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)

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Document

Equivalent to an $and operand

Usage

From source file:org.opencb.cellbase.mongodb.db.network.ProteinProteinInteractionMongoDBAdaptor.java

License:Apache License

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

    // Fiilter all by interactor ID
    List<Object> interactors = options.getList("interactor", null);
    if (interactors != null && interactors.size() > 0) {
        BasicDBList interactorDBList = new BasicDBList();
        interactorDBList.addAll(interactors);

        BasicDBList or = new BasicDBList();
        DBObject orA = new BasicDBObject("interactorA.xrefs.id", new BasicDBObject("$in", interactorDBList));
        DBObject orB = new BasicDBObject("interactorB.xrefs.id", new BasicDBObject("$in", interactorDBList));
        or.add(orA);/* www. j  ava 2s.  c  o  m*/
        or.add(orB);
        //            builder = builder.or(orA, orB);
        builder = builder.and(new BasicDBObject("$or", or));
    }

    // Filter all by Interaction Type (name and PSIMI)
    List<Object> type = options.getList("type", null);
    if (type != null && type.size() > 0) {
        BasicDBList typeDBList = new BasicDBList();
        typeDBList.addAll(type);

        BasicDBList or = new BasicDBList();
        DBObject orName = new BasicDBObject("type.name", new BasicDBObject("$in", typeDBList));
        DBObject orPsimi = new BasicDBObject("type.psimi", new BasicDBObject("$in", typeDBList));
        or.add(orName);
        or.add(orPsimi);
        //            builder = builder.or(orName, orPsimi);
        builder = builder.and(new BasicDBObject("$or", or));
    }

    // Filter all by source database
    List<Object> database = options.getList("database", null);
    if (database != null && database.size() > 0) {
        BasicDBList databaseDBList = new BasicDBList();
        databaseDBList.addAll(database);
        builder = builder.and("source.name").in(databaseDBList);
    }

    // Filter all by detection method (name and PSIMI)
    List<Object> detectionMethod = options.getList("detectionMethod", null);
    if (detectionMethod != null && detectionMethod.size() > 0) {
        BasicDBList detectionMethodDBList = new BasicDBList();
        detectionMethodDBList.addAll(detectionMethod);

        BasicDBList or = new BasicDBList();
        DBObject orName = new BasicDBObject("detectionMethod.name",
                new BasicDBObject("$in", detectionMethodDBList));
        DBObject orPsimi = new BasicDBObject("detectionMethod.psimi",
                new BasicDBObject("$in", detectionMethodDBList));
        or.add(orName);
        or.add(orPsimi);
        //            builder = builder.or(orName, orPsimi);
        builder = builder.and(new BasicDBObject("$or", or));
    }

    // Filter all by status
    List<Object> status = options.getList("status", null);
    if (status != null && status.size() > 0) {
        BasicDBList statusDBList = new BasicDBList();
        statusDBList.addAll(status);
        builder = builder.and("status").in(statusDBList);
    }

    //        List<Object> type = options.getList("type", null);
    //        if (type != null && type.size() > 0) {
    //            BasicDBList typeDBList = new BasicDBList();
    //            typeDBList.addAll(type);
    //            builder = builder.and("type.name").in(typeDBList);
    //        }

    //        String type = options.getString("type", null);
    //        if (type != null && !type.equals("")) {
    //            builder = builder.and("type.name").is(type);
    //        }

    System.out.println(builder.get().toString());
    //      options = addExcludeReturnFields("transcripts", options);
    return executeQuery("result", builder.get(), options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllByPositionList(List<Position> positionList, QueryOptions options) {
    //  db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156})

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

    List<DBObject> queries = new ArrayList<>();
    for (Position position : positionList) {
        String chunkId = position.getChromosome() + "_"
                + getChunkId(position.getPosition(), regulatoryRegionChunkSize) + "_"
                + regulatoryRegionChunkSize / 1000 + "k";
        BasicDBList chunksId = new BasicDBList();
        chunksId.add(chunkId);/*  w  w w . j a  va 2  s.  co  m*/
        QueryBuilder builder = QueryBuilder.start("_chunkIds").in(chunksId).and("start")
                .is(position.getPosition());
        if (featureType != null) {
            builder.and("featureType").is(featureType);
        }
        if (featureClass != null) {
            builder.and("featureClass").is(featureClass);
        }

        //        System.out.println("Query: " + builder.get());
        queries.add(builder.get());
    }

    System.out.println("Query: " + queries);

    //        options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(positionList, queries, options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllByRegionList(List<Region> regionList, QueryOptions options) {
    //  db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156})
    QueryBuilder builder = new QueryBuilder();

    List<Object> featureType = options.getAsList("featureType");
    List<Object> featureClass = options.getAsList("featureClass");

    //        options = addExcludeReturnFields("chunkIds", options);

    List<DBObject> queries = new ArrayList<>();
    for (Region region : regionList) {
        int firstChunkId = getChunkId(region.getStart(), regulatoryRegionChunkSize);
        int lastChunkId = getChunkId(region.getEnd(), regulatoryRegionChunkSize);
        BasicDBList chunksId = new BasicDBList();
        for (int j = firstChunkId; j <= lastChunkId; j++) {
            String chunkId = region.getChromosome() + "_" + j + "_" + regulatoryRegionChunkSize / 1000 + "k";
            chunksId.add(chunkId);/*from   ww  w .  j a  v a2s  .  c  om*/
        }

        //            logger.info(chunksId.toString());

        builder = builder.start("_chunkIds").in(chunksId).and("start").lessThanEquals(region.getEnd())
                .and("end").greaterThanEquals(region.getStart());

        if (featureType != null && featureType.size() > 0) {
            BasicDBList featureTypeDBList = new BasicDBList();
            featureTypeDBList.addAll(featureType);
            builder = builder.and("featureType").in(featureTypeDBList);
        }

        if (featureClass != null && featureClass.size() > 0) {
            BasicDBList featureClassDBList = new BasicDBList();
            featureClassDBList.addAll(featureClass);
            builder = builder.and("featureClass").in(featureClassDBList);
        }

        queries.add(builder.get());
    }
    //        System.out.println(">>"+regionList);
    //        System.out.println(">>"+builder.get().toString());
    return executeQueryList2(regionList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.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  a 2 s  .co 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 BasicDBObject("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 BasicDBObject("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(builder.get());
    return executeQuery("result", builder.get(), options);
}

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

License:Apache License

private QueryBuilder addClinvarFilters(QueryBuilder builder, QueryOptions options) {
    List<DBObject> filterSteps = new ArrayList<>();
    builder.and(new BasicDBObject("clinvarSet", new BasicDBObject("$exists", 1)));
    builder = addClinvarRcvFilter(builder, options);
    builder = addClinvarRsFilter(builder, options);
    builder = addClinvarSoTermFilter(builder, options);
    builder = addClinvarTypeFilter(builder, options);
    builder = addClinvarReviewFilter(builder, options);
    builder = addClinvarClinicalSignificanceFilter(builder, options);
    builder = addClinvarRegionFilter(builder, options);
    builder = addClinvarGeneFilter(builder, options);
    builder = addClinvarPhenotypeFilter(builder, options);
    ///*w ww  .j a  v  a 2  s . c  o  m*/
    //        // Filtering steps repeated twice to avoid undwind over all clinical records
    //        pipeline.addAll(filterSteps);
    ////        pipeline.add(new BasicDBObject("$unwind", "$clinvarList"));
    ////        pipeline.addAll(filterSteps);
    //        pipeline.add(new BasicDBObject("$limit", 100));

    return builder;
}

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

License:Apache License

private QueryBuilder addClinvarPhenotypeFilter(QueryBuilder builder, QueryOptions options) {
    List<String> phenotypeList = options.getAsStringList("phenotype", "\\|");
    if (phenotypeList != null && phenotypeList.size() > 0) {
        logger.info("phenotype filter activated, phenotype list: " + phenotypeList.toString());

        builder = builder.and(
                new BasicDBObject("clinvarSet.referenceClinVarAssertion.traitSet.trait.name.elementValue.value",
                        new BasicDBObject("$in", getClinvarPhenotypeRegex(phenotypeList))));

    }/* w  w  w  .j  ava  2 s . c om*/
    return builder;
}

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

License:Apache License

private QueryBuilder addClinvarGeneFilter(QueryBuilder builder, QueryOptions options) {
    //        List<String> geneList = (List<String>) options.get("gene");
    List<String> geneList = options.getAsStringList("gene");
    System.out.println("geneList = " + geneList);
    if (geneList != null && geneList.size() > 0) {
        logger.info("gene filter activated, gene list: " + geneList.toString());
        builder = builder.and(new BasicDBObject(
                "clinvarSet.referenceClinVarAssertion.measureSet.measure.measureRelationship.symbol.elementValue.value",
                new BasicDBObject("$in", geneList)));
    }//  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

private QueryBuilder addClinvarRegionFilter(QueryBuilder builder, QueryOptions options) {
    List<Region> regionList = Region.parseRegions((String) options.get("region"));
    //        List<Region> regionList = (List<Region>) options.get("region");
    if (regionList != null && regionList.size() > 0) {
        logger.info("region filter activated, region list: " + regionList.toString());
        builder = builder.and(getClinvarRegionFilterDBObject(regionList));

    }/*from w w w  .j  a v  a  2  s  .c o m*/
    return builder;
}

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

License:Apache License

private QueryBuilder addClinvarClinicalSignificanceFilter(QueryBuilder builder, QueryOptions options) {
    List<String> clinicalSignificanceList = (List<String>) options.getAsStringList("significance");
    //        List<String> clinicalSignificanceList = (List<String>) options.get("significance");
    if (clinicalSignificanceList != null && clinicalSignificanceList.size() > 0) {
        for (int i = 0; i < clinicalSignificanceList.size(); i++) {
            clinicalSignificanceList.set(i, clinicalSignificanceList.get(i).replace("_", " "));
        }/*  w w w .  j a  va2s .c om*/
        logger.info("Clinical significance filter activated, clinical significance list: "
                + clinicalSignificanceList.toString());
        builder = builder
                .and(new BasicDBObject("clinvarSet.referenceClinVarAssertion.clinicalSignificance.description",
                        new BasicDBObject("$in", clinicalSignificanceList)));
    }
    return builder;
}

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

License:Apache License

private QueryBuilder addClinvarReviewFilter(QueryBuilder builder, QueryOptions options) {
    List<String> reviewStatusList = (List<String>) options.getAsStringList("review");
    //        List<String> reviewStatusList = (List<String>) options.get("review");
    if (reviewStatusList != null && reviewStatusList.size() > 0) {
        for (int i = 0; i < reviewStatusList.size(); i++) {
            reviewStatusList.set(i, reviewStatusList.get(i).toUpperCase());
        }//from   w  ww  . j a  v a2  s.  com
        logger.info("Review staus filter activated, review status list: " + reviewStatusList.toString());
        builder = builder
                .and(new BasicDBObject("clinvarSet.referenceClinVarAssertion.clinicalSignificance.reviewStatus",
                        new BasicDBObject("$in", reviewStatusList)));
    }
    return builder;
}