Example usage for com.mongodb BasicDBList BasicDBList

List of usage examples for com.mongodb BasicDBList BasicDBList

  1. HOME
  2. Java
  3. com.mongodb
  4. com.mongodb.*
  5. BasicDBList
  6. BasicDBList

Introduction

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

Prototype

BasicDBList

Source Link

Usage

From source file:org.opencb.opencga.storage.mongodb.alignment.CoverageMongoDBWriter.java

License:Apache License

private void secureInsert(DBObject query, DBObject object, String chromosome, int start, int size) {
    boolean documentExists = true;
    boolean fileExists = true;

    //Check if the document exists
    {//from w  w w.  jav  a 2s .c  o m
        QueryResult countId = collection.count(query);
        if (countId.getNumResults() == 1 && countId.getResultType().equals(Long.class.getCanonicalName())) {
            if ((Long) countId.getResult().get(0) < 1) {
                DBObject document = BasicDBObjectBuilder.start().append(FILES_FIELD, new BasicDBList())
                        .append(CHR_FIELD, chromosome).append(START_FIELD, start).append(SIZE_FIELD, size)
                        .get();
                document.putAll(query); //{_id:<chunkId>, files:[]}
                collection.insert(document, null); //Insert a document with empty files array.
                fileExists = false;
            }
        } else {
            logger.error(countId.getErrorMsg(), countId);
        }
    }

    if (documentExists) {
        //Check if the file exists
        BasicDBObject fileQuery = new BasicDBObject(FILES_FIELD + "." + FILE_ID_FIELD, fileId);
        fileQuery.putAll(query);
        QueryResult countFile = collection.count(fileQuery);
        if (countFile.getNumResults() == 1 && countFile.getResultType().equals(Long.class.getCanonicalName())) {
            if ((Long) countFile.getResult().get(0) < 1) {
                fileExists = false;
            }
        } else {
            logger.error(countFile.getErrorMsg(), countFile);
        }
    }

    if (fileExists) {
        BasicDBObject fileQuery = new BasicDBObject(FILES_FIELD + "." + FILE_ID_FIELD, fileId);
        fileQuery.putAll(query);

        BasicDBObject fileObject = new BasicDBObject();
        for (String key : object.keySet()) {
            fileObject.put(FILES_FIELD + ".$." + key, object.get(key));
        }
        //            DBObject update = new BasicDBObject("$set", new BasicDBObject(FILES_FIELD, fileObject));
        DBObject update = new BasicDBObject("$set", fileObject);

        //db.<collectionName>.update({_id:<chunkId>  , "files.id":<fileId>}, {$set:{"files.$.<objKey>":<objValue>}})
        collection.update(fileQuery, update, updateOptions);
    } else {
        BasicDBObject fileObject = new BasicDBObject(FILE_ID_FIELD, fileId);
        fileObject.putAll(object);
        DBObject update = new BasicDBObject("$addToSet", new BasicDBObject(FILES_FIELD, fileObject));

        //db.<collectionName>.update({_id:<chunkId>} , {$addToSet:{files:{id:<fileId>, <object>}}})
        collection.update(query, update, updateOptions);
    }
}

From source file:org.opencb.opencga.storage.mongodb.variant.adaptors.VariantMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getFrequency(Query query, Region region, int regionIntervalSize) {
    // db.variants.aggregate( { $match: { $and: [ {chr: "1"}, {start: {$gt: 251391, $lt: 2701391}} ] }},
    //                        { $group: { _id: { $subtract: [ { $divide: ["$start", 20000] }, { $divide: [{$mod: ["$start", 20000]},
    // 20000] } ] },
    //                                  totalCount: {$sum: 1}}})

    QueryOptions options = new QueryOptions();

    // If interval is not provided is set to the value that returns 200 values
    if (regionIntervalSize <= 0) {
        //            regionIntervalSize = options.getInt("interval", (region.getEnd() - region.getStart()) / 200);
        regionIntervalSize = (region.getEnd() - region.getStart()) / 200;
    }/* w  ww  .j a  va2  s  .c o  m*/

    Document start = new Document("$gt", region.getStart());
    start.append("$lt", region.getEnd());

    BasicDBList andArr = new BasicDBList();
    andArr.add(new Document(DocumentToVariantConverter.CHROMOSOME_FIELD, region.getChromosome()));
    andArr.add(new Document(DocumentToVariantConverter.START_FIELD, start));

    // Parsing the rest of options
    Document mongoQuery = parseQuery(query);
    if (!mongoQuery.isEmpty()) {
        andArr.add(mongoQuery);
    }
    Document match = new Document("$match", new Document("$and", andArr));

    //        qb.and("_at.chunkIds").in(chunkIds);
    //        qb.and(DBObjectToVariantConverter.END_FIELD).greaterThanEquals(region.getStart());
    //        qb.and(DBObjectToVariantConverter.START_FIELD).lessThanEquals(region.getEnd());
    //
    //        List<String> chunkIds = getChunkIds(region);
    //        DBObject regionObject = new Document("_at.chunkIds", new Document("$in", chunkIds))
    //                .append(DBObjectToVariantConverter.END_FIELD, new Document("$gte", region.getStart()))
    //                .append(DBObjectToVariantConverter.START_FIELD, new Document("$lte", region.getEnd()));

    BasicDBList divide1 = new BasicDBList();
    divide1.add("$start");
    divide1.add(regionIntervalSize);

    BasicDBList divide2 = new BasicDBList();
    divide2.add(new Document("$mod", divide1));
    divide2.add(regionIntervalSize);

    BasicDBList subtractList = new BasicDBList();
    subtractList.add(new Document("$divide", divide1));
    subtractList.add(new Document("$divide", divide2));

    Document subtract = new Document("$subtract", subtractList);
    Document totalCount = new Document("$sum", 1);
    Document g = new Document("_id", subtract);
    g.append("features_count", totalCount);
    Document group = new Document("$group", g);
    Document sort = new Document("$sort", new Document("_id", 1));

    //        logger.info("getAllIntervalFrequencies - (>_)>");
    //        System.out.println(options.toString());
    //        System.out.println(match.toString());
    //        System.out.println(group.toString());
    //        System.out.println(sort.toString());

    long dbTimeStart = System.currentTimeMillis();
    QueryResult output = variantsCollection.aggregate(/*"$histogram", */Arrays.asList(match, group, sort),
            options);
    long dbTimeEnd = System.currentTimeMillis();

    Map<Long, Document> ids = new HashMap<>();
    // Create DBObject for intervals with features inside them
    for (Document intervalObj : (List<Document>) output.getResult()) {
        Long auxId = Math.round((Double) intervalObj.get("_id")); //is double

        Document intervalVisited = ids.get(auxId);
        if (intervalVisited == null) {
            intervalObj.put("_id", auxId);
            intervalObj.put("start", getChunkStart(auxId.intValue(), regionIntervalSize));
            intervalObj.put("end", getChunkEnd(auxId.intValue(), regionIntervalSize));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", Math.log((int) intervalObj.get("features_count")));
            ids.put(auxId, intervalObj);
        } else {
            Double sum = (Double) intervalVisited.get("features_count")
                    + Math.log((int) intervalObj.get("features_count"));
            intervalVisited.put("features_count", sum.intValue());
        }
    }

    // Create DBObject for intervals without features inside them
    BasicDBList resultList = new BasicDBList();
    int firstChunkId = getChunkId(region.getStart(), regionIntervalSize);
    int lastChunkId = getChunkId(region.getEnd(), regionIntervalSize);
    Document intervalObj;
    for (int chunkId = firstChunkId; chunkId <= lastChunkId; chunkId++) {
        intervalObj = ids.get((long) chunkId);
        if (intervalObj == null) {
            intervalObj = new Document();
            intervalObj.put("_id", chunkId);
            intervalObj.put("start", getChunkStart(chunkId, regionIntervalSize));
            intervalObj.put("end", getChunkEnd(chunkId, regionIntervalSize));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", 0);
        }
        resultList.add(intervalObj);
    }

    QueryResult queryResult = new QueryResult(region.toString(), ((Long) (dbTimeEnd - dbTimeStart)).intValue(),
            resultList.size(), resultList.size(), null, null, resultList);
    return queryResult;
}

From source file:org.opencb.opencga.storage.mongodb.variant.DBObjectToVariantConverter.java

License:Apache License

@Override
public DBObject convertToStorageType(Variant variant) {
    // Attributes easily calculated
    BasicDBObject mongoVariant = new BasicDBObject("_id", buildStorageId(variant))
            //                .append(IDS_FIELD, object.getIds())    //Do not include IDs.
            .append(CHROMOSOME_FIELD, variant.getChromosome()).append(START_FIELD, variant.getStart())
            .append(END_FIELD, variant.getEnd()).append(LENGTH_FIELD, variant.getLength())
            .append(REFERENCE_FIELD, variant.getReference()).append(ALTERNATE_FIELD, variant.getAlternate())
            .append(TYPE_FIELD, variant.getType().name());

    // Internal fields used for query optimization (dictionary named "_at")
    BasicDBObject _at = new BasicDBObject();
    mongoVariant.append("_at", _at);

    // Two different chunk sizes are calculated for different resolution levels: 1k and 10k
    BasicDBList chunkIds = new BasicDBList();
    String chunkSmall = variant.getChromosome() + "_"
            + variant.getStart() / VariantMongoDBWriter.CHUNK_SIZE_SMALL + "_"
            + VariantMongoDBWriter.CHUNK_SIZE_SMALL / 1000 + "k";
    String chunkBig = variant.getChromosome() + "_" + variant.getStart() / VariantMongoDBWriter.CHUNK_SIZE_BIG
            + "_" + VariantMongoDBWriter.CHUNK_SIZE_BIG / 1000 + "k";
    chunkIds.add(chunkSmall);/*from w  ww.  j  a  v a 2  s.c o m*/
    chunkIds.add(chunkBig);
    _at.append("chunkIds", chunkIds);

    // Transform HGVS: Map of lists -> List of map entries
    BasicDBList hgvs = new BasicDBList();
    for (Map.Entry<String, Set<String>> entry : variant.getHgvs().entrySet()) {
        for (String value : entry.getValue()) {
            hgvs.add(new BasicDBObject(HGVS_TYPE_FIELD, entry.getKey()).append(HGVS_NAME_FIELD, value));
        }
    }
    mongoVariant.append(HGVS_FIELD, hgvs);

    // Files
    if (variantSourceEntryConverter != null) {
        BasicDBList mongoFiles = new BasicDBList();
        for (VariantSourceEntry archiveFile : variant.getSourceEntries().values()) {
            mongoFiles.add(variantSourceEntryConverter.convertToStorageType(archiveFile));
        }
        mongoVariant.append(STUDIES_FIELD, mongoFiles);
    }

    //        // Annotations
    mongoVariant.append(ANNOTATION_FIELD, Collections.emptyList());
    //        if (variantAnnotationConverter != null) {
    //            if (object.getAnnotation() != null) {
    //                DBObject annotation = variantAnnotationConverter.convertToStorageType(object.getAnnotation());
    //                mongoVariant.append(ANNOTATION_FIELD, annotation);
    //            }
    //        }

    // Statistics
    if (statsConverter != null) {
        List mongoStats = statsConverter.convertCohortsToStorageType(variant.getSourceEntries());
        mongoVariant.put(STATS_FIELD, mongoStats);
    }

    return mongoVariant;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getFrequency(Query query, Region region, int regionIntervalSize) {
    // db.variants.aggregate( { $match: { $and: [ {chr: "1"}, {start: {$gt: 251391, $lt: 2701391}} ] }},
    //                        { $group: { _id: { $subtract: [ { $divide: ["$start", 20000] }, { $divide: [{$mod: ["$start", 20000]}, 20000] } ] },
    //                                  totalCount: {$sum: 1}}})

    QueryOptions options = new QueryOptions();

    // If interval is not provided is set to the value that returns 200 values
    if (regionIntervalSize <= 0) {
        //            regionIntervalSize = options.getInt("interval", (region.getEnd() - region.getStart()) / 200);
        regionIntervalSize = (region.getEnd() - region.getStart()) / 200;
    }//w ww  . ja v  a  2  s . c  o  m

    BasicDBObject start = new BasicDBObject("$gt", region.getStart());
    start.append("$lt", region.getEnd());

    BasicDBList andArr = new BasicDBList();
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.CHROMOSOME_FIELD, region.getChromosome()));
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.START_FIELD, start));

    // Parsing the rest of options
    QueryBuilder qb = new QueryBuilder();
    //        DBObject optionsMatch = parseQueryOptions(options, qb).get();
    DBObject optionsMatch = parseQuery(query, qb).get();
    if (!optionsMatch.keySet().isEmpty()) {
        andArr.add(optionsMatch);
    }
    DBObject match = new BasicDBObject("$match", new BasicDBObject("$and", andArr));

    //        qb.and("_at.chunkIds").in(chunkIds);
    //        qb.and(DBObjectToVariantConverter.END_FIELD).greaterThanEquals(region.getStart());
    //        qb.and(DBObjectToVariantConverter.START_FIELD).lessThanEquals(region.getEnd());
    //
    //        List<String> chunkIds = getChunkIds(region);
    //        DBObject regionObject = new BasicDBObject("_at.chunkIds", new BasicDBObject("$in", chunkIds))
    //                .append(DBObjectToVariantConverter.END_FIELD, new BasicDBObject("$gte", region.getStart()))
    //                .append(DBObjectToVariantConverter.START_FIELD, new BasicDBObject("$lte", region.getEnd()));

    BasicDBList divide1 = new BasicDBList();
    divide1.add("$start");
    divide1.add(regionIntervalSize);

    BasicDBList divide2 = new BasicDBList();
    divide2.add(new BasicDBObject("$mod", divide1));
    divide2.add(regionIntervalSize);

    BasicDBList subtractList = new BasicDBList();
    subtractList.add(new BasicDBObject("$divide", divide1));
    subtractList.add(new BasicDBObject("$divide", divide2));

    BasicDBObject subtract = new BasicDBObject("$subtract", subtractList);
    DBObject totalCount = new BasicDBObject("$sum", 1);
    BasicDBObject g = new BasicDBObject("_id", subtract);
    g.append("features_count", totalCount);
    DBObject group = new BasicDBObject("$group", g);
    DBObject sort = new BasicDBObject("$sort", new BasicDBObject("_id", 1));

    //        logger.info("getAllIntervalFrequencies - (>_)>");
    //        System.out.println(options.toString());
    //        System.out.println(match.toString());
    //        System.out.println(group.toString());
    //        System.out.println(sort.toString());

    long dbTimeStart = System.currentTimeMillis();
    QueryResult output = variantsCollection.aggregate(/*"$histogram", */Arrays.asList(match, group, sort),
            options);
    long dbTimeEnd = System.currentTimeMillis();

    Map<Long, DBObject> ids = new HashMap<>();
    // Create DBObject for intervals with features inside them
    for (DBObject intervalObj : (List<DBObject>) output.getResult()) {
        Long _id = Math.round((Double) intervalObj.get("_id"));//is double

        DBObject intervalVisited = ids.get(_id);
        if (intervalVisited == null) {
            intervalObj.put("_id", _id);
            intervalObj.put("start", getChunkStart(_id.intValue(), regionIntervalSize));
            intervalObj.put("end", getChunkEnd(_id.intValue(), regionIntervalSize));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", Math.log((int) intervalObj.get("features_count")));
            ids.put(_id, intervalObj);
        } else {
            Double sum = (Double) intervalVisited.get("features_count")
                    + Math.log((int) intervalObj.get("features_count"));
            intervalVisited.put("features_count", sum.intValue());
        }
    }

    // Create DBObject for intervals without features inside them
    BasicDBList resultList = new BasicDBList();
    int firstChunkId = getChunkId(region.getStart(), regionIntervalSize);
    int lastChunkId = getChunkId(region.getEnd(), regionIntervalSize);
    DBObject intervalObj;
    for (int chunkId = firstChunkId; chunkId <= lastChunkId; chunkId++) {
        intervalObj = ids.get((long) chunkId);
        if (intervalObj == null) {
            intervalObj = new BasicDBObject();
            intervalObj.put("_id", chunkId);
            intervalObj.put("start", getChunkStart(chunkId, regionIntervalSize));
            intervalObj.put("end", getChunkEnd(chunkId, regionIntervalSize));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", 0);
        }
        resultList.add(intervalObj);
    }

    QueryResult queryResult = new QueryResult(region.toString(), ((Long) (dbTimeEnd - dbTimeStart)).intValue(),
            resultList.size(), resultList.size(), null, null, resultList);

    return queryResult;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Override
@Deprecated/* ww  w. j av  a 2s.  c  om*/
public QueryResult getVariantFrequencyByRegion(Region region, QueryOptions options) {
    // db.variants.aggregate( { $match: { $and: [ {chr: "1"}, {start: {$gt: 251391, $lt: 2701391}} ] }}, 
    //                        { $group: { _id: { $subtract: [ { $divide: ["$start", 20000] }, { $divide: [{$mod: ["$start", 20000]}, 20000] } ] }, 
    //                                  totalCount: {$sum: 1}}})

    if (options == null) {
        options = new QueryOptions();
    }

    int interval = options.getInt("interval", 20000);

    BasicDBObject start = new BasicDBObject("$gt", region.getStart());
    start.append("$lt", region.getEnd());

    BasicDBList andArr = new BasicDBList();
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.CHROMOSOME_FIELD, region.getChromosome()));
    andArr.add(new BasicDBObject(DBObjectToVariantConverter.START_FIELD, start));

    // Parsing the rest of options
    QueryBuilder qb = new QueryBuilder();
    DBObject optionsMatch = parseQueryOptions(options, qb).get();
    if (!optionsMatch.keySet().isEmpty()) {
        andArr.add(optionsMatch);
    }
    DBObject match = new BasicDBObject("$match", new BasicDBObject("$and", andArr));

    //        qb.and("_at.chunkIds").in(chunkIds);
    //        qb.and(DBObjectToVariantConverter.END_FIELD).greaterThanEquals(region.getStart());
    //        qb.and(DBObjectToVariantConverter.START_FIELD).lessThanEquals(region.getEnd());
    //
    //        List<String> chunkIds = getChunkIds(region);
    //        DBObject regionObject = new BasicDBObject("_at.chunkIds", new BasicDBObject("$in", chunkIds))
    //                .append(DBObjectToVariantConverter.END_FIELD, new BasicDBObject("$gte", region.getStart()))
    //                .append(DBObjectToVariantConverter.START_FIELD, new BasicDBObject("$lte", region.getEnd()));

    BasicDBList divide1 = new BasicDBList();
    divide1.add("$start");
    divide1.add(interval);

    BasicDBList divide2 = new BasicDBList();
    divide2.add(new BasicDBObject("$mod", divide1));
    divide2.add(interval);

    BasicDBList subtractList = new BasicDBList();
    subtractList.add(new BasicDBObject("$divide", divide1));
    subtractList.add(new BasicDBObject("$divide", divide2));

    BasicDBObject substract = new BasicDBObject("$subtract", subtractList);

    DBObject totalCount = new BasicDBObject("$sum", 1);

    BasicDBObject g = new BasicDBObject("_id", substract);
    g.append("features_count", totalCount);
    DBObject group = new BasicDBObject("$group", g);

    DBObject sort = new BasicDBObject("$sort", new BasicDBObject("_id", 1));

    //        logger.info("getAllIntervalFrequencies - (>_)>");
    //        System.out.println(options.toString());
    //
    //        System.out.println(match.toString());
    //        System.out.println(group.toString());
    //        System.out.println(sort.toString());

    long dbTimeStart = System.currentTimeMillis();
    QueryResult output = variantsCollection.aggregate(/*"$histogram", */Arrays.asList(match, group, sort),
            options);
    long dbTimeEnd = System.currentTimeMillis();

    Map<Long, DBObject> ids = new HashMap<>();
    // Create DBObject for intervals with features inside them
    for (DBObject intervalObj : (List<DBObject>) output.getResult()) {
        Long _id = Math.round((Double) intervalObj.get("_id"));//is double

        DBObject intervalVisited = ids.get(_id);
        if (intervalVisited == null) {
            intervalObj.put("_id", _id);
            intervalObj.put("start", getChunkStart(_id.intValue(), interval));
            intervalObj.put("end", getChunkEnd(_id.intValue(), interval));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", Math.log((int) intervalObj.get("features_count")));
            ids.put(_id, intervalObj);
        } else {
            Double sum = (Double) intervalVisited.get("features_count")
                    + Math.log((int) intervalObj.get("features_count"));
            intervalVisited.put("features_count", sum.intValue());
        }
    }

    // Create DBObject for intervals without features inside them
    BasicDBList resultList = new BasicDBList();
    int firstChunkId = getChunkId(region.getStart(), interval);
    int lastChunkId = getChunkId(region.getEnd(), interval);
    DBObject intervalObj;
    for (int chunkId = firstChunkId; chunkId <= lastChunkId; chunkId++) {
        intervalObj = ids.get((long) chunkId);
        if (intervalObj == null) {
            intervalObj = new BasicDBObject();
            intervalObj.put("_id", chunkId);
            intervalObj.put("start", getChunkStart(chunkId, interval));
            intervalObj.put("end", getChunkEnd(chunkId, interval));
            intervalObj.put("chromosome", region.getChromosome());
            intervalObj.put("features_count", 0);
        }
        resultList.add(intervalObj);
    }

    QueryResult queryResult = new QueryResult(region.toString(), ((Long) (dbTimeEnd - dbTimeStart)).intValue(),
            resultList.size(), resultList.size(), null, null, resultList);

    return queryResult;
}

From source file:org.opendaylight.controller.samples.onftappingapp.MatchCriteria.java

License:Apache License

public BasicDBObject getAsDocument() {
    BasicDBObject document = new BasicDBObject();

    document.put("refCount", this.getReferenceCount());
    document.put("name", this.getName());
    document.put("enabled", this.getEnabled());
    document.put("reflexive", this.getReflexive());
    document.put("priority", this.getPriority());

    List<Object> matchFieldsDoc = new BasicDBList();
    for (int i = 0; i < matchFieldList.size(); i++) {
        MatchField matchField = matchFieldList.get(i);
        matchFieldsDoc.add(matchField.getAsDocument());
    }//  www .ja  v  a 2 s. c  o m
    document.put("matchFields", matchFieldsDoc);

    return document;
}

From source file:org.opendaylight.controller.samples.onftappingapp.PortRangeList.java

License:Apache License

public BasicDBObject getAsDocument() {
    BasicDBObject document = new BasicDBObject();

    List<Object> dbList = new BasicDBList();
    for (PortRange portRange : this.portList) {
        dbList.add(portRange.getAsDocument());
    }/*from w w  w.  j  a v a 2 s  .  c o m*/

    document.put("portRanges", dbList);
    return document;
}

From source file:org.opendaylight.controller.samples.onftappingapp.TapPolicy.java

License:Apache License

public BasicDBObject getAsDocument() {
    BasicDBObject document = new BasicDBObject();

    document.put("name", getName());
    document.put("description", getDescription());
    document.put("enabled", isEnabled());
    document.put("creationDate", new Date());

    // Add Match Criteria ID list Sub-document
    BasicDBList matchCriteriaListDoc = new BasicDBList();
    for (int i = 0; i < matchCriteriaIdList.size(); i++) {
        String matchCriteriaId = matchCriteriaIdList.get(i);
        matchCriteriaListDoc.add(matchCriteriaId);
    }/*from   www.  j a  v a 2s  .  c om*/
    document.put("matchCriteria", matchCriteriaListDoc);

    // Add SwitchAndPort Sub-document
    BasicDBList switchAndPortListDoc = new BasicDBList();
    for (SwitchAndPort switchAndPort : switchAndPortList) {
        switchAndPortListDoc.add(switchAndPort.getAsDocument());
    }
    document.put("switchAndPort", switchAndPortListDoc);

    // Add Capture Device Sub-document
    BasicDBList captureDevListDoc = new BasicDBList();
    for (int i = 0; i < captureDevIdList.size(); i++) {
        String captureDevId = captureDevIdList.get(i);
        captureDevListDoc.add(captureDevId);
    }
    document.put("captureDev", captureDevListDoc);

    // Add Port Chain Sub-document
    BasicDBList portChainListDoc = new BasicDBList();
    for (int i = 0; i < portChainIdList.size(); i++) {
        String portChainId = portChainIdList.get(i);
        portChainListDoc.add(portChainId);
    }
    document.put("portChain", portChainListDoc);

    return document;
}

From source file:org.opengrid.data.impl.PlenarioDataProvider.java

private String getJsonFromFilterList(String value, String key)
        throws ParseException, UnsupportedEncodingException {
    StringBuilder sb = new StringBuilder();

    BasicDBList q_list = new BasicDBList();
    q_list = (BasicDBList) JSON.parse(value);
    Iterator iter = q_list.iterator();

    if (key.equals("[$and]") || key.equals("$and")) {
        sb.append("{\"op\": \"and\", \"val\": [");
    } else {/*from w ww . ja va 2s . c o  m*/
        sb.append("{\"op\": \"or\", \"val\": [");
    }

    while (iter.hasNext()) {
        // {\"$and\":[{\"current_activity\":\"1\"},{\"police_district\":2},{\"$and\":[{\"current_activity\":\"1\"},{\"creation_date\":{\"$gt\":1474651260000}}]}]}
        LinkedHashMap<String, Object> q_filter = new LinkedHashMap<String, Object>();
        q_filter = (LinkedHashMap<String, Object>) JSON
                .parse(((LinkedHashMap<String, Object>) (iter.next())).toString());

        sb.append(getSingleFilter(q_filter));

        if (iter.hasNext()) {
            sb.append(",");
        }
    }

    sb.append("]}");

    return sb.toString();
}

From source file:org.opengrid.data.impl.PlenarioDataProvider.java

private boolean IgnoreDataset(String datasetName) {
    LinkedHashMap<String, Object> q = new LinkedHashMap<String, Object>();
    q = (LinkedHashMap<String, Object>) JSON
            .parse(FileUtil.getJsonFileContents("json/plenario_datasets_to_ignore.json"));

    for (Map.Entry<String, Object> entry : q.entrySet()) {

        BasicDBList q_list = new BasicDBList();
        q_list = (BasicDBList) JSON.parse(entry.getValue().toString());
        Iterator iter = q_list.iterator();

        while (iter.hasNext()) {
            LinkedHashMap<String, String> q_filter = new LinkedHashMap<String, String>();
            q_filter = (LinkedHashMap<String, String>) JSON
                    .parse(((LinkedHashMap<String, String>) (iter.next())).toString());
            String q_filter_key = q_filter.get("id");
            if (q_filter_key.equals(datasetName)) {
                return true;
            }/*from w w  w  .  j av  a  2 s.  c  o  m*/
        }
    }

    return false;
}