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.opencga.storage.mongodb.variant.VariantSourceMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getAllSourcesByStudyIds(List<String> studyIds, QueryOptions options) {
    MongoDBCollection coll = db.getCollection(collectionName);
    QueryBuilder qb = QueryBuilder.start();
    //        getStudyIdFilter(studyIds, qb);
    options.put("studyId", studyIds);
    parseQueryOptions(options, qb);//from  www . j  av a  2 s  .  c om

    return coll.find(qb.get(), null, variantSourceConverter, options);
}

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From source file:org.openmhealth.reference.data.mongodb.MongoAuthenticationTokenBin.java

License:Apache License

@Override
public AuthenticationToken getToken(final String token) throws OmhException {

    // Get the connection to the authentication token bin with the Jackson
    // wrapper.//from  w  w  w .jav  a2s .  c  om
    JacksonDBCollection<MongoAuthenticationToken, Object> collection = JacksonDBCollection
            .wrap(MongoDao.getInstance().getDb().getCollection(DB_NAME), MongoAuthenticationToken.class);

    // Build the query.
    QueryBuilder queryBuilder = QueryBuilder.start();

    // Add the authentication token to the query.
    queryBuilder.and(AuthenticationToken.JSON_KEY_TOKEN).is(token);

    // Add the expiration timer to ensure that this token has not expired.
    queryBuilder.and(MongoAuthenticationToken.JSON_KEY_EXPIRES).greaterThan(System.currentTimeMillis());

    // Execute query.
    DBCursor<MongoAuthenticationToken> result = collection.find(queryBuilder.get());

    // If multiple authentication tokens were returned, that is a violation
    // of the system.
    if (result.count() > 1) {
        throw new OmhException("Multiple copies of the same authentication token " + "exist: " + token);
    }

    // If no tokens were returned, then return null.
    if (result.count() == 0) {
        return null;
    } else {
        return result.next();
    }
}

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From source file:org.openmhealth.reference.data.mongodb.MongoDataSet.java

License:Apache License

@Override
public MultiValueResult<Data> getData(final String owner, final String schemaId, final long version,
        final ColumnList columnList, final long numToSkip, final long numToReturn) {

    // Get the connection to the database.
    DB db = MongoDao.getInstance().getDb();

    // Get the connection to the data with the Jackson wrapper.
    JacksonDBCollection<MongoData, Object> collection = JacksonDBCollection.wrap(db.getCollection(DB_NAME),
            MongoData.class);

    // Build the query.
    QueryBuilder queryBuilder = QueryBuilder.start();

    // Only select data for a single user.
    queryBuilder.and(Data.JSON_KEY_OWNER).is(owner);

    // Only select data for a given schema.
    queryBuilder.and(Schema.JSON_KEY_ID).is(schemaId);

    // Only select data for a given version of the the given schema.
    queryBuilder.and(Schema.JSON_KEY_VERSION).is(version);

    // Create the projection.
    DBObject projection = new BasicDBObject();
    // Add the owner field.
    projection.put(Data.JSON_KEY_OWNER, 1);
    // Add the schema ID field.
    projection.put(Schema.JSON_KEY_ID, 1);
    // Add the schema version.
    projection.put(Schema.JSON_KEY_VERSION, 1);
    // Add the meta-data field.
    projection.put(Data.JSON_KEY_METADATA, 1);
    // Add all of the data or add only the specified columns if given.
    if (columnList.size() == 0) {
        projection.put(Data.JSON_KEY_DATA, 1);
    } else {//from w w w .  j ava2s. c  om
        if ((columnList != null) && (columnList.size() > 0)) {
            for (String column : columnList.toList()) {
                projection.put(Data.JSON_KEY_DATA + ColumnList.COLUMN_SEPARATOR + column, 1);
            }
        }
    }

    // Build the query.
    DBCursor<MongoData> dbResult = collection.find(queryBuilder.get(), projection);

    // Build the sort field by sorting in reverse chronological order.
    DBObject sort = new BasicDBObject();
    sort.put(Data.JSON_KEY_METADATA + ColumnList.COLUMN_SEPARATOR + MetaData.JSON_KEY_TIMESTAMP, -1);
    dbResult.sort(sort);

    // Page the results and return the multi-value result.
    return new MongoMultiValueResultCursor<Data>(
            dbResult.skip((new Long(numToSkip)).intValue()).limit((new Long(numToReturn)).intValue()));
}

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From source file:org.openmhealth.reference.data.mongodb.MongoRegistry.java

License:Apache License

public Schema getSchema(final String schemaId, final long schemaVersion) {
    // Get the connection to the database.
    DB db = MongoDao.getInstance().getDb();

    // Get the connection to the registry with the Jackson wrapper.
    JacksonDBCollection<MongoSchema, Object> collection = JacksonDBCollection.wrap(db.getCollection(DB_NAME),
            MongoSchema.class, Object.class, JSON_MAPPER);

    // Build the query
    QueryBuilder queryBuilder = QueryBuilder.start();

    // Add the schema ID.
    queryBuilder.and(MongoSchema.JSON_KEY_ID).is(schemaId);

    // Add the schema version.
    queryBuilder.and(MongoSchema.JSON_KEY_VERSION).is(schemaVersion);

    // Execute query.
    DBCursor<MongoSchema> result = collection.find(queryBuilder.get());

    // Return null or the schema based on what the query returned.
    if (result.count() == 0) {
        return null;
    } else {//from   w w  w.j a va  2 s  . c o m
        return result.next();
    }
}

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From source file:org.openmhealth.reference.data.mongodb.MongoUserBin.java

License:Apache License

@Override
public User getUser(final String username) throws OmhException {
    // Validate the parameter.
    if (username == null) {
        throw new OmhException("The username is null.");
    }/*  w  ww  . j a va  2s .com*/

    // Get the authentication token collection.
    JacksonDBCollection<MongoUser, Object> collection = JacksonDBCollection.wrap(
            MongoDao.getInstance().getDb().getCollection(DB_NAME), MongoUser.class, Object.class, JSON_MAPPER);

    // Build the query.
    QueryBuilder queryBuilder = QueryBuilder.start();

    // Add the authentication token to the query
    queryBuilder.and(MongoUser.JSON_KEY_USERNAME).is(username);

    // Execute query.
    DBCursor<MongoUser> result = collection.find(queryBuilder.get());

    // If multiple authentication tokens were returned, that is a violation
    // of the system.
    if (result.count() > 1) {
        throw new OmhException("Multiple users exist with the same username: " + username);
    }

    // If no tokens were returned, then return null.
    if (result.count() == 0) {
        return null;
    } else {
        return result.next();
    }
}

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From source file:org.openmhealth.reference.data.mongodb.MongoUserBin.java

License:Apache License

@Override
public User getUserFromRegistrationId(final String registrationId) throws OmhException {

    // Validate the parameter.
    if (registrationId == null) {
        throw new OmhException("The registration ID is null.");
    }//from   w w w. ja  v a2s .  c  o  m

    // Get the authentication token collection.
    JacksonDBCollection<MongoUser, Object> collection = JacksonDBCollection.wrap(
            MongoDao.getInstance().getDb().getCollection(DB_NAME), MongoUser.class, Object.class, JSON_MAPPER);

    // Build the query.
    QueryBuilder queryBuilder = QueryBuilder.start();

    // Add the authentication token to the query
    queryBuilder.and(MongoUser.JSON_KEY_REGISTRATION_KEY).is(registrationId);

    // Execute query.
    DBCursor<MongoUser> result = collection.find(queryBuilder.get());

    // If multiple authentication tokens were returned, that is a violation
    // of the system.
    if (result.count() > 1) {
        throw new OmhException("Multiple users exist with the same registration ID: " + registrationId);
    }

    // If no tokens were returned, then return null.
    if (result.count() == 0) {
        return null;
    } else {
        return result.next();
    }
}

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From source file:org.ossmeter.platform.AbstractHistoricalMetricProvider.java

License:Open Source License

public List<Pongo> getHistoricalMeasurements(MetricProviderContext context, Project project, Date start,
        Date end) {/*from w w  w .  j  a va 2 s  . c o  m*/

    DB db = context.getProjectDB(project);
    DBCollection collection = db.getCollection(this.getCollectionName());

    QueryBuilder builder = QueryBuilder.start();
    if (start != null) {
        builder.and("__datetime").greaterThanEquals(start.toJavaDate());
    }
    if (end != null) {
        builder.and("__datetime").lessThanEquals(end.toJavaDate());
    }

    BasicDBObject query = (BasicDBObject) builder.get();

    Iterator<DBObject> it = collection.find(query).iterator();

    List<Pongo> pongoList = new ArrayList<Pongo>();

    while (it.hasNext()) {
        DBObject dbObject = it.next();
        pongoList.add(PongoFactory.getInstance().createPongo(dbObject));
    }

    return pongoList;

}

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From source file:org.ossmeter.platform.client.api.MetricVisualisationResource.java

License:Open Source License

public Representation doRepresent() {
    String projectName = (String) getRequest().getAttributes().get("projectid");
    String metricId = (String) getRequest().getAttributes().get("metricid");

    String agg = getQueryValue("agg");
    String start = getQueryValue("startDate");
    String end = getQueryValue("endDate");

    QueryBuilder builder = QueryBuilder.start();
    if (agg != null && agg != "") {
        //         builder.... // TODO
    }/* w  ww  .  j  a  va2s  .  c  o m*/
    try {
        if (start != null && start != "") {
            builder.and("__datetime").greaterThanEquals(new Date(start).toJavaDate());
        }
        if (end != null && end != "") {
            builder.and("__datetime").lessThanEquals(new Date(end).toJavaDate());
        }
    } catch (ParseException e) {
        return Util.generateErrorMessageRepresentation(generateRequestJson(projectName, metricId),
                "Invalid date. Format must be YYYYMMDD.");
    }

    BasicDBObject query = (BasicDBObject) builder.get();

    ProjectRepository projectRepo = platform.getProjectRepositoryManager().getProjectRepository();

    Project project = projectRepo.getProjects().findOneByShortName(projectName);
    if (project == null) {
        getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
        return Util.generateErrorMessageRepresentation(generateRequestJson(projectName, metricId),
                "No project was found with the requested name.");
    }

    MetricVisualisationExtensionPointManager manager = MetricVisualisationExtensionPointManager.getInstance();
    manager.getRegisteredVisualisations();

    MetricVisualisation vis = manager.findVisualisationById(metricId);

    if (vis == null) {
        return Util.generateErrorMessageRepresentation(generateRequestJson(projectName, metricId),
                "No visualiser found with specified ID.");
    }

    DB db = platform.getMetricsRepository(project).getDb();
    JsonNode visualisation = vis.visualise(db, query);

    StringRepresentation resp = new StringRepresentation(visualisation.toString());
    resp.setMediaType(MediaType.APPLICATION_JSON);
    return resp;
}

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From source file:org.ossmeter.platform.client.api.RawMetricResource.java

License:Open Source License

/**
 * TODO: Incomplete. [12th Sept, 2013]//from   w ww.j a  v a 2 s  .  co  m
 * @return
 */
public Representation doRepresent() {
    String projectId = (String) getRequest().getAttributes().get("projectid");
    String metricId = (String) getRequest().getAttributes().get("metricid");

    // FIXME: This and MetricVisualisationResource.java are EXACTLY the same.
    String agg = getQueryValue("agg");
    String start = getQueryValue("startDate");
    String end = getQueryValue("endDate");

    QueryBuilder builder = QueryBuilder.start();
    if (agg != null && agg != "") {
        //         builder.... // TODO
    }
    try {
        if (start != null && start != "") {
            builder.and("__datetime").greaterThanEquals(new Date(start).toJavaDate());
        }
        if (end != null && end != "") {
            builder.and("__datetime").lessThanEquals(new Date(end).toJavaDate());
        }
    } catch (ParseException e) {
        return Util.generateErrorMessageRepresentation(generateRequestJson(projectId, metricId),
                "Invalid date. Format must be YYYYMMDD.");
    }

    BasicDBObject query = (BasicDBObject) builder.get();

    ProjectRepository projectRepo = platform.getProjectRepositoryManager().getProjectRepository();

    Project project = projectRepo.getProjects().findOneByShortName(projectId);
    if (project == null) {
        getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
        return Util.generateErrorMessageRepresentation(generateRequestJson(projectId, metricId),
                "No project was found with the requested name.");
    }

    // Get collection from DB
    DB projectDB = platform.getMetricsRepository(project).getDb();

    MetricVisualisationExtensionPointManager manager = MetricVisualisationExtensionPointManager.getInstance();
    manager.getRegisteredVisualisations();
    MetricVisualisation vis = manager.findVisualisationById(metricId);

    if (vis == null) {
        return Util.generateErrorMessageRepresentation(generateRequestJson(projectId, metricId),
                "No visualiser found with specified ID.");
    }

    // TODO: okay, so we only allow people to get raw HISTORIC metrics? How would we
    //        return multiple collections???
    // TODO: Can we stream it? Page it? Filter and agg?

    DBCursor cursor = projectDB.getCollection(vis.getMetricId()).find(query);
    ArrayNode results = mapper.createArrayNode();

    while (cursor.hasNext()) {
        try {
            results.add(mapper.readTree(cursor.next().toString()));
        } catch (JsonProcessingException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    cursor.close();

    return Util.createJsonRepresentation(results);
}

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From source file:org.ossmeter.platform.client.api.SparkResource.java

License:Open Source License

public Representation doRepresent() {
    // Check cache
    String sd = SparkCache.getSparkCache().getSparkData(getRequest().getResourceRef().toString());

    if (sd != null) {
        JsonNode obj;//from   w  w  w. j a va 2s . c o  m
        try {
            System.out.println("SD: " + sd);
            obj = mapper.readTree(sd);
            return Util.createJsonRepresentation(obj);
        } catch (Exception e) {
            e.printStackTrace(); // FIXME
            getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
            ObjectNode node = mapper.createObjectNode();
            node.put("status", "error");
            node.put("msg", "Error whilst retrieving sparkline.");
            return Util.createJsonRepresentation(node);
        }
    }

    // Miss. Hit database.
    String projectId = (String) getRequest().getAttributes().get("projectid");
    String metric = (String) getRequest().getAttributes().get("metricid");

    String[] metrics = metric.split("\\+");
    System.err.println("metrics to get: " + metrics);
    ArrayNode sparks = mapper.createArrayNode();
    for (String metricId : metrics) {

        String agg = getQueryValue("agg");
        String start = getQueryValue("startDate");
        String end = getQueryValue("endDate");

        QueryBuilder builder = QueryBuilder.start();
        if (agg != null && agg != "") {
            //         builder.... // TODO
        }
        try {
            if (start != null && start != "") {
                builder.and("__datetime").greaterThanEquals(new Date(start).toJavaDate());
            }
            if (end != null && end != "") {
                builder.and("__datetime").lessThanEquals(new Date(end).toJavaDate());
            }
        } catch (ParseException e) {
            getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
            ObjectNode node = mapper.createObjectNode();
            node.put("status", "error");
            node.put("msg", "Invalid date. Format must be YYYYMMDD.");
            node.put("request", generateRequestJson(projectId, metricId));
            return Util.createJsonRepresentation(node);
        }

        BasicDBObject query = (BasicDBObject) builder.get();

        ProjectRepository projectRepo = platform.getProjectRepositoryManager().getProjectRepository();
        Project project = projectRepo.getProjects().findOneByShortName(projectId);
        if (project == null) {
            getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
            return Util.createJsonRepresentation(
                    generateErrorMessage(mapper, "No project matched that requested.", projectId, metricId));

        }

        MetricVisualisationExtensionPointManager manager = MetricVisualisationExtensionPointManager
                .getInstance();
        Map<String, MetricVisualisation> registeredVisualisations = manager.getRegisteredVisualisations();
        System.out.println("registered visualisations: " + registeredVisualisations.keySet());
        MetricVisualisation vis = manager.findVisualisationById(metricId);

        if (vis == null) {
            getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
            return Util.createJsonRepresentation(generateErrorMessage(mapper,
                    "No visualiser found with specified ID.", projectId, metricId));
        }

        DB db = platform.getMetricsRepository(project).getDb();

        System.setProperty("java.awt.headless", "true");

        byte[] sparky;
        try {
            sparky = vis.getSparky(db, query);
            ObjectNode sparkData = vis.getSparkData();

            if (sparky != null) {
                String uuid = UUID.randomUUID().toString();
                SparkCache.getSparkCache().putSpark(uuid, sparky);
                sparkData.put("spark", "/spark/" + uuid);
            }
            sparkData.put("metricId", metricId);
            sparkData.put("projectId", projectId);

            // And add to the return list
            sparks.add(sparkData);
        } catch (ParseException e) {
            //            getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
            // TODO Log this as series - needs investigating by admin
            sparks.add(generateErrorMessage(mapper, "Error whilst generating sparkle. Unable to parse data.",
                    projectId, metricId));
        } catch (UnsparkableVisualisationException e) {
            //            getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
            sparks.add(generateErrorMessage(mapper,
                    "Visualisation not sparkable. Metrics must be time series in order to be sparkable.",
                    projectId, metricId));
        } catch (IOException e) {
            e.printStackTrace(); // FIXME
            //            getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
            sparks.add(generateErrorMessage(mapper, "Error whilst generating sparkle.", projectId, metricId));
        }
    }

    // Put in the cache

    if (sparks.size() == 1) {
        SparkCache.getSparkCache().putSparkData(getRequest().getResourceRef().toString(),
                (ObjectNode) sparks.get(0));
        return Util.createJsonRepresentation(sparks.get(0));
    } else {
        SparkCache.getSparkCache().putSparkData(getRequest().getResourceRef().toString(), sparks);
        return Util.createJsonRepresentation(sparks);
    }
}

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