Examples of org.mmisw.ont.mmiuri.MmiUri

org.mmisw.ont.mmiuri.MmiUri

.org in the example) and the "root" directory component (ont in the example).

The following requested URI is used as example to illustrate the various operations:

 http://mmisw.org/ont/mmi/someVocab.owl/someTerm

Note that the "extension" (.owl) can also be indicated in the term component, eg.,

 http://mmisw.org/ont/mmi/someVocab/someTerm.owl

The two strings refer to the same ontology and term.

Note that the extension is NOT included in any of the report operations except {@link #getExtension()}.

As a concrete example with all the main operations:

 MmiUri mmiUri = new MmiUri("http://mmisw.org/ont/mmi/someVocab/someTerm.owl"); assertEquals("http://mmisw.org/ont/mmi/someVocab",          mmiUri.getOntologyUri()); assertEquals("http://mmisw.org/ont/mmi/someVocab/someTerm", mmiUri.getTermUri()); assertEquals("mmi",       mmiUri.getAuthority()); assertEquals(null,        mmiUri.getVersion()); assertEquals("someVocab", mmiUri.getTopic()); assertEquals("someTerm",  mmiUri.getTerm()); assertEquals(".owl",      mmiUri.getExtension()); assertEquals("http://mmisw.org/ont/",  mmiUri.getUntilRoot());

@author Carlos Rueda

                    String withUriParam = null;


                    if ( OntServiceUtil.isOntResolvableUri(ontologyUri) ) {
                        // prefer to show the unversioned URI
                        try {
                            MmiUri mmiUri = new MmiUri(ontologyUri);
                            version = mmiUri.getVersion();
                            ontologyUri = mmiUri.copyWithVersion(null).getOntologyUri();
                        }
                        catch (URISyntaxException ignore) {
                        }
                    }
                    else {

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    if (USE_UNVERSIONED) {
      model = JenaUtil2.loadModel("file:" + full_path, false);


      if (OntUtil.isOntResolvableUri(ontologyUri)) {
        MmiUri mmiUri;
        try {
          mmiUri = new MmiUri(ontologyUri);
          OntModel unversionedModel = UnversionedConverter
              .getUnversionedModel(model, mmiUri);


//          serialization = JenaUtil2.getOntModelAsString(
//              unversionedModel, "RDF/XML-ABBREV");
          
          // AG$: we don;t use the serialization; but here we need to update
          // the model reference to be unversionedModel:
          model = unversionedModel;


          ontologyUri = mmiUri.copyWithVersion(null).getOntologyUri();
        }
        catch (URISyntaxException e) {
          log.error("shouldn't happen", e);
          return;
        }

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    String ontologyUri = ontology.getUri();


    if (USE_UNVERSIONED) {


      if (OntUtil.isOntResolvableUri(ontologyUri)) {
        MmiUri mmiUri;
        try {
          mmiUri = new MmiUri(ontologyUri);
          ontologyUri = mmiUri.copyWithVersion(null).getOntologyUri();
        }
        catch (URISyntaxException e) {
          log.error("shouldn't happen", e);
          return;
        }

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   * @return the string that can be used as a link as stated above; null if value is not a URL.
   */
  public static String getLink(String value) {
    // try mmiUri:
    try {
      MmiUri mmiUri = new MmiUri(value);
      return mmiUri.getTermUri() + ".html";
    }
    catch (URISyntaxException e1) {
      // ignore. Try URL below.
    }

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  private static void populateList(AttrDef attrDef, String classUri) throws URISyntaxException {
    
    MmiUri classMmiUri = new MmiUri(classUri);
    String ontologUri = classMmiUri.getOntologyUri();
    String className = classMmiUri.getTerm();
    
    if ( log.isDebugEnabled() ) {
      log.debug("reading: " +classMmiUri.getTermUri()+ " individuals to populate " +className+ " list");
    }


    // read the ontology:
    OntModel ontModel = ModelFactory.createOntologyModel();
    ontModel.read(ontologUri);
    
    // add options here termporarily
    List<Option> list = new ArrayList<Option>();
    
    Resource classRes = ResourceFactory.createResource(classMmiUri.getTermUri());
    
    ExtendedIterator<Individual> iter = ontModel.listIndividuals(classRes);
    while ( iter.hasNext() ) {
      Resource idv = (Resource) iter.next();
      String idvName = idv.getLocalName();

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    // get the user RDF from the Ont service:
    String rdf = OntServiceUtil.getUsersRdf();
    
    // get the users RDF URI, assumed to be versioned:
    String generatedUsersUri = _getUsersUri(rdf);
    MmiUri mmiUri = new MmiUri(generatedUsersUri);
    String version = mmiUri.getVersion();
    
    // unversioned URI for purposes of geting possible prior version, set up auqportal filename, 
    // graphId, and report it in the result back to caller:
    final String unversUsersUri = mmiUri.copyWithVersion(null).getOntologyUri();
    
    // info from previous version if any:
    String ontologyId = null;
    String ontologyUserId = null;
    RegisteredOntologyInfo usersOntology = orrClient.getOntologyInfo(unversUsersUri);

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    // set some associated attributes for the registration:
    Map<String, String> newValues = _getValues(loginResult, "MMI ORR Groups",  version);
    String fileName = AquaUtil.getAquaportalFilename(unversGroupsUri);
    
    // the versioned form for the registration:
    String versionedUsersUri = new MmiUri(unversGroupsUri).copyWithVersion(version).getOntologyUri();
    
    String rdf = _getGroupsRdf(versionedUsersUri, version);
    // register:
    OntologyUploader createOnt = new OntologyUploader(
        versionedUsersUri , fileName, rdf ,

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