Example usage for com.mongodb QueryBuilder QueryBuilder

List of usage examples for com.mongodb QueryBuilder QueryBuilder

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Introduction

In this page you can find the example usage for com.mongodb QueryBuilder QueryBuilder.

Prototype

public QueryBuilder()

Source Link

Document

Creates a builder with an empty query

Usage

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult deleteStudy(String studyName, QueryOptions options) {
    if (options == null) {
        options = new QueryOptions();
    }//from ww  w .j a v  a 2 s .  co  m
    StudyConfiguration studyConfiguration = studyConfigurationManager.getStudyConfiguration(studyName, options)
            .first();
    DBObject query = parseQuery(new Query(VariantQueryParams.STUDIES.key(), studyConfiguration.getStudyId()),
            new QueryBuilder()).get();

    // { $pull : { files : {  sid : <studyId> } } }
    BasicDBObject update = new BasicDBObject("$pull",
            new BasicDBObject(DBObjectToVariantConverter.STUDIES_FIELD, new BasicDBObject(
                    DBObjectToVariantSourceEntryConverter.STUDYID_FIELD, studyConfiguration.getStudyId())));
    QueryResult<WriteResult> result = variantsCollection.update(query, update, new QueryOptions("multi", true));

    logger.debug("deleteStudy: query = {}", query);
    logger.debug("deleteStudy: update = {}", update);

    if (options.getBoolean("purge", false)) {
        BasicDBObject purgeQuery = new BasicDBObject(DBObjectToVariantConverter.STUDIES_FIELD,
                new BasicDBObject("$size", 0));
        variantsCollection.remove(purgeQuery, new QueryOptions("multi", true));
    }

    return result;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getFrequency(Query query, Region region, int regionIntervalSize) {
    // db.variants.aggregate( { $match: { $and: [ {chr: "1"}, {start: {$gt: 251391, $lt: 2701391}} ] }},
    //                        { $group: { _id: { $subtract: [ { $divide: ["$start", 20000] }, { $divide: [{$mod: ["$start", 20000]}, 20000] } ] },
    //                                  totalCount: {$sum: 1}}})

    QueryOptions options = new QueryOptions();

    // If interval is not provided is set to the value that returns 200 values
    if (regionIntervalSize <= 0) {
        //            regionIntervalSize = options.getInt("interval", (region.getEnd() - region.getStart()) / 200);
        regionIntervalSize = (region.getEnd() - region.getStart()) / 200;
    }// w w w.ja  va  2s  .  com

    BasicDBObject start = new BasicDBObject("$gt", region.getStart());
    start.append("$lt", region.getEnd());

    BasicDBList andArr = new BasicDBList();
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.CHROMOSOME_FIELD, region.getChromosome()));
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.START_FIELD, start));

    // Parsing the rest of options
    QueryBuilder qb = new QueryBuilder();
    //        DBObject optionsMatch = parseQueryOptions(options, qb).get();
    DBObject optionsMatch = parseQuery(query, qb).get();
    if (!optionsMatch.keySet().isEmpty()) {
        andArr.add(optionsMatch);
    }
    DBObject match = new BasicDBObject("$match", new BasicDBObject("$and", andArr));

    //        qb.and("_at.chunkIds").in(chunkIds);
    //        qb.and(DBObjectToVariantConverter.END_FIELD).greaterThanEquals(region.getStart());
    //        qb.and(DBObjectToVariantConverter.START_FIELD).lessThanEquals(region.getEnd());
    //
    //        List<String> chunkIds = getChunkIds(region);
    //        DBObject regionObject = new BasicDBObject("_at.chunkIds", new BasicDBObject("$in", chunkIds))
    //                .append(DBObjectToVariantConverter.END_FIELD, new BasicDBObject("$gte", region.getStart()))
    //                .append(DBObjectToVariantConverter.START_FIELD, new BasicDBObject("$lte", region.getEnd()));

    BasicDBList divide1 = new BasicDBList();
    divide1.add("$start");
    divide1.add(regionIntervalSize);

    BasicDBList divide2 = new BasicDBList();
    divide2.add(new BasicDBObject("$mod", divide1));
    divide2.add(regionIntervalSize);

    BasicDBList subtractList = new BasicDBList();
    subtractList.add(new BasicDBObject("$divide", divide1));
    subtractList.add(new BasicDBObject("$divide", divide2));

    BasicDBObject subtract = new BasicDBObject("$subtract", subtractList);
    DBObject totalCount = new BasicDBObject("$sum", 1);
    BasicDBObject g = new BasicDBObject("_id", subtract);
    g.append("features_count", totalCount);
    DBObject group = new BasicDBObject("$group", g);
    DBObject sort = new BasicDBObject("$sort", new BasicDBObject("_id", 1));

    //        logger.info("getAllIntervalFrequencies - (>_)>");
    //        System.out.println(options.toString());
    //        System.out.println(match.toString());
    //        System.out.println(group.toString());
    //        System.out.println(sort.toString());

    long dbTimeStart = System.currentTimeMillis();
    QueryResult output = variantsCollection.aggregate(/*"$histogram", */Arrays.asList(match, group, sort),
            options);
    long dbTimeEnd = System.currentTimeMillis();

    Map<Long, DBObject> ids = new HashMap<>();
    // Create DBObject for intervals with features inside them
    for (DBObject intervalObj : (List<DBObject>) output.getResult()) {
        Long _id = Math.round((Double) intervalObj.get("_id"));//is double

        DBObject intervalVisited = ids.get(_id);
        if (intervalVisited == null) {
            intervalObj.put("_id", _id);
            intervalObj.put("start", getChunkStart(_id.intValue(), regionIntervalSize));
            intervalObj.put("end", getChunkEnd(_id.intValue(), regionIntervalSize));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", Math.log((int) intervalObj.get("features_count")));
            ids.put(_id, intervalObj);
        } else {
            Double sum = (Double) intervalVisited.get("features_count")
                    + Math.log((int) intervalObj.get("features_count"));
            intervalVisited.put("features_count", sum.intValue());
        }
    }

    // Create DBObject for intervals without features inside them
    BasicDBList resultList = new BasicDBList();
    int firstChunkId = getChunkId(region.getStart(), regionIntervalSize);
    int lastChunkId = getChunkId(region.getEnd(), regionIntervalSize);
    DBObject intervalObj;
    for (int chunkId = firstChunkId; chunkId <= lastChunkId; chunkId++) {
        intervalObj = ids.get((long) chunkId);
        if (intervalObj == null) {
            intervalObj = new BasicDBObject();
            intervalObj.put("_id", chunkId);
            intervalObj.put("start", getChunkStart(chunkId, regionIntervalSize));
            intervalObj.put("end", getChunkEnd(chunkId, regionIntervalSize));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", 0);
        }
        resultList.add(intervalObj);
    }

    QueryResult queryResult = new QueryResult(region.toString(), ((Long) (dbTimeEnd - dbTimeStart)).intValue(),
            resultList.size(), resultList.size(), null, null, resultList);

    return queryResult;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult deleteAnnotation(String annotationId, Query query, QueryOptions queryOptions) {
    if (queryOptions == null) {
        queryOptions = new QueryOptions();
    }/*  w ww.ja  v a  2s.  com*/
    //        queryOptions.put(VariantQueryParams.STUDIES.key(), studyId);
    DBObject dbQuery = parseQuery(query, new QueryBuilder()).get();

    //        DBObject update = new BasicDBObject("$unset", new BasicDBObject(DBObjectToVariantConverter.ANNOTATION_FIELD, ""));
    DBObject update = new BasicDBObject("$set",
            new BasicDBObject(DBObjectToVariantConverter.ANNOTATION_FIELD + ".0", null));

    logger.debug("deleteAnnotation: query = {}", dbQuery);
    logger.debug("deleteAnnotation: update = {}", update);

    return variantsCollection.update(dbQuery, update, new QueryOptions("multi", true));
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

private QueryBuilder addScoreFilter(String key, List<String> list, QueryBuilder builder) {
    List<DBObject> ands = new ArrayList<>();
    for (Iterator<String> iterator = list.iterator(); iterator.hasNext();) {
        String elem = iterator.next();
        String[] populationFrequency = splitKeyValue(elem);
        QueryBuilder scoreBuilder = new QueryBuilder();
        scoreBuilder.and(DBObjectToVariantAnnotationConverter.SCORE_SOURCE_FIELD).is(populationFrequency[0]);
        addCompQueryFilter(DBObjectToVariantAnnotationConverter.SCORE_SCORE_FIELD, populationFrequency[1],
                scoreBuilder);// www .  j  av  a  2 s  . co  m
        ands.add(new BasicDBObject(key, new BasicDBObject("$elemMatch", scoreBuilder.get())));
    }
    if (!ands.isEmpty()) {
        builder.and(ands.toArray(new DBObject[ands.size()]));
    }
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

private QueryBuilder addFrequencyFilter(String key, String alleleFrequencyField, List<String> list,
        QueryBuilder builder) {// ww  w.  j a  va  2 s . c o m
    List<DBObject> ands = new ArrayList<>();
    for (Iterator<String> iterator = list.iterator(); iterator.hasNext();) {
        String elem = iterator.next();
        String[] split = elem.split(":");
        if (split.length == 2) {
            String study = split[0];
            String population = split[1];
            //                String frequency = split[2];
            String[] populationFrequency = splitKeyValue(population);
            QueryBuilder frequencyBuilder = new QueryBuilder();
            frequencyBuilder.and(DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCY_STUDY_FIELD)
                    .is(study);
            //                frequencyBuilder.and(DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCY_POP_FIELD).is(population);
            frequencyBuilder.and(DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCY_POP_FIELD)
                    .is(populationFrequency[0]);
            //                addCompQueryFilter(alleleFrequencyField, frequency, frequencyBuilder);
            System.out.println("populationFrequency = " + Arrays.toString(populationFrequency));
            addCompQueryFilter(alleleFrequencyField, populationFrequency[1], frequencyBuilder);
            ands.add(new BasicDBObject(key, new BasicDBObject("$elemMatch", frequencyBuilder.get())));
        } else {
            logger.error("Bad score filter: " + elem);
            iterator.remove(); //Remove the malformed query params.
        }
    }
    if (!ands.isEmpty()) {
        builder.and(ands.toArray(new DBObject[ands.size()]));
    }
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Override
@Deprecated//  w  w  w .  j ava2  s .c o  m
public QueryResult getVariantFrequencyByRegion(Region region, QueryOptions options) {
    // db.variants.aggregate( { $match: { $and: [ {chr: "1"}, {start: {$gt: 251391, $lt: 2701391}} ] }}, 
    //                        { $group: { _id: { $subtract: [ { $divide: ["$start", 20000] }, { $divide: [{$mod: ["$start", 20000]}, 20000] } ] }, 
    //                                  totalCount: {$sum: 1}}})

    if (options == null) {
        options = new QueryOptions();
    }

    int interval = options.getInt("interval", 20000);

    BasicDBObject start = new BasicDBObject("$gt", region.getStart());
    start.append("$lt", region.getEnd());

    BasicDBList andArr = new BasicDBList();
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.CHROMOSOME_FIELD, region.getChromosome()));
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.START_FIELD, start));

    // Parsing the rest of options
    QueryBuilder qb = new QueryBuilder();
    DBObject optionsMatch = parseQueryOptions(options, qb).get();
    if (!optionsMatch.keySet().isEmpty()) {
        andArr.add(optionsMatch);
    }
    DBObject match = new BasicDBObject("$match", new BasicDBObject("$and", andArr));

    //        qb.and("_at.chunkIds").in(chunkIds);
    //        qb.and(DBObjectToVariantConverter.END_FIELD).greaterThanEquals(region.getStart());
    //        qb.and(DBObjectToVariantConverter.START_FIELD).lessThanEquals(region.getEnd());
    //
    //        List<String> chunkIds = getChunkIds(region);
    //        DBObject regionObject = new BasicDBObject("_at.chunkIds", new BasicDBObject("$in", chunkIds))
    //                .append(DBObjectToVariantConverter.END_FIELD, new BasicDBObject("$gte", region.getStart()))
    //                .append(DBObjectToVariantConverter.START_FIELD, new BasicDBObject("$lte", region.getEnd()));

    BasicDBList divide1 = new BasicDBList();
    divide1.add("$start");
    divide1.add(interval);

    BasicDBList divide2 = new BasicDBList();
    divide2.add(new BasicDBObject("$mod", divide1));
    divide2.add(interval);

    BasicDBList subtractList = new BasicDBList();
    subtractList.add(new BasicDBObject("$divide", divide1));
    subtractList.add(new BasicDBObject("$divide", divide2));

    BasicDBObject substract = new BasicDBObject("$subtract", subtractList);

    DBObject totalCount = new BasicDBObject("$sum", 1);

    BasicDBObject g = new BasicDBObject("_id", substract);
    g.append("features_count", totalCount);
    DBObject group = new BasicDBObject("$group", g);

    DBObject sort = new BasicDBObject("$sort", new BasicDBObject("_id", 1));

    //        logger.info("getAllIntervalFrequencies - (>_)>");
    //        System.out.println(options.toString());
    //
    //        System.out.println(match.toString());
    //        System.out.println(group.toString());
    //        System.out.println(sort.toString());

    long dbTimeStart = System.currentTimeMillis();
    QueryResult output = variantsCollection.aggregate(/*"$histogram", */Arrays.asList(match, group, sort),
            options);
    long dbTimeEnd = System.currentTimeMillis();

    Map<Long, DBObject> ids = new HashMap<>();
    // Create DBObject for intervals with features inside them
    for (DBObject intervalObj : (List<DBObject>) output.getResult()) {
        Long _id = Math.round((Double) intervalObj.get("_id"));//is double

        DBObject intervalVisited = ids.get(_id);
        if (intervalVisited == null) {
            intervalObj.put("_id", _id);
            intervalObj.put("start", getChunkStart(_id.intValue(), interval));
            intervalObj.put("end", getChunkEnd(_id.intValue(), interval));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", Math.log((int) intervalObj.get("features_count")));
            ids.put(_id, intervalObj);
        } else {
            Double sum = (Double) intervalVisited.get("features_count")
                    + Math.log((int) intervalObj.get("features_count"));
            intervalVisited.put("features_count", sum.intValue());
        }
    }

    // Create DBObject for intervals without features inside them
    BasicDBList resultList = new BasicDBList();
    int firstChunkId = getChunkId(region.getStart(), interval);
    int lastChunkId = getChunkId(region.getEnd(), interval);
    DBObject intervalObj;
    for (int chunkId = firstChunkId; chunkId <= lastChunkId; chunkId++) {
        intervalObj = ids.get((long) chunkId);
        if (intervalObj == null) {
            intervalObj = new BasicDBObject();
            intervalObj.put("_id", chunkId);
            intervalObj.put("start", getChunkStart(chunkId, interval));
            intervalObj.put("end", getChunkEnd(chunkId, interval));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", 0);
        }
        resultList.add(intervalObj);
    }

    QueryResult queryResult = new QueryResult(region.toString(), ((Long) (dbTimeEnd - dbTimeStart)).intValue(),
            resultList.size(), resultList.size(), null, null, resultList);

    return queryResult;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Deprecated
public QueryResult deleteStudy(int studyId, QueryOptions queryOptions) {

    if (queryOptions == null) {
        queryOptions = new QueryOptions();
    }//w  ww  . j av  a2s. co m
    queryOptions.put(VariantQueryParams.STUDIES.key(), studyId);
    DBObject query = parseQueryOptions(queryOptions, new QueryBuilder()).get();

    // { $pull : { files : {  sid : <studyId> } } }
    BasicDBObject update = new BasicDBObject("$pull",
            new BasicDBObject(DBObjectToVariantConverter.STUDIES_FIELD,
                    new BasicDBObject(DBObjectToVariantSourceEntryConverter.STUDYID_FIELD, studyId)));
    QueryResult<WriteResult> result = variantsCollection.update(query, update, new QueryOptions("multi", true));

    logger.debug("deleteStudy: query = {}", query);
    logger.debug("deleteStudy: update = {}", update);

    if (queryOptions.getBoolean("purge", false)) {
        BasicDBObject purgeQuery = new BasicDBObject(DBObjectToVariantConverter.STUDIES_FIELD,
                new BasicDBObject("$size", 0));
        variantsCollection.remove(purgeQuery, new QueryOptions("multi", true));
    }

    return result;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Deprecated
QueryResult deleteAnnotation(int annotationId, int studyId, QueryOptions queryOptions) {

    if (queryOptions == null) {
        queryOptions = new QueryOptions();
    }/*from  w w  w . j  a  v  a 2  s . c  o  m*/
    queryOptions.put(VariantQueryParams.STUDIES.key(), studyId);
    DBObject query = parseQueryOptions(queryOptions, new QueryBuilder()).get();

    DBObject update = new BasicDBObject("$unset",
            new BasicDBObject(DBObjectToVariantConverter.ANNOTATION_FIELD, ""));

    logger.debug("deleteAnnotation: query = {}", query);
    logger.debug("deleteAnnotation: update = {}", update);

    return variantsCollection.update(query, update, new QueryOptions("multi", true));
}

From source file:org.wrml.contrib.runtime.service.mongo.MongoService.java

License:Apache License

private DBObject createMongoQuery(final SearchCriteria searchCriteria) {

    QueryBuilder queryBuilder = null;// ww  w .j  a  v  a  2 s  . co m

    final List<SearchCriterion> and = searchCriteria.getAnd();
    if (and != null && !and.isEmpty()) {

        queryBuilder = new QueryBuilder();

        for (final SearchCriterion searchCriterion : and) {

            final String referenceSlot = searchCriterion.getReferenceSlot();
            queryBuilder.and(referenceSlot);
            addQueryCriterion(searchCriterion, queryBuilder);

        }

    }

    final List<SearchCriterion> or = searchCriteria.getOr();
    if (or != null && !or.isEmpty()) {

        final DBObject[] orQueryCriterionArray = new DBObject[or.size()];
        for (int i = 0; i < or.size(); i++) {
            final SearchCriterion searchCriterion = or.get(i);
            final String referenceSlot = searchCriterion.getReferenceSlot();
            final QueryBuilder orQueryCriterionBuilder = QueryBuilder.start(referenceSlot);
            addQueryCriterion(searchCriterion, orQueryCriterionBuilder);
            orQueryCriterionArray[i] = orQueryCriterionBuilder.get();
        }

        final QueryBuilder orQueryBuilder = new QueryBuilder();
        orQueryBuilder.or(orQueryCriterionArray);

        if (queryBuilder != null) {
            // AND the OR clause together with the AND query
            queryBuilder.and(orQueryBuilder.get());
        } else {
            queryBuilder = orQueryBuilder;
        }
    }

    if (queryBuilder == null) {
        return null;
    }

    final DBObject mongoQuery = queryBuilder.get();
    return mongoQuery;
}