Example usage for com.mongodb QueryBuilder get

List of usage examples for com.mongodb QueryBuilder get

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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.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());
    }/*ww  w  .  j  a va2s .c  o m*/
    return executeQueryList(idList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.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);
        }/*from   w  w  w.  j ava2 s  . com*/
    }
    return executeQuery("result", builder.get(), options, mongoVariationPhenotypeDBCollection);
}

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  ww w  .  jav  a 2s . 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 executeQueryList(ids, queries, options, db.getCollection("variation_phenotype_annotation"));
}

From source file:org.opencb.cellbase.mongodb.db.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, mongoVariationPhenotypeDBCollection);
}

From source file:org.opencb.cellbase.mongodb.db.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());
    }/* w  w  w .j  a v a  2  s  . c  o m*/
    return executeQueryList(phenotypeList, queries, options, mongoVariationPhenotypeDBCollection);
}

From source file:org.opencb.cellbase.mongodb.db.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  www . j a va 2 s . c om*/
        }
        return executeQueryList(ids, queries, options, db.getCollection("variation_phenotype_annotation"));
    } 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 executeQueryList(ids, queries, options);
    }
}

From source file:org.opencb.cellbase.mongodb.db.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);//from   w  w w .  ja va 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, mongoDBCollection2);

    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.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);/*from   w w  w . j  av  a 2s  . 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, mongoDBCollection2);
    //        results = executeQueryList(variations, queries, options, mongoDBCollection);

    return results;
}

From source file:org.opencb.cellbase.mongodb.db.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());
    }/*  w  w w  . java 2  s. co m*/

    return executeQueryList(idList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.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  v  a 2  s  . com*/
    return executeQueryList(geneList, queries, options);
}