Example usage for com.mongodb BasicDBList BasicDBList

List of usage examples for com.mongodb BasicDBList BasicDBList

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

Prototype

BasicDBList

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Usage

From source file:org.obiba.magma.datasource.mongodb.converter.VariableConverter.java

License:Open Source License

public static DBObject marshall(Variable variable) {
    BasicDBObjectBuilder builder = BasicDBObjectBuilder.start() //
            .add("name", variable.getName()) //
            .add("valueType", variable.getValueType().getName()) //
            .add("entityType", variable.getEntityType()) //
            .add("mimeType", variable.getMimeType()) //
            .add("repeatable", variable.isRepeatable()) //
            .add("occurrenceGroup", variable.getOccurrenceGroup()) //
            .add("referencedEntityType", variable.getReferencedEntityType()) //
            .add("unit", variable.getUnit()).add("index", variable.getIndex());

    if (variable.hasCategories()) {
        Collection<Object> list = new BasicDBList();
        for (Category category : variable.getCategories()) {
            list.add(marshall(category));
        }//from w w w  .ja  v  a 2  s.  com
        builder.add("categories", list);
    }

    if (variable.hasAttributes()) {
        Collection<Object> list = new BasicDBList();
        for (Attribute attribute : variable.getAttributes()) {
            list.add(marshall(attribute));
        }
        builder.add("attributes", list);
    }

    return builder.get();
}

From source file:org.obiba.magma.datasource.mongodb.converter.VariableConverter.java

License:Open Source License

private static DBObject marshall(Category category) {
    BasicDBObjectBuilder builder = BasicDBObjectBuilder.start() //
            .add("name", category.getName()).add("missing", category.isMissing());
    if (category.hasAttributes()) {
        Collection<Object> list = new BasicDBList();
        for (Attribute attribute : category.getAttributes()) {
            list.add(marshall(attribute));
        }/*from   www . j  a  v  a  2  s  . c o m*/
        builder.add("attributes", list);
    }
    return builder.get();
}

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

License:Apache License

@Deprecated
@Override/*from www .  j a v  a  2 s  . c om*/
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        // Max region size is 10000bp
        if (region.getEnd() - region.getStart() > 10000) {
            region.setEnd(region.getStart() + 10000);
        }

        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), this.chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosomeInfo() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds);
        /****/

        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());

        //            logger.debug(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);
        //            BasicDBList list = (BasicDBList) queryResult.getResult();
        List list = queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            Document chunk = (Document) list.get(j);
            String source = chunk.getString("source");
            List<Float> valuesList;
            if (!typeMap.containsKey(source)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(source, valuesList);
            } else {
                valuesList = typeMap.get(source);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInteger("start")) {
                pos = region.getStart() - chunk.getInteger("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInteger("start") <= region.getEnd()); pos++) {
                //                    System.out.println("valuesList SIZE = " + valuesList.size());
                //                    System.out.println("pos = " + pos);
                //                    System.out.println("DIV " + (chunk.getInt("start") - region.getStart()));
                //                    System.out.println("valuesChunk = " + valuesChunk.get(pos));
                //                    System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart()));
                valuesList.set(pos + chunk.getInteger("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        //            ConservationScoreRegion conservedRegionChunk;
        GenomicScoreRegion<Float> conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            //                conservedRegionChunk = new ConservationScoreRegion(region.getChromosome(), region.getStart(),
            //                        region.getEnd(), elem.getKey(), elem.getValue());
            conservedRegionChunk = new GenomicScoreRegion<>(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

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

License:Apache License

@Override
public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<Integer> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);// ww  w.j a v  a 2 s  . c  om
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            //                    integerChunkIds.add(chunkId);
            //                }
            //    //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds);
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(integerChunkIds);
            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());

        //            logger.debug(builder.get().toString());

    }
    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    //        List<QueryResult> queryResults = executeQueryList(ids, queries, options);

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        List<Document> list = (List<Document>) queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            Document chunk = list.get(j);

            if (!chunk.isEmpty()) {
                BasicDBList valuesChunk = (BasicDBList) chunk.get("values");
                if (valuesChunk != null) { // TODO: temporary patch to skip empty chunks - remove as soon as conservation is reloaded
                    String source = chunk.getString("source");
                    List<Float> valuesList;
                    if (!typeMap.containsKey(source)) {
                        valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                        for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                            valuesList.add(null);
                        }
                        typeMap.put(source, valuesList);
                    } else {
                        valuesList = typeMap.get(source);
                    }

                    valuesChunk = (BasicDBList) chunk.get("values");
                    int pos = 0;
                    if (region.getStart() > chunk.getInteger("start")) {
                        pos = region.getStart() - chunk.getInteger("start");
                    }

                    for (; pos < valuesChunk.size()
                            && (pos + chunk.getInteger("start") <= region.getEnd()); pos++) {
                        valuesList.set(pos + chunk.getInteger("start") - region.getStart(),
                                new Float((Double) valuesChunk.get(pos)));
                    }
                } else {
                    continue;
                }

            }

            BasicDBList resultList = new BasicDBList();
            for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
                for (Float value : elem.getValue()) {
                    if (value != null) {
                        resultList.add(new Score(new Double(value), elem.getKey()));
                    }
                }
            }
            if (!resultList.isEmpty()) {
                queryResult.setResult(resultList);
            } else {
                queryResult.setResult(null);
            }
        }
    }
    return queryResults;
}

From source file:org.opencb.cellbase.lib.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);/*www.j ava 2  s . c o  m*/
        builder = builder.and("biotype").in(biotypeIds);
    }

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

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

License:Apache License

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

    List<Object> biotypes = options.getList("biotype", null);
    BasicDBList biotypeIds = new BasicDBList();
    if (biotypes != null && biotypes.size() > 0) {
        biotypeIds.addAll(biotypes);// w  ww  .  java2  s.  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(new Document(builder.get().toMap()));
        ids.add(region.toString());
    }
    return executeQueryList2(ids, queries, options);
    //        return executeQueryList(ids, queries, options);
}

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

License:Apache License

@Override
public QueryResult getVariantAnnotation(String ensemblTranscriptId, Integer position, String aaReference,
        String aaAlternate, QueryOptions queryOptions) {

    QueryResult queryResult = new QueryResult();
    queryResult.setId(ensemblTranscriptId + "/" + position + "/" + aaAlternate);
    long dbTimeStart = System.currentTimeMillis();

    ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation();
    proteinVariantAnnotation.setPosition(position);
    proteinVariantAnnotation.setReference(aaReference);
    proteinVariantAnnotation.setAlternate(aaAlternate);
    proteinVariantAnnotation/*from w  ww  .  ja  va2  s .  com*/
            .setSubstitutionScores(getProteinSubstitutionScores(ensemblTranscriptId, position, aaAlternate));

    QueryResult proteinVariantData = null;
    String shortAlternativeAa = aaShortName.get(aaAlternate);
    if (shortAlternativeAa != null) {
        List<Bson> pipeline = new ArrayList<>();

        //            BasicDBList andDBList1 = new BasicDBList();
        //            andDBList1.add(new Document("dbReference.id", ensemblTranscriptId));
        //            andDBList1.add(new Document("feature.location.position.position", position));
        //            andDBList1.add(new Document("feature.variation", shortAlternativeAa));
        //            pipeline.add(new Document("$match", new Document("$and", andDBList1)));

        pipeline.add(new Document("$match", new Document("dbReference.id", ensemblTranscriptId)));

        Document projection = new Document();
        projection.put("accession", 1);
        projection.put("keyword", 1);
        projection.put("feature", 1);
        pipeline.add(new Document("$project", projection));

        pipeline.add(new Document("$unwind", "$feature"));

        BasicDBList andDBList2 = new BasicDBList();
        andDBList2.add(new Document("feature.location.position.position", position));
        andDBList2.add(new Document("feature.variation", shortAlternativeAa));
        Document firstOr = new Document("$and", andDBList2);
        BasicDBList andDBList3 = new BasicDBList();
        andDBList3.add(new Document("feature.location.end.position", new Document("$gte", position)));
        andDBList3.add(new Document("feature.location.begin.position", new Document("$lte", position)));
        Document secondOr = new Document();
        secondOr.put("$and", andDBList3);
        BasicDBList orList = new BasicDBList();
        orList.add(firstOr);
        orList.add(secondOr);
        pipeline.add(new Document("$match", new Document("$or", orList)));
        //            pipeline.add(new Document("$match", firstOr));
        //
        Document groupFields = new Document();
        groupFields.put("_id", "$accession");
        groupFields.put("keyword", new Document("$addToSet", "$keyword"));
        groupFields.put("feature", new Document("$addToSet", "$feature"));
        pipeline.add(new Document("$group", groupFields));

        //TODO:terminar el pipeline de agregacion
        //            QueryBuilder builder = QueryBuilder.start("dbReference.id").is(ensemblTranscriptId)
        //                    .and("feature.location.position.position").is(position)
        //                    .and("feature.variation").is(shortAlternativeAa);
        //
        //            Document firstOr = new Document();
        //            firstOr.put("location.position.position", position);
        //            firstOr.put("variation", shortAlternativeAa);
        //
        //            BasicDBList andList = new BasicDBList();
        //            andList.add(new Document("location.end.position", new Document("$gte", position)));
        //            andList.add(new Document("location.begin.position", new Document("$lte", position)));
        //            Document secondOr = new Document();
        //            secondOr.put("$and", andList);
        //
        //            BasicDBList orList = new BasicDBList();
        //            orList.add(firstOr);
        //            orList.add(secondOr);
        //
        //            Document elemMatch = new Document();
        //            elemMatch.put("$elemMatch", new Document("$or", orList));
        //
        //            Document projection = new Document();
        //            projection.put("feature", elemMatch);
        //
        //            QueryOptions localQueryOptions = new QueryOptions();
        //            localQueryOptions.put("elemMatch",projection);
        //            localQueryOptions.put("include","accession,keyword,feature");
        //            proteinVariantData = executeQuery(ensemblTranscriptId + "_" + String.valueOf(position) + "_"
        //                            + aaAlternate, new Document(builder.get().toMap()), localQueryOptions);
        proteinVariantData = executeAggregation2(
                ensemblTranscriptId + "_" + String.valueOf(position) + "_" + aaAlternate, pipeline,
                new QueryOptions());
        if (proteinVariantData.getNumResults() > 0) {
            proteinVariantAnnotation = processProteinVariantData(proteinVariantAnnotation, shortAlternativeAa,
                    (Document) proteinVariantData.getResult().get(0));
        }
    }

    long dbTimeEnd = System.currentTimeMillis();
    queryResult.setDbTime(Long.valueOf(dbTimeEnd - dbTimeStart).intValue());

    if (proteinVariantAnnotation.getSubstitutionScores() != null
            || proteinVariantAnnotation.getUniprotAccession() != null) {
        queryResult.setNumResults(1);
        queryResult.setResult(Collections.singletonList(proteinVariantAnnotation));
    }
    return queryResult;

}

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

License:Apache License

@Override
public List<QueryResult> getAllByDBNameList(List<String> ids, QueryOptions options) {

    // Mel de romer
    //db.core.aggregate(
    //{$match: {"transcripts.xrefs.id": "ENST00000544455"}},
    //{$unwind: "$transcripts"},
    //{$unwind: "$transcripts.xrefs"},
    //{$match: {"transcripts.xrefs.dbNameShort":{$in:["go"]}}},
    //{$group:{_id:{id:"$transcripts.xrefs.id", dbNameShort:"$transcripts.xrefs.dbNameShort", description:"$transcripts.xrefs.description"}}},
    //{$project:{"_id":0,"id":"$_id.id","dbNameShort":"$_id.dbNameShort","description":"$_id.description"}})

    // Biotype if gene given: db.core.find({"transcripts.xrefs.id": "BRCA2"}, {"biotype":1})
    // Biotype if protein/transcript given: db.core.aggregate({$match: {"transcripts.xrefs.id": "ENST00000470094"}},
    // {$unwind: "$transcripts"}, {$match: {"transcripts.xrefs.id": "ENST00000470094"}}, {$group:{_id:{biotype:"$transcripts.biotype"}}},
    // {$project:{"transcripts.biotype":1}})
    List<List<Bson>> commandsList = new ArrayList<>(ids.size());
    for (String id : ids) {
        List<Bson> commands = new ArrayList<>(ids.size());

        Document match = new Document("$match", new Document("transcripts.xrefs.id", id));
        Document unwind = new Document("$unwind", "$transcripts");
        Document unwind2 = new Document("$unwind", "$transcripts.xrefs");

        commands.add(match);//from   w w w  .  j ava  2s .  c o m
        commands.add(unwind);
        commands.add(match);
        commands.add(unwind2);

        //Check dbname option exists
        List<Object> list = options.getList("dbname", null);
        if (list != null && list.size() > 0) {
            BasicDBList dbnameDBList = new BasicDBList();
            dbnameDBList.addAll(list);
            Document dbnameMatch = new Document("$match",
                    new Document("transcripts.xrefs.dbName", new Document("$in", dbnameDBList)));
            commands.add(dbnameMatch);
        }

        Document group = new Document("$group", new Document("_id",
                new Document("id", "$transcripts.xrefs.id").append("dbName", "$transcripts.xrefs.dbName")
                        .append("dbDisplayName", "$transcripts.xrefs.dbDisplayName")
                        .append("description", "$transcripts.xrefs.description")));
        commands.add(group);

        Document project = new Document("$project",
                new Document("_id", 0).append("id", "$_id.id").append("dbName", "$_id.dbName")
                        .append("dbDisplayName", "$_id.dbDisplayName")
                        .append("description", "$_id.description"));
        commands.add(project);

        //ArrayList to array
        //            Document[] commandsArray = commands.toArray(new Document[0]);

        commandsList.add(commands);
    }
    return executeAggregationList2(ids, commandsList, 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 w  w  . j a  v a 2 s.co 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);/*from  ww w.  j  a v  a  2  s. c om*/
        }

        //            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);
}