Example usage for com.mongodb QueryBuilder and

List of usage examples for com.mongodb QueryBuilder and

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Introduction

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

Prototype

@SuppressWarnings("unchecked")
public QueryBuilder and(final DBObject... ands)

Source Link

Document

Equivalent to an $and operand

Usage

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

License:Apache License

private QueryBuilder addClinvarTypeFilter(QueryBuilder builder, QueryOptions options) {
    List<String> typeList = (List<String>) options.getAsStringList("type");
    //        List<String> typeList = (List<String>) options.get("type");
    if (typeList != null && typeList.size() > 0) {
        for (int i = 0; i < typeList.size(); i++) {
            typeList.set(i, typeList.get(i).replace("_", " "));
        }/*www .j  a v a  2s. co m*/
        logger.info("Type filter activated, type list: " + typeList.toString());
        builder = builder.and(new BasicDBObject("clinvarSet.referenceClinVarAssertion.measureSet.measure.type",
                new BasicDBObject("$in", typeList)));
    }
    return builder;
}

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

License:Apache License

private QueryBuilder addClinvarSoTermFilter(QueryBuilder builder, QueryOptions options) {
    List<String> soList = (List<String>) options.getAsStringList("so");
    //        List<String> soList = (List<String>) options.get("so");
    if (soList != null && soList.size() > 0) {
        logger.info("So filter activated, SO list: " + soList.toString());
        builder = builder.and(
                new BasicDBObject("annot.consequenceTypes.soTerms.soName", new BasicDBObject("$in", soList)));
    }//w  w  w .  j  av a2s.co  m
    return builder;
}

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

License:Apache License

private QueryBuilder addClinvarRsFilter(QueryBuilder builder, QueryOptions options) {
    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));
        }//from  w w w  . j av  a 2s.  c o m
        builder = builder
                .and(new BasicDBObject("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.id",
                        new BasicDBObject("$in", rsList)));
        builder = builder.and(
                new BasicDBObject("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.type", "rs"));
    }
    return builder;
}

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

License:Apache License

private QueryBuilder addClinvarRcvFilter(QueryBuilder builder, QueryOptions options) {
    //        List<String> rcvList = (List<String>) options.get("rcv");
    List<String> rcvList = (List<String>) options.getAsStringList("rcv");
    if (rcvList != null && rcvList.size() > 0) {
        logger.info("rcv filter activated, rcv list: " + rcvList.toString());
        builder = builder.and(new BasicDBObject("clinvarSet.referenceClinVarAssertion.clinVarAccession.acc",
                new BasicDBObject("$in", rcvList)));
    }/*from  w ww  . ja  v  a2 s  .  c o  m*/
    return builder;
}

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

License:Apache License

@Override
public List<QueryResult> getAllByGenomicVariantList(List<GenomicVariant> variantList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(variantList.size());
    List<QueryResult> queryResultList;
    for (GenomicVariant genomicVariant : variantList) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(genomicVariant.getChromosome()).and("start")
                .is(genomicVariant.getPosition()).and("alternate").is(genomicVariant.getAlternative());
        if (genomicVariant.getReference() != null) {
            builder = builder.and("reference").is(genomicVariant.getReference());
        }/* w ww  .j  ava  2s.c  o m*/
        queries.add(builder.get());
        ids.add(genomicVariant.toString());
    }

    queryResultList = executeQueryList2(ids, queries, options);

    for (QueryResult queryResult : queryResultList) {
        List<BasicDBObject> clinicalList = (List<BasicDBObject>) queryResult.getResult();

        List<Cosmic> cosmicList = new ArrayList<>();
        List<Gwas> gwasList = new ArrayList<>();
        List<Clinvar> clinvarList = new ArrayList<>();

        for (Object clinicalObject : clinicalList) {
            BasicDBObject clinical = (BasicDBObject) clinicalObject;

            if (isCosmic(clinical)) {
                Cosmic cosmic = getCosmic(clinical);
                //                    if (cosmicList == null) {
                //                        cosmicList = new ArrayList<>();
                //                    }
                cosmicList.add(cosmic);
            } else if (isGwas(clinical)) {
                Gwas gwas = getGwas(clinical);
                //                    if (gwasList == null) {
                //                        gwasList = new ArrayList<>();
                //                    }
                gwasList.add(gwas);

            } else if (isClinvar(clinical)) {
                Clinvar clinvar = getClinvar(clinical);
                //                    if (clinvarList == null) {
                //                        clinvarList = new ArrayList<>();
                //                    }
                clinvarList.add(clinvar);
            }
        }
        Map<String, Object> clinicalData = new HashMap<>();
        if (cosmicList != null && cosmicList.size() > 0) {
            clinicalData.put("cosmic", cosmicList);
        }
        if (gwasList != null && gwasList.size() > 0) {
            clinicalData.put("gwas", gwasList);
        }
        if (clinvarList != null && clinvarList.size() > 0) {
            clinicalData.put("clinvar", clinvarList);
        }
        if (!clinicalData.isEmpty()) {
            // FIXME quick solution to compile
            //            queryResult.setResult(clinicalData);
            queryResult.setResult(Arrays.asList(clinicalData));
            queryResult.setNumResults(cosmicList.size() + clinvarList.size() + gwasList.size());
        } else {
            queryResult.setResult(null);
            queryResult.setNumResults(0);
        }
    }

    return queryResultList;
}

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

License:Apache License

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

    /**//from ww w . j a v  a 2  s  .co  m
     * If source is present in options is it parsed and prepare first,
     * otherwise ti will be done for each iteration of regions.
     */
    List<Object> source = options.getList("source", null);
    BasicDBList sourceIds = new BasicDBList();
    if (source != null && source.size() > 0) {
        sourceIds.addAll(source);
    }

    //        List<Region> regions = Region.parseRegions(options.getString("region"));
    List<String> ids = new ArrayList<>(regions.size());
    for (Region region : regions) {
        if (region != null && !region.equals("")) {
            // If regions is 1 position then query can be optimize using chunks
            if (region.getStart() == region.getEnd()) {
                String chunkId = getChunkIdPrefix(region.getChromosome(), region.getStart(),
                        variationChunkSize);
                System.out.println(chunkId);
                builder = QueryBuilder.start("_chunkIds").is(chunkId).and("end")
                        .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
            } else {
                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                        .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
            }

            if (sourceIds != null && sourceIds.size() > 0) {
                builder = builder.and("source").in(sourceIds);
            }

            queries.add(builder.get());
            ids.add(region.toString());
        }
    }
    return executeQueryList2(ids, queries, options, mongoVariationPhenotypeDBCollection2);
}

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

License:Apache License

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

    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(builder.get());/* w ww. j  a va 2s.c  om*/
            ids.add(region.toString());
        }
        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("transcriptVariations.consequenceTypes").in(consequenceTypeDBList);
            }
            queries.add(builder.get());
            ids.add(region.toString());
        }

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

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

License:Apache License

@Override
public List<QueryResult> getIdByVariantList(List<GenomicVariant> variations, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(variations.size());
    List<QueryResult> results;

    for (GenomicVariant variation : variations) {
        String chunkId = getChunkIdPrefix(variation.getChromosome(), variation.getPosition(),
                variationChunkSize);/*  w  w w  . ja  v a  2s . c om*/
        QueryBuilder builder = QueryBuilder.start("_chunkIds").is(chunkId).and("chromosome")
                .is(variation.getChromosome()).and("start").is(variation.getPosition()).and("alternate")
                .is(variation.getAlternative());
        if (variation.getReference() != null) {
            builder = builder.and("reference").is(variation.getReference());
        }

        queries.add(builder.get());
    }

    results = executeQueryList2(variations, queries, options, mongoDBCollection);

    for (QueryResult result : results) {
        List<String> idList = new LinkedList();

        BasicDBList idListObject = (BasicDBList) result.getResult();
        for (Object idObject : idListObject) {
            DBObject variantObject = (DBObject) idObject;
            idList.add(variantObject.get("id").toString());
        }

        //            result.setResult(Joiner.on(",").skipNulls().join(idList));
        result.setResult(idList);
    }

    return results;
}

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

License:Apache License

@Override
public List<QueryResult> getAllByVariantList(List<GenomicVariant> variations, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(variations.size());
    List<QueryResult> results;

    for (GenomicVariant variation : variations) {
        String chunkId = getChunkIdPrefix(variation.getChromosome(), variation.getPosition(),
                variationChunkSize);/*  www.jav  a2 s  .c o  m*/

        QueryBuilder builder = QueryBuilder.start("_chunkIds").is(chunkId).and("chromosome")
                .is(variation.getChromosome()).and("start").is(variation.getPosition()).and("alternate")
                .is(variation.getAlternative());

        if (variation.getReference() != null) {
            builder = builder.and("reference").is(variation.getReference());
        }

        queries.add(builder.get());
    }

    results = executeQueryList2(variations, queries, options, mongoDBCollection);
    //        results = executeQueryList(variations, queries, options, mongoDBCollection);

    return results;
}

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

License:Apache License

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

    /**//from  www .  ja va  2  s . c o m
     * If source is present in options is it parsed and prepare first,
     * otherwise ti will be done for each iteration of regions.
     */
    List<Object> source = options.getList("source", null);
    BasicDBList sourceIds = new BasicDBList();
    if (source != null && source.size() > 0) {
        sourceIds.addAll(source);
    }

    //        List<Region> regions = Region.parseRegions(options.getString("region"));
    List<String> ids = new ArrayList<>(regions.size());
    for (Region region : regions) {
        if (region != null && !region.equals("")) {
            // If regions is 1 position then query can be optimize using chunks
            if (region.getStart() == region.getEnd()) {
                String chunkId = getChunkIdPrefix(region.getChromosome(), region.getStart(),
                        variationChunkSize);
                System.out.println(chunkId);
                builder = QueryBuilder.start("_chunkIds").is(chunkId).and("end")
                        .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
            } else {
                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                        .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
            }

            if (sourceIds != null && sourceIds.size() > 0) {
                builder = builder.and("source").in(sourceIds);
            }

            queries.add(builder.get());
            ids.add(region.toString());
        }
    }
    return executeQueryList(ids, queries, options, db.getCollection("variation_phenotype_annotation"));
}