Example usage for com.mongodb BasicDBObjectBuilder start

Introduction

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

Prototype

public static BasicDBObjectBuilder start() 

Source Link

Document

Creates a builder intialized with an empty document.

Usage

From source file:org.obiba.magma.datasource.mongodb.MongoDBValueTable.java

License:Open Source License

/**
 * Drop the files from the {@link com.mongodb.gridfs.GridFS} for this table.
 *//* w  w w.ja va2s  .  com*/
private void dropFiles() {
    GridFS gridFS = getMongoDBDatasource().getMongoDBFactory().getGridFS();
    BasicDBObjectBuilder metaDataQuery = BasicDBObjectBuilder.start() //
            .add("metadata.datasource", getDatasource().getName()) //
            .add("metadata.table", getName());
    gridFS.remove(metaDataQuery.get());
}

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From source file:org.obiba.magma.datasource.mongodb.MongoDBVariableValueSourceFactory.java

License:Open Source License

@Override
public Set<VariableValueSource> createSources() {
    ImmutableSet.Builder<VariableValueSource> builder = ImmutableSet.builder();
    try (DBCursor variableCursor = table.getVariablesCollection().find(new BasicDBObject())
            .sort(BasicDBObjectBuilder.start().add("_id", 1).get())) {
        while (variableCursor.hasNext()) {
            builder.add(new MongoDBVariableValueSource(table, variableCursor.next().get("name").toString()));
        }/*from w  w  w. j a  v a2s .  c  o  m*/
    }
    return builder.build();
}

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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  ww  .ja  v a2  s  .  co 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);
    }
}

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

License:Apache License

private QueryResult _getAllIntervalFrequencies(Region region, QueryOptions options) {
    long startTime = System.currentTimeMillis();
    MongoDBCollection collection = mongoDataStore.getCollection(CoverageMongoDBWriter.COVERAGE_COLLECTION_NAME);

    int size = region.getEnd() - region.getStart();
    String fileId = options.getString(QO_FILE_ID);
    //        boolean histogram = options.getBoolean(QO_HISTOGRAM, size < 2000);
    boolean histogram = true;
    int batchSize = histogram ? options.getInt(QO_INTERVAL_SIZE, 1000) : 1000;
    String batchName = MeanCoverage.sizeToNameConvert(batchSize);

    String coverageType;//from w  w  w  . ja v  a  2 s .  c o m
    ComplexTypeConverter complexTypeConverter;
    if (histogram) {
        complexTypeConverter = new DBObjectToMeanCoverageConverter();
        coverageType = CoverageMongoDBWriter.AVERAGE_FIELD;
    } else {
        complexTypeConverter = new DBObjectToRegionCoverageConverter();
        coverageType = CoverageMongoDBWriter.COVERAGE_FIELD;
    }
    List<String> regions = new LinkedList<>();

    for (int i = region.getStart() / batchSize; i <= (region.getEnd() - 1) / batchSize; i++) {
        regions.add(region.getChromosome() + "_" + i + "_" + batchName);
    }

    //db.alignment.find( { _id:{$in:regions}}, { files: {$elemMatch : {id:fileId} }, "files.cov":0 , "files.id":0 } )}
    DBObject query = new BasicDBObject(CoverageMongoDBWriter.ID_FIELD, new BasicDBObject("$in", regions));
    DBObject projection = BasicDBObjectBuilder.start()
            //                .append(CoverageMongoWriter.FILES_FIELD+"."+CoverageMongoWriter.FILE_ID_FIELD,fileId)
            .append(CoverageMongoDBWriter.FILES_FIELD,
                    new BasicDBObject("$elemMatch",
                            new BasicDBObject(CoverageMongoDBWriter.FILE_ID_FIELD, fileId)))
            .append(CoverageMongoDBWriter.FILES_FIELD + "." + coverageType, true)

            //.append(CoverageMongoWriter.FILES_FIELD+"."+DBObjectToRegionCoverageConverter.COVERAGE_FIELD, true)
            //.append(CoverageMongoWriter.FILES_FIELD+"."+DBObjectToMeanCoverageConverter.AVERAGE_FIELD, true)
            //.append(CoverageMongoWriter.FILES_FIELD+"."+CoverageMongoWriter.FILE_ID_FIELD, true)
            .get();

    System.out.println("db." + CoverageMongoDBWriter.COVERAGE_COLLECTION_NAME + ".find(" + query.toString()
            + ", " + projection.toString() + ")");

    QueryResult queryResult = collection.find(query, projection, complexTypeConverter, null);
    queryResult.setId(region.toString());
    queryResult.setTime((int) (System.currentTimeMillis() - startTime));
    return queryResult;
}

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From source file:org.opentaps.notes.repository.impl.NoteRepositoryImpl.java

License:Open Source License

private static BasicDBObject noteToDbObject(Note note) {
    if (note == null) {
        return null;
    }/* www  .ja  v  a2s.co  m*/
    BasicDBObject noteDoc = (BasicDBObject) BasicDBObjectBuilder.start()
            .add(Note.Fields.noteId.getName(), note.getNoteId())
            .add(Note.Fields.noteText.getName(), note.getNoteText())
            .add(Note.Fields.clientDomain.getName(), note.getClientDomain()).get();

    User user = note.getCreatedByUser();
    if (user != null) {
        BasicDBObject userDoc = (BasicDBObject) BasicDBObjectBuilder.start().get();
        @SuppressWarnings("unchecked")
        Dictionary<String, Object> props = user.getProperties();
        if (props != null && !props.isEmpty()) {
            Enumeration<String> keys = props.keys();
            while (keys.hasMoreElements()) {
                String key = keys.nextElement();
                userDoc.append(key, props.get(key));
            }
        }
        noteDoc.append(Note.Fields.createdByUser.getName(), userDoc);
    }

    // look for custom fields
    for (String field : note.getAttributeNames()) {
        noteDoc.put(field, note.getAttribute(field));
    }

    return noteDoc;
}

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From source file:org.seadpdt.impl.ROServicesImpl.java

License:Apache License

@POST
@Path("/")
@Consumes(MediaType.APPLICATION_JSON)/*from   w ww . j a  va 2s. c o  m*/
@Produces(MediaType.APPLICATION_JSON)
public Response startROPublicationProcess(String publicationRequestString,
        @QueryParam("requestUrl") String requestURL, @QueryParam("oreId") String oreId)
        throws URISyntaxException {
    String messageString = "";
    Document request = Document.parse(publicationRequestString);
    Document content = (Document) request.get("Aggregation");
    if (content == null) {
        messageString += "Missing Aggregation ";
    }
    Document preferences = (Document) request.get("Preferences");
    if (preferences == null) {
        messageString += "Missing Preferences ";
    }
    Object repository = request.get("Repository");
    if (repository == null) {
        messageString += "Missing Respository ";
    } else {
        FindIterable<Document> iter = repositoriesCollection.find(new Document("orgidentifier", repository));
        if (iter.first() == null) {
            messageString += "Unknown Repository: " + repository + " ";
        }

    }

    if (messageString.equals("")) {
        // Get organization from profile(s)
        // Add to base document
        Object creatorObject = content.get("Creator");
        String ID = (String) content.get("Identifier");
        BasicBSONList affiliations = new BasicBSONList();
        if (creatorObject != null) {
            if (creatorObject instanceof ArrayList) {
                Iterator<String> iter = ((ArrayList<String>) creatorObject).iterator();

                while (iter.hasNext()) {
                    String creator = iter.next();
                    List<String> orgs = getOrganizationforPerson(creator);
                    if (!orgs.isEmpty()) {
                        affiliations.addAll(orgs);
                    }
                }

            } else {
                // BasicDBObject - single value
                List<String> orgs = getOrganizationforPerson((String) creatorObject);
                if (!orgs.isEmpty()) {
                    affiliations.addAll(orgs);
                }
            }
        }

        request.append("Affiliations", affiliations);

        // Add first status message

        List<DBObject> statusreports = new ArrayList<DBObject>();
        DBObject status = BasicDBObjectBuilder.start()
                .add("date", DateFormat.getDateTimeInstance().format(new Date(System.currentTimeMillis())))
                .add("reporter", Constants.serviceName).add("stage", "Receipt Acknowledged")
                .add("message", "request recorded and processing will begin").get();
        statusreports.add(status);
        request.append("Status", statusreports);
        // Create initial status message - add
        // Add timestamp
        // Generate ID - by calling Workflow?
        // Add doc, return 201

        String newMapURL = requestURL + "/" + ID + "/oremap";
        URI uri = new URI(newMapURL);
        uri = uri.normalize();
        content.put("@id", uri.toString() + "#aggregation");
        content.put("authoratativeMap", oreId);

        publicationsCollection.insertOne(request);
        URI resource = null;
        try {
            resource = new URI("./" + ID);
        } catch (URISyntaxException e) {
            // Should not happen given simple ids
            e.printStackTrace();
        }
        return Response.created(resource).entity(new Document("identifier", ID)).build();
    } else {
        return Response.status(ClientResponse.Status.BAD_REQUEST).entity(messageString).build();
    }
}

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From source file:org.sglover.checksum.dao.mongo.MongoChecksumDAO.java

License:Open Source License

private DBObject toDBObject(NodeChecksums documentChecksums) {
    BasicDBObjectBuilder checksumsObjectBuilder = BasicDBObjectBuilder.start();
    for (Map.Entry<Integer, List<Checksum>> checksums : documentChecksums.getChecksums().entrySet()) {
        List<DBObject> checksumDBObjects = new LinkedList<>();
        for (Checksum checksum : checksums.getValue()) {
            DBObject checksumDBObject = toDBObject(checksum);
            checksumDBObjects.add(checksumDBObject);
        }//from  w w w  . j av  a 2 s. c  om
        checksumsObjectBuilder.add(String.valueOf(checksums.getKey()), checksumDBObjects);
    }
    DBObject dbObject = BasicDBObjectBuilder.start("n", documentChecksums.getNodeId())
            .add("ni", documentChecksums.getNodeInternalId()).add("v", documentChecksums.getNodeVersion())
            .add("l", documentChecksums.getVersionLabel()).add("b", documentChecksums.getBlockSize())
            .add("nb", documentChecksums.getNumBlocks()).add("c", checksumsObjectBuilder.get()).get();
    return dbObject;
}

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