Beispiel #1
0
  /** returns the literal value of the node reachable from subject via predicate */
  public static String getObjectLiteral(Model r, Resource subject, Resource predicate)
      throws ModelException {

    RDFNode obj = getObject(r, subject, predicate);
    if (obj instanceof Literal) return obj.toString();
    else return null;
  }
  /**
   * Query SPARQL endpoint with a SELECT query
   *
   * @param qExec QueryExecution encapsulating the query
   * @return model retrieved by querying the endpoint
   */
  private Model getSelectModel(QueryExecution qExec) {
    Model model = ModelFactory.createDefaultModel();
    Graph graph = model.getGraph();
    ResultSet results = qExec.execSelect();

    while (results.hasNext()) {
      QuerySolution sol = results.next();
      String subject;
      String predicate;
      RDFNode object;

      try {
        subject = sol.getResource("s").toString();
        predicate = sol.getResource("p").toString();
        object = sol.get("o");
      } catch (NoSuchElementException e) {
        logger.error("SELECT query does not return a (?s ?p ?o) Triple");
        continue;
      }

      Node objNode;
      if (object.isLiteral()) {
        Literal obj = object.asLiteral();
        objNode = NodeFactory.createLiteral(obj.getString(), obj.getDatatype());
      } else {
        objNode = NodeFactory.createLiteral(object.toString());
      }

      graph.add(
          new Triple(NodeFactory.createURI(subject), NodeFactory.createURI(predicate), objNode));
    }

    return model;
  }
Beispiel #3
0
  public static void main(String args[]) {

    OntModel m = ModelFactory.createOntologyModel();
    OntDocumentManager dm = m.getDocumentManager();
    dm.addAltEntry(
        "http://www.eswc2006.org/technologies/ontology",
        "file:" + JENA + "src/examples/resources/eswc-2006-09-21.rdf");
    m.read("http://www.eswc2006.org/technologies/ontology");

    // create an empty model
    Model model = ModelFactory.createDefaultModel();

    // create the resource
    Resource johnSmith = model.createResource(personURI);

    // add the property
    johnSmith.addProperty(VCARD.FN, fullName);

    johnSmith.addProperty(
        VCARD.N,
        model.createResource().addProperty(VCARD.Given, "jon").addProperty(VCARD.Family, "Smit"));

    // list the statements in the Model
    StmtIterator iter = model.listStatements();

    // print out the predicate, subject and object of each statement
    while (iter.hasNext()) {
      Statement stmt = iter.nextStatement(); // get next statement
      Resource subject = stmt.getSubject(); // get the subject
      Property predicate = stmt.getPredicate(); // get the predicate
      RDFNode object = stmt.getObject(); // get the object

      System.out.print(subject.toString());
      System.out.print(" " + predicate.toString() + " ");
      if (object instanceof Resource) {
        System.out.print(object.toString());
      } else {
        // object is a literal
        System.out.print(" \"" + object.toString() + "\"");
      }

      System.out.println(" .");
    }
  }
 public Collection<URI> getSupportedFacets(URI needUri) throws NoSuchNeedException {
   List<URI> ret = new LinkedList<URI>();
   Need need = DataAccessUtils.loadNeed(needRepository, needUri);
   Model content = rdfStorageService.loadContent(need);
   if (content == null) return ret;
   Resource baseRes = content.getResource(content.getNsPrefixURI(""));
   StmtIterator stmtIterator = baseRes.listProperties(WON.HAS_FACET);
   while (stmtIterator.hasNext()) {
     RDFNode object = stmtIterator.nextStatement().getObject();
     if (object.isURIResource()) {
       ret.add(URI.create(object.toString()));
     }
   }
   return ret;
 }
  @Test
  public void testSelectToWurcsSparql() throws SparqlException, UnsupportedEncodingException {
    GlycoSequenceToWurcsSelectSparql s = new GlycoSequenceToWurcsSelectSparql("glycoct");
    SparqlEntity se = new SparqlEntity();
    se.setValue(
        GlycoSequenceToWurcsSelectSparql.FromSequence,
        "RES\n1b:a-dgal-HEX-1:5\n2s:n-acetyl\n3b:b-dgal-HEX-1:5\n4b:b-dglc-HEX-1:5\n5s:n-acetyl\n6b:b-dgal-HEX-1:5\n7b:a-lgal-HEX-1:5|6:d\n8b:b-dglc-HEX-1:5\n9s:n-acetyl\n10b:b-dglc-HEX-1:5\n11s:n-acetyl\n12b:b-dgal-HEX-1:5\n13b:a-lgal-HEX-1:5|6:d\nLIN\n1:1d(2+1)2n\n2:1o(3+1)3d\n3:3o(3+1)4d\n4:4d(2+1)5n\n5:4o(4+1)6d\n6:6o(2+1)7d\n7:3o(6+1)8d\n8:8d(2+1)9n\n9:1o(6+1)10d\n10:10d(2+1)11n\n11:10o(4+1)12d\n12:12o(2+1)13d"
            .replaceAll("\n", "\\\\n"));
    s.setSparqlEntity(se);
    logger.debug(s.getSparql());
    Query query =
        QueryFactory.create(s.getSparql().replaceAll("null", "").replace("?Sequence", ""));
    //        QueryExecution qe =
    // QueryExecutionFactory.sparqlService("http://localhost:3030/glycobase/query",query);
    QueryExecution qe =
        QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query);
    ResultSet rs = qe.execSelect();

    List<SparqlEntity> results = new ArrayList<SparqlEntity>();

    while (rs.hasNext()) {
      QuerySolution row = rs.next();
      Iterator<String> columns = row.varNames();
      SparqlEntity se2 = new SparqlEntity();
      while (columns.hasNext()) {
        String column = columns.next();
        RDFNode cell = row.get(column);

        if (cell.isResource()) {
          Resource resource = cell.asResource();
          // do something maybe with the OntModel???
          if (resource.isLiteral()) se.setValue(column, resource.asLiteral().getString());
          else se.setValue(column, resource.toString());
        } else if (cell.isLiteral()) {
          se.setValue(column, cell.asLiteral().getString());
        } else if (cell.isAnon()) {
          se.setValue(column, "anon");
        } else {
          se.setValue(column, cell.toString());
        }
      }
      results.add(se);
    }

    for (SparqlEntity entity : results) {
      System.out.println("results: " + entity.getValue("PrimaryId"));
    }
  }
  @Test
  public void testKBtoWurcsSparqlTranslation() throws SparqlException {

    List<Translation> translations = Ebean.find(Translation.class).findList();
    HashSet<String> resultList = new HashSet<>();

    String ct = "";

    for (Translation translation : translations) {
      System.out.println("id check " + translation.id + " ct " + translation.ct);
      if (translation.ct == null) continue;

      if (translation.structure.id > 0) {

        ct = translation.ct;

        GlycoSequenceToWurcsSelectSparql s = new GlycoSequenceToWurcsSelectSparql("glycoct");
        SparqlEntity se = new SparqlEntity();
        ct = StringUtils.chomp(ct);
        System.out.println("ct on top: " + ct);
        if (ct != null) {
          se.setValue(
              GlycoSequenceToWurcsSelectSparql.FromSequence,
              ct.replaceAll("\n", "\\\\n")
                  .replaceAll("x\\(", "u\\(")
                  .replaceAll("\\)x", "\\)u")
                  .trim());
          s.setSparqlEntity(se);
          logger.debug(s.getSparql());

          Query query =
              QueryFactory.create(s.getSparql().replaceAll("null", "").replace("?Sequence", ""));
          System.out.println(
              "Id "
                  + translation.structure.id
                  + " Query: "
                  + s.getSparql().replaceAll("null", "").replace("?Sequence", ""));
          QueryExecution qe =
              QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query);
          ResultSet rs = qe.execSelect();

          List<SparqlEntity> results = new ArrayList<>();
          HashSet<String> resultsList = new HashSet<>();

          while (rs.hasNext()) {
            QuerySolution row = rs.next();
            Iterator<String> columns = row.varNames();
            SparqlEntity se2 = new SparqlEntity();
            while (columns.hasNext()) {
              String column = columns.next();
              RDFNode cell = row.get(column);

              if (cell.isResource()) {
                Resource resource = cell.asResource();
                // do something maybe with the OntModel???
                if (resource.isLiteral()) se.setValue(column, resource.asLiteral().getString());
                else se.setValue(column, resource.toString());
              } else if (cell.isLiteral()) {
                se.setValue(column, cell.asLiteral().getString());
              } else if (cell.isAnon()) {
                se.setValue(column, "anon");
              } else {
                se.setValue(column, cell.toString());
              }
            }
            results.add(se);
          }

          for (SparqlEntity entity : results) {
            // System.out.println("results: " + entity.getValue("PrimaryId"));
            resultList.add(
                translation.structure.id + "\t" + entity.getValue("PrimaryId").toString());
          }
        }
      }
    }

    for (String c : resultList) {
      System.out.println(c);
    }
  }
  @Test
  public void testKBtoWurcsSparql() throws SparqlException {

    List<Structure> structures = Ebean.find(Structure.class).findList();
    HashSet<String> resultList = new HashSet<>();

    String ct = "";

    for (Structure structure : structures) {
      if (structure.id >= 7400) {

        if (structure.glycanst.startsWith("v--")) {
          structure.glycanst = structure.glycanst.replace("v--", "FreeEnd--");
        }

        if (structure.glycanst.startsWith("FreenEnd")) {
          structure.glycanst = structure.glycanst.replace("FreenEnd", "FreeEnd");
        }

        if (structure.glycanst.startsWith("FreeEnd?")) {
          structure.glycanst = structure.glycanst.replace("FreeEnd?", "FreeEnd--?");
        }

        if (structure.glycanst.startsWith("<Gly") || structure.glycanst.contains("0.0000u")) {
          continue;
        }

        System.out.println(structure.getGlycanst());

        BuilderWorkspace workspace = new BuilderWorkspace(new GlycanRendererAWT());
        workspace.setNotation("cfg"); // cfgbw | uoxf | uoxfcol | text
        GlycanRenderer renderer = workspace.getGlycanRenderer();
        org.eurocarbdb.application.glycanbuilder.Glycan glycan =
            org.eurocarbdb.application.glycanbuilder.Glycan.fromString(structure.glycanst.trim());
        if (glycan != null) {
          ct = glycan.toGlycoCTCondensed();
          System.out.println("this was the ct: " + ct);
          GlycoSequenceToWurcsSelectSparql s = new GlycoSequenceToWurcsSelectSparql("glycoct");
          SparqlEntity se = new SparqlEntity();
          ct = StringUtils.chomp(ct);
          se.setValue(
              GlycoSequenceToWurcsSelectSparql.FromSequence,
              ct.replaceAll("\n", "\\\\n")
                  .replaceAll("x\\(", "u\\(")
                  .replaceAll("\\)x", "\\)u")
                  .trim());
          s.setSparqlEntity(se);
          logger.debug(s.getSparql());

          Query query =
              QueryFactory.create(s.getSparql().replaceAll("null", "").replace("?Sequence", ""));
          System.out.println(
              "Id "
                  + structure.id
                  + " Query: "
                  + s.getSparql().replaceAll("null", "").replace("?Sequence", ""));
          QueryExecution qe =
              QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query);
          ResultSet rs = qe.execSelect();

          List<SparqlEntity> results = new ArrayList<>();
          HashSet<String> resultsList = new HashSet<>();

          while (rs.hasNext()) {
            QuerySolution row = rs.next();
            Iterator<String> columns = row.varNames();
            SparqlEntity se2 = new SparqlEntity();
            while (columns.hasNext()) {
              String column = columns.next();
              RDFNode cell = row.get(column);

              if (cell.isResource()) {
                Resource resource = cell.asResource();
                // do something maybe with the OntModel???
                if (resource.isLiteral()) se.setValue(column, resource.asLiteral().getString());
                else se.setValue(column, resource.toString());
              } else if (cell.isLiteral()) {
                se.setValue(column, cell.asLiteral().getString());
              } else if (cell.isAnon()) {
                se.setValue(column, "anon");
              } else {
                se.setValue(column, cell.toString());
              }
            }
            results.add(se);
          }

          for (SparqlEntity entity : results) {
            // System.out.println("results: " + entity.getValue("PrimaryId"));
            resultList.add(structure.id + "\t" + entity.getValue("PrimaryId").toString());
          }
        }
      }
    }
    PrintWriter writer = null;
    try {
      writer =
          new PrintWriter(
              new OutputStreamWriter(new FileOutputStream("/tmp/HashSet.txt"), "UTF-8"));
    } catch (UnsupportedEncodingException e) {
      e.printStackTrace();
    } catch (FileNotFoundException e) {
      e.printStackTrace();
    }
    for (String c : resultList) {
      System.out.println(c);
      writer.println(c);
    }
  }
  public static void main(String[] args) {

    List<String> obj = new ArrayList<String>();

    Scanner input = new Scanner(System.in);

    System.out.print("Enter URI: ");

    String userIn = input.nextLine();

    // create an empty Model
    Model model = ModelFactory.createDefaultModel();

    // read the RDF/XML file
    model.read(userIn);

    // write it to standard out
    // model.write(System.out);

    // list the statements in the Model
    StmtIterator iter = model.listStatements();

    System.out.println();

    // print out the predicate, subject and object of each statement
    while (iter.hasNext()) {
      Statement stmt = iter.nextStatement(); // get next statement
      Resource subject = stmt.getSubject(); // get the subject
      Property predicate = stmt.getPredicate(); // get the predicate
      RDFNode object = stmt.getObject(); // get the object

      System.out.print(subject.toString());
      System.out.print(" -> " + predicate.toString() + " -> ");
      if (object instanceof Resource) {
        System.out.print(object.toString() + "\n");
      } else {
        // object is a literal
        System.out.print(" \"" + object.toString() + "\"\n");
      }
    }

    /* for(int i = 0; i < (obj.size()); i++){

    	String sparqlQueryString1=
    								"SELECT ?s ?o "+
    								"WHERE {"+
    								"?s ?p ?o ."+
    								"?o <bif:contains> \""+obj.get(i)+"\" ."+
    								"}"+
    								"limit 10";

    		      Query query = QueryFactory.create(sparqlQueryString1);
    		      QueryExecution qexec = QueryExecutionFactory.sparqlService("http://pubmed.bio2rdf.org/sparql", query);

    		      ResultSet results = qexec.execSelect();
    		      System.out.println("Query: "+obj.get(i));
    		      ResultSetFormatter.out(System.out, results, query);

    		     qexec.close() ;
    } */

  }