-- ...
p1: UML!Property(
		
	upper <-a.associationEnds.first().conformance.upperBound,
	lower <- a.associationEnds.first().conformance.lowerBound,
	name <- a.associationEnds.first().name,
	type <- firstMemberType,
	opposite <- p2,
	isComposite <- true
),

p2: UML!Property(
		
		upper <-a.associationEnds.last().conformance.upperBound,
		lower <- a.associationEnds.last().conformance.lowerBound,
		name <- a.associationEnds.last().name,
		type <- secondMemberType,
		opposite <- p1
	),

as:UML!Association(
		name <- a.name,
		ownedEnd <- Set{p2}
		navigableOwnedEnd <- Set{p1}
		)
	do {
p1.applyStereotype(thisModule.getStereotype('xsdElement')); -- here an exception is thrown: see below
}

Here appear some other resulting stacktraces.
......

Caused by: java.lang.IllegalArgumentException: org.eclipse.uml2.uml.internal.impl.StereotypeImpl@21ee05 (name: xsdElement, visibility: <unset>) (isLeaf: false, isAbstract: false) (isActive: false)
	at org.eclipse.uml2.uml.internal.operations.ElementOperations.applyStereotype(ElementOperations.java:1413)
	at org.eclipse.uml2.uml.internal.impl.ElementImpl.applyStereotype(ElementImpl.java:510)
	... 18 more

myClass.applyStereotype(stereotype);

Exception in thread "main" java.lang.IllegalArgumentException: org.eclipse.uml2.uml.internal.impl.StereotypeImpl@90832e (name: TestComponent, visibility: <unset>) (isLeaf: false, isAbstract: false, isFinalSpecialization: false) (isActive: false)
	at org.eclipse.uml2.uml.internal.operations.ElementOperations.applyStereotype(ElementOperations.java:1413)
	at org.eclipse.uml2.uml.internal.impl.ElementImpl.applyStereotype(ElementImpl.java:510)
	at test.main(test.java:65)

testModel.applyProfile(profModel); //testModel is a org.eclipse.uml2.uml.Model
                                   //profModel is a org.eclipse.uml2.uml.Profile

UMLResourcesUtil.init(RESOURCE_SET);

import java.io.IOException;

import org.eclipse.emf.common.util.URI;
import org.eclipse.emf.ecore.EPackage;
import org.eclipse.emf.ecore.EcorePackage;
import org.eclipse.emf.ecore.resource.Resource;
import org.eclipse.emf.ecore.resource.ResourceSet;
import org.eclipse.emf.ecore.resource.impl.ResourceSetImpl;
import org.eclipse.emf.ecore.util.EcoreUtil;
import org.eclipse.uml2.uml.Element;
import org.eclipse.uml2.uml.Model;
import org.eclipse.uml2.uml.Package;
import org.eclipse.uml2.uml.Profile;
import org.eclipse.uml2.uml.Stereotype;
import org.eclipse.uml2.uml.UMLPackage;
import org.eclipse.uml2.uml.resource.UMLResource;
import org.eclipse.uml2.uml.resource.XMI212UMLResource;
import org.eclipse.uml2.uml.resources.util.UMLResourcesUtil;

/**
 * @author Mauro Faella
 *
 */
public class Test {
	static private ResourceSet RESOURCE_SET = new ResourceSetImpl();
	
	public static void main(String[] args) {
		
		UMLResourcesUtil.init(RESOURCE_SET);
		URI uriModel = URI.createFileURI("Test").appendFileExtension(UMLResource.FILE_EXTENSION);
		URI uriProf = URI.createFileURI("StandardProfileL2").appendFileExtension(XMI212UMLResource.FILE_EXTENSION);
		Resource umlModel = RESOURCE_SET.getResource(uriModel, true);
		Resource umlProfile = RESOURCE_SET.getResource(uriProf, true);
		//To avoid reference problem in uml file 
		umlProfile.setURI(URI.createFileURI(uriProf.segmentsList().get(uriProf.segmentCount()-1)));
		Model testModel = (Model) EcoreUtil.getObjectByType(umlModel.getContents()
				, UMLPackage.Literals.MODEL);
		Profile profModel = (Profile) EcoreUtil.getObjectByType(umlProfile.getContents()
				, UMLPackage.Literals.PROFILE);
		if (profModel.isDefined()){
			System.out.println("is Defined");
		}else{
			EPackage profileModel = (EPackage) EcoreUtil.getObjectByType(umlProfile.getContents()
					, EcorePackage.Literals.EPACKAGE);
			System.out.println("is Not Defined");
			profModel.createMetamodelReference((Package) profileModel);
			profModel.define();
		}
		testModel.applyProfile(profModel);
		System.out.println("applied: "+testModel.isProfileApplied(profModel));
		org.eclipse.uml2.uml.Package myPkg = (org.eclipse.uml2.uml.Package) testModel.getPackagedElement("myPkg");
		Element myClass = myPkg.getPackagedElement("Class1");
		try {
			umlModel.save(null);
			System.out.println("Saved");
		} catch (IOException e) {
			e.printStackTrace();
		}
		Stereotype stereotype = profModel.getOwnedStereotype("Type");
		myClass.applyStereotype(stereotype);
		try {
			umlModel.save(null);
		} catch (IOException e) {
			e.printStackTrace();
		}
	} 
}

String JAR_FILE_ECLIPSE_UML2_UML_RESOURCES = "jar:file:C:/org.eclipse.uml2.uml.resources_4.0.1.v20120913-1441.jar!/";
File test = new File(JAR_FILE_ECLIPSE_UML2_UML_RESOURCES.substring(9,JAR_FILE_ECLIPSE_UML2_UML_RESOURCES.length()-2)).getAbsoluteFile();
if (!test.exists()){
                throw new NullPointerException("JAR_FILE_ECLIPSE_UML2_UML_RESOURCES PATH ERROR, "+test.toString()+"not found!");
}
_resourceSet.getPackageRegistry().put(UMLPackage.eNS_URI, UMLPackage.eINSTANCE);
_resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put(UMLResource.FILE_EXTENSION,UMLResource.Factory.INSTANCE);
Map<URI, URI> _resourceSetURIMap = _resourceSet.getURIConverter().getURIMap();
URI uri = URI.createURI(JAR_FILE_ECLIPSE_UML2_UML_RESOURCES);
_resourceSetURIMap.put(URI.createURI(UMLResource.LIBRARIES_PATHMAP), uri.appendSegment("libraries").appendSegment(""));
_resourceSetURIMap.put(URI.createURI(UMLResource.METAMODELS_PATHMAP), uri.appendSegment("metamodels").appendSegment(""));
_resourceSetURIMap.put(URI.createURI(UMLResource.PROFILES_PATHMAP), uri.appendSegment("profiles").appendSegment(""));