Example usage for com.mongodb QueryBuilder start

Introduction

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

Prototype

public static QueryBuilder start(final String key)

Source Link

Document

Creates a new query with a document key

Usage

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

License:Apache License

@Override
public List<QueryResult> getAllByEnsemblTranscriptIdList(List<String> transcriptIdList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(transcriptIdList.size());

    if (options.containsKey("aaPosition")) {
        if (options.containsKey("aaChange")) {
            addIncludeReturnFields(/*from w  ww.j a v a2s  .c  o m*/
                    "aaPositions." + options.getString("aaPosition") + "." + options.getString("aaChange"),
                    options);
        } else {
            addIncludeReturnFields("aaPositions." + options.getString("aaPosition"), options);
        }
    }

    for (String id : transcriptIdList) {
        QueryBuilder builder = QueryBuilder.start("transcriptId").is(id);
        queries.add(builder.get());
    }

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList(transcriptIdList, queries, options);
}

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

License:Apache License

public QueryResult getByAaChange(String transcriptId, Integer aaPosition, String newAa,
        QueryOptions queryOptions) {// www. ja v a2s. com

    QueryBuilder builder = QueryBuilder.start("transcriptId").is(transcriptId);
    QueryResult allChangesQueryResult = executeQuery(transcriptId, builder.get(), queryOptions);

    QueryResult proteinSubstitionScoresQueryResult = new QueryResult();
    proteinSubstitionScoresQueryResult.setDbTime(allChangesQueryResult.getDbTime());
    proteinSubstitionScoresQueryResult.setId(transcriptId + "-" + aaPosition + "-" + newAa);

    String currentAaShortName;
    Map aaPositions;
    if (allChangesQueryResult.getNumResults() > 0 && (currentAaShortName = aaShortName.get(newAa)) != null
            && (aaPositions = ((HashMap) ((BasicDBObject) allChangesQueryResult.getResult().get(0))
                    .get("aaPositions"))) != null) {
        proteinSubstitionScoresQueryResult.setNumResults(1);
        proteinSubstitionScoresQueryResult.setResult(Arrays.asList(
                ((BasicDBObject) aaPositions.get(Integer.toString(aaPosition))).get(currentAaShortName)));
    } else {
        proteinSubstitionScoresQueryResult.setNumResults(0);
    }

    return proteinSubstitionScoresQueryResult;
}

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

License:Apache License

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

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList(idList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.regulatory.RegulatoryRegionMongoDBAdaptor.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("name").is(id);
        //          System.out.println("Query: " + builder.get());
        queries.add(builder.get());//from ww  w.j a  va2 s .c  o  m
    }
    //        options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(idList, queries, 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);//from   www .j  ava 2 s . c  om
        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 a 2s  . co m*/
        }

        //            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);//ww  w .j a va  2  s . c o  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.regulatory.TfbsMongoDBAdaptor.java

License:Apache License

/**
 * PARTICULAR METHODS FOR TFBS CLASS//w  w w .j a  va  2  s. com
 */
@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("name").is(id).and("featureType").is("TF_binding_site_motif");
        //            System.out.println("Query: " + builder.get());
        queries.add(builder.get());
    }
    options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("xrefs.id").is(id);
        queries.add(builder.get());/*ww w .  ja va2s.c  o m*/
    }
    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllEffectsByVariantList(List<GenomicVariant> variants, QueryOptions options) {
    List<QueryResult> queryResults = new ArrayList<>(variants.size());
    List<DBObject> queries = new ArrayList<>(variants.size());
    for (GenomicVariant genomicVariant : variants) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(genomicVariant.getChromosome()).and("start")
                .lessThanEquals(genomicVariant.getPosition()).and("end")
                .greaterThanEquals(genomicVariant.getPosition());
        queries.add(builder.get());/*  w  ww  .j a  va2s.c  o m*/
    }

    options = addExcludeReturnFields("transcripts.xrefs", options);

    BasicDBObject returnFields = getReturnFields(options);
    BasicDBList list = executeFind(queries.get(0), returnFields, options, db.getCollection("core"));
    long dbTimeStart, dbTimeEnd;

    GenomicVariantEffectPredictor genomicVariantEffectPredictor = new GenomicVariantEffectPredictor();
    //            List<Gene> genes = jsonObjectMapper.readValue(list.toString(), new TypeReference<List<Gene>>() { });
    List<Gene> genes = new ArrayList<>();
    dbTimeStart = System.currentTimeMillis();
    List<GenomicVariantEffect> a = genomicVariantEffectPredictor.getAllEffectsByVariant(variants.get(0), genes,
            null);
    dbTimeEnd = System.currentTimeMillis();

    QueryResult queryResult = new QueryResult();
    queryResult.setDbTime(Long.valueOf(dbTimeEnd - dbTimeStart).intValue());
    queryResult.setNumResults(list.size());
    queryResult.setResult(a);

    queryResults.add(queryResult);

    return queryResults;
}