Ejemplo n.º 1
0
  @Test
  public void testSparql() {

    String queryStr = "select distinct ?Concept where {[] a ?Concept} LIMIT 10";
    Query query = QueryFactory.create(queryStr);

    // Remote execution.
    try (QueryExecution qexec =
        QueryExecutionFactory.sparqlService("http://dbpedia.org/sparql", query)) {
      // Set the DBpedia specific timeout.
      ((QueryEngineHTTP) qexec).addParam("timeout", "10000");

      // Execute.
      ResultSet rs = qexec.execSelect();
      ResultSetFormatter.out(System.out, rs, query);
    } catch (Exception e) {
      e.printStackTrace();
    }
  }
Ejemplo n.º 2
0
  @Test
  public void testDOQuery2() {

    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 *\n"
            + "from <http://purl.obolibrary.org/obo/merged/DOID>\n"
            + "\n"
            + "WHERE {\n"
            + "   <http://purl.obolibrary.org/obo/DOID_1485> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?o\n"
            + "}";

    Query query = QueryFactory.create(queryString);
    System.out.println("String: " + queryString);
    QueryExecution qExe =
        QueryExecutionFactory.sparqlService("http://sparql.hegroup.org/sparql/", query);
    ResultSet results = qExe.execSelect();
    ResultSetFormatter.out(System.out, results, query);
  }
Ejemplo n.º 3
0
  @Override
  public EntityDefinition open(Assembler a, Resource root, Mode mode) {
    String prologue = "PREFIX : <" + NS + ">   PREFIX list: <http://jena.apache.org/ARQ/list#> ";
    Model model = root.getModel();

    String qs1 =
        StrUtils.strjoinNL(
            prologue,
            "SELECT * {",
            "  ?eMap  :entityField  ?entityField ;",
            "         :map ?map ;",
            "         :defaultField ?dftField .",
            "  OPTIONAL {",
            "    ?eMap :graphField ?graphField",
            "  }",
            "  OPTIONAL {",
            "    ?eMap :langField ?langField",
            "  }",
            "  OPTIONAL {",
            "    ?eMap :uidField ?uidField",
            "  }",
            "}");
    ParameterizedSparqlString pss = new ParameterizedSparqlString(qs1);
    pss.setIri("eMap", root.getURI());

    Query query1 = QueryFactory.create(pss.toString());
    QueryExecution qexec1 = QueryExecutionFactory.create(query1, model);
    ResultSet rs1 = qexec1.execSelect();
    List<QuerySolution> results = ResultSetFormatter.toList(rs1);
    if (results.size() == 0) {
      Log.warn(this, "Failed to find a valid EntityMap for : " + root);
      throw new TextIndexException("Failed to find a valid EntityMap for : " + root);
    }

    if (results.size() != 1) {
      Log.warn(this, "Multiple matches for EntityMap for : " + root);
      throw new TextIndexException("Multiple matches for EntityMap for : " + root);
    }

    QuerySolution qsol1 = results.get(0);
    String entityField = qsol1.getLiteral("entityField").getLexicalForm();
    String graphField =
        qsol1.contains("graphField") ? qsol1.getLiteral("graphField").getLexicalForm() : null;
    String langField =
        qsol1.contains("langField") ? qsol1.getLiteral("langField").getLexicalForm() : null;
    String defaultField =
        qsol1.contains("dftField") ? qsol1.getLiteral("dftField").getLexicalForm() : null;
    String uniqueIdField =
        qsol1.contains("uidField") ? qsol1.getLiteral("uidField").getLexicalForm() : null;

    Multimap<String, Node> mapDefs = HashMultimap.create();
    Map<String, Analyzer> analyzerDefs = new HashMap<>();

    Statement listStmt = root.getProperty(TextVocab.pMap);
    while (listStmt != null) {
      RDFNode n = listStmt.getObject();
      if (!n.isResource()) {
        throw new TextIndexException("Text list node is not a resource : " + n);
      }
      Resource listResource = n.asResource();
      if (listResource.equals(RDF.nil)) {
        break; // end of the list
      }

      Statement listEntryStmt = listResource.getProperty(RDF.first);
      if (listEntryStmt == null) {
        throw new TextIndexException("Text map list is not well formed.  No rdf:first property");
      }
      n = listEntryStmt.getObject();
      if (!n.isResource()) {
        throw new TextIndexException("Text map list entry is not a resource : " + n);
      }
      Resource listEntry = n.asResource();

      Statement fieldStatement = listEntry.getProperty(TextVocab.pField);
      if (fieldStatement == null) {
        throw new TextIndexException("Text map entry has no field property");
      }
      n = fieldStatement.getObject();
      if (!n.isLiteral()) {
        throw new TextIndexException("Text map entry field property has no literal value : " + n);
      }
      String field = n.asLiteral().getLexicalForm();

      Statement predicateStatement = listEntry.getProperty(TextVocab.pPredicate);
      if (predicateStatement == null) {
        throw new TextIndexException("Text map entry has no predicate property");
      }
      n = predicateStatement.getObject();
      if (!n.isURIResource()) {
        throw new TextIndexException(
            "Text map entry predicate property has non resource value : " + n);
      }
      mapDefs.put(field, n.asNode());

      Statement analyzerStatement = listEntry.getProperty(TextVocab.pAnalyzer);
      if (analyzerStatement != null) {
        n = analyzerStatement.getObject();
        if (!n.isResource()) {
          throw new TextIndexException("Text map entry analyzer property is not a resource : " + n);
        }
        Resource analyzerResource = n.asResource();
        Analyzer analyzer = (Analyzer) a.open(analyzerResource);
        analyzerDefs.put(field, analyzer);
      }

      // move on to the next element in the list
      listStmt = listResource.getProperty(RDF.rest);
    }

    // Primary field/predicate
    if (defaultField != null) {
      Collection<Node> c = mapDefs.get(defaultField);
      if (c.isEmpty())
        throw new TextIndexException("No definition of primary field '" + defaultField + "'");
    }

    EntityDefinition docDef = new EntityDefinition(entityField, defaultField);
    docDef.setGraphField(graphField);
    docDef.setLangField(langField);
    docDef.setUidField(uniqueIdField);
    for (String f : mapDefs.keys()) {
      for (Node p : mapDefs.get(f)) docDef.set(f, p);
    }
    for (String f : analyzerDefs.keySet()) {
      docDef.setAnalyzer(f, analyzerDefs.get(f));
    }
    return docDef;
  }
Ejemplo n.º 4
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);
  }
Ejemplo n.º 5
0
  @Test
  public void testWURCS() {

    String ct =
        "RES\n"
            + "1b:b-dglc-HEX-1:5\n"
            + "2s:n-acetyl\n"
            + "3b:b-dglc-HEX-1:5\n"
            + "4s:n-acetyl\n"
            + "5b:b-dman-HEX-1:5\n"
            + "6b:a-dman-HEX-1:5\n"
            + "7b:a-dman-HEX-1:5\n"
            + "8b:a-dman-HEX-1:5\n"
            + "9b:a-dman-HEX-1:5\n"
            + "10b:a-dman-HEX-1:5\n"
            + "LIN\n"
            + "1:1d(2+1)2n\n"
            + "2:1o(4+1)3d\n"
            + "3:3d(2+1)4n\n"
            + "4:3o(4+1)5d\n"
            + "5:5o(3+1)6d\n"
            + "6:6o(2+1)7d\n"
            + "7:5o(6+1)8d\n"
            + "8:8o(3+1)9d\n"
            + "9:8o(6+1)10d\n"
            + "UND\n"
            + "UND1:100.0:100.0\n"
            + "ParentIDs:7|9|10\n"
            + "SubtreeLinkageID1:o(2+1)d\n"
            + "RES\n"
            + "11b:a-dman-HEX-1:5";

    ct = ct.replaceAll("\n", "\\\\n");

    String queryString =
        "PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>\n"
            + "PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>\n"
            + "PREFIX  xsd:  <http://www.w3.org/2001/XMLSchema#>\n"
            + "\n"
            + "SELECT DISTINCT ?Sequence\n"
            + "FROM <http://rdf.glytoucan.org>\n"
            + "FROM <http://rdf.glytoucan.org/sequence/wurcs>\n"
            + "\n"
            + "WHERE {\n"
            + "?SaccharideURI a glycan:saccharide .\n"
            + "?SaccharideURI glycan:has_glycosequence ?GlycanSequenceURI .\n"
            + "?GlycanSequenceURI glycan:has_sequence ?Sequence .\n"
            + "?GlycanSequenceURI glycan:in_carbohydrate_format glycan:carbohydrate_format_wurcs .\n"
            + "?SaccharideURI glycan:has_glycosequence ?FormatGlycoSequenceURI .\n"
            + "?FormatGlycoSequenceURI glycan:in_carbohydrate_format glycan:carbohydrate_format_glycoct .\n"
            + "?FormatGlycoSequenceURI glycan:has_sequence"
            + " \""
            + ct
            + "\""
            + "^^xsd:string ."
            + "}";

    System.out.println("String: " + queryString);

    Query query = QueryFactory.create(queryString);

    QueryExecution qExe =
        QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query);
    ResultSet results = qExe.execSelect();
    ResultSetFormatter.out(System.out, results, query);
  }
Ejemplo n.º 6
0
  @Test
  public void testGlycotoucanCTSearch() {

    List<Structure> structures = Ebean.find(Structure.class).findList();
    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);
        ct = glycan.toGlycoCTCondensed();

        // System.out.println(ct);
        //  }
        // }

        /*String ct = "RES\\n" +
                "1b:a-dgal-HEX-1:5\\n" +
                "2s:n-acetyl\\n" +
                "3b:b-dgal-HEX-1:5\\n" +
                "4b:a-lgal-HEX-1:5|6:d\\n" +
                "5b:a-dgal-HEX-1:5\\n" +
                "6s:n-acetyl\\n" +
                "7b:b-dglc-HEX-1:5\\n" +
                "8s:n-acetyl\\n" +
                "LIN\\n" +
                "1:1d(2+1)2n\\n" +
                "2:1o(3+1)3d\\n" +
                "3:3o(2+1)4d\\n" +
                "4:3o(3+1)5d\\n" +
                "5:5d(2+1)6n\\n" +
                "6:1o(6+1)7d\\n" +
                "7:7d(2+1)8n";

        ct = "RES\n" +
                "1b:b-dglc-HEX-1:5\n" +
                "2s:n-acetyl\n" +
                "3b:b-dglc-HEX-1:5\n" +
                "4s:n-acetyl\n" +
                "5b:b-dman-HEX-1:5\n" +
                "6b:a-dman-HEX-1:5\n" +
                "7b:a-dman-HEX-1:5\n" +
                "8b:a-lgal-HEX-1:5|6:d\n" +
                "LIN\n" +
                "1:1d(2+1)2n\n" +
                "2:1o(4+1)3d\n" +
                "3:3d(2+1)4n\n" +
                "4:3o(4+1)5d\n" +
                "5:5o(3+1)6d\n" +
                "6:5o(6+1)7d\n" +
                "7:1o(6+1)8d\n" +
                "UND\n" +
                "UND1:100.0:100.0\n" +
                "ParentIDs:1|3|5|6|7|8\n" +
                "SubtreeLinkageID1:x(-1+1)x\n" +
                "RES\n" +
                "9b:b-dglc-HEX-1:5\n" +
                "10s:n-acetyl\n" +
                "11b:a-lgal-HEX-1:5|6:d\n" +
                "12b:b-dgal-HEX-1:5\n" +
                "13b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d\n" +
                "14s:n-acetyl\n" +
                "LIN\n" +
                "8:9d(2+1)10n\n" +
                "9:9o(3+1)11d\n" +
                "10:9o(4+1)12d\n" +
                "11:12o(-1+2)13d\n" +
                "12:13d(5+1)14n\n" +
                "UND2:100.0:100.0\n" +
                "ParentIDs:1|3|5|6|7|8\n" +
                "SubtreeLinkageID1:x(-1+1)x\n" +
                "RES\n" +
                "15b:b-dglc-HEX-1:5\n" +
                "16s:n-acetyl\n" +
                "17b:a-lgal-HEX-1:5|6:d\n" +
                "18b:b-dgal-HEX-1:5\n" +
                "LIN\n" +
                "13:15d(2+1)16n\n" +
                "14:15o(3+1)17d\n" +
                "15:15o(4+1)18d\n" +
                "UND3:100.0:100.0\n" +
                "ParentIDs:1|3|5|6|7|8\n" +
                "SubtreeLinkageID1:x(-1+1)x\n" +
                "RES\n" +
                "19b:b-dglc-HEX-1:5\n" +
                "20s:n-acetyl\n" +
                "21b:b-dgal-HEX-1:5\n" +
                "LIN\n" +
                "16:19d(2+1)20n\n" +
                "17:19o(4+1)21d";
                */

        ct = ct.replaceAll("\n", "\\\\n").replaceAll("x\\(", "u\\(").replaceAll("\\)x", "\\)u");
        System.out.println("new ct: " + ct);

        String queryString =
            "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n"
                + "PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>\n"
                + "PREFIX wurcs: <http://www.glycoinfo.org/glyco/owl/wurcs#>\n"
                + "SELECT DISTINCT ?glycan ?c\n"
                + "# FROM <http://rdf.glycoinfo.org/wurcs/0.5.0>\n"
                + "# FROM <http://rdf.glycoinfo.org/wurcs/0.5.0/ms>\n"
                + "WHERE {\n"
                + "  ?glycan a \tglycan:glycosequence ;\n"
                + "\tglycan:in_carbohydrate_format  glycan:carbohydrate_format_glycoct ;\n"
                + "\tglycan:has_sequence\n"
                + "\t\t?c filter(contains(?c, \"RES\\n1b:b-dglc-HEX-1\")) .\n"
                +
                // "\t\t?c filter(contains(?c, \"" + ct + "\" )) .\n" +
                "\n"
                + "  }\n"
                + "  ORDER BY ?glycan\n"
                + "limit 10";

        System.out.println("String: " + queryString + "\t\tID: " + structure.id);

        Query query = QueryFactory.create(queryString);

        QueryExecution qExe =
            QueryExecutionFactory.sparqlService("http://test.ts.glytoucan.org/sparql", query);
        ResultSet results = qExe.execSelect();
        ResultSetFormatter.out(System.out, results, query);
      }
    }
  }