import java.io.File;
import java.net.URL;
import org.eclipse.emf.common.util.URI;
import org.eclipse.emf.ecore.resource.Resource;
import org.eclipse.emf.ecore.resource.Resource.Factory;
import org.eclipse.emf.ecore.resource.ResourceSet;
import org.eclipse.emf.ecore.resource.URIConverter;
import org.eclipse.emf.ecore.resource.impl.ResourceSetImpl;
import org.eclipse.emf.ecore.util.EcoreUtil;
import org.eclipse.uml2.uml.*;
import org.eclipse.uml2.uml.Class;
import org.eclipse.uml2.uml.Package;
import org.eclipse.uml2.uml.UMLPackage.Literals;
import org.eclipse.uml2.uml.resource.UMLResource;

public class SampleProfile
{

  private static final ResourceSet RESOURCE_SET = new ResourceSetImpl();

  protected static void registerPathmaps( URI baseUri )
  {
    System.out.println( "baseUri = " + baseUri );
    URIConverter.URI_MAP.put(URI.createURI( UMLResource.LIBRARIES_PATHMAP ), baseUri.appendSegment( "libraries" ).appendSegment( "" ));
    URIConverter.URI_MAP.put(URI.createURI( UMLResource.METAMODELS_PATHMAP ), baseUri.appendSegment( "metamodels" ).appendSegment( "" ));
    URIConverter.URI_MAP.put(URI.createURI( UMLResource.PROFILES_PATHMAP ), baseUri.appendSegment( "profiles" ).appendSegment( "" ));
  }

  protected static Package load( URI uri )
    throws Exception
  {
    System.out.println( "uri = " + uri );
    Resource resource = RESOURCE_SET.getResource( uri, true );
    return (Package) EcoreUtil.getObjectByType( resource.getContents(), Literals.PACKAGE );
  }

  public static void main( String[] args )
    throws Exception
  {
    // This line needs to be here, to force running of the UMLPackage
    //  static initializer, otherwise loading the meta-model will return null
    UMLPackage.eINSTANCE.getName();
    
    Factory.Registry.INSTANCE.getExtensionToFactoryMap().put(
      UMLResource.FILE_EXTENSION,
      UMLResource.Factory.INSTANCE
    );

    final String umlProfile = "metamodels/UML.metamodel.uml";
    final URL url = SampleProfile.class.getClassLoader().getResource( umlProfile );
    String baseUrl = url.toString();
    baseUrl = baseUrl.substring( 0, baseUrl.length() - umlProfile.length() );
    registerPathmaps( URI.createURI( baseUrl ));

    Model umlMetamodel = (Model) load( URI.createURI( UMLResource.UML_METAMODEL_URI ) );
    System.out.println( "umlMetamodel = " + umlMetamodel );

    final Model sampleModel = UMLFactory.eINSTANCE.createModel();
    sampleModel.setName( "Sample Model" );

    final Profile sampleProfile = UMLFactory.eINSTANCE.createProfile();
    sampleProfile.setName( "Sample Profile" );


    // The model should be added to a resource before creating/applying stereotypes
    //  otherwise EMF won't persist the created stereotypes
    final File outputFile = new File( "sample_model.uml" );
    final URI outputUri = URI.createFileURI( outputFile.getAbsolutePath() );
    final Resource resource = RESOURCE_SET.createResource( outputUri );
    resource.getContents().add( sampleModel );
    resource.getContents().add( sampleProfile );

    final Stereotype ejbStereo = sampleProfile.createOwnedStereotype( "EJB" );
    extendMetaclass( umlMetamodel, sampleProfile, UMLPackage.Literals.CLASS.getName(), ejbStereo );

    sampleProfile.define();

    final Package samplePackage = sampleModel.createNestedPackage( "sample" );
    samplePackage.applyProfile( sampleProfile );

    final Class sampleClass = samplePackage.createOwnedClass( "TimeEntry", false );
    sampleClass.applyStereotype( ejbStereo );    

    resource.save( null );
  }

  private static void extendMetaclass( final Model umlMetamodel,
                                       final Profile profile,
                                       final String name,
                                       final Stereotype stereotype )
  {
    // The isRequired argument must be false, otherwise all classes will inherit the stereotype
    //  by default
    stereotype.createExtension( referenceMetaclass( umlMetamodel, profile, name ), false );
  }

  private static org.eclipse.uml2.uml.Class referenceMetaclass( final Model umlMetamodel,
                                                                final Profile profile,
                                                                final String name )
  {
    final Class metaclass = (Class) umlMetamodel.getOwnedType( name );
    if ( !profile.getReferencedMetaclasses().contains( metaclass ) )
    {
      profile.createMetaclassReference( metaclass );
    }
    return metaclass;
  }
}

<?xml version="1.0" encoding="UTF-8"?>
<xmi:XMI xmi:version="2.1" xmlns:xmi="http://schema.omg.org/spec/XMI/2.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:SampleProfile="http:///schemas/SampleProfile/_AHok4AQEEeClQKRD-V5YLA/0" xmlns:ecore="http://www.eclipse.org/emf/2002/Ecore" xmlns:uml="http://www.eclipse.org/uml2/3.0.0/UML" xsi:schemaLocation="http:///schemas/SampleProfile/_AHok4AQEEeClQKRD-V5YLA/0 #_AHs2UQQEEeClQKRD-V5YLA">
  <uml:Model xmi:id="_AG9PcAQEEeClQKRD-V5YLA" name="Sample Model">
    <packagedElement xmi:type="uml:Package" xmi:id="_AHs2VgQEEeClQKRD-V5YLA" name="sample">
      <packagedElement xmi:type="uml:Class" xmi:id="_AHxHwAQEEeClQKRD-V5YLA" name="TimeEntry"/>
      <profileApplication xmi:id="_AHtdYAQEEeClQKRD-V5YLA" appliedProfile="_AG9PcQQEEeClQKRD-V5YLA">
        <eAnnotations xmi:id="_AHvSkAQEEeClQKRD-V5YLA" source="http://www.eclipse.org/uml2/2.0.0/UML" references="_AHs2UQQEEeClQKRD-V5YLA"/>
      </profileApplication>
    </packagedElement>
  </uml:Model>
  <uml:Profile xmi:id="_AG9PcQQEEeClQKRD-V5YLA" name="Sample Profile" metaclassReference="_AHO8QAQEEeClQKRD-V5YLA">
    <eAnnotations xmi:id="_AHs2UAQEEeClQKRD-V5YLA" source="http://www.eclipse.org/uml2/2.0.0/UML">
      <contents xmi:type="ecore:EPackage" xmi:id="_AHs2UQQEEeClQKRD-V5YLA" name="SampleProfile" nsURI="http:///schemas/SampleProfile/_AHok4AQEEeClQKRD-V5YLA/0" nsPrefix="SampleProfile">
        <eClassifiers xmi:type="ecore:EClass" xmi:id="_AHs2UgQEEeClQKRD-V5YLA" name="EJB">
          <eAnnotations xmi:id="_AHs2UwQEEeClQKRD-V5YLA" source="http://www.eclipse.org/uml2/2.0.0/UML" references="_AHASwAQEEeClQKRD-V5YLA"/>
          <eStructuralFeatures xmi:type="ecore:EReference" xmi:id="_AHs2VAQEEeClQKRD-V5YLA" name="base_Class" ordered="false" lowerBound="1">
            <eType xmi:type="ecore:EClass" href="http://www.eclipse.org/uml2/3.0.0/UML#//Class"/>
          </eStructuralFeatures>
        </eClassifiers>
      </contents>
    </eAnnotations>
    <elementImport xmi:id="_AHO8QAQEEeClQKRD-V5YLA">
      <importedElement xmi:type="uml:Class" href="pathmap://UML_METAMODELS/UML.metamodel.uml#Class"/>
    </elementImport>
    <packagedElement xmi:type="uml:Stereotype" xmi:id="_AHASwAQEEeClQKRD-V5YLA" name="EJB">
      <ownedAttribute xmi:id="_AHT0wAQEEeClQKRD-V5YLA" name="base_Class" association="_AHTNsAQEEeClQKRD-V5YLA">
        <type xmi:type="uml:Class" href="pathmap://UML_METAMODELS/UML.metamodel.uml#Class"/>
      </ownedAttribute>
    </packagedElement>
    <packagedElement xmi:type="uml:Extension" xmi:id="_AHTNsAQEEeClQKRD-V5YLA" name="Class_EJB" memberEnd="_AHTNsQQEEeClQKRD-V5YLA _AHT0wAQEEeClQKRD-V5YLA">
      <ownedEnd xmi:type="uml:ExtensionEnd" xmi:id="_AHTNsQQEEeClQKRD-V5YLA" name="extension_EJB" type="_AHASwAQEEeClQKRD-V5YLA" aggregation="composite" association="_AHTNsAQEEeClQKRD-V5YLA"/>
    </packagedElement>
  </uml:Profile>
  <SampleProfile:EJB xmi:id="_AHzkAAQEEeClQKRD-V5YLA" base_Class="_AHxHwAQEEeClQKRD-V5YLA"/>
</xmi:XMI>