Example usage for com.mongodb.client.model Projections excludeId

List of usage examples for com.mongodb.client.model Projections excludeId

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Introduction

In this page you can find the example usage for com.mongodb.client.model Projections excludeId.

Prototype

public static Bson excludeId()

Source Link

Document

Creates a projection that excludes the _id field.

Usage

From source file:com.spleefleague.core.listeners.EnvironmentListener.java

@EventHandler(priority = EventPriority.HIGH)
public void rankCheck(AsyncPlayerPreLoginEvent e) {
    Document dbo = SpleefLeague.getInstance().getPluginDB().getCollection("Players")
            .find(new Document("uuid", e.getUniqueId().toString()))
            .projection(Projections.fields(Projections.include("rank"), Projections.excludeId())).first();
    if (dbo != null) {
        Rank rank = Rank.DEFAULT;/* w  ww .j  av a  2s.  c om*/
        try {
            rank = Rank.valueOf(dbo.getString("rank"));
        } catch (Exception ignored) {
        }
        if (rank == null || (!rank.hasPermission(SpleefLeague.getInstance().getMinimumJoinRank())
                && !SpleefLeague.getInstance().getExtraJoinRanks().contains(rank))) {
            e.setLoginResult(AsyncPlayerPreLoginEvent.Result.KICK_WHITELIST);
            e.setKickMessage(ChatColor.RED + "You are not of rank to join this server!");
        }
    }
}

From source file:module.ExportGeo.java

License:Open Source License

public ExportGeo() {

    String gseNumber = "GSE2109";

    // ===== Connection =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

    MongoCollection<Document> collection = db.getCollection("samples");

    // ===== Find exp_group in the database =====

    List<Document> docExpGroup = collection.find(Filters.in("series", gseNumber))
            .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId()))
            .into(new ArrayList<Document>());

    List<Document> docParam = collection.find(Filters.in("series", gseNumber))
            .projection(Projections.fields(Projections.include("parameters"), Projections.excludeId()))
            .into(new ArrayList<Document>());

    mongoClient.close();//w ww .jav a2 s  .c o m

    // ===== Load Exp Group into a matrix =====

    List<String> headerExpGroup = new ArrayList<String>();
    List<Object> dataExpGroup = new ArrayList<Object>();

    for (int i = 0; i < docExpGroup.size(); i++) {
        Map<String, String> expGroup = (Map<String, String>) docExpGroup.get(i).get("exp_group");
        if (i == 0) {
            headerExpGroup.addAll(expGroup.keySet());
        }

        String[] dataLine = new String[headerExpGroup.size()];
        for (int j = 0; j < headerExpGroup.size(); j++) {
            dataLine[j] = expGroup.get(headerExpGroup.get(j));
        }
        dataExpGroup.add(dataLine);
    }

    // ===== Load Params into a matrix =====

    Set<String> headerParamSet = new HashSet<String>();
    List<String> headerParam = new ArrayList<String>();
    List<Object> dataParam = new ArrayList<Object>();

    for (int i = 0; i < docParam.size(); i++) {
        Map<String, String> param = (Map<String, String>) docParam.get(i).get("parameters");
        headerParamSet.addAll(param.keySet());
    }
    headerParam.addAll(headerParamSet);
    Collections.sort(headerParam);

    for (int i = 0; i < docParam.size(); i++) {
        Map<String, String> param = (Map<String, String>) docParam.get(i).get("parameters");
        String[] dataLine = new String[headerParam.size()];
        for (int j = 0; j < headerParam.size(); j++) {
            dataLine[j] = param.get(headerParam.get(j));
        }
        // System.out.println(Arrays.toString(dataLine));
        dataParam.add(dataLine);

    }

    // === Output ===

    String fileName = this.getOutputDirectory() + this.getDirSeparator() + "Export_Mongo_" + gseNumber + "_"
            + dateFormat.format(new Date()) + ".xlsx";
    System.out.println(fileName);
    XSSFWorkbook workbook = fileService.createWorkbook();
    fileService.addSheet(workbook, "exp_group" + dateFormat.format(new Date()), headerExpGroup, dataExpGroup);
    fileService.addSheet(workbook, "parameters_" + dateFormat.format(new Date()), headerParam, dataParam);
    fileService.writeWorkbook(workbook, fileName);

}

From source file:module.test.CustomExport.java

License:Open Source License

public CustomExport() {

    // ===== Connection =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

    MongoCollection<Document> collection = db.getCollection("samples");

    // ===== Find exp_group in the database =====

    // === Query 1 ===
    /*/*ww  w. ja v a 2 s  .c o  m*/
    String queryName = "breast_cancer_GPL570";
    List<Bson> filters = new ArrayList<Bson>();
    filters.add(Filters.eq("exp_group.id_platform", "GPL570"));
    filters.add(Filters.eq("exp_group.id_topology_group", "C50"));
    filters.add(Filters.eq("exp_group.id_tissue_status", 3)); // tumoral
     */

    // === Query 2 ===
    /*
    String queryName = "breast_normal_GPL570";
    List<Bson> filters = new ArrayList<Bson>();
    filters.add(Filters.eq("exp_group.id_platform", "GPL570"));
    filters.add(Filters.eq("exp_group.id_topology_group", "C50"));
    filters.add(Filters.eq("exp_group.id_tissue_status", 1)); // normal
    */

    // === Query 3 ===
    String queryName = "breast_cancer_with_survival_GPL570";
    List<Bson> filters = new ArrayList<Bson>();
    filters.add(Filters.eq("exp_group.id_platform", "GPL570"));
    filters.add(Filters.eq("exp_group.id_topology_group", "C50"));
    filters.add(Filters.eq("exp_group.id_tissue_status", 3)); // tumoral
    filters.add(Filters.or(Filters.ne("exp_group.os_months", null), Filters.ne("exp_group.dfss_months", null),
            Filters.ne("exp_group.relapsed", null), Filters.ne("exp_group.dead", null)));

    Bson filter = Filters.and(filters);
    Long nbSamples = collection.count(filter);
    List<String> listSeries = collection.distinct("exp_group.main_gse_number", filter, String.class)
            .into(new ArrayList<String>());
    queryName = queryName + "_" + nbSamples + "_samples_" + listSeries.size() + "_series";

    List<Document> docExpGroup = collection.find(filter)
            .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId()))
            .into(new ArrayList<Document>());

    List<Document> docParam = collection.find(filter)
            .projection(Projections.fields(Projections.include("parameters"), Projections.excludeId()))
            .into(new ArrayList<Document>());

    mongoClient.close();

    // ===== Load Exp Group into a matrix =====

    List<String> headerExpGroup = new ArrayList<String>();
    List<Object> dataExpGroup = new ArrayList<Object>();

    for (int i = 0; i < docExpGroup.size(); i++) {
        Map<String, String> expGroup = (Map<String, String>) docExpGroup.get(i).get("exp_group");
        if (i == 0) {
            headerExpGroup.addAll(expGroup.keySet());
        }

        Object[] dataLine = new Object[headerExpGroup.size()];
        for (int j = 0; j < headerExpGroup.size(); j++) {
            dataLine[j] = expGroup.get(headerExpGroup.get(j));
        }
        dataExpGroup.add(dataLine);
    }

    // ===== Load Params into a matrix =====

    Set<String> headerParamSet = new HashSet<String>();
    List<String> headerParam = new ArrayList<String>();
    List<Object> dataParam = new ArrayList<Object>();

    for (int i = 0; i < docParam.size(); i++) {
        Map<String, String> param = (Map<String, String>) docParam.get(i).get("parameters");
        headerParamSet.addAll(param.keySet());
    }
    headerParam.addAll(headerParamSet);
    Collections.sort(headerParam);

    for (int i = 0; i < docParam.size(); i++) {
        Map<String, String> param = (Map<String, String>) docParam.get(i).get("parameters");
        Object[] dataLine = new Object[headerParam.size()];
        for (int j = 0; j < headerParam.size(); j++) {
            dataLine[j] = param.get(headerParam.get(j));
        }
        // System.out.println(Arrays.toString(dataLine));
        dataParam.add(dataLine);

    }

    // === Output ===

    String fileName = this.getOutputDirectory() + this.getDirSeparator() + "EpiMed_database_" + queryName + "_"
            + dateFormat.format(new Date()) + ".xlsx";
    System.out.println(fileName);
    XSSFWorkbook workbook = fileService.createWorkbook();
    fileService.addSheet(workbook, "exp_group_" + dateFormat.format(new Date()), headerExpGroup, dataExpGroup);
    fileService.addSheet(workbook, "parameters_" + dateFormat.format(new Date()), headerParam, dataParam);
    fileService.writeWorkbook(workbook, fileName);

}

From source file:org.opencb.cellbase.lib.impl.GeneMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getTfbs(Query query, QueryOptions queryOptions) {
    Bson bsonQuery = parseQuery(query);//  w  w w .  j av a  2 s  .  c  o  m
    Bson match = Aggregates.match(bsonQuery);

    // We parse user's exclude options, ONLY _id can be added if exists
    Bson includeAndExclude;
    Bson exclude = null;
    if (queryOptions != null && queryOptions.containsKey("exclude")) {
        List<String> stringList = queryOptions.getAsStringList("exclude");
        if (stringList.contains("_id")) {
            exclude = Aggregates.project(Projections.exclude("_id"));
        }
    }
    if (exclude != null) {
        includeAndExclude = Aggregates
                .project(Projections.fields(Projections.excludeId(), Projections.include("transcripts.tfbs")));
    } else {
        includeAndExclude = Aggregates.project(Projections.include("transcripts.tfbs"));
    }

    Bson unwind = Aggregates.unwind("$transcripts");
    Bson unwind2 = Aggregates.unwind("$transcripts.tfbs");

    // This project the three fields of Xref to the top of the object
    Document document = new Document("tfName", "$transcripts.tfbs.tfName");
    document.put("pwm", "$transcripts.tfbs.pwm");
    document.put("chromosome", "$transcripts.tfbs.chromosome");
    document.put("start", "$transcripts.tfbs.start");
    document.put("end", "$transcripts.tfbs.end");
    document.put("strand", "$transcripts.tfbs.strand");
    document.put("relativeStart", "$transcripts.tfbs.relativeStart");
    document.put("relativeEnd", "$transcripts.tfbs.relativeEnd");
    document.put("score", "$transcripts.tfbs.score");
    Bson project = Aggregates.project(document);

    return mongoDBCollection.aggregate(Arrays.asList(match, includeAndExclude, unwind, unwind2, project),
            queryOptions);
}

From source file:org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.java

License:Apache License

protected static Bson getProjection(Bson projection, QueryOptions options) {
    Bson projectionResult = null;/*from w  w  w  . ja va 2 s . c o  m*/
    List<Bson> projections = new ArrayList<>();

    // It is too risky to merge projections, if projection alrady exists we return it as it is, otherwise we create a new one.
    if (projection != null) {
        //            projections.add(projection);
        return projection;
    }

    if (options != null) {
        // Select which fields are excluded and included in the query
        // Read and process 'include'/'exclude'/'elemMatch' field from 'options' object

        Bson include = null;
        if (options.containsKey(QueryOptions.INCLUDE)) {
            Object includeObject = options.get(QueryOptions.INCLUDE);
            if (includeObject != null) {
                if (includeObject instanceof Bson) {
                    include = (Bson) includeObject;
                } else {
                    List<String> includeStringList = options.getAsStringList(QueryOptions.INCLUDE, ",");
                    if (includeStringList != null && includeStringList.size() > 0) {
                        include = Projections.include(includeStringList);
                    }
                }
            }
        }

        Bson exclude = null;
        boolean excludeId = false;
        if (options.containsKey(QueryOptions.EXCLUDE)) {
            Object excludeObject = options.get(QueryOptions.EXCLUDE);
            if (excludeObject != null) {
                if (excludeObject instanceof Bson) {
                    exclude = (Bson) excludeObject;
                } else {
                    List<String> excludeStringList = options.getAsStringList(QueryOptions.EXCLUDE, ",");
                    if (excludeStringList != null && excludeStringList.size() > 0) {
                        exclude = Projections.exclude(excludeStringList);
                        excludeId = excludeStringList.contains("_id");
                    }
                }
            }
        }

        // If both include and exclude exist we only add include
        if (include != null) {
            projections.add(include);
            // MongoDB allows to exclude _id when include is present
            if (excludeId) {
                projections.add(Projections.excludeId());
            }
        } else {
            if (exclude != null) {
                projections.add(exclude);
            }
        }

        if (options.containsKey(MongoDBCollection.ELEM_MATCH)) {
            Object elemMatch = options.get(MongoDBCollection.ELEM_MATCH);
            if (elemMatch != null && elemMatch instanceof Bson) {
                projections.add((Bson) elemMatch);
            }
        }

        //            List<String> includeStringList = options.getAsStringList(MongoDBCollection.INCLUDE, ",");
        //            if (includeStringList != null && includeStringList.size() > 0) {
        //                projections.add(Projections.include(includeStringList));
        ////                for (Object field : includeStringList) {
        ////                    projection.put(field.toString(), 1);
        ////                }
        //            } else {
        //                List<String> excludeStringList = options.getAsStringList(MongoDBCollection.EXCLUDE, ",");
        //                if (excludeStringList != null && excludeStringList.size() > 0) {
        //                    projections.add(Projections.exclude(excludeStringList));
        ////                    for (Object field : excludeStringList) {
        ////                        projection.put(field.toString(), 0);
        ////                    }
        //                }
        //            }
    }

    if (projections.size() > 0) {
        projectionResult = Projections.fields(projections);
    }

    return projectionResult;
}

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoProjectDBAdaptor.java

License:Apache License

@Override
public QueryResult<AclEntry> getProjectAcl(long projectId, String userId) throws CatalogDBException {
    long startTime = startQuery();
    /*//  w  w w  .  ja v a2 s  .co  m
    DBObject match1 = new BasicDBObject("$match", new BasicDBObject("projects.id", projectId));
    DBObject project = new BasicDBObject("$project", BasicDBObjectBuilder
        .start("_id", false)
        .append("projects.acl", true)
        .append("projects.id", true).get());
    DBObject unwind1 = new BasicDBObject("$unwind", "$projects");
    DBObject match2 = new BasicDBObject("$match", new BasicDBObject("projects.id", projectId));
    DBObject unwind2 = new BasicDBObject("$unwind", "$projects.acl");
    DBObject match3 = new BasicDBObject("$match", new BasicDBObject("projects.acl.userId", userId));
            
    */
    Bson match1 = Aggregates.match(Filters.eq("projects.id", projectId));
    //        Bson project = Projections.fields(Projections.excludeId(), Projections.include("projects.acl", "projects.id"));
    Bson project = Aggregates.project(
            Projections.fields(Projections.excludeId(), Projections.include("projects.acl", "projects.id")));
    Bson unwind1 = Aggregates.unwind("$projects");
    Bson match2 = Aggregates.match(Filters.eq("projects.id", projectId));
    Bson unwind2 = Aggregates.unwind("$projects.acl");
    Bson match3 = Aggregates.match(Filters.eq("projects.acl.userId", userId));

    List<Bson> operations = new LinkedList<>();
    operations.add(match1);
    operations.add(project);
    operations.add(unwind1);
    operations.add(match2);
    operations.add(unwind2);
    operations.add(match3);

    QueryResult aggregate = userCollection.aggregate(operations, null);
    List<AclEntry> acls = new LinkedList<>();
    if (aggregate.getNumResults() != 0) {
        //            DBObject aclObject = (DBObject) ((DBObject) ((DBObject) aggregate.getResult().get(0)).get("projects")).get("acl");
        Document aclObject = (Document) ((Document) ((Document) aggregate.getResult().get(0)).get("projects"))
                .get("acl");
        AclEntry acl = parseObject(aclObject, AclEntry.class);
        acls.add(acl);
    }
    return endQuery("get project ACL", startTime, acls);
}