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.MutationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByDiseaseList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("primaryHistology").is(id);
        queries.add(builder.get());
    }/*from   w ww.  j  av a  2  s . c om*/

    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

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

    return executeQueryList2(geneNameList, queries, options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllByProteinIdList(List<String> proteinIdList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    for (String id : proteinIdList) {
        QueryBuilder builder = QueryBuilder.start("protein").is(id);
        queries.add(builder.get());
    }/*from  w  w  w . j a  v  a2 s .  c  o m*/

    return executeQueryList2(proteinIdList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.variation.MutationMongoDBAdaptor.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());
    for (Region region : regions) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
        queries.add(builder.get());
        ids.add(region.toString());//from w  ww  .j  a  va  2s  .com
    }

    return executeQueryList2(ids, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.variation.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  ww  .  j  av a  2s  .  co m
    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllByTranscriptIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("transcriptVariations.transcriptId").is(id);
        queries.add(builder.get());
    }/*from www.  j a  v  a2s .  c om*/
    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

@Override
public QueryResult getAllPhenotypes(QueryOptions options) {
    //        return executeDistinct("distinct", "phenotype", mongoVariationPhenotypeDBCollection);
    QueryBuilder builder = new QueryBuilder();
    if (options.containsKey("phenotype")) {
        String pheno = options.getString("phenotype");
        if (pheno != null && !pheno.equals("")) {
            builder = builder.start("phenotype").is(pheno);
        }//  w  ww .  j  a v  a  2  s  .c  o m
    }
    return executeQuery("result", builder.get(), options);
    //        return executeQuery("result", builder.get(), options, mongoVariationPhenotypeDBCollection);
}

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  ava2  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 executeQueryList2(ids, queries, options, mongoVariationPhenotypeDBCollection2);
}

From source file:org.opencb.cellbase.mongodb.db.variation.VariationMongoDBAdaptor.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, mongoVariationPhenotypeDBCollection2);
}

From source file:org.opencb.cellbase.mongodb.db.variation.VariationMongoDBAdaptor.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. jav a 2s . co  m*/
    return executeQueryList2(phenotypeList, queries, options, mongoVariationPhenotypeDBCollection2);
}