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.lib.db.core.ProteinMongoDBAdaptor.java

License:Apache License

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

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

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

    //<<<<<<< HEAD
    //        String currentAaShortName = aaShortName.get(newAa);
    //        Map aaPositions = ((HashMap) ((Document) allChangesQueryResult.getResult().get(0)).get("aaPositions"));
    //        if (allChangesQueryResult.getNumResults() > 0 && currentAaShortName != null && aaPositions != null) {
    //            Document positionDBObject = (Document) aaPositions.get(Integer.toString(aaPosition));
    //            if (positionDBObject != null) {
    //                Object aaObject = positionDBObject.get(currentAaShortName);
    //                if (aaObject != null) {
    //                    proteinSubstitionScoresQueryResult.setNumResults(1);
    //                    proteinSubstitionScoresQueryResult.setResult(Arrays.asList(aaObject));
    //=======
    if (allChangesQueryResult.getNumResults() > 0) {
        String currentAaShortName = aaShortName.get(newAa);
        Map aaPositions = ((HashMap) ((Document) allChangesQueryResult.getResult().get(0)).get("aaPositions"));
        if (currentAaShortName != null && aaPositions != null) {
            Document positionDBObject = (Document) aaPositions.get(Integer.toString(aaPosition));
            if (positionDBObject != null) {
                Object aaObject = positionDBObject.get(currentAaShortName);
                if (aaObject != null) {
                    proteinSubstitionScoresQueryResult.setNumResults(1);
                    proteinSubstitionScoresQueryResult.setResult(Arrays.asList(aaObject));
                } else {
                    proteinSubstitionScoresQueryResult.setErrorMsg("Unaccepted AA " + currentAaShortName
                            + ". Available AA changes for transcript " + transcriptId + ", position "
                            + aaPosition + ": " + positionDBObject.keySet().toString());
                    return proteinSubstitionScoresQueryResult;
                }
                //>>>>>>> develop
            } else {
                proteinSubstitionScoresQueryResult.setErrorMsg("Unaccepted position "
                        + Integer.toString(aaPosition) + ". Available positions for transcript " + transcriptId
                        + ": " + aaPositions.keySet().toString());
                return proteinSubstitionScoresQueryResult;
            }
        } else {
            proteinSubstitionScoresQueryResult.setNumResults(0);
        }
    }

    return proteinSubstitionScoresQueryResult;
}

---

From source file:org.opencb.cellbase.lib.db.core.XRefsMongoDBAdaptor.java

License:Apache License

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

    for (String id : ids) {
        QueryBuilder builder = QueryBuilder.start("transcripts.xrefs.id").regex(Pattern.compile("^" + id));
        queries.add(new Document(builder.get().toMap()));
    }/*  ww w.  ja v  a2  s  .  co  m*/
    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);
}

---

From source file:org.opencb.cellbase.lib.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 {// w  w w . ja  v a 2s .  co  m
        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", new Document(builder.get().toMap()), options, mongoDBCollection);
}

---

From source file:org.opencb.cellbase.lib.db.regulatory.RegulatoryRegionMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<Document> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("name").is(id);
        //          System.out.println("Query: " + new Document(builder.get().toMap()));
        queries.add(new Document(builder.get().toMap()));
    }//from  w  w w  . j  a  v  a 2s .co  m
    //        options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.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<Document> 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);// w  ww .  ja va  2 s  .  c o  m
        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: " + new Document(builder.get().toMap()));
        queries.add(new Document(builder.get().toMap()));
    }

    System.out.println("Query: " + queries);

    //        options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(positionList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.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<Document> 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);//ww w .j  a  v a  2 s  .c  o  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(new Document(builder.get().toMap()));
    }
    //        System.out.println(">>"+regionList);
    //        System.out.println(">>"+new Document(builder.get().toMap()).toString());
    return executeQueryList2(regionList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.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);//from w w  w  .j  a v a  2s . c  om

    // 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 Document("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 Document("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(new Document(builder.get().toMap()));
    return executeQuery("result", new Document(builder.get().toMap()), options);
}

---

From source file:org.opencb.cellbase.lib.db.regulatory.TfbsMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<Document> 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(new Document(builder.get().toMap()));
    }/* w  w w . j  ava  2s .  c o m*/
    options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(idList, queries, options);
}

---

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

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<Document> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("xrefs.id").is(id);
        queries.add(new Document(builder.get().toMap()));
    }//from   w  w w  .  j  a v  a  2s. c  om
    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

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

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

        QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());

        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());/*from   w  w w.jav a2  s .c  o  m*/
    }
    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
• »