Examples with TripleInfo org.nextprot.api.rdf.domain.TripleInfo used on opensource projects

Example 1 with TripleInfo

use of org.nextprot.api.rdf.domain.TripleInfo in project nextprot-api by calipho-sib.

the class RdfHelpServiceImpl method getRdfTypeFullInfoList.

@Cacheable("rdfhelp")
@Override
public synchronized List<RdfTypeInfo> getRdfTypeFullInfoList() {
    long t0 = System.currentTimeMillis();
    Set<String> rdfTypesNames = getRdfTypesNames();
    List<Future<RdfTypeInfo>> rdfFutureTypes = new ArrayList<Future<RdfTypeInfo>>();
    List<RdfTypeInfo> rdfTypes = Collections.synchronizedList(new ArrayList<RdfTypeInfo>());
    ExecutorService executor = Executors.newFixedThreadPool(NUMBER_THREADS);
    for (String rdfTypeName : rdfTypesNames) {
        // LOGGER.info("step1 - found rdf:type name " + rdfTypeName);
        Future<RdfTypeInfo> futureRdfTypeInfo = executor.submit(new FillRdfTypeInfoTask(this, rdfTypeName));
        rdfFutureTypes.add(futureRdfTypeInfo);
    }
    executor.shutdown();
    try {
        executor.awaitTermination(1, TimeUnit.DAYS);
    } catch (InterruptedException e) {
        e.printStackTrace();
        throw new NextProtException(e.getLocalizedMessage());
    }
    for (Future<RdfTypeInfo> futureRdfTypeInfo : rdfFutureTypes) {
        try {
            rdfTypes.add(futureRdfTypeInfo.get());
        } catch (InterruptedException e) {
            e.printStackTrace();
        } catch (ExecutionException e) {
            e.printStackTrace();
        }
    }
    // now populate parent and parent triples of each type
    for (RdfTypeInfo rti : rdfTypes) {
        // LOGGER.info("step2 - updating rdf:type " + rti.getTypeName());
        for (RdfTypeInfo parent : rdfTypes) {
            List<TripleInfo> triples = parent.findTriplesWithObjectType(rti.getTypeName());
            if (triples.size() > 0) {
                // LOGGER.info("step3 - linking parent rdf:type " + parent.getTypeName()  + " to rdf:type " + rti.getTypeName() + " , triple size: " + triples.size());
                rti.addParent(parent.getTypeName());
                for (TripleInfo triple : triples) rti.addParentTriple(triple);
            }
        }
    }
    Map<String, RdfTypeInfo> fullMap = new HashMap<String, RdfTypeInfo>();
    for (RdfTypeInfo rti : rdfTypes) {
        fullMap.put(rti.getTypeName(), rti);
    }
    if (fullMap.containsKey(":Entry"))
        buildPathToOrigin(fullMap, fullMap.get(":Entry"), "?entry ", 0);
    long seconds = (System.currentTimeMillis() - t0) / 1000;
    String duration = String.format("%d:%02d:%02d", seconds / 3600, (seconds % 3600) / 60, (seconds % 60)) + " [H:MM:SS]";
    LOGGER.info("errors: " + errorCount);
    LOGGER.info("duration: " + duration);
    return rdfTypes;
}

Example 2 with TripleInfo

use of org.nextprot.api.rdf.domain.TripleInfo in project nextprot-api by calipho-sib.

the class RdfHelpServiceImpl method buildPathToOrigin.

private static void buildPathToOrigin(final Map<String, RdfTypeInfo> fullMap, RdfTypeInfo currentEntry, String currentPath, int currenDepth) {
    if (currenDepth > 20)
        return;
    for (TripleInfo childTripleInfo : currentEntry.getTriples()) {
        RdfTypeInfo childTypeInfo = fullMap.get(childTripleInfo.getObjectType());
        if (childTypeInfo != null && !currentPath.contains(childTripleInfo.getPredicate()) && !childTripleInfo.getPredicate().equals(":interaction")) {
            String nextPath = currentPath + childTripleInfo.getPredicate();
            childTypeInfo.addPathToOrigin(nextPath);
            buildPathToOrigin(fullMap, childTypeInfo, nextPath + "/", currenDepth + 1);
        }
    }
}

Example 3 with TripleInfo

use of org.nextprot.api.rdf.domain.TripleInfo in project nextprot-api by calipho-sib.

the class RdfHelpServiceImpl method getTripleInfoList.

@Override
public List<TripleInfo> getTripleInfoList(String rdfType) {
    String queryBase = sparqlDictionary.getSparqlWithPrefixes("typepred");
    Set<TripleInfo> tripleList = new TreeSet<TripleInfo>();
    try {
        String query = sparqlDictionary.getSparqlOnly("prefix");
        query += queryBase.replace(":SomeRdfType", rdfType);
        QueryExecution qExec = sparqlService.queryExecution(query);
        ResultSet rs = qExec.execSelect();
        while (rs.hasNext()) {
            QuerySolution sol = rs.next();
            TripleInfo ti = new TripleInfo();
            String pred = (String) getDataFromSolutionVar(sol, "pred");
            String sspl = (String) getDataFromSolutionVar(sol, "subjSample");
            String ospl = (String) getDataFromSolutionVar(sol, "objSample", true);
            String spl = sspl + " " + pred + " " + ospl + " .";
            ti.setTripleSample(spl);
            ti.setPredicate(pred);
            ti.setSubjectType((String) getDataFromSolutionVar(sol, "subjType"));
            String objectType = (String) getDataFromSolutionVar(sol, "objType");
            if (objectType.length() == 0) {
                objectType = getObjectTypeFromSample(sol, "objSample");
                ti.setLiteralType(true);
            }
            ti.setObjectType(objectType);
            ti.setTripleCount(Integer.valueOf((String) getDataFromSolutionVar(sol, "objCount")));
            LOGGER.info(ti);
            tripleList.add(ti);
        }
        qExec.close();
    } catch (Exception e) {
        incrementErrors();
        System.err.println("Error with " + rdfType);
        e.printStackTrace();
        LOGGER.error("Error with " + rdfType, e);
    }
    return new ArrayList<TripleInfo>(tripleList);
}

Example 4 with TripleInfo

use of org.nextprot.api.rdf.domain.TripleInfo in project nextprot-api by calipho-sib.

the class RdfHelpServiceImpl method getRdfTypeFullInfo.

@Override
public RdfTypeInfo getRdfTypeFullInfo(String rdfTypeName) {
    RdfTypeInfo rdfTypeInfo = new RdfTypeInfo();
    rdfTypeInfo.setTypeName(rdfTypeName);
    Map<String, String> properties = getRdfTypeProperties(rdfTypeName);
    if (!properties.isEmpty()) {
        rdfTypeInfo.setTypeName(properties.get("rdfType"));
        rdfTypeInfo.setRdfsLabel(properties.get("label"));
        rdfTypeInfo.setRdfsComment(properties.get("comment"));
        rdfTypeInfo.setInstanceCount(Integer.valueOf(properties.get("instanceCount")));
        rdfTypeInfo.setInstanceSample(properties.get("instanceSample"));
    }
    List<TripleInfo> triples = getTripleInfoList(rdfTypeInfo.getTypeName());
    Set<String> values = null;
    if (completeSetOfValuesForTypes.contains(rdfTypeInfo.getTypeName())) {
        values = getRdfTypeValues(rdfTypeName, Integer.MAX_VALUE);
    } else {
        values = getRdfTypeValues(rdfTypeName, 20);
    }
    rdfTypeInfo.setValues(values);
    for (TripleInfo triple : triples) {
        rdfTypeInfo.addTriple(triple);
        if (triple.isLiteralType() && (!triple.getObjectType().equals(RdfConstants.BLANK_OBJECT_TYPE))) {
            String typeLiteral = rdfTypeName + "/" + triple.getPredicate();
            Set<String> exampleValues = null;
            if (completeSetOfValuesForLiteral.contains(typeLiteral)) {
                exampleValues = getValuesForTriple(rdfTypeName, triple.getPredicate(), Integer.MAX_VALUE);
            } else {
                exampleValues = getValuesForTriple(rdfTypeName, triple.getPredicate(), 50);
            }
            triple.setValues(exampleValues);
        }
    }
    return rdfTypeInfo;
}