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.GeneMongoDBAdaptor.java

License:Apache License

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

    List<Object> biotypes = options.getList("biotypes", null);
    if (biotypes != null && biotypes.size() > 0) {
        BasicDBList biotypeIds = new BasicDBList();
        biotypeIds.addAll(biotypes);/*from  w  w  w.  jav  a  2s.  co  m*/
        builder = builder.and("biotype").in(biotypeIds);
    }

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

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

License:Apache License

@Override
public QueryResult next(String chromosome, int position, QueryOptions options) {
    if (options.getString("strand") == null || options.getString("strand").equals("")
            || (options.getString("strand").equals("1") || options.getString("strand").equals("+"))) {
        // db.core.find({chromosome: "1", start: {$gt: 1000000}}).sort({start: 1}).limit(1)
        QueryBuilder builder = QueryBuilder.start("chromosome").is(chromosome).and("start")
                .greaterThanEquals(position);
        // options.put("sortAsc", "start");
        options.put("sort", new HashMap<String, String>().put("start", "asc"));
        options.put("limit", 1);
        // mongoDBCollection.find().sort(new BasicDBObject("", "")).limit(1);
        return executeQuery("result", builder.get(), options);
    } else {//from  ww  w . j a va 2s .c o m
        QueryBuilder builder = QueryBuilder.start("chromosome").is(chromosome).and("end")
                .lessThanEquals(position);
        // options.put("sortDesc", "end");
        options.put("sort", new HashMap<String, String>().put("end", "desc"));
        options.put("limit", 1);
        //              mongoDBCollection.find().sort(new BasicDBObject("", "")).limit(1);
        return executeQuery("result", builder.get(), options);
    }
}

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

License:Apache License

@Override
public List<org.opencb.datastore.core.QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    //      QueryBuilder builder = QueryBuilder.start("transcripts.xrefs.id").in(idList);

    List<DBObject> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("transcripts.xrefs.id").is(id);
        queries.add(builder.get());
    }//from   w w  w  .j  ava  2 s . com

    //        options = addExcludeReturnFields("transcripts", options);
    //        return executeQueryList(idList, queries, options);
    return executeQueryList2(idList, queries, null);
}

---

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

License:Apache License

@Override
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    /****///from  w  w w.ja v a 2s.  c om
    String chunkIdSuffix = this.chunkSize / 1000 + "k";
    /****/

    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> chunkIds;
    List<Integer> integerChunkIds;
    for (Region region : regions) {
        chunkIds = new ArrayList<>();
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        int regionChunkStart = getChunk(region.getStart());
        int regionChunkEnd = getChunk(region.getEnd());
        for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            String chunkIdStr = region.getChromosome() + "_" + chunkId + "_" + chunkIdSuffix;
            chunkIds.add(chunkIdStr);
            integerChunkIds.add(chunkId);
        }
        //            QueryBuilder builder = QueryBuilder.start("sequenceName").is(region.getChromosome()).and("_chunkIds").in(chunkIds);
        QueryBuilder builder = QueryBuilder.start("_chunkIds").in(chunkIds);
        /****/
        queries.add(builder.get());
        ids.add(region.toString());

        logger.info(builder.get().toString());
    }

    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);

        List list = queryResult.getResult();
        StringBuilder sb = new StringBuilder();
        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            sb.append(chunk.get("sequence"));
        }

        int startStr = getOffset(region.getStart());
        int endStr = getOffset(region.getStart()) + (region.getEnd() - region.getStart()) + 1;

        String subStr = "";

        if (getChunk(region.getStart()) > 0) {
            if (sb.toString().length() > 0 && sb.toString().length() >= endStr) {
                subStr = sb.toString().substring(startStr, endStr);
            }
        } else {
            if (sb.toString().length() > 0 && sb.toString().length() + 1 >= endStr) {
                subStr = sb.toString().substring(startStr - 1, endStr - 1);
            }
        }
        GenomeSequenceFeature genomeSequenceFeature = new GenomeSequenceFeature(region.getChromosome(),
                region.getStart(), region.getEnd(), 1, ((BasicDBObject) list.get(0)).getString("sequenceType"),
                ((BasicDBObject) list.get(0)).getString("assembly"), subStr);
        //            GenomeSequenceChunk genomeSequenceChunk = new GenomeSequenceChunk(region.getSequenceName(), region.getStart(), region.getEnd(), subStr);

        queryResult.setResult(Arrays.asList(genomeSequenceFeature));
    }

    return queryResults;
}

---

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

License:Apache License

public QueryResult next(String chromosome, int position, QueryOptions options,
        MongoDBCollection mongoDBCollection) {
    QueryBuilder builder;
    if (options.getString("strand") == null || options.getString("strand").equals("")
            || (options.getString("strand").equals("1") || options.getString("strand").equals("+"))) {
        builder = QueryBuilder.start("chromosome").is(chromosome).and("start").greaterThanEquals(position);
        options.put("sort", new HashMap<String, String>().put("start", "asc"));
        options.put("limit", 1);
    } else {//from  ww w.  j  a  v a 2  s . com
        builder = QueryBuilder.start("chromosome").is(chromosome).and("end").lessThanEquals(position);
        options.put("sort", new HashMap<String, String>().put("end", "desc"));
        options.put("limit", 1);
    }
    return executeQuery("result", builder.get(), options, mongoDBCollection);
}

---

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

License:Apache License

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

    List<Object> biotypes = options.getList("disease", null);
    if (biotypes != null && biotypes.size() > 0) {
        BasicDBList biotypeIds = new BasicDBList();
        biotypeIds.addAll(biotypes);/*from   w  w  w  .ja va2  s  .co m*/
        builder = builder.and("primaryHistology").in(biotypeIds);
    }

    return executeQuery("result", builder.get(), options);
}

---

From source file:org.opencb.cellbase.mongodb.db.MutationMongoDBAdaptor.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("id").is(id);
        queries.add(builder.get());
    }/*from   w w w  . j  a  v  a 2s .c  o  m*/

    return executeQueryList(idList, queries, options);
}

---

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

    return executeQueryList(idList, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.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());
    }/*  w  w w. j  a v a2  s.c  o m*/

    return executeQueryList(geneNameList, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.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  . ja  va2  s  . c  o m

    return executeQueryList(proteinIdList, queries, options);
}

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