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.core.GeneMongoDBAdaptor.java

License:Apache License

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

    List<String> biotypes = options.getAsStringList("biotype");
    if (biotypes != null && biotypes.size() > 0) {
        BasicDBList biotypeIds = new BasicDBList();
        biotypeIds.addAll(biotypes);//from  ww w.  ja v  a  2 s. com
        builder = builder.and("biotype").in(biotypeIds);
    }

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

---

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

License:Apache License

@Override
public List<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 www. j  av a 2s.c om*/

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

---

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

License:Apache License

@Override
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();

    List<Object> biotypes = options.getList("biotype", null);
    BasicDBList biotypeIds = new BasicDBList();
    if (biotypes != null && biotypes.size() > 0) {
        biotypeIds.addAll(biotypes);//from w ww.j  ava2s  .  c  o  m
    }

    List<String> ids = new ArrayList<>(regions.size());
    for (Region region : regions) {

        QueryBuilder builder = null;
        // If regions is 1 position then query can be optimize using chunks
        if (region.getStart() == region.getEnd()) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), geneChunkSize)).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 (biotypeIds.size() > 0) {
            builder = builder.and("biotype").in(biotypeIds);
        }
        queries.add(builder.get());
        ids.add(region.toString());
    }
    return executeQueryList2(ids, queries, options);
    //        return executeQueryList(ids, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.core.GenomeMongoDBAdaptor.java

License:Apache License

@Deprecated
public QueryResult speciesInfoTmp(String id, QueryOptions options) {
    // reading application.properties file

    //        String[] speciesArray = applicationProperties.getProperty("SPECIES").split(",");

    //        List<DBObject> queries = new ArrayList<>(1);
    //        for (String id : idList) {
    QueryBuilder builder = QueryBuilder.start("species").is(id);

    //        queries.add(builder.get());
    //        }//from   www  .  j a  v  a2  s  .  c o  m

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

}

---

From source file:org.opencb.cellbase.mongodb.db.core.GenomeMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllSequencesByRegionList(List<Region> regions, QueryOptions options) {
    /****//*from ww w .  j av  a  2  s  .  co  m*/
    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 = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        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, genomeSequenceCollection);
    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 (getChunkId(region.getStart(), this.chunkSize) > 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);
            }
        }
        logger.info("((BasicDBObject)list.get(0)).getString(\"sequenceType\") = {}",
                ((BasicDBObject) list.get(0)).getString("sequenceType"));
        logger.info("((BasicDBObject)list.get(0)).getString(\"assembly\") = {}",
                ((BasicDBObject) list.get(0)).getString("assembly"));
        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.core.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());
    }/*from   ww  w.  j  ava2 s .  c om*/

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

---

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

License:Apache License

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

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

---

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

License:Apache License

@Override
public List<QueryResult> getAllFunctionPredictionByEnsemblTranscriptIdList(List<String> transcriptIdList,
        QueryOptions options) {/*  www.j  a v  a  2s.c  o m*/
    List<DBObject> queries = new ArrayList<>(transcriptIdList.size());

    if (options.containsKey("aaPosition")) {
        if (options.containsKey("aaChange")) {
            addIncludeReturnFields(
                    "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 executeQueryList2(transcriptIdList, queries, options, proteinFunctionalPredictionCollection);
}

---

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

License:Apache License

public QueryResult getFunctionPredictionByAaChange(String transcriptId, Integer aaPosition, String newAa,
        QueryOptions queryOptions) {/*  w w  w. ja va 2s .  co  m*/

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

    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.core.XRefsMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getByStartsWithQueryList(List<String> ids, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();

    for (String id : ids) {
        QueryBuilder qb = QueryBuilder.start("transcripts.xrefs.id").regex(Pattern.compile("^" + id));
        queries.add(qb.get());
    }/*from   www.  j a  v a2  s  .com*/
    int limit = options.getInt("limit", 50);
    if (limit > 50) {
        options.put("limit", 50);
    }
    System.out.println(options.getInt("limit"));
    options.put("include", Arrays.asList("chromosome", "start", "end", "id", "name"));

    return executeQueryList2(ids, queries, options);
}

---

• «
• 1
• 2
• 3
• 4
• 5
• 6
• 7
• 8
• 9
• 10
• 11
• 12
• 13
• 14
• 15
• 16
• 17
• 18
• 19
• 20
• 21
• 22
• 23
• 24
• 25
• 26
• 27
• 28
• 29
• »