Example usage for com.mongodb BasicDBObject toString

Introduction

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

Prototype

@SuppressWarnings("deprecation")
public String toString() 

Source Link

Document

Returns a JSON serialization of this object

The output will look like: {"a":1, "b":["x","y","z"]} }

Usage

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

License:Apache License

public QueryResult getIntervalFrequencies(Region region, QueryOptions options) {
    //  MONGO QUERY TO IMPLEMENT
    //    db.variation.aggregate({$match: {$and: [{chromosome: "1"}, {start: {$gt: 251391, $lt: 2701391}}]}}, {$group: {_id: {$subtract: [{$divide: ["$start", 40000]}, {$divide: [{$mod: ["$start", 40000]}, 40000]}]}, totalCount: {$sum: 1}}})
    //        {//from  w  ww .ja v  a  2 s.  c  o m
    //            $match: {
    //                $and: [{
    //                    chromosome: "1"
    //                }, {
    //                    start: {
    //                        $gt: 251391,
    //                                $lt: 2701391
    //                    }
    //                }
    //                ]
    //            }
    //        }, {
    //            $group: {
    //                _id: {
    //                    $subtract: [{
    //                        $divide: ["$start", 40000]
    //                    }, {
    //                        $divide: [{
    //                            $mod: ["$start", 40000]
    //                        },
    //                        40000
    //                        ]
    //                    }
    //                    ]
    //                },
    //                totalCount: {
    //                    $sum: 1
    //                }
    //            }
    //        }

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

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

    BasicDBList andArr = new BasicDBList();
    andArr.add(new BasicDBObject("chromosome", region.getChromosome()));
    andArr.add(new BasicDBObject("start", start));

    BasicDBObject match = new BasicDBObject("$match", new BasicDBObject("$and", andArr));

    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);
    BasicDBObject group = new BasicDBObject("$group", g);

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

    logger.info("getIntervalFrequencies - (>_)>");
    System.out.println(options.toString());

    System.out.println(match.toString());
    System.out.println(group.toString());
    System.out.println(sort.toString());

    QueryResult<DBObject> aggregationOutput = mongoDBCollection.aggregate(Arrays.asList(match, group, sort),
            options);
    Map<Long, DBObject> ids = new HashMap<>();
    for (DBObject intervalObj : aggregationOutput.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());
        }
    }

    /****/
    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();
    queryResult.setResult(resultList);
    queryResult.setId(region.toString());
    queryResult.setResultType("frequencies");

    return queryResult;

    /***************************/
    //        QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getSequenceName()).and("end")
    //                .greaterThan(region.getStart()).and("start").lessThan(region.getEnd());
    //
    //        int numIntervals = (region.getEnd() - region.getStart()) / interval + 1;
    //        int[] intervalCount = new int[numIntervals];
    //
    //        List<Variation> variationList = executeQuery(builder.get(), Arrays.asList("id,chromosome,end,strand,type,reference,alternate,alleleString,species,assembly,source,version,transcriptVariations,xrefs,featureId,featureAlias,variantFreq,validationStatus"));
    //
    //        System.out.println("Variation index");
    //        System.out.println("numIntervals: " + numIntervals);
    //        for (Variation variation : variationList) {
    //            System.out.print("gsnp start:" + variation.getStart() + " ");
    //            if (variation.getStart() >= region.getStart() && variation.getStart() <= region.getEnd()) {
    //                int intervalIndex = (variation.getStart() - region.getStart()) / interval; // truncate
    //                System.out.print(intervalIndex + " ");
    //                intervalCount[intervalIndex]++;
    //            }
    //        }
    //        System.out.println("Variation index");
    //
    //        int intervalStart = region.getStart();
    //        int intervalEnd = intervalStart + interval - 1;
    //        BasicDBList intervalList = new BasicDBList();
    //        for (int i = 0; i < numIntervals; i++) {
    //            BasicDBObject intervalObj = new BasicDBObject();
    //            intervalObj.put("start", intervalStart);
    //            intervalObj.put("end", intervalEnd);
    //            intervalObj.put("interval", i);
    //            intervalObj.put("value", intervalCount[i]);
    //            intervalList.add(intervalObj);
    //            intervalStart = intervalEnd + 1;
    //            intervalEnd = intervalStart + interval - 1;
    //        }
    //
    //        System.out.println(region.getSequenceName());
    //        System.out.println(region.getStart());
    //        System.out.println(region.getEnd());
    //        return intervalList.toString();
}

---

From source file:org.restheart.hal.metadata.MapReduce.java

License:Open Source License

/**
 * @param aVars RequestContext.getAggregationVars()
 * @return the map function with bound aggregation variables
 *//*from w  w  w . ja v a2  s. c  o m*/
public String getResolvedMap(BasicDBObject aVars) {
    if (aVars == null || aVars.isEmpty()) {
        return map;
    } else {
        String escapedAVars = "\"" + aVars.toString().replaceAll("\"", "\\\\\\\\\"") + "\"";

        String ret = map == null ? null : map.replaceAll(Matcher.quoteReplacement("$") + "vars", escapedAVars);

        return ret;
    }
}

---

From source file:org.restheart.hal.metadata.MapReduce.java

License:Open Source License

/**
 * @param aVars RequestContext.getAggregationVars()
 * @return the reduce function with bound aggregation variables
 *//*from  www.  j av  a  2 s.c om*/
public String getResolvedReduce(BasicDBObject aVars) {
    if (aVars == null || aVars.isEmpty()) {
        return map;
    } else {
        String escapedAVars = "\"" + aVars.toString().replaceAll("\"", "\\\\\\\\\"") + "\"";

        String ret = reduce == null ? null
                : reduce.replaceAll(Matcher.quoteReplacement("$") + "vars", escapedAVars);

        return ret;
    }
}

---

From source file:org.restheart.handlers.schema.JsonMetaSchemaChecker.java

License:Open Source License

@Override
public boolean check(HttpServerExchange exchange, RequestContext context, BasicDBObject contentToCheck,
        DBObject args) {// w w w  .  j  av  a 2  s .  c o m
    if (contentToCheck == null) {
        return false;
    }

    try {
        schema.validate(new JSONObject(contentToCheck.toString()));
    } catch (ValidationException ve) {
        context.addWarning(ve.getMessage());
        ve.getCausingExceptions().stream().map(ValidationException::getMessage).forEach(context::addWarning);

        return false;
    }

    return true;
}

---

From source file:org.restheart.test.performance.LoadPutPT.java

License:Open Source License

/**
 *
 * @throws IOException/* w  w  w.ja  v  a 2  s.c  om*/
 */
public void put() throws Exception {
    BasicDBObject content = new BasicDBObject("random", Math.random());

    Response resp = httpExecutor.execute(Request.Post(url).bodyString(content.toString(), halCT)
            .addHeader(Headers.CONTENT_TYPE_STRING, Representation.HAL_JSON_MEDIA_TYPE));

    HttpResponse httpResp = resp.returnResponse();
    assertNotNull(httpResp);
    HttpEntity entity = httpResp.getEntity();
    assertNotNull(entity);
    StatusLine statusLine = httpResp.getStatusLine();
    assertNotNull(statusLine);

    assertEquals("check status code", HttpStatus.SC_CREATED, statusLine.getStatusCode());
}

---

From source file:org.sipfoundry.sipxconfig.mongo.MongoReplicaSetManager.java

License:Open Source License

public void forceReconfig() {
    try {//  ww  w .j  a  v a2 s. c o  m
        String id = "_id";
        BasicDBObject config = new BasicDBObject();
        config.put(id, "sipxecs");
        config.put("version", 1);
        BasicDBList members = new BasicDBList();
        BasicDBObject primary = new BasicDBObject();
        primary.put(id, 0);
        primary.put(HOST, format("%s:%d", m_primaryFqdn, MongoSettings.SERVER_PORT));
        primary.put("priority", 2);
        members.add(primary);
        config.put(MEMBERS, members);
        String command = format(COMMAND_FORCE_RECONFIG, config.toString());
        BasicBSONObject result = MongoUtil.runCommand(m_localDb.getDb(), command);
        MongoUtil.checkForError(result);
    } catch (MongoCommandException e) {
        LOG.warn("Failed to force replica set reconfiguration", e);
        throw new UserException("&err.failed.forceReconfig");
    }
}

---

From source file:org.socialhistoryservices.security.MongoUserDetailService.java

License:Open Source License

public void createUser(MongoUserDetails user) {

    if (user.getPassword() != null)
        user.setPassword(HashPassword.encrypt(HASH, user.getPassword()));

    final DBCollection coll = coll();
    BasicDBObject query = new BasicDBObject("username", user.getUsername());
    DBObject tmp = coll.findOne(query);/*from w  w  w  . ja va 2s  . com*/
    if (tmp != null) {
        if (user.getPassword() == null) {
            user.setPassword((String) tmp.get("password"));
        }
        if (user.getAuthorities().size() == 0) {
            BasicDBList authorities = (BasicDBList) tmp.get("authorities");
            for (Object authority : authorities) {
                user.getAuthorities()
                        .add(new org.socialhistoryservices.security.MongoAuthority((String) authority));
            }
        }
    }

    BasicDBObject document = new BasicDBObject();
    document.put("username", user.getUsername());
    document.put("password", user.getPassword());
    document.put("enabled", user.isEnabled());
    document.put("accountNonExpired", user.isAccountNonExpired());
    document.put("accountNonLocked", user.isAccountNonLocked());
    document.put("credentialsNonExpired", user.isCredentialsNonExpired());
    BasicDBList authorities = new BasicDBList();
    for (GrantedAuthority authority : user.getAuthorities()) {
        authorities.add(authority.getAuthority());
    }
    document.put("authorities", authorities);
    final WriteResult result = coll.update(query, document, true, false, WriteConcern.SAFE);
    if (result.getN() == 0)
        log.error(new Exception("Adding the user failed: " + result.getError()));
    log.info("Persisted:\n" + document.toString());
}

---

From source file:parser.mongodbContoller.java

public void add_page_data(pageData PageData) {
    try {//from ww w . java 2 s.  com
        DB PageDataDB = MongoDbClient.getDB(PageDataDBName);

        if (!PageDataDB.collectionExists(PageDataCollectionName)) {
            DBObject DBOptions = BasicDBObjectBuilder.start().get();

            PageDataDB.createCollection(PageDataCollectionName, DBOptions);
        }

        BasicDBObject PageDataDocument = new BasicDBObject();
        //adds page url
        PageDataDocument.append("Web_Url", PageData.getPageUrl());
        //adds page description
        if (PageData.getPageDescription() != null) {
            PageDataDocument.append("Page_Description", PageData.getPageDescription());

        }
        //adds keyword frequencies
        if (PageData.get_keyword_frequencies_map() != null) {
            PageDataDocument.append("Keywords", new BasicDBObject(PageData.get_keyword_frequencies_map()));
        }
        //adds term frequencies
        if (PageData.get_term_frequencies_map() != null) {
            PageDataDocument.append("Terms", new BasicDBObject(PageData.get_term_frequencies_map()));
        }
        System.out.println("Inserting; \n " + PageDataDocument.toString());
        System.out.println("Inserted " + PageDataDB.getCollection(PageDataCollectionName)
                .insert(PageDataDocument, WriteConcern.FSYNCED).getN() + " Documents");

        System.out.println("Last error:\n" + PageDataDB.getLastError());

    } catch (Exception e) {
        e.printStackTrace();
    }
}

---

From source file:project.ac.mongoservice.MongoDB.java

/**
 * Web service operation/*from   w ww.  j  av  a  2s .c  o  m*/
 *
 * @param className
 * @param atribute
 * @param data
 * @return
 */
//<editor-fold defaultstate="collapsed" desc="Metodo :: find(String, String, String)">
@WebMethod(operationName = "find")
public String find(@WebParam(name = "className") String className, @WebParam(name = "atribute") String atribute,
        @WebParam(name = "data") String data) {
    LinkedList<BasicDBObject> r;
    String found = "";

    try {
        BasicDBObject obj = (BasicDBObject) Class.forName(className).newInstance();
        DBObject fileData = chargeJson();
        MongoHandler mongoHandler = new MongoHandler("service", fileData);
        r = (LinkedList<BasicDBObject>) mongoHandler.find(obj.getClass(), atribute, data);

        if (r.size() == 0) {
            return "Object not Found or Doesnt Exist";
        } else {
            for (BasicDBObject ob : r) {
                found += ob.toString() + "&&";
            }
            return found;
        }
    } catch (UnknownHostException ex) {
        return "Object Coundnt be Found";
    } catch (ClassNotFoundException | InstantiationException | IllegalAccessException ex) {
        return "The Class Coundnt be Charged";
    }
}

---

From source file:project.ac.mongoservice.MongoDB.java

/**
 * Web service operation//from   www. j  a  v  a2 s. c  o m
 *
 * @param className
 * @return
 */
//<editor-fold defaultstate="collapsed" desc="Metodo :: findAll(String)">
@WebMethod(operationName = "findAll")
public String findAll(@WebParam(name = "className") String className) {
    LinkedList<BasicDBObject> rAll;
    String foundAll = "";

    try {
        BasicDBObject obj = (BasicDBObject) Class.forName(className).newInstance();
        DBObject fileData = chargeJson();
        MongoHandler mongoHandler = new MongoHandler("service", fileData);
        rAll = (LinkedList<BasicDBObject>) mongoHandler.findAll(obj.getClass());

        if (rAll.size() == 0) {
            return "Objects not Found or Dont Exist";
        } else {
            for (BasicDBObject ob : rAll) {
                foundAll += ob.toString() + "&&";
            }
            return foundAll;
        }
    } catch (UnknownHostException ex) {
        return "Objects Coundnt be Found";
    } catch (ClassNotFoundException | InstantiationException | IllegalAccessException ex) {
        return "The Class Coundnt be Charged";
    }
}

---

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