Example usage for com.mongodb BasicDBList BasicDBList

List of usage examples for com.mongodb BasicDBList BasicDBList

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

Prototype

BasicDBList

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Usage

From source file:org.opencb.cellbase.lib.db.regulatory.RegulatoryRegionMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult next(String chromosome, int position, QueryOptions options) {

    String featureType = options.getString("featureType", null);
    String featureClass = options.getString("featureClass", null);

    BasicDBList chunksId = new BasicDBList();
    String chunkId = chromosome + "_" + getChunkId(position, regulatoryRegionChunkSize) + "_"
            + regulatoryRegionChunkSize / 1000 + "k";
    chunksId.add(chunkId);/*from   w ww  .j  a v a2s . c  o  m*/

    // TODO: Add query to find next item considering next chunk
    // db.regulatory_region.find({ "chromosome" : "19" , "start" : { "$gt" : 62005} , "featureType"
    // : "TF_binding_site_motif"}).sort({start:1}).limit(1)

    QueryBuilder builder;
    if (options.getString("strand") == null
            || (options.getString("strand").equals("1") || options.getString("strand").equals("+"))) {
        // db.core.find({chromosome: "1", start: {$gt: 1000000}}).sort({start: 1}).limit(1)
        builder = QueryBuilder.start("_chunkIds").in(chunksId).and("chromosome").is(chromosome).and("start")
                .greaterThan(position);
        options.put("sort", new Document("start", 1));
        options.put("limit", 1);
    } else {
        builder = QueryBuilder.start("_chunkIds").in(chunksId).and("chromosome").is(chromosome).and("end")
                .lessThan(position);
        options.put("sort", new Document("end", -1));
        options.put("limit", 1);
    }

    if (featureType != null) {
        builder.and("featureType").is(featureType);
    }
    if (featureClass != null) {
        builder.and("featureClass").is(featureClass);
    }
    System.out.println(new Document(builder.get().toMap()));
    return executeQuery("result", new Document(builder.get().toMap()), options);
}

From source file:org.opencb.cellbase.lib.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

private Document getFilters(QueryOptions options) {
    Document filtersDBObject = new Document();
    if (filteringOptionsEnabled(options)) {
        Document commonFiltersDBObject = getCommonFilters(options);
        BasicDBList sourceSpecificFilterList = new BasicDBList();
        List<String> sourceContent = options.getAsStringList("source");
        if (sourceContent == null || sourceContent.isEmpty() || includeContains(sourceContent, "clinvar")) {
            sourceSpecificFilterList.add(getClinvarFilters(options));
        }/* w  w w.j av a 2s. c  o  m*/
        if (sourceContent == null || sourceContent.isEmpty() || includeContains(sourceContent, "cosmic")) {
            sourceSpecificFilterList.add(getCosmicFilters(options));
        }
        if (sourceContent == null || sourceContent.isEmpty() || includeContains(sourceContent, "gwas")) {
            sourceSpecificFilterList.add(getGwasFilters(options));
        }
        if (sourceSpecificFilterList.size() > 0 && commonFiltersDBObject != null) {
            BasicDBList filtersDBList = new BasicDBList();
            filtersDBList.add(commonFiltersDBObject);
            filtersDBList.add(new Document("$or", sourceSpecificFilterList));
            filtersDBObject.put("$and", filtersDBList);
        } else if (commonFiltersDBObject != null) {
            filtersDBObject = commonFiltersDBObject;
        } else if (sourceSpecificFilterList.size() > 0) {
            filtersDBObject = new Document("$or", sourceSpecificFilterList);
        }
    }
    return filtersDBObject;
}

From source file:org.opencb.cellbase.lib.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

private Document getCommonFilters(QueryOptions options) {
    BasicDBList filterList = new BasicDBList();
    addIfNotNull(filterList, getSoTermFilter(options.getAsStringList("so")));
    addIfNotNull(filterList, getRegionFilter(Region.parseRegions((String) options.get("region"))));
    addIfNotNull(filterList, getGeneFilter(options.getAsStringList("gene")));
    addIfNotNull(filterList, getPhenotypeFilter(options.getString("phenotype")));

    if (filterList.size() > 0) {
        return new Document("$and", filterList);
    } else {// w  w w  .ja v  a2 s. c o m
        return null;
    }
}

From source file:org.opencb.cellbase.lib.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

private Document getClinvarFilters(QueryOptions options) {
    BasicDBList filterList = new BasicDBList();
    filterList.add(new Document("source", "clinvar"));
    addIfNotNull(filterList, getClinvarRcvFilter(options.getAsStringList("rcv")));
    addIfNotNull(filterList, getClinvarRsFilter(options.getAsStringList("rs")));
    addIfNotNull(filterList, getClinvarTypeFilter(options.getAsStringList("type")));
    addIfNotNull(filterList, getClinvarReviewFilter(options.getAsStringList("review")));
    addIfNotNull(filterList, getClinvarClinicalSignificanceFilter(options.getAsStringList("significance")));

    return new Document("$and", filterList);
}

From source file:org.opencb.cellbase.lib.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

private Document getClinvarRegionFilterDBObject(List<Region> regionList) {
    BasicDBList orDBList = new BasicDBList();
    for (Region region : regionList) {
        BasicDBList andDBList = new BasicDBList();
        andDBList.add(new Document("chromosome", region.getChromosome()));
        andDBList.add(new Document("end", new Document("$gte", region.getStart())));
        andDBList.add(new Document("start", new Document("$lte", region.getEnd())));
        orDBList.add(new Document("$and", andDBList));
    }//from  w  w w. ja v  a2 s  .co  m

    return new Document("$or", orDBList);
}

From source file:org.opencb.cellbase.lib.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

private Document getClinvarRsFilter(List<String> rsStringList) {
    //        List<String> rsStringList = options.getAsStringList("rs");
    //        List<String> rsStringList = (List<String>) options.get("rs");
    if (rsStringList != null && rsStringList.size() > 0) {
        logger.info("rs filter activated, res list: " + rsStringList.toString());
        List<String> rsList = new ArrayList<>(rsStringList.size());
        for (String rsString : rsStringList) {
            rsList.add(rsString.substring(2));
        }/*w  w  w .ja va2 s.  co  m*/
        BasicDBList filterList = new BasicDBList();
        filterList.add(new Document("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.id",
                new Document("$in", rsList)));
        filterList.add(new Document("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.type", "rs"));
        return new Document("$and", filterList);
    }
    return null;
}

From source file:org.opencb.cellbase.lib.db.variation.MutationMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getAll(QueryOptions options) {
    QueryBuilder builder = new QueryBuilder();

    List<Object> biotypes = options.getList("disease", null);
    if (biotypes != null && biotypes.size() > 0) {
        BasicDBList biotypeIds = new BasicDBList();
        biotypeIds.addAll(biotypes);/*from w w  w .java  2 s  .co  m*/
        builder = builder.and("primaryHistology").in(biotypeIds);
    }

    return executeQuery("result", new Document(builder.get().toMap()), options);
}

From source file:org.opencb.cellbase.lib.db.variation.VariationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());

    // TODO: do not allow phenotype queries on the variation collection.
    // TODO: phenotype queries shall be answered by the clinicalMongoDBAdaptor
    String phenotype = options.getString("phenotype");
    if (phenotype != null && !phenotype.equals("")) {
        for (Region region : regions) {
            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                    .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
            builder = builder.and("phenotype").is(phenotype);
            queries.add(new Document(builder.get().toMap()));
            ids.add(region.toString());/* w  w w  .j  a  va  2 s  . co  m*/
        }
        return executeQueryList2(ids, queries, options, mongoVariationPhenotypeDBCollection2);
    } else {
        String consequenceTypes = options.getString("consequence_type", null);
        BasicDBList consequenceTypeDBList = new BasicDBList();
        if (consequenceTypes != null && !consequenceTypes.equals("")) {
            for (String ct : consequenceTypes.split(",")) {
                consequenceTypeDBList.add(ct);
            }
        }

        for (Region region : regions) {
            // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getSequenceName())
            // .and("end").greaterThan(region.getStart()).and("start").lessThan(region.getEnd());
            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                    .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
            if (consequenceTypeDBList.size() > 0) {
                builder = builder.and("annotation.consequenceTypes.sequenceOntologyTerms.name")
                        .in(consequenceTypeDBList);
            }
            queries.add(new Document(builder.get().toMap()));
            ids.add(region.toString());
        }

        return executeQueryList2(ids, queries, options);
    }
}

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

License:Apache License

public List<QueryResult> getAllByRegionList(List regionList, QueryOptions options) {
    //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);/*from ww  w  .j  a v  a2 s  .com*/
        }
        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());

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

    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        //            BasicDBList list = (BasicDBList) queryResult.getResult();
        List list = queryResult.getResult();

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

        //            int start = region.getStart();

        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++) {
                //                    System.out.println("valuesList SIZE = " + valuesList.size());
                //                    System.out.println("pos = " + pos);
                //                    System.out.println("DIV " + (chunk.getInt("start") - region.getStart()));
                //                    System.out.println("valuesChunk = " + valuesChunk.get(pos));
                //                    System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart()));
                valuesList.set(pos + chunk.getInteger("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        //            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);
    }

    return queryResults;
}

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

License:Apache License

@Override
@Deprecated//  w  w w . ja v a2s. co  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;
}