.out.println("artifact = " + artifact);
}
A sorted set of artifacts is returned. To modify the sorting order, provide a custom comparator:
new ArtifactVersionCollector(Comparator.comparing(Artifact::getVersion)).collect();
This way the list of artifacts is returned sorted by version numbers.
Find a specific artifact
ArtifactVersionCollector.findArtifact("foo.bar", "foobar");
Fetches the version details for a specific artifact.
Find artifacts with matching groupId(s)
Find all artifacts with groupId foo.bar (exact match):
ArtifactVersionCollector.findArtifactsByGroupId("foo.bar", true);
Find all artifacts where groupId starts with foo.bar:
ArtifactVersionCollector.findArtifactsByGroupId("foo.bar", false);
Sort result by version number:
new ArtifactVersionCollector(Comparator.comparing(Artifact::getVersion)).artifactsByGroupId("foo.", false);
Implement custom actions on list of artifacts
By supplying a lambda, the very first example could be implemented like this:
ArtifactVersionCollector.iterateArtifacts(a -> {
System.out.println(a);
return false;
});
Installation
Add these two tags to all pom.xml files, or maybe to a company master pom somewhere:
<build>
<plugins>
<plugin>
<groupId>de.westemeyer</groupId>
<artifactId>artifact-version-maven-plugin</artifactId>
<version>1.1.0</version>
<executions>
<execution>
<goals>
<goal>generate-service</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>de.westemeyer</groupId>
<artifactId>artifact-version-service</artifactId>
<version>1.1.0</version>
</dependency>
</dependencies>

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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.example</groupId>
<artifactId>WDProject</artifactId>
<version>1.0-SNAPSHOT</version>
<name>WDProject</name>
<url>http://www.nosite.com</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<selenium.version>3.141.59</selenium.version>
<webdrivermanager.version>3.7.1</webdrivermanager.version>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/io.github.bonigarcia/webdrivermanager -->
<dependency>
<groupId>io.github.bonigarcia</groupId>
<artifactId>webdrivermanager</artifactId>
<version>${webdrivermanager.version}</version>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-api</artifactId>
<version>${selenium.version}</version>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-server</artifactId>
<version>${selenium.version}</version>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-remote-driver</artifactId>
<version>${selenium.version}</version>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-java</artifactId>
<version>${selenium.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.lingala.zip4j</groupId>
<artifactId>zip4j</artifactId>
<version>2.2.4</version>
</dependency>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-model</artifactId>
<version>3.3.9</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>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
Although what you want is to search for a specific dependency, the below code retrieves all the details of the dependencies available in pom file.
You just need to create a wrapper method to retrieve details of specific dependencies.
import org.apache.maven.model.Model;
import org.apache.maven.model.io.xpp3.MavenXpp3Reader;
import org.codehaus.plexus.util.xml.pull.XmlPullParserException;
import java.io.FileReader;
import java.io.IOException;
class SampleMavenDependencyReader {
public static void main(String[] args) throws IOException, XmlPullParserException {
MavenXpp3Reader reader = new MavenXpp3Reader();
Model model = reader.read(new FileReader("/Users/nonadmin/bins/projects/IdeaProjects/WDProject/pom.xml"));
for (int i = 0; i < model.getDependencies().size(); i++) {
System.out.println(model.getDependencies().get(i));
}
}
}
OUTPUT
Dependency {groupId=junit, artifactId=junit, version=4.11, type=jar}
Dependency {groupId=io.github.bonigarcia, artifactId=webdrivermanager, version=${webdrivermanager.version}, type=jar}
Dependency {groupId=org.seleniumhq.selenium, artifactId=selenium-api, version=${selenium.version}, type=jar}
Dependency {groupId=org.seleniumhq.selenium, artifactId=selenium-server, version=${selenium.version}, type=jar}
Dependency {groupId=org.seleniumhq.selenium, artifactId=selenium-remote-driver, version=${selenium.version}, type=jar}
Dependency {groupId=org.seleniumhq.selenium, artifactId=selenium-java, version=${selenium.version}, type=jar}
Dependency {groupId=net.lingala.zip4j, artifactId=zip4j, version=2.2.4, type=jar}
Dependency {groupId=org.apache.maven, artifactId=maven-model, version=3.3.9, type=jar}~~~

Including classes and jars from a local war file with maven

I have a War file that has dependencies and class files that I need in it that I am trying to include in my project with Maven. Inside the War file, there is a WEB-INF that contains those libs and classes. I have tried everything that I know to try to get this going, but my knowledge of Maven is limited.
I have tried simply listing the War as a dependency and following the process described here to install the third-party library, but when I do that Maven says it can't find my packages that I need when I try to install.
I have tried overlaying the War as described here with no luck.
I have tried maven-warpath-plugin but didn't really have any luck either.
Should any of these tools solve my problem? Is how I am trying to solve the problem possible in this way? Or am I completely off base?
Here are the important parts of my pom.xml from using the maven-warpath-plugin:
<build>
...
<pluginManagement>
<plugins>
<plugin>
<groupId>org.appfuse</groupId>
<artifactId>maven-warpath-plugin</artifactId>
<version>1.0-SNAPSHOT</version>
<extensions>true</extensions>
<executions>
<execution>
<goals>
<goal>add-classes</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
...
</build>
<repositories>
<repository>
<id>data-local</id>
<name>data</name>
<url>file://${project.basedir}/o</url>
</repository>
</repositories>
<dependencies>
...
<dependency>
<groupId>my.local.dep</groupId>
<artifactId>MyLocalDep</artifactId>
<version>1.1.1.1</version>
<type>war</type>
</dependency>
<dependency>
<groupId>my.local.dep</groupId>
<artifactId>MyLocalDep</artifactId>
<version>1.1.1.1</version>
<type>warpath</type>
</dependency>
</dependencies>

Unpack the war in a separate clean step first and add the unpacked jars as system dependency in the main step.
Idea is from here: https://stackoverflow.com/a/6120395/503025

How do you replace the class of a Maven dependency?

There is a class in a maven dependency that is incompatible with Java 8.
How do you properly fix that problem?
Right now I'm doing the following:
Create a package with the same name
Create a class with the same name in that package
Copy and paste the code
Fix the incompatible API call
The problem is that this class contains API calls to restricted classes and although I changed the Eclipse compiler settings (Window -> Preferences -> Java -> Compiler -> Error/Warnings -> Deprecated and restricted API -> Forbidden reference (access rule): Error -> Warning) to allow access the project will only compile sometimes. If it doesn't compile I'll get a "can't find symbol" error.
Edit:
Here are the details you asked for:
Dependency: http://mvnrepository.com/artifact/com.sun.xml.wss/xws-security/3.0
Class: EncryptionProcessor
Necessary change:
// Change line 1053 FROM:
// _dataEncryptor = XMLCipher.getInstance(dataEncAlgo, _dataCipher);
// TO:
_dataEncryptor = XMLCipher.getInstance(dataEncAlgo);
Edit-2:
Maven build error:
[ERROR] symbol: class XMLCipher
[ERROR] location: class com.sun.xml.wss.impl.apachecrypto.EncryptionProcessor
[ERROR] /C:/Users/{name}/development/eclipse_workspace/git/xws-security/src/main/java/com/sun/xml/wss/impl/apachecrypto/EncryptionProcessor.java:[1482,98] cannot find symbol

Here is a detailed guide describing what I did exactly:
Create new Maven project in Eclipse
Configure Maven settings of new project (Important: Use the same group and artifact ID and only change the version number)
<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.sun.xml.wss</groupId>
<artifactId>xws-security</artifactId>
<version>3.0-java8-fix</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.version>1.8</java.version>
</properties>
</project>
Add dependency of bugged JAR
<dependencies>
<dependency>
<groupId>com.sun.xml.wss</groupId>
<artifactId>xws-security</artifactId>
<version>3.0</version>
<exclusions>
<exclusion>
<artifactId>xmldsig</artifactId>
<groupId>javax.xml.crypto</groupId>
</exclusion>
<exclusion>
<artifactId>activation</artifactId>
<groupId>javax.activation</groupId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
Create Java file in the same package of class that needs to be fixed
package com.sun.xml.wss.impl.apachecrypto;
public class EncryptionProcessor {
// The FIX goes here
}
Add Maven shade build plug in to handle creation of patched JAR file (this is not the only plug in to handle this kind of task - e.g. dependency:unpack)
<build>
<plugins>
<!-- plug in for creation of patched JAR file -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<filters>
<filter>
<artifact>com.sun.xml.wss:xws-security:3.0</artifact>
<includes>
<include>**/*.class</include>
<include>**/*.xml</include>
</includes>
<excludes>
<exlude>
com/sun/xml/wss/impl/apachecrypto/EncryptionProcessor.class
</exlude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
Include patched JAR in other projects as necessary (Note: If you experience ClassNotFoundExceptions or similar errors do this: Right-click on the project -> Properties -> Maven -> "Resolve dependencies from Workspace projects":false)
In case you are not familiar with Maven. Here is the complete pom.xml: http://pastebucket.com/88444

Similar to Steven S.'s answer, but using the maven-dependency-plugin. Based on this blog post.
I changed the name of the patched library (not the version), but it depends on your needs what works better for you.
The dependency on the original library should be marked as <optional>true</optional>. Otherwise, the projects that depend on your patched library will also depend on the original library, which means that both the patched and the original version will be on the classpath, which can lead to all kinds of problems.
If your project is a child project, you can still use a completely different groupId and version than your parent pom. Doesn't matter.
You can exclude the classes you patch from unpacking, but it's probably not necessary, because Maven will first unpack the original library and then compile your new version, which means that the original classes are overwritten. Nice!
<?xml version="1.0"?>
<project xmlns="http://maven.apache.org/POM/4.0.0">
<modelVersion>4.0.0</modelVersion>
<!-- remove this if you don't have a parent pom -->
<parent>
<groupId>my.company</groupId>
<artifactId>my.company</artifactId>
<version>1.2.3</version>
<relativePath>../pom.xml</relativePath>
</parent>
<groupId>com.foo</groupId>
<artifactId>foo-bar-patched</artifactId>
<version>4.5.6</version>
<build>
<plugins>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>com.foo</groupId>
<artifactId>foo-bar</artifactId>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
<!-- excludes are probably not necessary -->
<!-- <excludes>**/Foo.class,**/Bar.class</excludes> -->
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>com.foo</groupId>
<artifactId>foo-bar</artifactId>
<version>4.5.6</version>
<optional>true</optional>
</dependency>
</dependencies>
</project>

General solution:
download all project sources
apply your modification
use version control so that change isn't lost
change version in pom.xml, for example from 3.0 to 3.0-patched
launch maven build
copy generated artifacts to you repository/Artifactory, if you use one
change dependency version in your own project

Maven: javax.servlet specification deployed

I've a web application configured with Maven which uses a library, also configured with Maven and when I package geronimo-servlet_3.0_spec-1.0.jar is included in WEB-INF/lib and I don't understand why.
I check the library with mvn dependency:tree
$ mvn dependency:tree | grep geronimo
[INFO] +- org.apache.geronimo.specs:geronimo-servlet_3.0_spec:jar:1.0:provided
I check my web app:
$ mvn dependency:tree | grep geronimo
$
However when I run mvn:package the file gets included in WEB-INF/lib.
When I run mvn tomcat:run I can see:
INFO: validateJarFile(/home/stivlo/workspace/private/src/main/webapp/WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class
Why and how to avoid? Thank you.
UPDATE 1: as requested I add the 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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.obliquid</groupId>
<artifactId>test-webapp</artifactId>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<name>private webapp</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<repositories>
<!-- For Jakarta ORO -->
<repository>
<id>mvnsearch</id>
<name>Maven Search</name>
<url>http://www.mvnsearch.org/maven2/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.8.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.4</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<finalName>private</finalName>
</build>
</project>
UPDATE 2: I followed the advice of Stephen C and modified the build section as follows:
<build>
<finalName>private</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war</artifactId>
<version>2.1</version>
<configuration>
<overlays>
<overlay>
<groupId>org.obliquid</groupId>
<artifactId>test-webapp</artifactId>
<excludes>
<exclude>WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar</exclude>
</excludes>
</overlay>
</overlays>
</configuration>
</plugin>
</plugins>
</build>
However geronimo*.jar still gets included. I guess I've made a mistake in this configuration.
UPDATE 3: Stephen C. says that I should use
the groupId the artifactId of the WAR
file that contains the JAR file(s)
that you are trying to exclude.
I didn't know that WAR files could have a groupId and artifactId, in fact in my pom.xml I don't see any. My project builds a WAR file and has a groupId and an artifactId and those were the ones I tested above without success.
The dependency causing the problem is the following (is a JAR, not a WAR):
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
If I try to use the groupId and artifactId listed in this dependency I've the following error:
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-war-plugin:2.1.1:war
(default-war) on project test-webapp:
overlay [ id
org.obliquid.helpers:obliquid-helpers]
is not a dependency of the project. ->
[Help 1]
If I try to use the groupId and artifactId of the JAR included by org.obliquid.helpers:
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>)
I have the same error.
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-war-plugin:2.1.1:war
(default-war) on project test-webapp:
overlay [ id
org.apache.geronimo.specs:geronimo-servlet_3.0_spec]
is not a dependency of the project. ->
[Help 1]
Reading the War plugin documentation, I found a section about creating skinny WARs. So I tried the following:
<build>
<finalName>private</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.1.1</version>
<configuration>
<packagingExcludes>WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar</packagingExcludes>
</configuration>
</plugin>
</plugins>
</build>
Still without any success, geronimo-servlet_3.0_spec-1.0.jar is still there!
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.1.1:war (default-war) on project test-webapp: overlay [ id org.obliquid.helpers:obliquid-helpers] is not a dependency of the project. -> [Help 1]
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.1.1:war (default-war) on project test-webapp: overlay [ id org.apache.geronimo.specs:geronimo-servlet_3.0_spec] is not a dependency of the project. -> [Help 1]
UPDATE 4: I discovered that the target/private.war file is not a zip of target/private/ directory, but the exclusions are done at packaging time and not by deleting files in target/private/ -- This means, I've to re-test all the things I did before.
Suggestion of gouki: doesn't work, the JAR is still there also in the WAR file.
Suggestion of Stephen C., maybe mis-understood: actually I just noticed that the pom.xml is always invalid whatever groupId/artifactId I put of the three possibilities explained above. So they didn't work for me.
What I found in the documentation (packagingExcludes), works.
Now, if I had to choose one of he answers I would choose Stephen C., because he helped me pointing at the documentation of the WAR plugin (I was reading in the wrong places). However I'd accept an answer that doesn't work, at least in the way I tried (probably wrong). So I'm not going to accept any answer, and add a new answer myself with the final working configuration.
UPDATE 5: I post the relevant part of the pom.xml of obliquid-helpers, that mentions geronimo-servlet_3.0_spec. I've marked it optional and with scope provided, still it gets included by a web-app, unless I mark it as "packagingExclude" in the maven-war-plugin configuration.
<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.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<packaging>jar</packaging>
<name>obliquid-helpers</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<repositories>
[...]
</repositories>
<dependencies>
[...]
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
<version>1.0</version>
<scope>provided</scope>
<optional>true</optional>
</dependency>
</dependencies>
</project>

Clearly, something has a dependency on that JAR file. If it is not showing up in the dependency tree, perhaps it is due to a dependency of your webapp WAR file on another WAR file that has this dependency.
If that is the case, then you could get add an <excludes> to the <overlay> element of the build descriptor for the WAR file plugin; e.g.
...
<build>
<finalName>webapp</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.1</version>
<configuration>
<overlays>
<overlay>
<groupId>xxx</groupId>
<artifactId>yyy</artifactId>
<excludes>
<exclude>WEB-INF/lib/whatever.jar</exclude>
</excludes>
</overlay>
</overlays>
</configuration>
</plugin>
</plugins>
</build>
...
If you are using WAR file overlays, you should always include the clean target in the build. Otherwise you can get old dependencies hanging around in the WAR file. (IIRC, there is a Warning in the Maven output each time you build an overlaid WAR without cleaning!)
In fact, this could be the root cause of your problems. For instance, if previously you had the "geronimo" as an ordinary dependency and you haven't run mvn clean since then, the JAR file could still be hanging around.

Based from your pom.xml, the only dependency that might have dependency on geronimo servlet is
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
Can you try excluding the geronimo in this dependency?
<dependency>
<groupId>org.obliquid.helpers</groupId>
<artifactId>obliquid-helpers</artifactId>
<version>0.9-SNAPSHOT</version>
<scope>compile</scope>
<exclusions>
<exclusion>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-servlet_3.0_spec</artifactId>
</exclusion>
</exclusions>
</dependency>

First I want to thank gouki and Stephen C. for helping me. However their proposed solution didn't work for me. I'm grateful to them, but I can't accept their answer, because it would be misleading since it didn't work for this problem. I've upvoted Stephen C. answer, because he pointed me to the right documentation, which was essential to solve the problem.
Reading the WAR plugin documentation, especially the war:war mojo section, I've found an example on how to create Skinny WARs, which did the trick. So here is below the working configuration, to be added to the build section:
<build>
<finalName>private</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.1.1</version>
<configuration>
<packagingExcludes>WEB-INF/lib/geronimo-servlet_3.0_spec-1.0.jar</packagingExcludes>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
The archive part is probably not really needed, but I will find out when I deploy the WAR. The part that does the trick is the packagingExcludes tag, that can contain a comma separated list of tokens to exclude from the WAR before packaging.