Example usage for com.mongodb QueryBuilder get

List of usage examples for com.mongodb QueryBuilder get

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Introduction

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

Prototype

public DBObject get()

Source Link

Document

Creates a DBObject query to be used for the driver's find operations

Usage

From source file:org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor.java

License:Apache License

@Override
@Deprecated//from w  w w .j av a  2s  . c o  m
public List<QueryResult> getAllScoresByRegionList(List regionList, QueryOptions options) {
    //TODO not finished yet
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regionList.size());
    List<Integer> integerChunkIds;

    List<Region> regions = regionList;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(),
                MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE);
        int regionChunkEnd = getChunkId(region.getEnd(),
                MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds").is(getChunkIdPrefix(region.getChromosome(),
                    region.getStart(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            //                    integerChunkIds.add(chunkId);
            //                }
            //    //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds);
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        /****/

        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());

        //            logger.debug(builder.get().toString());

    }
    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    //        List<QueryResult> queryResults = executeQueryList(ids, queries, options);

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        List<Document> list = (List<Document>) queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            Document chunk = list.get(j);

            if (!chunk.isEmpty()) {
                //                    BasicDBList valuesChunk = (BasicDBList) chunk.get("values");
                ArrayList valuesChunk = chunk.get("values", ArrayList.class);

                if (valuesChunk != null) { // TODO: temporary patch to skip empty chunks - remove as soon as conservation is reloaded
                    String source = chunk.getString("source");
                    List<Float> valuesList;
                    if (!typeMap.containsKey(source)) {
                        valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                        for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                            valuesList.add(null);
                        }
                        typeMap.put(source, valuesList);
                    } else {
                        valuesList = typeMap.get(source);
                    }

                    //                        valuesChunk = (BasicDBList) chunk.get("values");
                    valuesChunk = chunk.get("values", ArrayList.class);
                    int pos = 0;
                    if (region.getStart() > chunk.getInteger("start")) {
                        pos = region.getStart() - chunk.getInteger("start");
                    }

                    for (; pos < valuesChunk.size()
                            && (pos + chunk.getInteger("start") <= region.getEnd()); pos++) {
                        valuesList.set(pos + chunk.getInteger("start") - region.getStart(),
                                new Float((Double) valuesChunk.get(pos)));
                    }
                } else {
                    continue;
                }

            }

            BasicDBList resultList = new BasicDBList();
            for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
                for (Float value : elem.getValue()) {
                    if (value != null) {
                        resultList.add(new Score(new Double(value), elem.getKey(), null));
                    }
                }
            }
            if (!resultList.isEmpty()) {
                queryResult.setResult(resultList);
            } else {
                queryResult.setResult(null);
            }
        }

    }
    return queryResults;
}

From source file:org.opencb.cellbase.lib.impl.GenomeMongoDBAdaptor.java

License:Apache License

@Override
//    public List<QueryResult<ConservationScoreRegion>> getConservation(List<Region> regionList, QueryOptions options) {
public List<QueryResult<GenomicScoreRegion<Float>>> getConservation(List<Region> regionList,
        QueryOptions options) {/*from   w  ww.j  a  v  a 2s  . c  om*/
    //TODO not finished yet
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regionList.size());
    List<String> integerChunkIds;

    List<Region> regions = regionList;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        // Max region size is 10000bp
        if (region.getEnd() - region.getStart() > 10000) {
            region.setEnd(region.getStart() + 10000);
        }

        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(),
                MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE);
        int regionChunkEnd = getChunkId(region.getEnd(),
                MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds").is(getChunkIdPrefix(region.getChromosome(),
                    region.getStart(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosomeInfo() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds);
        /****/

        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());
    }

    List<QueryResult> queryResults = executeQueryList2(ids, queries, options, conservationMongoDBCollection);
    //        List<QueryResult<ConservationScoreRegion>> conservationQueryResults = new ArrayList<>();
    List<QueryResult<GenomicScoreRegion<Float>>> conservationQueryResults = new ArrayList<>();

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        //            QueryResult<ConservationScoreRegion> conservationQueryResult = new QueryResult<>();
        QueryResult<GenomicScoreRegion<Float>> conservationQueryResult = new QueryResult<>();

        //            BasicDBList list = (BasicDBList) queryResult.getResult();
        List list = queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap<>();
        for (int j = 0; j < list.size(); j++) {
            Document chunk = (Document) list.get(j);
            String source = chunk.getString("source");
            List<Float> valuesList;
            if (!typeMap.containsKey(source)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(source, valuesList);
            } else {
                valuesList = typeMap.get(source);
            }

            //                BasicDBList valuesChunk = (BasicDBList) chunk.get("values");
            ArrayList valuesChunk = chunk.get("values", ArrayList.class);

            int pos = 0;
            if (region.getStart() > chunk.getInteger("start")) {
                pos = region.getStart() - chunk.getInteger("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInteger("start") <= region.getEnd()); pos++) {
                valuesList.set(pos + chunk.getInteger("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }

        //            BasicDBList resultList = new BasicDBList();
        //            List<ConservationScoreRegion> resultList = new ArrayList<>();
        List<GenomicScoreRegion<Float>> resultList = new ArrayList<>();
        //            ConservationScoreRegion conservedRegionChunk;
        GenomicScoreRegion<Float> conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            //                conservedRegionChunk = new ConservationScoreRegion(region.getChromosome(), region.getStart(), region.getEnd(),
            //                        elem.getKey(), elem.getValue());
            conservedRegionChunk = new GenomicScoreRegion<>(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        //            queryResult.setResult(resultList);
        conservationQueryResult.setResult(resultList);
        conservationQueryResults.add(conservationQueryResult);
    }

    return conservationQueryResults;
}

From source file:org.opencb.cellbase.lib.impl.VariantMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult<Score> getFunctionalScoreVariant(Variant variant, QueryOptions queryOptions) {
    String chromosome = variant.getChromosome();
    int position = variant.getStart();
    String reference = variant.getReference();
    String alternate = variant.getAlternate();

    String chunkId = getChunkIdPrefix(chromosome, position,
            MongoDBCollectionConfiguration.VARIATION_FUNCTIONAL_SCORE_CHUNK_SIZE);
    QueryBuilder builder = QueryBuilder.start("_chunkIds").is(chunkId);
    //                .and("chromosome").is(chromosome)
    //                .and("start").is(position);
    //        System.out.println(chunkId);
    QueryResult result = executeQuery(chromosome + "_" + position + "_" + reference + "_" + alternate,
            new Document(builder.get().toMap()), queryOptions, caddDBCollection);

    //        System.out.println("result = " + result);

    List<Score> scores = new ArrayList<>();
    for (Object object : result.getResult()) {
        //            System.out.println("object = " + object);
        Document dbObject = (Document) object;
        int chunkStart = dbObject.getInteger("start");
        int chunkEnd = dbObject.getInteger("end");
        // CADD positions are not continuous through the whole chromosome. Several documents may be associated with
        // the same chunk id: we have to be sure that current document contains queried position. Only two documents
        // will contain queried position - one for raw and one for scaled values
        if (position >= chunkStart && position <= chunkEnd) {
            int offset = (position - chunkStart);
            ArrayList basicDBList = dbObject.get("values", ArrayList.class);

            //                long l1 = 0L; // TODO: delete
            //                try { // TODO: delete
            long l1 = Long.parseLong(basicDBList.get(offset).toString());
            //                                 l1 = (Long) basicDBList.get(offset);
            //                } catch (Exception e) {  // TODO: delete
            //                    logger.error("problematic variant: {}", variant.toString());
            //                    throw e;
            //                }

            if (dbObject.getString("source").equalsIgnoreCase("cadd_raw")) {
                float value = 0f;
                switch (alternate.toLowerCase()) {
                case "a":
                    //                            value = ((short) (l1 >> 48) - 10000) / DECIMAL_RESOLUTION;
                    value = (((short) (l1 >> 48)) / DECIMAL_RESOLUTION) - 10;
                    break;
                case "c":
                    value = (((short) (l1 >> 32)) / DECIMAL_RESOLUTION) - 10;
                    break;
                case "g":
                    value = (((short) (l1 >> 16)) / DECIMAL_RESOLUTION) - 10;
                    break;
                case "t":
                    value = (((short) (l1 >> 0)) / DECIMAL_RESOLUTION) - 10;
                    break;
                default:
                    break;
                }//from   w ww .j  a  v a  2 s.  co  m
                scores.add(Score.newBuilder().setScore(value).setSource(dbObject.getString("source"))
                        .setDescription(null)
                        //                        .setDescription("")
                        .build());
            }

            if (dbObject.getString("source").equalsIgnoreCase("cadd_scaled")) {
                float value = 0f;
                switch (alternate.toLowerCase()) {
                case "a":
                    value = ((short) (l1 >> 48)) / DECIMAL_RESOLUTION;
                    break;
                case "c":
                    value = ((short) (l1 >> 32)) / DECIMAL_RESOLUTION;
                    break;
                case "g":
                    value = ((short) (l1 >> 16)) / DECIMAL_RESOLUTION;
                    break;
                case "t":
                    value = ((short) (l1 >> 0)) / DECIMAL_RESOLUTION;
                    break;
                default:
                    break;
                }
                scores.add(Score.newBuilder().setScore(value).setSource(dbObject.getString("source"))
                        .setDescription(null)
                        //                        .setDescription("")
                        .build());
            }
        }
    }

    result.setResult(scores);
    return result;
}

From source file:org.opencb.cellbase.mongodb.db.ChromosomeMongoDBAdaptor.java

License:Apache License

public QueryResult speciesInfoTmp(String id, QueryOptions options) {
    // reading application.properties file

    //        String[] speciesArray = applicationProperties.getProperty("SPECIES").split(",");

    //        List<DBObject> queries = new ArrayList<>(1);
    //        for (String id : idList) {
    QueryBuilder builder = QueryBuilder.start("species").is(id);

    //        queries.add(builder.get());
    //        }/*from w  w  w  .j  a  va2 s.  c o  m*/

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQuery(id, builder.get(), options);

}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllClinvarByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(idList.size());
    options.addToListOption("include", "clinvarList");
    options.addToListOption("include", "chromosome");
    options.addToListOption("include", "start");
    options.addToListOption("include", "end");
    options.addToListOption("include", "reference");
    options.addToListOption("include", "alternate");
    for (String id : idList) {
        if (id.toLowerCase().startsWith("rcv")) {
            QueryBuilder builder = addClinvarQueryFilters(QueryBuilder
                    .start("clinvarList.clinvarSet.referenceClinVarAssertion.clinVarAccession.acc").is(id),
                    options);//from  www  .j  a  v a 2  s  .  c o  m
            queries.add(builder.get());
        } else if (id.toLowerCase().startsWith("rs")) {
            QueryBuilder builder = addClinvarQueryFilters(QueryBuilder.start(
                    "clinvarList.clinvarSet.referenceClinVarAssertion.measureSet.measure.attributeSet.xref.type")
                    .is("rs")
                    .and("clinvarList.clinvarSet.referenceClinVarAssertion.measureSet.measure.attributeSet.xref.id")
                    .is(id), options);
            queries.add(builder.get());
        }
    }
    return prepareClinvarQueryResultList(executeQueryList2(idList, queries, options));
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllClinvarByGeneList(List<String> geneList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(geneList.size());
    options.addToListOption("include", "clinvarList");
    options.addToListOption("include", "chromosome");
    options.addToListOption("include", "start");
    options.addToListOption("include", "end");
    options.addToListOption("include", "reference");
    options.addToListOption("include", "alternate");
    for (String gene : geneList) {
        QueryBuilder builder = addClinvarQueryFilters(QueryBuilder.start(
                "clinvarList.clinvarSet.referenceClinVarAssertion.measureSet.measure.measureRelationship.symbol.elementValue.value")
                .is(gene), options);/*from ww  w.  j a va2  s .  co m*/
        queries.add(builder.get());
    }

    return prepareClinvarQueryResultList(executeQueryList2(geneList, queries, options));
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private QueryBuilder addClinvarPhenotypeFilter(QueryBuilder builder, QueryOptions options) {
    List<Object> phenotypeList = options.getList("phenotype", null);
    if (phenotypeList != null && phenotypeList.size() > 0) {
        QueryBuilder phenotypeQueryBuilder = QueryBuilder.start();
        for (Object phenotype : phenotypeList) {
            String phenotypeString = (String) phenotype;
            phenotypeQueryBuilder = phenotypeQueryBuilder
                    .or(QueryBuilder.start("referenceClinVarAssertion.traitSet.trait.name.elementValue.value")
                            .text(phenotypeString).get());
        }//w  w  w .j a  v  a2 s .  c  o m
        builder = builder.and(phenotypeQueryBuilder.get());
    }
    return builder;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private QueryBuilder addClinvarRegionFilter(QueryBuilder builder, QueryOptions options) {
    List<Object> regions = options.getList("region", null);
    BasicDBList regionList = new BasicDBList();
    if (regions != null) {
        Region region = (Region) regions.get(0);
        QueryBuilder regionQueryBuilder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        for (int i = 1; i < regions.size(); i++) {
            region = (Region) regions.get(i);
            regionQueryBuilder = regionQueryBuilder.or(QueryBuilder.start("chromosome")
                    .is(region.getChromosome()).and("end").greaterThanEquals(region.getStart()).and("start")
                    .lessThanEquals(region.getEnd()).get());
        }/*w  w w  .  ja v  a  2s  .c  om*/
        builder = builder.and(regionQueryBuilder.get());
    }
    return builder;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private QueryBuilder addClinvarIdFilter(QueryBuilder builder, QueryOptions options) {
    List<Object> idList = options.getList("id", null);
    if (idList != null && idList.size() > 0) {
        QueryBuilder idQueryBuilder = QueryBuilder.start();
        for (Object id : idList) {
            String idString = (String) id;
            if (idString.toLowerCase().startsWith("rs")) {
                idQueryBuilder = idQueryBuilder.or(QueryBuilder.start(
                        "clinvarList.clinvarSet.referenceClinVarAssertion.measureSet.measure.attributeSet.xref.type")
                        .is("rs")
                        .and("clinvarList.clinvarSet.referenceClinVarAssertion.measureSet.measure.attributeSet.xref.id")
                        .is(Integer.valueOf(idString.substring(2))).get());
            } else if (idString.toLowerCase().startsWith("rcv")) {
                idQueryBuilder = idQueryBuilder.or(QueryBuilder
                        .start("clinvarList.clinvarSet.referenceClinVarAssertion.clinVarAccession.acc")
                        .is(idString).get());
            }/*from  w  ww  .  j av  a  2 s . c o  m*/
        }
        builder = builder.and(idQueryBuilder.get());
    }
    return builder;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllClinvarByRegionList(List<Region> regions, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();

    options.addToListOption("include", "clinvarList");
    options.addToListOption("include", "chromosome");
    options.addToListOption("include", "start");
    options.addToListOption("include", "end");
    options.addToListOption("include", "reference");
    options.addToListOption("include", "alternate");
    List<String> ids = new ArrayList<>(regions.size());
    for (Region region : regions) {

        // If regions is 1 position then query can be optimize using chunks
        QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        builder = addClinvarQueryFilters(builder, options);
        System.out.println(builder.get().toString());
        queries.add(builder.get());//from   w w w .  j  a v  a 2s.  c  om
        ids.add(region.toString());
    }
    return prepareClinvarQueryResultList(executeQueryList2(ids, queries, options));
}