Ejemplo n.º 1
0
 /**
  * Example the conclusions graph for introduction of restrictions which require a comprehension
  * rewrite and declare new (anon) classes for those restrictions.
  */
 public void comprehensionAxioms(Model premises, Model conclusions) {
   // Comprehend all restriction declarations and note them in a map
   Map<Resource, Resource> comprehension = new HashMap<>();
   StmtIterator ri = conclusions.listStatements(null, RDF.type, OWL.Restriction);
   while (ri.hasNext()) {
     Resource restriction = ri.nextStatement().getSubject();
     StmtIterator pi = restriction.listProperties(OWL.onProperty);
     while (pi.hasNext()) {
       Resource prop = (Resource) pi.nextStatement().getObject();
       StmtIterator vi = restriction.listProperties();
       while (vi.hasNext()) {
         Statement rs = vi.nextStatement();
         if (!rs.getPredicate().equals(OWL.onProperty)) {
           // Have a restriction on(prop) of type rs in the conclusions
           // So assert a premise that such a restriction could exisit
           Resource comp =
               premises
                   .createResource()
                   .addProperty(RDF.type, OWL.Restriction)
                   .addProperty(OWL.onProperty, prop)
                   .addProperty(rs.getPredicate(), rs.getObject());
           comprehension.put(restriction, comp);
         }
       }
     }
   }
   // Comprehend any intersectionOf lists. Introduce anon class which has the form
   // of the intersection expression.
   // Rewrite queries of the form (X intersectionOf Y) to the form
   //   (X equivalentClass ?CC) (?CC intersectionOf Y)
   StmtIterator ii = conclusions.listStatements(null, OWL.intersectionOf, (RDFNode) null);
   List<Statement> intersections = new ArrayList<>();
   while (ii.hasNext()) {
     intersections.add(ii.nextStatement());
   }
   for (Statement is : intersections) {
     // Declare in the premises that such an intersection exists
     Resource comp =
         premises
             .createResource()
             .addProperty(RDF.type, OWL.Class)
             .addProperty(
                 OWL.intersectionOf, mapList(premises, (Resource) is.getObject(), comprehension));
     // Rewrite the conclusions to be a test for equivalence between the class being
     // queried and the comprehended interesection
     conclusions.remove(is);
     conclusions.add(is.getSubject(), OWL.equivalentClass, comp);
   }
   // Comprehend any oneOf lists
   StmtIterator io = conclusions.listStatements(null, OWL.oneOf, (RDFNode) null);
   while (io.hasNext()) {
     Statement s = io.nextStatement();
     Resource comp = premises.createResource().addProperty(OWL.oneOf, s.getObject());
   }
 }
Ejemplo n.º 2
0
  public static String RenderTemplatePage(Bindings b, String templateName) throws IOException {

    MediaType mt = MediaType.TEXT_HTML;
    Resource config = model.createResource("eh:/root");
    Mode prefixMode = Mode.PreferPrefixes;
    ShortnameService sns = new StandardShortnameService();

    List<Resource> noResults = CollectionUtils.list(root.inModel(model));
    Graph resultGraph = graphModel.getGraph();

    resultGraph.getPrefixMapping().setNsPrefix("api", API.NS);
    resultGraph.add(Triple.create(root.asNode(), API.items.asNode(), RDF.nil.asNode()));

    APIResultSet rs = new APIResultSet(resultGraph, noResults, true, true, "details", View.ALL);
    VelocityRenderer vr = new VelocityRenderer(mt, null, config, prefixMode, sns);

    VelocityRendering vx = new VelocityRendering(b, rs, vr);

    VelocityEngine ve = vx.createVelocityEngine();
    VelocityContext vc = vx.createVelocityContext(b);

    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    Writer w = new OutputStreamWriter(bos, "UTF-8");
    Template t = ve.getTemplate(templateName);

    t.merge(vc, w);
    w.close();

    return bos.toString();
  }
Ejemplo n.º 3
0
 /**
  * Helper. Adds to the target model a translation of the given RDF list with each element replaced
  * according to the map.
  */
 private Resource mapList(Model target, Resource list, Map<Resource, Resource> map) {
   if (list.equals(RDF.nil)) {
     return RDF.nil;
   } else {
     Resource head = (Resource) list.getRequiredProperty(RDF.first).getObject();
     Resource rest = (Resource) list.getRequiredProperty(RDF.rest).getObject();
     Resource mapElt = target.createResource();
     Resource mapHead = map.get(head);
     if (mapHead == null) mapHead = head;
     mapElt.addProperty(RDF.first, mapHead);
     mapElt.addProperty(RDF.rest, mapList(target, rest, map));
     return mapElt;
   }
 }
Ejemplo n.º 4
0
 /** Initialize the result model. */
 public void initResults() {
   testResults = ModelFactory.createDefaultModel();
   jena2 = testResults.createResource(BASE_RESULTS_URI + "#jena2");
   jena2.addProperty(
       RDFS.comment,
       testResults.createLiteral(
           "<a xmlns=\"http://www.w3.org/1999/xhtml\" href=\"http://jena.sourceforce.net/\">Jena2</a> includes a rule-based inference engine for RDF processing, "
               + "supporting both forward and backward chaining rules. Its OWL rule set is designed to provide sound "
               + "but not complete instance resasoning for that fragment of OWL/Full limited to the OWL/lite vocabulary. In"
               + "particular it does not support unionOf/complementOf.",
           true));
   jena2.addProperty(RDFS.label, "Jena2");
   testResults.setNsPrefix("results", OWLResults.NS);
 }
Ejemplo n.º 5
0
 /** Run a single test of any sort, performing any appropriate logging and error reporting. */
 public void runTest(Resource test) {
   System.out.println("Running " + test);
   boolean success = false;
   boolean fail = false;
   try {
     success = doRunTest(test);
   } catch (Exception e) {
     fail = true;
     System.out.print("\nException: " + e);
     e.printStackTrace();
   }
   testCount++;
   if (success) {
     System.out.print((testCount % 40 == 0) ? ".\n" : ".");
     System.out.flush();
     passCount++;
   } else {
     System.out.println("\nFAIL: " + test);
   }
   Resource resultType = null;
   if (fail) {
     resultType = OWLResults.FailingRun;
   } else {
     if (test.hasProperty(RDF.type, OWLTest.NegativeEntailmentTest)
         || test.hasProperty(RDF.type, OWLTest.ConsistencyTest)) {
       resultType = success ? OWLResults.PassingRun : OWLResults.FailingRun;
     } else {
       resultType = success ? OWLResults.PassingRun : OWLResults.IncompleteRun;
     }
   }
   // log to the rdf result format
   Resource result =
       testResults
           .createResource()
           .addProperty(RDF.type, OWLResults.TestRun)
           .addProperty(RDF.type, resultType)
           .addProperty(OWLResults.test, test)
           .addProperty(OWLResults.system, jena2);
 }
  /**
   * agINFRA Social visualization components aux. tool
   *
   * @param args
   * @throws FileNotFoundException
   */
  public static void main(String[] args) throws FileNotFoundException {

    System.out.println("Hello");

    // PARAMS
    if (args.length != 5) {
      System.out.println(
          "Proper Arguments are: [Dataset files full path] [URL store] [URI graph base] [Destination directory] [commit to 4store]");
      System.out.println(
          "Example: java -jar xxxxx.jar /home/carlos/Desktop/agINFRA-workflow/workflow/loms/bioe/ http://localhost:81 http://laclo.laflor /home/carlos/Desktop/agINFRA-workflow/workflow/loms/bioerdf/ false");
      System.exit(0);
    }

    String dspath = args[0];
    String urlStore = args[1];
    String uriGraph = args[2];
    String destination = args[3];
    String commit4store_arg = args[4];

    /*String dspath = "/home/carlos/workspace/WebAPI/ds/";
    String urlStore = "http://4store.ipb.ac.rs:81";
    String uriGraph = "http://aginfra.eu";
    String localCouchdbProxy = "localhost";
    String commit4store_arg = "no";*/

    boolean commit4store = false;
    if (commit4store_arg.equals("commit")) commit4store = true;

    String output = "0"; // valor de retorno
    String status = "ERROR";
    String errorDescription = "";
    String tmpMetadataFile = "";
    // check if type is valid
    boolean bContinuar = true;
    // StorageService service;
    ArrayList<KeyValue> keyValues = new ArrayList<KeyValue>();
    HashMap fileDatasetMap = new HashMap();

    /*
    //Fetch and download IPB metadata sets.
    //CouchDB via PHP local proxy
    //http://agro.ipb.ac.rs/agcouchdb/_design/datasets/_view/list?limit=10
    //http://localhost/ag_couch_proxy/proxy-IPB-datasets.php
    try{
    	System.out.println("Connecting IPB CouchDB...");

    	String url = "http://"+localCouchdbProxy+"/ag_couch_proxy/proxy-IPB-datasets.php?dspath="+dspath;
    	WebResource webResource = Client.create().resource(url);
    	//System.out.println(url);
    	ClientResponse response = webResource.accept(MediaType.APPLICATION_JSON,MediaType.TEXT_HTML,MediaType.WILDCARD).get(ClientResponse.class);
    	if (response.getStatus() != 200) {
    	   throw new RuntimeException("Failed : HTTP error code : " + response.getStatus());
    	}


    	//String response_str = response.getEntity(String.class);	//I don't know why this does not work when running in shell
    	String response_str = getStringFromInputStream(response.getEntityInputStream());
    	//System.out.println(response_str);	//debug

    	System.out.println("Finished IPB call");



    	System.out.println("Reading Dataset Map...");

    	//READ CSV
    	//create BufferedReader to read csv file
              StringTokenizer st = null;
              int lineNumber = 0, tokenNumber = 0;

              //read comma separated file line by line
              Scanner scanner = new Scanner(response_str);
              while (scanner.hasNextLine())
              {
                      lineNumber++;
                      String strLine = scanner.nextLine();

                      //break comma separated line using ","
                      st = new StringTokenizer(strLine, ",");

                      String datasetFile = "";
                      String datasetName = "";

                      while(st.hasMoreTokens())
                      {
                              //display csv values
                              tokenNumber++;
                              //System.out.println("Line # " + lineNumber +", Token # " + tokenNumber + ", Token : "+ st.nextToken());
                              if(tokenNumber == 1)
                              	datasetFile = st.nextToken();
                              if(tokenNumber == 2)
                              	datasetName = st.nextToken();
                      }

                      fileDatasetMap.put(datasetFile,datasetName);

                      //reset token number
                      tokenNumber = 0;

              }

              System.out.println("Finished Map reading");

    } catch (Exception e) {
    	e.printStackTrace();
    }
    */

    /*
    //foreach dataset.tar.gz **
    //Iterate
    File root = new File("ds/");
    Collection files = FileUtils.listFiles(root, null, false);

    //mini db processed files
    ArrayList processed = new ArrayList();
          try {
          	BufferedReader br = new BufferedReader(new FileReader("processed.txt"));
              String line;
          	while((line = br.readLine()) != null) {
          		processed.add(line);
    	}
    } catch (IOException e) {
    	e.printStackTrace();
    }

    System.out.println("Iterating all downloaded datasets tgz files...");
    int dsCount = 0;

    for (Iterator iterator = files.iterator(); iterator.hasNext();) {
    	File dsFile = (File) iterator.next();
    	String inputDataset = dsFile.getAbsolutePath();

    	dsCount = dsCount + 1;
    	System.out.println("  Processing "+dsCount+":"+inputDataset);	//debug

    	//po5i: mini db processed files
    	if(processed.contains(inputDataset)){
    		System.out.println("    >>Already processed... skipping... ");
    		continue;
    	}
    	else
    	{
    		processed.add(inputDataset);
    		try {
    			FileWriter fileWritter = new FileWriter("processed.txt",true);
    			BufferedWriter bufferWritter = new BufferedWriter(fileWritter);
       	        bufferWritter.write(inputDataset+"\n");
       	        bufferWritter.close();
    		} catch (IOException e) {
    			e.printStackTrace();
    		}
    	}

    	//Set the GraphID
    	String graphID = (String) fileDatasetMap.get(dsFile.getName());
    	System.out.println("    Graph:: "+graphID);



    	//Uncompress the dataset and iterate throughout the files
    	try {
    		FileInputStream fin = new FileInputStream(inputDataset);
    		BufferedInputStream in = new BufferedInputStream(fin);
    		FileOutputStream out = new FileOutputStream("ds/archive.tar");
    		GzipCompressorInputStream gzIn;
    		gzIn = new GzipCompressorInputStream(in);
    		final byte[] buffer = new byte[1024];
    		int n = 0;
    		while (-1 != (n = gzIn.read(buffer))) {
    		    out.write(buffer, 0, n);
    		}
    		out.close();
    		gzIn.close();

    		//read the tar
    		File input = new File("ds/archive.tar"); //getFile("ds/archive.tar");
            InputStream is = new FileInputStream(input);
            ArchiveInputStream in1 = new ArchiveStreamFactory().createArchiveInputStream("tar", is);
            TarArchiveEntry entry = (TarArchiveEntry)in1.getNextEntry();

            while (entry != null) {// create a file with the same name as the tarEntry
                File destPath = new File("ds/extract/" + entry.getName());
                if (entry.isDirectory()) {
                    destPath.mkdirs();
                } else {
                    destPath.createNewFile();
                    OutputStream out1 = new FileOutputStream(destPath);
                    IOUtils.copy(in1, out1);
                    out1.close();
                }
                entry = (TarArchiveEntry)in1.getNextEntry();
            }

            in1.close();
    	} catch (Exception e) {
    		e.printStackTrace();
    	}*/

    // Iterate on extracted files
    try {
      File root1 = new File(dspath);
      Collection files1 = FileUtils.listFiles(root1, null, true);
      // new File(dspath+"../rdf").mkdir();

      for (Iterator iterator1 = files1.iterator(); iterator1.hasNext(); ) {
        File lomFile = (File) iterator1.next();
        String inputFile = lomFile.getAbsolutePath();

        // System.out.println("      Processing:"+inputFile);	//debug

        if (bContinuar) {
          // save metadata stream in a local file
          tmpMetadataFile = inputFile;
          String valid = "1";
          // valid = XMLValidator.validate(tmpMetadataFile,
          //		StorageService.getXSDFile(storageType));
          boolean hasSource = false;
          if (tmpMetadataFile.length() > 0) {
            // TODO: metadata validation
            // valid = "1";
            if (valid.equalsIgnoreCase("1")) {
              // generate id for the new material

              // output = graphID;
              // save metatada in rdf
              // obtain key-value pairs
              try {
                LOMParser.parseToKeyValue(tmpMetadataFile);
                if (!LOMParser.keyValues.isEmpty()) {
                  keyValues = LOMParser.keyValues;
                }
              } catch (MalformedURLException e1) {
                e1.printStackTrace();
              } catch (IOException e1) {
                e1.printStackTrace();
              }

              if (!keyValues.isEmpty()) {

                int canSave = 1;

                if (canSave > 0) {

                  // 4store
                  // save to rdf this triple (slow)
                  // HandleGraph graph = new HandleGraph(urlStore,uriGraph);
                  // result = graph.AppendTriple(graphID, keyValues);

                  // 4store
                  // prepare RDF file (better)
                  try {
                    // HELP: http://www.roseindia.net/tutorials/rdf/generateRDF.shtml

                    Model model = ModelFactory.createDefaultModel();

                    for (KeyValue kv : keyValues) {
                      String s = uriGraph + "/" + lomFile.getName();
                      // String p = URLEncoder.encode(kv.getKey(),"UTF-8");
                      String p = kv.getKey().replaceAll("[^\\w\\s\\.]", "_");
                      String v = kv.getValue();

                      // obtener el autor del CDATA en variable v
                      if (v.contains("CDATA")) {
                        v = v.replace("<![CDATA[", "");
                        v = v.replace("]]>", "");

                        VCardEngine vcardEngine = new VCardEngine();
                        VCard vcard = vcardEngine.parse(v);
                        if (vcard.hasFN()) v = vcard.getFN().getFormattedName();
                        else if (vcard.hasN()) v = vcard.getN().getFamilyName();
                        else {
                          // format string it can be parsed.

                          StringBuffer sb;
                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("VERSION:"), "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf(" FN:") + 1, "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf(" N:") + 1, "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("ORG:"), "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("EMAIL:"), "\n");
                          v = sb.toString();

                          sb = new StringBuffer(v);
                          sb.insert(v.indexOf("END:"), "\n");
                          v = sb.toString();

                          vcard = vcardEngine.parse(v);
                          if (vcard.hasFN()) v = vcard.getFN().getFormattedName();
                          else if (vcard.hasN()) v = vcard.getN().getFamilyName();
                          else {
                            System.out.println(" ~ ~ Problem with:::" + v);
                            System.out.println(" ~ ~ When Processing:" + inputFile); // debug
                          }

                          // System.out.println(" ~ author is: "+v);
                        }
                      }

                      // System.out.println("p: "+p+"\t\t\t v: "+v);

                      Property lom_prop = model.createProperty("http://ltsc.ieee.org/xsd/LOM#" + p);
                      Resource node = model.createResource(s).addProperty(lom_prop, v);
                    }

                    FileOutputStream fop = null;
                    File rdfFile =
                        new File(destination + lomFile.getName().replace(".xml", ".rdf"));
                    fop = new FileOutputStream(rdfFile);

                    // model.write(System.out);
                    model.write(fop);

                    // 4store
                    if (commit4store) {
                      HandleGraph graph = new HandleGraph(urlStore, uriGraph);
                      int result = graph.AppendGraph(rdfFile.getAbsolutePath()); // returns 0-1
                    }

                  } catch (Exception e) {
                    e.printStackTrace();
                  }
                  // break;	//debug

                }
                output = "1";
              } else {
                output = "0";
                errorDescription = "Could not handle metadata to key-value";
              }

            } else {
              errorDescription = "XML Validation:" + valid;
            }
          } else {
            errorDescription = "Could not handle metadata file";
          }
        }
      }
    } catch (Exception e) {
      e.printStackTrace();
    }

    /*//break;	//debug

    			//Borrar todo lo de ds/extract/, rdf y el archive.tar para liberar espacio
    			try {
    				FileUtils.deleteDirectory(new File("ds/extract/"));
    				FileUtils.deleteDirectory(new File("ds/rdf/"));
    				FileUtils.deleteQuietly(new File("ds/archive.tar"));

    			} catch (IOException e) {
    				e.printStackTrace();
    			}

    		}
    */

    // prepare response
    if (output.contentEquals("0")) status = "ERROR: " + errorDescription;
    else status = "OK";

    System.out.println(status);
  }