dependencies of dependency are not included

Question

I have a java application that has some dependencies, among them another project with its own dependencies. Whenever I run it from Netbeans or with mvn exec is fine but when I try to package it, even though it's successfully built, at run time I get the following error:

Exception in thread "main" org.openrdf.rio.UnsupportedRDFormatException: No parser factory available for RDF format Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl)
    at org.openrdf.rio.Rio.createParser(Rio.java:198)
    at org.openrdf.rio.Rio.createParser(Rio.java:213)
    at org.openrdf.repository.util.RDFLoader.loadInputStreamOrReader(RDFLoader.java:318)
    at org.openrdf.repository.util.RDFLoader.load(RDFLoader.java:222)
    at org.openrdf.repository.util.RDFLoader.load(RDFLoader.java:104)
    at org.openrdf.repository.base.RepositoryConnectionBase.add(RepositoryConnectionBase.java:217)
    at net.antidot.semantic.rdf.model.impl.sesame.SesameDataSet.loadDataFromFile(SesameDataSet.java:160)

so the problem is that the sesame rio parsers seem not to be included even though I can see them in my maven repository. I include all the dependencies at the included project. I also tried to exclude them and explicitly add them to my main project and it again failed.

Any suggestions?

my dependencies tree:

[INFO] --- maven-dependency-plugin:2.1:tree (default-cli) @ RMLMapper ---
[INFO] be.ugent.mmlab:RMLMapper:jar:0.1
[INFO] +- junit:junit:jar:4.11:test
[INFO] |  \- org.hamcrest:hamcrest-core:jar:1.3:test
[INFO] +- xom:xom:jar:1.2.5:compile
[INFO] |  +- xml-apis:xml-apis:jar:1.3.03:compile
[INFO] |  +- xerces:xercesImpl:jar:2.8.0:compile
[INFO] |  \- xalan:xalan:jar:2.7.0:compile
[INFO] +- jlibs:jlibs-xmldog:jar:1.0:compile
[INFO] |  +- jlibs:jlibs-xml:jar:1.0:compile
[INFO] |  |  +- jlibs:jlibs-core:jar:1.0:compile
[INFO] |  |  \- jlibs:jlibs-nbp:jar:1.0:compile
[INFO] |  \- jaxen:jaxen:jar:1.1.1:compile
[INFO] +- com.jayway.jsonpath:json-path:jar:0.8.1:compile
[INFO] |  +- net.minidev:json-smart:jar:1.1.1:compile
[INFO] |  \- commons-lang:commons-lang:jar:2.6:compile
[INFO] +- com.jayway.jsonpath:json-path-assert:jar:0.9.1:test
[INFO] |  \- org.hamcrest:hamcrest-library:jar:1.3:test
[INFO] +- net.antidot:db2triples:jar:1.0.2:compile
[INFO] |  +- commons-logging:commons-logging:jar:1.1.2:compile
[INFO] |  +- mysql:mysql-connector-java:jar:5.1.25:compile
[INFO] |  +- postgresql:postgresql:jar:9.1-901.jdbc4:compile
[INFO] |  \- org.slf4j:slf4j-simple:jar:1.6.1:runtime
[INFO] +- org.openrdf.sesame:sesame-runtime:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-model:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-repository-api:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-repository-manager:jar:2.7.12:compile
[INFO] |  |  +- org.openrdf.sesame:sesame-repository-event:jar:2.7.12:compile
[INFO] |  |  +- org.openrdf.sesame:sesame-sail-memory:jar:2.7.12:compile
[INFO] |  |  +- org.openrdf.sesame:sesame-http-client:jar:2.7.12:compile
[INFO] |  |  |  \- commons-httpclient:commons-httpclient:jar:3.1:compile
[INFO] |  |  \- org.openrdf.sesame:sesame-http-protocol:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-repository-http:jar:2.7.12:compile
[INFO] |  |  +- org.openrdf.sesame:sesame-queryparser-api:jar:2.7.12:compile
[INFO] |  |  \- org.openrdf.sesame:sesame-queryresultio-api:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-repository-sparql:jar:2.7.12:compile
[INFO] |  |  +- org.openrdf.sesame:sesame-queryparser-sparql:jar:2.7.12:compile
[INFO] |  |  \- org.openrdf.sesame:sesame-queryresultio-sparqlxml:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-repository-contextaware:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-repository-sail:jar:2.7.12:compile
[INFO] |  |  \- org.openrdf.sesame:sesame-rio-trig:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-sail-api:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-sail-federation:jar:2.7.12:compile
[INFO] |  +- org.slf4j:slf4j-api:jar:1.6.1:compile
[INFO] |  +- org.openrdf.sesame:sesame-queryparser-serql:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-queryresultio-binary:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-queryresultio-sparqljson:jar:2.7.12:runtime
[INFO] |  |  \- com.fasterxml.jackson.core:jackson-core:jar:2.2.1:runtime
[INFO] |  +- org.openrdf.sesame:sesame-queryresultio-text:jar:2.7.12:runtime
[INFO] |  |  \- net.sf.opencsv:opencsv:jar:2.0:runtime
[INFO] |  +- org.openrdf.sesame:sesame-repository-dataset:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-rio-languages:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-rio-binary:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-rio-nquads:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-rio-n3:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-rio-rdfjson:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-rio-rdfxml:jar:2.7.12:runtime
[INFO] |  +- org.openrdf.sesame:sesame-rio-trix:jar:2.7.12:runtime
[INFO] |  \- org.openrdf.sesame:sesame-sail-rdbms:jar:2.7.12:runtime
[INFO] |     \- commons-dbcp:commons-dbcp:jar:1.3:runtime
[INFO] |        \- commons-pool:commons-pool:jar:1.5.4:runtime
[INFO] +- org.openrdf.sesame:sesame-sail-nativerdf:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-sail-inferencer:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-queryalgebra-evaluation:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-queryalgebra-model:jar:2.7.12:compile
[INFO] |  +- org.openrdf.sesame:sesame-query:jar:2.7.12:compile
[INFO] |  \- org.openrdf.sesame:sesame-util:jar:2.7.12:compile
[INFO] +- com.sun.org.apache:jaxp-ri:jar:1.4:compile
[INFO] |  \- javax.xml.parsers:jaxp-api:jar:1.4:compile
[INFO] +- net.sourceforge.javacsv:javacsv:jar:2.0:compile
[INFO] +- commons-io:commons-io:jar:1.3.2:compile
[INFO] +- net.sf.saxon:Saxon-HE:jar:compressed:9.5.1-4:compile
[INFO] +- org.jodd:jodd-lagarto:jar:3.5:compile
[INFO] |  +- org.jodd:jodd-log:jar:3.5:compile
[INFO] |  \- org.jodd:jodd-core:jar:3.5:compile
[INFO] +- org.jsoup:jsoup:jar:1.7.3:compile
[INFO] +- org.apache.httpcomponents:httpclient:jar:4.2.2:compile
[INFO] |  +- org.apache.httpcomponents:httpcore:jar:4.2.2:compile
[INFO] |  \- commons-codec:commons-codec:jar:1.6:compile
[INFO] +- com.github.fge:uri-template:jar:0.9:compile
[INFO] |  +- com.github.fge:msg-simple:jar:1.1:compile
[INFO] |  |  \- com.github.fge:btf:jar:1.2:compile
[INFO] |  +- com.google.guava:guava:jar:16.0.1:compile
[INFO] |  \- com.google.code.findbugs:jsr305:jar:2.0.1:compile
[INFO] +- org.openrdf.sesame:sesame-rio-api:jar:2.7.12:compile
[INFO] +- org.openrdf.sesame:sesame-rio-datatypes:jar:2.7.12:compile
[INFO] +- org.openrdf.sesame:sesame-rio-turtle:jar:2.7.12:compile
[INFO] +- org.openrdf.sesame:sesame-rio-ntriples:jar:2.7.12:compile
[INFO] +- org.openrdf.sesame:sesame-rio-n3:pom:2.7.12:compile
[INFO] +- org.openrdf.sesame:sesame-rio:pom:2.7.12:compile
[INFO] \- commons-cli:commons-cli:jar:1.2:compile

Answer 1

starting from your considerations I found a solution for building a fat-jar of my application including Sesame. I had to use another maven plugin, which is shade and the configuration for my build is as follows:

<build>
<plugins>
  <plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-shade-plugin</artifactId>
    <version>2.3</version>
    <executions>
      <execution>
        <phase>package</phase>
        <goals>
          <goal>shade</goal>
        </goals>
        <configuration>
          <transformers>
            <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
              <mainClass>my.package.main.MyMain</mainClass>
            </transformer>
            <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
          </transformers>
          <filters>
            <filter>
              <artifact>*:*</artifact>
              <excludes>
                <exclude>META-INF/*.SF</exclude>
                <exclude>META-INF/*.DSA</exclude>
                <exclude>META-INF/*.RSA</exclude>
              </excludes>
            </filter>
          </filters>
        </configuration>
      </execution>
    </executions>
  </plugin>
</plugins>
</build>

The most interesting parts are:

• mainClass element: to specify the main
• ServicesResourceTransformer: the core of our problem with sesame, which is the META-INF/services/ dir. This transformer helps in merging the dependancies services META-INF (as better explained in http://maven.apache.org/plugins/maven-shade-plugin/examples/resource-transformers.html#ServicesResourceTransformer )
• filters: to sign the jar (further details on: http://zhentao-li.blogspot.it/2012/06/maven-shade-plugin-invalid-signature.html )

Hope it helps. Cheers, Riccardo