/**
* Gets current query or constructs one on demand.
*
* @return The current query.
*/
private Query getQuery() {
if (query == null) {
query = queryFactory.constructQuery(sortPropertyIds, ascendingStates);
queryCount++;
}
return query;
}
private static Query toQuery(Element pattern) {
Query query = QueryFactory.make();
query.setQueryPattern(pattern);
query.setQuerySelectType();
query.setQueryResultStar(true);
return query;
}
public List<ResourceName> queryMDS(PackageName packageName) {
MDSInstance mdsInstance;
List<ResourceName> resources = new ArrayList<ResourceName>();
try {
mdsInstance = storeInitializer.getMDSInstance();
packageName = (packageName == null) ? PackageName.createPackageName("/") : packageName;
NameCondition condition =
ConditionFactory.createNameCondition(packageName.getAbsoluteName(), "%");
ResourceQuery query = QueryFactory.createResourceQuery(mdsInstance, condition);
Iterator<QueryResult> contents = query.execute();
if (contents == null) {
return resources;
}
while (contents.hasNext()) {
QueryResult result = contents.next();
if (result.getResultType() == QueryResult.ResultType.PACKAGE_RESULT) {
PackageResult pack = (PackageResult) result;
resources.add(pack.getPackageName());
} else {
DocumentResult doc = (DocumentResult) result;
resources.add(doc.getDocumentName());
}
}
return resources;
} catch (MDSAccessException e) {
throw new IllegalArgumentException("Could not connect to MDS, check login data", e);
} catch (InvalidReferenceException e) {
throw new IllegalArgumentException("Could not find/read " + packageName, e);
} catch (InvalidReferenceTypeException e) {
throw new IllegalArgumentException("No correct type!", e);
}
}
/**
* Queries the {@link #rdfEndpoint(String)} with each of the {@link #rdfQueries} and harvests the
* results of the query.
*/
private void harvestFromEndpoint() {
Query query;
QueryExecution qExec;
for (String rdfQuery : rdfQueries) {
if (closed) break;
logger.info(
"Harvesting with query: [{}] on index [{}] and type [{}]", rdfQuery, indexName, typeName);
try {
query = QueryFactory.create(rdfQuery);
} catch (QueryParseException qpe) {
logger.error("Could not parse [{}]. Please provide a relevant query. {}", rdfQuery, qpe);
continue;
}
qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
try {
harvest(qExec);
} catch (Exception e) {
logger.error("Exception [{}] occurred while harvesting", e.getLocalizedMessage());
} finally {
qExec.close();
}
}
}
/**
* Create a QueryExecution that will access a SPARQL service over HTTP
*
* @param service URL of the remote service
* @param query Query string to execute
* @param defaultGraphURIs List of URIs to make up the default graph
* @param namedGraphURIs List of URIs to make up the named graphs
* @return QueryExecution
*/
public static QueryExecution sparqlService(
String service, String query, List<String> defaultGraphURIs, List<String> namedGraphURIs) {
checkNotNull(service, "URL for service is null");
// checkNotNull(defaultGraphURIs, "List of default graph URIs is null") ;
// checkNotNull(namedGraphURIs, "List of named graph URIs is null") ;
checkArg(query);
return sparqlService(service, QueryFactory.create(query), defaultGraphURIs, namedGraphURIs);
}
@BeforeMethod
public void setup() {
mockFactory = mock(QueryFactory.class);
mockQueryFilter = mock(QueryFilter.class);
given(mockFactory.createFilter()).willReturn(mockQueryFilter);
mockAndBuilder = mock(QueryFilter.QueryFilterBuilder.class);
mockOrBuilder = mock(QueryFilter.QueryFilterBuilder.class);
given(mockQueryFilter.and()).willReturn(mockAndBuilder);
given(mockQueryFilter.or()).willReturn(mockOrBuilder);
}
@Test
public void testCreatingFilterPatternQuery() {
Query query = QueryFactory.createQuery();
query.from(
QueryFactory.sequenceStream(
Sequence.next(
QueryFactory.inputStream("e1", "Stream1"),
QueryFactory.inputStream("e2", "Stream1")),
Expression.value(2000)));
query.insertInto("OutStream");
query.select(
QueryFactory.outputSelector()
.select("symbol", Expression.variable("e1", "symbol"))
.select("avgPrice", "avg", Expression.variable("e2", 0, "price"))
.groupBy("e1", "symbol")
.having(
Condition.compare(
Expression.variable("avgPrice"),
Condition.Operator.GREATER_THAN,
Expression.value(50))));
}
/**
* Tests whether a query gives the same results when run both with and without a given optimizer
*
* @param queryStr Query
* @param ds Dataset
* @param opt Optimizer
* @param expected Expected number of results
*/
public static void test(String queryStr, Dataset ds, Symbol opt, int expected) {
Query q = QueryFactory.create(queryStr);
if (!q.isSelectType()) Assert.fail("Only SELECT queries are testable with this method");
Op op = Algebra.compile(q);
// Track current state
boolean isEnabled = ARQ.isTrue(opt);
boolean isDisabled = ARQ.isFalse(opt);
try {
// Run first without optimization
ARQ.set(opt, false);
ResultSetRewindable rs;
try (QueryExecution qe = QueryExecutionFactory.create(q, ds)) {
rs = ResultSetFactory.makeRewindable(qe.execSelect());
if (expected != rs.size()) {
System.err.println("Non-optimized results not as expected");
TextOutput output = new TextOutput((SerializationContext) null);
output.format(System.out, rs);
rs.reset();
}
Assert.assertEquals(expected, rs.size());
}
// Run with optimization
ARQ.set(opt, true);
ResultSetRewindable rsOpt;
try (QueryExecution qeOpt = QueryExecutionFactory.create(q, ds)) {
rsOpt = ResultSetFactory.makeRewindable(qeOpt.execSelect());
if (expected != rsOpt.size()) {
System.err.println("Optimized results not as expected");
TextOutput output = new TextOutput((SerializationContext) null);
output.format(System.out, rsOpt);
rsOpt.reset();
}
Assert.assertEquals(expected, rsOpt.size());
}
Assert.assertTrue(ResultSetCompare.isomorphic(rs, rsOpt));
} finally {
// Restore previous state
if (isEnabled) {
ARQ.set(opt, true);
} else if (isDisabled) {
ARQ.set(opt, false);
} else {
ARQ.unset(opt);
}
}
}
@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"));
}
}
protected void execute(String queryString, HttpAction action) {
String queryStringLog = ServletOps.formatForLog(queryString);
if (action.verbose) action.log.info(format("[%d] Query = \n%s", action.id, queryString));
else action.log.info(format("[%d] Query = %s", action.id, queryStringLog));
Query query = null;
try {
// NB syntax is ARQ (a superset of SPARQL)
query = QueryFactory.create(queryString, QueryParseBase, Syntax.syntaxARQ);
queryStringLog = formatForLog(query);
validateQuery(action, query);
} catch (ActionErrorException ex) {
throw ex;
} catch (QueryParseException ex) {
ServletOps.errorBadRequest(
"Parse error: \n" + queryString + "\n\r" + messageForQueryException(ex));
}
// Should not happen.
catch (QueryException ex) {
ServletOps.errorBadRequest("Error: \n" + queryString + "\n\r" + ex.getMessage());
}
// Assumes finished whole thing by end of sendResult.
try {
action.beginRead();
Dataset dataset = decideDataset(action, query, queryStringLog);
try (QueryExecution qExec = createQueryExecution(query, dataset); ) {
SPARQLResult result = executeQuery(action, qExec, query, queryStringLog);
// Deals with exceptions itself.
sendResults(action, result, query.getPrologue());
}
} catch (QueryParseException ex) {
// Late stage static error (e.g. bad fixed Lucene query string).
ServletOps.errorBadRequest(
"Query parse error: \n" + queryString + "\n\r" + messageForQueryException(ex));
} catch (QueryCancelledException ex) {
// Additional counter information.
incCounter(action.getEndpoint().getCounters(), QueryTimeouts);
throw ex;
} finally {
action.endRead();
}
}
@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();
}
}
/**
* Returns the string value of the first of the properties in the uriDescriptionList for the given
* resource (as an URI). In case the resource does not have any of the properties mentioned, its
* URI is returned. The value is obtained by querying the endpoint and the endpoint is queried
* repeatedly until it gives a response (value or the lack of it)
*
* <p>It is highly recommended that the list contains properties like labels or titles, with test
* values.
*
* @param uri - the URI for which a label is required
* @return a String value, either a label for the parameter or its value if no label is obtained
* from the endpoint
*/
private String getLabelForUri(String uri) {
String result;
if (uriLabelCache.containsKey(uri)) {
return uriLabelCache.get(uri);
}
for (String prop : uriDescriptionList) {
String innerQuery = "SELECT ?r WHERE {<" + uri + "> <" + prop + "> ?r } LIMIT 1";
try {
Query query = QueryFactory.create(innerQuery);
QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
boolean keepTrying = true;
while (keepTrying) {
keepTrying = false;
try {
ResultSet results = qExec.execSelect();
if (results.hasNext()) {
QuerySolution sol = results.nextSolution();
result = EEASettings.parseForJson(sol.getLiteral("r").getLexicalForm());
if (!result.isEmpty()) {
uriLabelCache.put(uri, result);
return result;
}
}
} catch (Exception e) {
keepTrying = true;
logger.warn("Could not get label for uri {}. Retrying.", uri);
} finally {
qExec.close();
}
}
} catch (QueryParseException qpe) {
logger.error("Exception for query {}. The label cannot be obtained", innerQuery);
}
}
return uri;
}
@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);
}
/**
* Get a set of unique queryObjName returned from a select query
*
* <p>Used to retrieve sets of modified objects used in sync
*
* @param rdfQuery query to execute
* @param queryObjName name of the object returned
* @return set of values for queryObjectName in the rdfQuery result
*/
HashSet<String> executeSyncQuery(String rdfQuery, String queryObjName) {
HashSet<String> rdfUrls = new HashSet<String>();
Query query;
try {
query = QueryFactory.create(rdfQuery);
} catch (QueryParseException qpe) {
logger.warn(
"Could not parse [{}]. Please provide a relevant query. {}",
rdfQuery,
qpe.getLocalizedMessage());
return null;
}
QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
try {
ResultSet results = qExec.execSelect();
while (results.hasNext()) {
QuerySolution sol = results.nextSolution();
try {
String value = sol.getResource(queryObjName).toString();
rdfUrls.add(value);
} catch (NoSuchElementException e) {
logger.error("Encountered a NoSuchElementException: " + e.getLocalizedMessage());
return null;
}
}
} catch (Exception e) {
logger.error(
"Encountered a [{}] while querying the endpoint for sync", e.getLocalizedMessage());
return null;
} finally {
qExec.close();
}
return rdfUrls;
}
public static void main(String... argv) {
String queryString = "SELECT * { ?s ?p ?o }";
Query query = QueryFactory.create(queryString);
Store store = SDBFactory.connectStore("sdb.ttl");
// Must be a DatasetStore to trigger the SDB query engine.
// Creating a graph from the Store, and adding it to a general
// purpose dataset will not necesarily exploit full SQL generation.
// The right answers will be obtained but slowly.
Dataset ds = DatasetStore.create(store);
QueryExecution qe = QueryExecutionFactory.create(query, ds);
try {
ResultSet rs = qe.execSelect();
ResultSetFormatter.out(rs);
} finally {
qe.close();
}
// Close the SDB conenction which also closes the underlying JDBC connection.
store.getConnection().close();
store.close();
}
/**
* Create a QueryExecution that will access a SPARQL service over HTTP
*
* @param service URL of the remote service
* @param query Query string to execute
* @param defaultGraph URI of the default graph
* @return QueryExecution
*/
public static QueryExecution sparqlService(String service, String query, String defaultGraph) {
checkNotNull(service, "URL for service is null");
// checkNotNull(defaultGraph, "IRI for default graph is null") ;
checkArg(query);
return sparqlService(service, QueryFactory.create(query), defaultGraph);
}
private static Query makeQuery(String queryStr, Syntax syntax) {
return QueryFactory.create(queryStr, syntax);
}
@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;
}
/**
* Create a QueryExecution that will access a SPARQL service over HTTP
*
* @param service URL of the remote service
* @param query Query string to execute
* @return QueryExecution
*/
public static QueryExecution sparqlService(String service, String query) {
checkNotNull(service, "URL for service is null");
checkArg(query);
return sparqlService(service, QueryFactory.create(query));
}
public static Query createQuery(QueryType typeOfQuery) {
return QueryFactory.newQuery(typeOfQuery);
}
@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 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);
}
@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);
}
}
private static Query makeQuery(String queryStr) {
return QueryFactory.create(queryStr);
}
/**
* Starts a harvester with predefined queries to synchronize with the changes from the SPARQL
* endpoint
*/
public boolean sync() {
logger.info("Sync resources newer than {}", startTime);
String rdfQueryTemplate =
"PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> "
+ "SELECT DISTINCT ?resource WHERE { "
+ " GRAPH ?graph { %s }"
+ " ?graph <%s> ?time . %s "
+ " FILTER (?time > xsd:dateTime(\"%s\")) }";
String queryStr =
String.format(
rdfQueryTemplate, syncConditions, syncTimeProp, graphSyncConditions, startTime);
Set<String> syncUris = executeSyncQuery(queryStr, "resource");
if (syncUris == null) {
logger.error("Errors occurred during sync procedure. Aborting!");
return false;
}
/**
* If desired, query for old data that has the sync conditions modified
*
* <p>This option is useful in the case in which the application indexes resources that match
* some conditions. In this case, if they are modified and no longer match the initial
* conditions, they will not be synchronized. When syncOldData is True, the modified resources
* that no longer match the conditions are deleted.
*/
int deleted = 0;
int count = 0;
if (this.syncOldData) {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
queryStr =
String.format(
rdfQueryTemplate,
syncConditions,
syncTimeProp,
graphSyncConditions,
sdf.format(new Date(0)));
HashSet<String> allIndexURIs = executeSyncQuery(queryStr, "resource");
if (allIndexURIs == null) {
logger.error("Errors occurred during modified content sync query. Aborting!");
return false;
}
deleted = removeMissingUris(allIndexURIs);
}
/* Prepare a series of bulk uris to be described so we can make
* a smaller number of calls to the SPARQL endpoint. */
ArrayList<ArrayList<String>> bulks = new ArrayList<ArrayList<String>>();
ArrayList<String> currentBulk = new ArrayList<String>();
for (String uri : syncUris) {
currentBulk.add(uri);
if (currentBulk.size() == EEASettings.DEFAULT_BULK_SIZE) {
bulks.add(currentBulk);
currentBulk = new ArrayList<String>();
}
}
if (currentBulk.size() > 0) {
bulks.add(currentBulk);
}
/* Execute RDF queries for the resources in each bulk */
for (ArrayList<String> bulk : bulks) {
String syncQuery = getSyncQueryStr(bulk);
try {
Query query = QueryFactory.create(syncQuery);
QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
try {
Model constructModel = ModelFactory.createDefaultModel();
qExec.execConstruct(constructModel);
BulkRequestBuilder bulkRequest = client.prepareBulk();
/**
* When adding the model to ES do not use toDescribeURIs as the query already returned the
* correct labels.
*/
addModelToES(constructModel, bulkRequest, false);
count += bulk.size();
} catch (Exception e) {
logger.error("Error while querying for modified content. {}", e.getLocalizedMessage());
return false;
} finally {
qExec.close();
}
} catch (QueryParseException qpe) {
logger.warn(
"Could not parse Sync query. Please provide a relevant query. {}",
qpe.getLocalizedMessage());
return false;
}
}
logger.info(
"Finished synchronisation: Deleted {}, Updated {}/{}", deleted, count, syncUris.size());
return true;
}
@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);
}
@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);
}
}
}