/** Return a list of all tests of the given type, according to the current filters */
public List<Resource> findTestsOfType(Resource testType) {
ArrayList<Resource> result = new ArrayList<>();
StmtIterator si = testDefinitions.listStatements(null, RDF.type, testType);
while (si.hasNext()) {
Resource test = si.nextStatement().getSubject();
boolean accept = true;
// Check test status
Literal status = (Literal) test.getProperty(RDFTest.status).getObject();
if (approvedOnly) {
accept = status.getString().equals(STATUS_FLAGS[0]);
} else {
accept = false;
for (String STATUS_FLAG : STATUS_FLAGS) {
if (status.getString().equals(STATUS_FLAG)) {
accept = true;
break;
}
}
}
// Check for blocked tests
for (String BLOCKED_TEST : BLOCKED_TESTS) {
if (BLOCKED_TEST.equals(test.toString())) {
accept = false;
}
}
// End of filter tests
if (accept) {
result.add(test);
}
}
return result;
}
@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"));
}
}
/** Converts an ordinal property to an integer. */
public static int getOrd(Resource r) throws ModelException {
if (r == null) return -1;
String uri = r.toString();
if (!isRDF(uri)) return -1;
int pos = getNamespaceEnd(uri);
if (pos > 0 && pos + 1 < uri.length()) {
try {
int n = Integer.parseInt(uri.substring(pos + 1));
if (n >= 1) return n;
} catch (Exception any) {
}
}
return -1;
}
@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() ;
} */
}