/**
* 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;
}
/**
* Builds a String result for Elastic Search from an RDFNode
*
* @param node An RDFNode representing the value of a property for a given resource
* @return If the RDFNode has a Literal value, among Boolean, Byte, Double, Float, Integer Long,
* Short, this value is returned, converted to String
* <p>If the RDFNode has a String Literal value, this value will be returned, surrounded by
* double quotes
* <p>If the RDFNode has a Resource value (URI) and toDescribeURIs is set to true, the value
* of @getLabelForUri for the resource is returned, surrounded by double quotes. Otherwise,
* the URI will be returned
*/
private String getStringForResult(RDFNode node, boolean getNodeLabel) {
String result = "";
boolean quote = false;
if (node.isLiteral()) {
Object literalValue = node.asLiteral().getValue();
try {
Class<?> literalJavaClass = node.asLiteral().getDatatype().getJavaClass();
if (literalJavaClass.equals(Boolean.class)
|| Number.class.isAssignableFrom(literalJavaClass)) {
result += literalValue;
} else {
result = EEASettings.parseForJson(node.asLiteral().getLexicalForm());
quote = true;
}
} catch (java.lang.NullPointerException npe) {
result = EEASettings.parseForJson(node.asLiteral().getLexicalForm());
quote = true;
}
} else if (node.isResource()) {
result = node.asResource().getURI();
if (getNodeLabel) {
result = getLabelForUri(result);
}
quote = true;
}
if (quote) {
result = "\"" + result + "\"";
}
return result;
}
/**
* Answer the string described by the value of the unique optional <code>classProperty</code>
* property of <code>root</code>, or null if there's no such property. The value may be a URI, in
* which case it must be a <b>java:</b> URI with content the class name; or it may be a literal,
* in which case its lexical form is its class name; otherwise, BOOM.
*/
public static String getOptionalClassName(Resource root, Property classProperty) {
RDFNode classNode = getUnique(root, classProperty);
return classNode == null
? null
: classNode.isLiteral()
? classNode.asNode().getLiteralLexicalForm()
: classNode.isResource() ? mustBeJava(classNode.asNode().getURI()) : null;
}
@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"));
}
}
@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;
}
@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);
}
}
/**
* Get JSON map for a given resource by applying the river settings
*
* @param rs resource being processed
* @param properties properties to be indexed
* @param model model returned by the indexing query
* @param getPropLabel if set to true all URI property values will be indexed as their label. The
* label is taken as the value of one of the properties set in {@link #uriDescriptionList}.
* @return map of properties to be indexed for res
*/
private Map<String, ArrayList<String>> getJsonMap(
Resource rs, Set<Property> properties, Model model, boolean getPropLabel) {
Map<String, ArrayList<String>> jsonMap = new HashMap<String, ArrayList<String>>();
ArrayList<String> results = new ArrayList<String>();
if (addUriForResource) {
results.add("\"" + rs.toString() + "\"");
jsonMap.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#about", results);
}
Set<String> rdfLanguages = new HashSet<String>();
for (Property prop : properties) {
NodeIterator niter = model.listObjectsOfProperty(rs, prop);
String property = prop.toString();
results = new ArrayList<String>();
String lang;
String currValue;
while (niter.hasNext()) {
RDFNode node = niter.next();
currValue = getStringForResult(node, getPropLabel);
if (addLanguage) {
if (node.isLiteral()) {
lang = node.asLiteral().getLanguage();
if (!lang.isEmpty()) {
rdfLanguages.add("\"" + lang + "\"");
}
}
}
String shortValue = currValue;
int currLen = currValue.length();
// Unquote string
if (currLen > 1) shortValue = currValue.substring(1, currLen - 1);
// If either whiteMap does contains shortValue
// or blackMap contains the value
// skip adding it to the index
boolean whiteMapCond =
whiteMap.containsKey(property) && !whiteMap.get(property).contains(shortValue);
boolean blackMapCond =
blackMap.containsKey(property) && blackMap.get(property).contains(shortValue);
if (whiteMapCond || blackMapCond) {
continue;
}
if (normalizeObj.containsKey(shortValue)) {
results.add("\"" + normalizeObj.get(shortValue) + "\"");
} else {
results.add(currValue);
}
}
// Do not index empty properties
if (results.isEmpty()) continue;
if (normalizeProp.containsKey(property)) {
property = normalizeProp.get(property);
if (jsonMap.containsKey(property)) {
jsonMap.get(property).addAll(results);
} else {
jsonMap.put(property, results);
}
} else {
jsonMap.put(property, results);
}
}
if (addLanguage) {
if (rdfLanguages.isEmpty() && !language.isEmpty()) rdfLanguages.add(language);
if (!rdfLanguages.isEmpty()) jsonMap.put("language", new ArrayList<String>(rdfLanguages));
}
for (Map.Entry<String, String> it : normalizeMissing.entrySet()) {
if (!jsonMap.containsKey(it.getKey())) {
ArrayList<String> res = new ArrayList<String>();
res.add("\"" + it.getValue() + "\"");
jsonMap.put(it.getKey(), res);
}
}
return jsonMap;
}