Пример #1
0
  @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"));
    }
  }
Пример #2
0
  @Test
  public void testDO() {
    String doid = "1485";
    String queryString =
        "prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n"
            + "prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n"
            + "prefix owl: <http://www.w3.org/2002/07/owl#>\n"
            + "\n"
            + "select ?s ?p ?o \n"
            + "from <http://purl.obolibrary.org/obo/merged/DOID>\n"
            + "\n"
            + "WHERE {\n"
            + "   <http://purl.obolibrary.org/obo/DOID_"
            + doid
            + "> ?p ?o\n"
            + "}";

    Query query = QueryFactory.create(queryString);
    QueryExecution qExe =
        QueryExecutionFactory.sparqlService("http://sparql.hegroup.org/sparql/", query);
    ResultSet results = qExe.execSelect();
    ResultSetFormatter.out(System.out, results, query);

    assertNotNull(results);

    /*Model model = ModelFactory.createDefaultModel();
    Selector selector = new SimpleSelector(null, model.getProperty("<http://www.geneontology.org/formats/oboInOwl#hasDbXref>"), (RDFNode) null);  // you need to cast the last null as otherwise the method is ambigious
    */

    List<String> dbXref = new ArrayList<>();
    List<String> iao = new ArrayList<>();
    List<String> exactSynonym = new ArrayList<>();
    List<String> alternativeId = new ArrayList<>();
    String diseaseLabel;

    while (results.hasNext()) {
      QuerySolution querySolution = results.nextSolution();

      if (querySolution.get("p").toString().matches("rdfs:label ")) {
        diseaseLabel = querySolution.get("o").toString();
      }

      if (querySolution
          .get("p")
          .toString()
          .matches("http://www.geneontology.org/formats/oboInOwl#hasDbXref")) {
        System.out.println(
            querySolution.get("p").toString() + "   " + querySolution.get("o").toString());
        dbXref.add(querySolution.get("o").toString());
      }

      if (querySolution.get("p").toString().matches("http://purl.obolibrary.org/obo/IAO_0000115")) {
        System.out.println(
            querySolution.get("p").toString() + "   " + querySolution.get("o").toString());
        iao.add(querySolution.get("o").toString());
      }

      if (querySolution
          .get("p")
          .toString()
          .matches("http://www.geneontology.org/formats/oboInOwl#hasExactSynonym")) {
        System.out.println(
            querySolution.get("p").toString() + "   " + querySolution.get("o").toString());
        exactSynonym.add(querySolution.get("o").toString());
      }

      if (querySolution
          .get("p")
          .toString()
          .matches("http://www.geneontology.org/formats/oboInOwl#hasAlternativeId")) {
        System.out.println(
            querySolution.get("p").toString() + "   " + querySolution.get("o").toString());
        alternativeId.add(querySolution.get("o").toString());
      }
    }

    assertNotNull(dbXref);
    assertNotNull(iao);
  }
Пример #3
0
  @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);
    }
  }
Пример #4
0
  @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);
    }
  }