Package edu.stanford.smi.protege.model

Examples of edu.stanford.smi.protege.model.Project

135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
   */
  public static POntology loadOntology(URI uri) throws IOntologyException{
    POntology ont = null;
    if(uri.toString().endsWith(".pprj")){
      ArrayList errors = new ArrayList();
      Project project = Project.loadProjectFromURI(uri,errors);
      if(!errors.isEmpty()){
        throw new IOntologyException("Problem loading PPRJ file "+uri,getException(errors));
      }
      ont =  new POntology((OWLModel) project.getKnowledgeBase());
    }else {
      try{
        ont = new POntology(ProtegeOWL.createJenaOWLModelFromURI(""+uri));
      }catch(Exception ex){
        throw new IOntologyException("Problem loading OWL file "+uri,ex);
View Full Code Here
336
337
338
339
340
341
342
343
344
345
346
347
348
   */
  public static POntology loadOntology(File uri) throws IOntologyException{
    // check if this is an pprj file
    if(uri.getName().endsWith(".pprj")){
      ArrayList errors = new ArrayList();
      Project project = Project.loadProjectFromFile(uri.getAbsolutePath(),errors);
      if(!errors.isEmpty()){
        throw new IOntologyException("Could not open "+uri,getException(errors));
      }
      return new POntology((OWLModel) project.getKnowledgeBase());
    }
    return loadOntology(uri.toURI());
  }
View Full Code Here
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
    if(info.containsKey("driver") || "database".equals(info.get("format"))){
      URI path = getURI();
     
      // load new KB
      KnowledgeBaseFactory factory = new MyOWLDatabaseKnowledgeBaseFactory();
      Project project = Project.createBuildProject(factory, errors);
      if(!errors.isEmpty())
        throw new IOntologyException(""+errors);
      loadNewSources(project, factory);
     
      // load data
      project.createDomainKnowledgeBase(factory, errors, true);
          if(!errors.isEmpty())
        throw new IOntologyException(""+errors);
             
        model = (OWLModel) project.getKnowledgeBase();      
     
          // make sure it is named correctly
          model.getNamespaceManager().setDefaultNamespace(path+"#");
      OWLUtil.renameOntology(model,model.getDefaultOWLOntology(),""+path);
     }else{
      // load regular ontology
      String u = ""+info.get("location");
      File f = new File(u);
      URI path = (f.exists())?f.toURI():URI.create(u);
     
      // check URI path, if doesn't exist simply use URI as location
      if("file".equals(path.getScheme()) && !(new File(path)).exists())
        path = getURI();
     
      if(path.toString().endsWith(".pprj")){
        Project project = Project.loadProjectFromURI(path,errors);
        if(!errors.isEmpty()){
          throw new IOntologyException("Problem loading PPRJ file "+path+"\n",getException(errors));
        }
        model = (OWLModel) project.getKnowledgeBase();
      }else {
        try{
          model = ProtegeOWL.createJenaOWLModelFromURI(""+path);
        }catch(Exception ex){
          throw new IOntologyException("Problem loading OWL file "+path,ex);
View Full Code Here
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
    String prefix="";
    if(getRepository() instanceof ProtegeRepository){
      prefix = ((ProtegeRepository)getRepository()).getOntologyPrefix();
    }
 
    Project currentProject = model.getProject();
    KnowledgeBaseFactory factory = new OWLDatabaseKnowledgeBaseFactory();
       
        // load new source information
        loadNewSources(currentProject, factory);
       
        // check completeness
        if (currentProject.hasCompleteSources()) {
          ArrayList errors = new ArrayList();
            currentProject.setIsReadonly(false);
            currentProject.save(errors);
            if(!errors.isEmpty())
              throw new IOntologyException("problem saving "+getURI(),getException(errors));      
        }
       
        // save included projects
View Full Code Here
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
   */
  public static POntology loadOntology(URI uri) throws IOntologyException{
    POntology ont = null;
    if(uri.toString().endsWith(".pprj")){
      ArrayList errors = new ArrayList();
      Project project = Project.loadProjectFromURI(uri,errors);
      if(!errors.isEmpty()){
        throw new IOntologyException("Problem loading PPRJ file "+uri,getException(errors));
      }
      ont =  new POntology((OWLModel) project.getKnowledgeBase());
    }else {
      try{
        ont = new POntology(ProtegeOWL.createJenaOWLModelFromURI(""+uri));
      }catch(Exception ex){
        throw new IOntologyException("Problem loading OWL file "+uri,ex);
View Full Code Here
336
337
338
339
340
341
342
343
344
345
346
347
348
   */
  public static POntology loadOntology(File uri) throws IOntologyException{
    // check if this is an pprj file
    if(uri.getName().endsWith(".pprj")){
      ArrayList errors = new ArrayList();
      Project project = Project.loadProjectFromFile(uri.getAbsolutePath(),errors);
      if(!errors.isEmpty()){
        throw new IOntologyException("Could not open "+uri,getException(errors));
      }
      return new POntology((OWLModel) project.getKnowledgeBase());
    }
    return loadOntology(uri.toURI());
  }
View Full Code Here
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
    if(info.containsKey("driver") || "database".equals(info.get("format"))){
      URI path = getURI();
     
      // load new KB
      KnowledgeBaseFactory factory = new MyOWLDatabaseKnowledgeBaseFactory();
      Project project = Project.createBuildProject(factory, errors);
      if(!errors.isEmpty())
        throw new IOntologyException(""+errors);
      loadNewSources(project, factory);
     
      // load data
      project.createDomainKnowledgeBase(factory, errors, true);
          if(!errors.isEmpty())
        throw new IOntologyException(""+errors);
             
        model = (OWLModel) project.getKnowledgeBase();      
     
          // make sure it is named correctly
          model.getNamespaceManager().setDefaultNamespace(path+"#");
      OWLUtil.renameOntology(model,model.getDefaultOWLOntology(),""+path);
     }else{
      // load regular ontology
      String u = ""+info.get("location");
      File f = new File(u);
      URI path = (f.exists())?f.toURI():URI.create(u);
     
      // check URI path, if doesn't exist simply use URI as location
      if("file".equals(path.getScheme()) && !(new File(path)).exists())
        path = getURI();
     
      if(path.toString().endsWith(".pprj")){
        Project project = Project.loadProjectFromURI(path,errors);
        if(!errors.isEmpty()){
          throw new IOntologyException("Problem loading PPRJ file "+path+"\n",getException(errors));
        }
        model = (OWLModel) project.getKnowledgeBase();
      }else {
        try{
          model = ProtegeOWL.createJenaOWLModelFromURI(""+path);
        }catch(Exception ex){
          throw new IOntologyException("Problem loading OWL file "+path,ex);
View Full Code Here
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
    String prefix="";
    if(getRepository() instanceof ProtegeRepository){
      prefix = ((ProtegeRepository)getRepository()).getOntologyPrefix();
    }
 
    Project currentProject = model.getProject();
    KnowledgeBaseFactory factory = new OWLDatabaseKnowledgeBaseFactory();
       
        // load new source information
        loadNewSources(currentProject, factory);
       
        // check completeness
        if (currentProject.hasCompleteSources()) {
          ArrayList errors = new ArrayList();
            currentProject.setIsReadonly(false);
            currentProject.save(errors);
            if(!errors.isEmpty())
              throw new IOntologyException("problem saving "+getURI(),getException(errors));      
        }
       
        // save included projects
View Full Code Here
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
        clamlFile = file;
    }

    @Override
    protected Project buildNewProject(KnowledgeBaseFactory factory) {
        Project project = createNewProject(factory);
        if (project != null) {
            try {
                importClamlCM((OWLModel) project.getKnowledgeBase());
                ClamlImport clamlImport = new ClamlImport((OWLModel) project.getKnowledgeBase());
                clamlImport.doImport(clamlFile);
            } catch (Exception ex) {
                Log.getLogger().log(Level.SEVERE, "Exception caught", ex);
                JOptionPane.showMessageDialog(Application.getMainWindow(), "Could not load " + clamlFile.getAbsolutePath() + "\n" + ex, "Error", JOptionPane.ERROR_MESSAGE);
            }
View Full Code Here
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
    return null;
  }
 
  private KnowledgeBase loadProject(URI uri) {
    ArrayList errors = new ArrayList();
    Project project = null;
    try {
      project = Project.loadProjectFromURI(uri, errors); 
    } catch (Exception e) {
      Log.getLogger().log(Level.SEVERE, "Errors at loading " + uri, e);
    }
   
    if (errors.size() > 0) {
      ProjectManager.getProjectManager().displayErrors("Errors at loading project " + uri, errors);
    }
   
    return project == null ? null : project.getKnowledgeBase();
  }
View Full Code Here
TOP

Related Classes of edu.stanford.smi.protege.model.Project

  • edu.mayo.informatics.icd.claml.ICDClaMLLinearizationHierarchicalStructure
  • edu.mayo.informatics.icd.claml.ICDClaMLPanel
  • edu.mayo.informatics.icd.claml.ICDClaMLXMLExporter
  • edu.pitt.dbmi.nlp.noble.ontology.protege.POntology
  • edu.pitt.ontology.protege.POntology
  • edu.stanford.bmir.icd.claml.ClamlCreateProjectPlugin
  • edu.stanford.bmir.icd.claml.ClamlImport
  • edu.stanford.bmir.icd.utils.ICD_API_Example
  • edu.stanford.bmir.protegex.icd.diff.TreeComponent
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.