Example usage for com.mongodb QueryBuilder get

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.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());
            ids.add(region.toString());/*from  ww  w  . java  2  s . c  om*/
        }
        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 . j  ava  2s  .co 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);

    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);//  w  w w  .j a  v a  2  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.variation.VariationPhenotypeAnnotationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("id").is(id);
        queries.add(builder.get());
    }//from  w  w  w.j  a  v  a  2s. c o  m

    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

@Override
public QueryResult getAllByPhenotype(String phenotype, QueryOptions options) {
    QueryBuilder builder = QueryBuilder.start("phenotype").is(phenotype);
    return executeQuery(phenotype, builder.get(), options);
}

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

License:Apache License

@Override
public QueryResult getAllByGene(String gene, QueryOptions options) {
    QueryBuilder builder = QueryBuilder.start("associatedGenes").is(gene);
    return executeQuery(gene, builder.get(), options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllByGeneList(List<String> geneList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(geneList.size());
    for (String id : geneList) {
        QueryBuilder builder = QueryBuilder.start("associatedGenes").is(id);
        queries.add(builder.get());
    }/*from  w  w  w  .j a  va2 s  . co  m*/
    return executeQueryList2(geneList, queries, options);
}

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

License:Apache License

@Override
public QueryResult getAllGenesByPhenotype(String phenotype, QueryOptions options) {
    QueryBuilder builder = QueryBuilder.start("phenotype").is(phenotype);
    return executeQuery(phenotype, builder.get(), options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllGenesByPhenotypeList(List<String> phenotypeList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(phenotypeList.size());
    for (String id : phenotypeList) {
        QueryBuilder builder = QueryBuilder.start("phenotype").is(id);
        queries.add(builder.get());
    }/*from w w  w.  j a va2s.c  o m*/
    return executeQueryList2(phenotypeList, queries, options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("id").is(id);
        queries.add(builder.get());
    }/* w  w w  .  ja v a2s. c o  m*/
    return executeQueryList(idList, queries, options);
}