@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); } }