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maven dependency not properly compile into war

I am using the Eclipse IDE and in the past, I have been developing a maven project depending on local sources (from github (sap-olingo)) as well as maven dependencies loaded as jar. I have now updated the github source and also all the dependencies which seems to break standard eclipse export functionalities (right click porject -> export -> war)
The webproject is working fine when using the maven install functionality and is loading all sources into the META-INF/lib classes, but when using the export as war from eclipse (which I did previously) it is missing to compile a proper dependency. Missing in the sense of that the jar is still present in the META-INF/lib directory of the war, but the content is empty and the size is only 1kb
When comparing the mvn clean install to the exported, there are rarely any differences. Except for the projects that are to be compiled during the runtime. Sizes of the libs in the mvn created war and the exported war roughly matches except for that one jar.
Is there a way to root cause that issue? I am using solely the maven integrated into the IDE which is why I doubt differences in the maven versions and or jdk.
Unfortunately I have no idea in where to start and what info you require
Thanks for your input
EDIT:
My projects pom:
<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>com.test</groupId>
<artifactId>odata</artifactId>
<packaging>war</packaging>
<version>4.0.0</version>
<name>odataMaven Webapp</name>
<url></url>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sap.olingo</groupId>
<artifactId>odata-jpa-processor</artifactId>
<version>0.3.7-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.microsoft.sqlserver</groupId>
<artifactId>mssql-jdbc</artifactId>
<version>6.1.0.jre8</version>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>javax.persistence</artifactId>
<version>2.1.0</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>eclipselink</artifactId>
<version>2.6.2</version>
</dependency>
</dependencies>
<build>
<finalName>odata</finalName>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.17</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>${project.build.source}</source>
<target>${project.build.source}</target>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.source>1.8</project.build.source>
</properties>
</project>
The odata-jpa-processor source/project is pulled from here. The problem exists solely with the olingo-jpa-metadata jar which is empty. All other maven dependencies are exported correctly.

How to disable karaf-maven-plugin 4 tight dependency constraint checks

Currently I am moving from karaf 3.0.5 to the newest version 4.0.2, I do assembly my own karaf with the karaf-maven-plugin. This is how my pom looks like.
<?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">
<parent>
<groupId>my.own.group</groupId>
<artifactId>assemble</artifactId>
<version>1.14.0-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
<artifactId>karaf-customize</artifactId>
<modelVersion>4.0.0</modelVersion>
<packaging>karaf-assembly</packaging>
<dependencies>
<dependency>
<groupId>org.apache.karaf.features</groupId>
<artifactId>framework</artifactId>
<version>${karaf.version}</version>
<type>kar</type>
</dependency>
<dependency>
<groupId>org.apache.karaf.features</groupId>
<artifactId>standard</artifactId>
<classifier>features</classifier>
<version>${karaf.version}</version>
<type>xml</type>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.apache.cxf.karaf</groupId>
<artifactId>apache-cxf</artifactId>
<classifier>features</classifier>
<version>${cxf.version}</version>
<type>xml</type>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.apache.karaf.features</groupId>
<artifactId>enterprise</artifactId>
<classifier>features</classifier>
<version>${karaf.version}</version>
<type>xml</type>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>my.own.group</groupId>
<artifactId>kar-archive</artifactId>
<version>1.14.0-SNAPSHOT</version>
<type>pom</type>
<optional>true</optional>
</dependency>
<dependency>
<groupId>my.own.group</groupId>
<artifactId>karaf-branding</artifactId>
<version>1.14.0-SNAPSHOT</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>com.alutam</groupId>
<artifactId>ziputils</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>wsdl4j</groupId>
<artifactId>wsdl4j</artifactId>
<version>1.6.3</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.karaf.tooling</groupId>
<artifactId>karaf-maven-plugin</artifactId>
<version>${karaf.version}</version>
<extensions>true</extensions>
<configuration>
<javase>1.8</javase>
<bootFeatures>
<feature>jasypt-encryption</feature>
<feature>config</feature>
<feature>standard</feature>
<feature>region</feature>
<feature>management</feature>
<feature>bundle</feature>
<feature>package</feature>
<feature>kar</feature>
<feature>ssh</feature>
<feature>http</feature>
<feature>cxf</feature>
<feature>service-wrapper</feature>
<feature>jdbc</feature>
<feature>system</feature>
</bootFeatures>
</configuration>
</plugin>
</plugins>
</build>
</project>
With this configuration I do get the following error for several dependencies.
Caused by: org.osgi.framework.BundleException: Unsupported 'Bundle-ManifestVersion' value: 1
at org.apache.karaf.features.internal.resolver.ResourceBuilder.doBuild(ResourceBuilder.java:88)
at org.apache.karaf.features.internal.resolver.ResourceBuilder.build(ResourceBuilder.java:78)
I guess it happens within this parser. The reason is some old third party libraries have only Bundle-ManifestVersion: 1 set within their manifest file.
With karaf-maven-plugin 3.x this didn't matter at all. In contrast the karaf-maven-plugin 4.x fails with message above.
The only way I know to fix this is either rebuild from source or repack the hole jar again.
Is there any other way like a configuration for the karaf-maven-plugin to disable this constraint check? Because it would be awful lot of work to get all of this bundles up an running, again.

I faced the same error when updating to Karaf 4 and you have two choices:
Osgify conflictive dependency using bndtools:
Download bnd tools
Open a shell where you have downloaded bnd-2.4.0.jar.
Type:
java -jar bnd-2.4.0.jar wrap -o osgify-dependency.jar dependency.jar
where dependency.jar is your third party and osgify-dependency.jar will be the output.
Deploy to maven repo overriding the previous maven coordinates, or deploy your thirdparty with different coordinates.
mvn deploy:deploy-file -Dfile osgify-dependency.jar ..
Enable the wrap protocol
Add to you maven karaf plugin wrap and wrapper features.
So you can use wrap protocol to fix your corrupted MANIFEST.MF
Inside some karaf features:
<bundle>wrap:mvn:group.id/third.party.artefact.id/version</bundle>
Inside your pom.xml notice feature wrap / wrapper.
<plugin>
<groupId>org.apache.karaf.tooling</groupId>
<artifactId>karaf-maven-plugin</artifactId>
<extensions>true</extensions>
<executions>
</executions>
<configuration>
<!-- no startupFeatures -->
<bootFeatures>
<feature>feature</feature>
<feature>jaas</feature>
<feature>shell</feature>
<feature>ssh</feature>
<feature>management</feature>
<feature>bundle</feature>
<feature>config</feature>
<feature>deployer</feature>
<feature>diagnostic</feature>
<feature>instance</feature>
<feature>kar</feature>
<feature>log</feature>
<feature>package</feature>
<feature>service</feature>
<feature>system</feature>
<feature>wrap</feature>
<feature>aries-blueprint</feature>
</bootFeatures>
<installedFeatures>
..
<feature>wrapper</feature>
</installedFeatures>
</configuration>
</plugin>
Here you have the full code where i tested:
https://github.com/antoniomaria/gazpachoquest/blob/master/karaf-assembly/pom.xml

execute goal mvn-failsafe-plugin: (failsafe-integration-tests) project x: suiteXmlFiles is configured, but there is no TestNG dependency

i am using maven failsafe plugin to execute the integration test cases along with cobertura plugin.
in the configuration of failsafe plugin, i have given suiteXmlFile which has all the integration tests
however, when run the following command , i am getting error
command is : mvn cobertura:cobertura-integration -DskipITs=false
and error is :
Failed to execute goal maven-failsafe-plugin:2.17:integration-test (failsafe-integration-tests) on project xx: suiteXmlFiles is configured, but there is no TestNG dependency
here is the snippet from pom.xml
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.17</version>
<configuration>
<suiteXmlFiles>
<suiteXmlFile>/home/adam/coberturaint/reporting/src/test/resources/testng/it-test.xml</suiteXmlFile>
</suiteXmlFiles>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8.8</version>
</dependency>
</dependencies>
</dependencyManagement>
</configuration>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8.8</version>
</dependency>
</dependencies>
</plugin>
i am using fail-safe plugin version : 2.17
i have mentioned the dependency of testng everywhere, but still i am getting dependency error
please suggest
regards

You need to go a different way cause the messages it already.
<?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>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8.8</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.17</version>
<configuration>
<suiteXmlFiles>
<suiteXmlFile>/home/adam/coberturaint/reporting/src/test/resources/testng/it-test.xml</suiteXmlFile>
</suiteXmlFiles>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>
Apart from that you need to call maven like this:
mvn verify
to run the integration-test phase. If you call Maven like this:
mvn cobertura:cobertura-integration
You have no life cycle which will not run the integration tests.
You should prevent using absolute paths in your pom file as you do with your suite file. The question is on the other hand why you need a suite file. In TestNG usually you don't need one.

Maven null dependency and multiple annotations on this line

Something has gone wrong with my pom and I have a blank dependency and artifactId in the xml but get the same error whether I delete the tags or not.
I am using eclipse with m2eclipse installed in my home folder on Linux Mint 14 with maven version 'Apache Maven 2.2.1 (rdebian-8)' installed
Here is 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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>TransferHandler</groupId>
<artifactId>TransferHandler</artifactId>
<version>0.0.1-SNAPSHOT</version>
<build>
<sourceDirectory>src</sourceDirectory>
<testSourceDirectory>test</testSourceDirectory>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId>
<version>1.4.6-rc1</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-vfs2</artifactId>
<version>2.0</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>com.jcraft</groupId>
<artifactId>jsch</artifactId>
<version>0.1.49</version>
</dependency>
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.2</version>
<classifier>ftp</classifier>
</dependency>
<dependency>
<groupId>commons-httpclient</groupId>
<artifactId>commons-httpclient</artifactId>
<version>3.1</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>3.2.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-io</artifactId>
<version>1.3.2</version>
</dependency>
<dependency>
<artifactId></artifactId>
</dependency>
</dependencies>
</project>
There are three error messages displayed:
On line1:
Multiple annotations found at this line:
- null (org.apache.maven.plugins:maven-resources-plugin:2.5:resources:default-resources:process-resources)
- null (org.apache.maven.plugins:maven-resources-plugin:2.5:testResources:default-testResources:process-test-
resources)
On line70:
Multiple annotations found at this line:
- Project build error: 'dependencies.dependency.groupId' for null::jar is
missing.
- Project build error: 'dependencies.dependency.version' for null::jar is
missing.
On line 71:
Project build error: 'dependencies.dependency.artifactId' for null::jar is missing.
It seems like the one on line 70 with the empty tags is the root cause (excerpt below) but I'm not sure.
<dependency>
<artifactId></artifactId>
</dependency>
Even if I delete the empty tags from the xml and refresh maven and the project the error remains. On my Dependencies tab I see a jar with a '?' next to it but can't delete it and in my Dependency Hierachy tab I see a ' : [compile]' jar but can delete or exclude it.
How can I remove this ghost/null jar?

Try This Header
<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">
Good Luck !

I found a way around the problem using git but was not able to solve it directly by removing the offending packages.
The work-around was to shutdown eclipse, remove the pom and then use git to discard changes in the working directory. Commands:
rm pom.xml
git checkout -- pom.xml
Then the pom should reappear returned to its state at the last commit (which luckily for me was before this error arose). Not a very satisfying answer but at least it worked. If anyone posts an answer and explanation to the heart of the real problem (ie why can't I remove a null package and how did it get there in the first place) I would still be happy to accept it.

Add my own bundle sources to pax-exam when building with pax-maven-plugin

I'm trying to build my OSGI bundle with pax-maven-build and in the same time test it with pax-exam. It have some bundle in provision than I can test with the following pax-exam test configuration:
#RunWith(JUnit4TestRunner.class)
#ExamReactorStrategy(AllConfinedStagedReactorFactory.class)
public class OSGILoaderTest {
#Inject
protected BundleContext bundleContext;
#Configuration
public Option[] config() throws MalformedURLException {
String projectRoot = // a path to my project
return options(
junitBundles(),
equinox(),
bundle(projectRoot + "libs/org.eclipse.core.variables_3.2.500.v20110511.jar"),
bundle(projectRoot + "libs/org.eclipse.core.contenttype_3.4.100.v20110423-0524.jar"),
bundle(projectRoot + "libs/org.eclipse.core.expressions_3.4.300.v20110228.jar"),
// etc...
);
}
#Test
public void getBundleContext() throws RodinDBException {
IRodinDB rodinDB = RodinCore.getRodinDB();
assertNotNull(rodinDB);
}
}
Here, I can see I can access to the IRodinDB instance from a jar I have provisonned.
Now I have code my own bundle, which is going to use all the jar provisionned. But I cannot even test my own code, for instance:
#Test
public void checkAccessToRodinDbTest() {
VTGService service = null;
assertTrue(true);
}
give an error at compilation time:
[ERROR] Failed to execute goal org.ops4j:maven-pax-plugin:1.5:testCompile (default-testCompile) : Compilation failure
[ERROR] cannot find symbol
[ERROR] symbol : class VTGService
It seems test compilation cannot see 'src/main/java', contrarly as expected by the default behavior of maven-compiler-plugin. But in my case, you can see than maven does not use the compiler plugin but instead maven-pax-plugin.
The question is: how can i test my own bundle with pax-exam ?
update1
It seems that this is a problem with recent version of maven-pax-plugin, as the basic example available in ops4j pax maven plugin (in section Using the Pax Plugin inside a POM) seems to suffer of the same problem.
update2
As requested by Dmytro, this is the pom.xml of my bundle:
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<parent>
<relativePath>../poms/compiled/</relativePath>
<groupId>fr.xlim.ssd.vtg.build</groupId>
<artifactId>compiled-bundle-settings</artifactId>
<version>0.1-SNAPSHOT</version>
</parent>
<properties>
<bundle.symbolicName>fr.xlim.ssd.vtg.bundle</bundle.symbolicName>
<bundle.namespace>fr.xlim.ssd.vtg.bundle</bundle.namespace>
</properties>
<modelVersion>4.0.0</modelVersion>
<groupId>fr.xlim.ssd.vtg</groupId>
<artifactId>fr.xlim.ssd.vtg.bundle</artifactId>
<version>0.1-SNAPSHOT</version>
<name>${bundle.symbolicName}</name>
<packaging>bundle</packaging>
<dependencies>
<dependency>
<type>pom</type>
<groupId>${project.parent.groupId}</groupId>
<artifactId>provision</artifactId>
<optional>true</optional>
</dependency>
<!-- not needed as equinox bundle are available in provision -->
<dependency>
<groupId>org.osgi</groupId>
<artifactId>osgi_R4_core</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>osgi_R4_compendium</artifactId>
<optional>true</optional>
</dependency-->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.9</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-junit4</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-inject</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.url</groupId>
<artifactId>pax-url-mvn</artifactId>
<version>1.3.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-container-native</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javax.inject</groupId>
<artifactId>javax.inject</artifactId>
<version>1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.exam</groupId>
<artifactId>pax-exam-link-mvn</artifactId>
<version>2.3.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.0.0</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
</plugins>
</build>
</project>
I am not sure it is the most elegant solution, but I created a new maven project when I can import my own bundle like in the source code of my question.
Is there an elegant way to add my own java sources directly as new bundle for test in the same Maven project ? It could be not possible (as the bundle assembly operation is done after the compilation and tests)...

I use the following setup to provision the bundle under test. When configuring the test, I provision the bundle using the reference-protocol (this is a non-standard feature of Equinox and Felix, see here):
#Configuration
public Option[] config() {
return options(
bundle("reference:file:target/classes"),
junitBundles(),
felix()
);
}
The test-cases also run when you specify knopplerfish() as the environment. I guess that is because the URL is resolved by Pax Exam, and not by the OSGi-runtime. I use the maven-bundle-plugin to build my bundles. To make this work as expected, you have to add the following configuration:
<build>
<plugins>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.3.7</version>
<extensions>true</extensions>
<executions>
<!-- This execution makes sure that the manifest is available
when the tests are executed -->
<execution>
<goals>
<goal>manifest</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Otherwise the manifest will not be available when the tests are run, since by default it is generated during the package-phase.
I hope I did not forget anything - please let me know if it worked for you!

Check PaxExam docs how to configure your Maven POM with PaxExam.
Samples here