Example usage for com.mongodb.client MongoCollection find

Introduction

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

Prototype

FindIterable<TDocument> find();

Source Link

Document

Finds all documents in the collection.

Usage

From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public Set<UUID> getUniqueUsers() {
    Set<UUID> uuids = new HashSet<>();
    MongoCollection<Document> c = database.getCollection(prefix + "users");
    try (MongoCursor<Document> cursor = c.find().iterator()) {
        while (cursor.hasNext()) {
            Document d = cursor.next();
            uuids.add(d.get("_id", UUID.class));
        }/*from  w ww . j av a2 s  .  c  o m*/
    }
    return uuids;
}

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From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public List<HeldPermission<UUID>> getUsersWithPermission(String permission) {
    ImmutableList.Builder<HeldPermission<UUID>> held = ImmutableList.builder();
    MongoCollection<Document> c = database.getCollection(prefix + "users");
    try (MongoCursor<Document> cursor = c.find().iterator()) {
        while (cursor.hasNext()) {
            Document d = cursor.next();
            UUID holder = d.get("_id", UUID.class);

            Set<NodeModel> nodes = new HashSet<>(nodesFromDoc(d));
            for (NodeModel e : nodes) {
                if (!e.getPermission().equalsIgnoreCase(permission)) {
                    continue;
                }/*from   w  w w.ja  va 2  s.c  om*/
                held.add(NodeHeldPermission.of(holder, e));
            }
        }
    }
    return held.build();
}

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From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public boolean loadAllGroups() {
    List<String> groups = new ArrayList<>();
    MongoCollection<Document> c = database.getCollection(prefix + "groups");
    try (MongoCursor<Document> cursor = c.find().iterator()) {
        while (cursor.hasNext()) {
            String name = cursor.next().getString("_id");
            groups.add(name);/*ww  w. j  a v a2 s .  c  om*/
        }
    }

    boolean success = true;
    for (String g : groups) {
        try {
            loadGroup(g);
        } catch (Exception e) {
            e.printStackTrace();
            success = false;
        }
    }

    if (!success) {
        throw new RuntimeException("Exception occurred whilst loading a group");
    }

    GroupManager gm = plugin.getGroupManager();
    gm.getAll().values().stream().filter(g -> !groups.contains(g.getName())).forEach(gm::unload);

    return true;
}

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From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public List<HeldPermission<String>> getGroupsWithPermission(String permission) {
    ImmutableList.Builder<HeldPermission<String>> held = ImmutableList.builder();
    MongoCollection<Document> c = database.getCollection(prefix + "groups");
    try (MongoCursor<Document> cursor = c.find().iterator()) {
        while (cursor.hasNext()) {
            Document d = cursor.next();

            String holder = d.getString("_id");
            Set<NodeModel> nodes = new HashSet<>(nodesFromDoc(d));
            for (NodeModel e : nodes) {
                if (!e.getPermission().equalsIgnoreCase(permission)) {
                    continue;
                }/*from   w  ww  . j  a  va2 s  . c o m*/
                held.add(NodeHeldPermission.of(holder, e));
            }
        }
    }
    return held.build();
}

---

From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public boolean loadAllTracks() {
    List<String> tracks = new ArrayList<>();
    MongoCollection<Document> c = database.getCollection(prefix + "tracks");
    try (MongoCursor<Document> cursor = c.find().iterator()) {
        while (cursor.hasNext()) {
            String name = cursor.next().getString("_id");
            tracks.add(name);//from   w w  w .  j av a 2  s .c  o m
        }
    }

    boolean success = true;
    for (String t : tracks) {
        try {
            loadTrack(t);
        } catch (Exception e) {
            e.printStackTrace();
            success = false;
        }
    }

    if (!success) {
        throw new RuntimeException("Exception occurred whilst loading a track");
    }

    TrackManager tm = plugin.getTrackManager();
    tm.getAll().values().stream().filter(t -> !tracks.contains(t.getName())).forEach(tm::unload);

    return true;
}

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From source file:module.script.epimed_ontology.AddEpimedGroupToSamples.java

License:Open Source License

public AddEpimedGroupToSamples() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();
    ClTopologyDao topologyDao = new ClTopologyDao(session);

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
    MongoCollection<Document> collectionSample = db.getCollection("sample");

    List<Document> samples = collectionSample.find().into(new ArrayList<Document>());

    for (int i = 0; i < samples.size(); i++) {
        Document sample = samples.get(i);
        Document expgroup = sample.get("exp_group", Document.class);

        String idTopology = expgroup.getString("id_topology");

        if (idTopology != null && !idTopology.isEmpty()) {

            ClTopology topology = topologyDao.find(idTopology);
            ClEpimedGroup grp1 = topology.getClEpimedGroup();
            ClEpimedGroup grp2 = grp1.getParent();
            ClEpimedGroup grp3 = grp2.getParent();
            expgroup.append("tissue_group_level1", grp1.getName());
            expgroup.append("tissue_group_level2", grp2.getName());
            expgroup.append("tissue_group_level3", grp3.getName());

            System.out.println((i + 1) + "/" + samples.size() + " " + expgroup);

            sample.append("exp_group", expgroup);
            collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")),
                    new Document("$set", sample));
        }//from   ww  w.  jav a 2s  . com

    }

    // === Commit transaction ===
    // session.getTransaction().commit();
    session.getTransaction().rollback();

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

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From source file:module.UpdateNumberSamples.java

License:Open Source License

public UpdateNumberSamples() {

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

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

    MongoCollection<Document> collectionSeries = db.getCollection("series");
    MongoCollection<Document> collectionSamples = db.getCollection("sample");

    // String [] listIdSeries = {"TISSUE_SPECIFIC_GENES_MM"};
    // List<Document> listSeries = collectionSeries.find(Filters.in("_id", listIdSeries)).into(new ArrayList<Document>());

    List<Document> listSeries = collectionSeries.find().into(new ArrayList<Document>());

    for (Document ser : listSeries) {
        System.out.println(ser);/*from   w  w  w  .  ja  v  a 2s.co m*/

        String idSeries = ser.getString("_id");
        Bson filter = Filters.in("series", idSeries);

        Long nbSamples = collectionSamples.count(filter);

        System.out.println(idSeries + " " + nbSamples);

        ser.append("nb_samples", nbSamples);
        collectionSeries.updateOne(Filters.eq("_id", idSeries), new Document("$set", ser));

    }

    mongoClient.close();

}

---

From source file:module.UpdateTissueStatus.java

License:Open Source License

public UpdateTissueStatus() {

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

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
    MongoCollection<Document> collectionSample = db.getCollection("sample");

    List<Document> samples = collectionSample.find().into(new ArrayList<Document>());
    ;//from  w ww. ja  v a 2s . c  om

    for (Document sample : samples) {

        Document expgroup = sample.get("exp_group", Document.class);
        Integer idTissueStatus = expgroup.getInteger("id_tissue_status");
        if (idTissueStatus != null) {
            if (idTissueStatus.equals(1)) {
                expgroup.put("tissue_status", "normal");
            }
            if (idTissueStatus.equals(2)) {
                expgroup.put("tissue_status", "pathological_non_tumoral");
            }
            if (idTissueStatus.equals(3)) {
                expgroup.put("tissue_status", "tumoral");
            }

            sample.put("exp_group", expgroup);

            System.out.println(sample.get("exp_group", Document.class));

            collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")),
                    new Document("$set", sample));

        }

    }

    mongoClient.close();

}

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From source file:mongodb.QuickTour.java

License:Apache License

/**
 * Run this main method to see the output of this quick example.
 *
 * @param args takes an optional single argument for the connection string
 *//* w  w  w  .  ja v a 2s .  co m*/
public static void main(final String[] args) {

    //represents a pool of connections to the database
    MongoClient mongoClient = new MongoClient("10.9.17.105", 27017);

    // get handle to "mydb" database
    MongoDatabase database = mongoClient.getDatabase("test");

    // get a handle to the "test" collection
    MongoCollection<Document> collection = database.getCollection("test");

    // drop all the data in it
    collection.drop();

    // make a document and insert it
    Document doc = new Document("name", "MongoDB").append("type", "database").append("count", 1).append("info",
            new Document("x", 203).append("y", 102));

    collection.insertOne(doc);

    // get it (since it's the only one in there since we dropped the rest earlier on)
    Document myDoc = collection.find().first();
    System.out.println(myDoc.toJson());

    // now, lets add lots of little documents to the collection so we can explore queries and cursors
    List<Document> documents = new ArrayList<Document>();
    for (int i = 0; i < 100; i++) {
        documents.add(new Document("i", i));
    }
    collection.insertMany(documents);
    System.out.println(
            "total # of documents after inserting 100 small ones (should be 101) " + collection.count());

    // find first
    myDoc = collection.find().first();
    System.out.println(myDoc.toJson());

    // lets get all the documents in the collection and print them out
    MongoCursor<Document> cursor = collection.find().iterator();
    try {
        while (cursor.hasNext()) {
            System.out.println(cursor.next().toJson());
        }
    } finally {
        cursor.close();
    }

    for (Document cur : collection.find()) {
        System.out.println(cur.toJson());
    }

    // now use a query to get 1 document out
    myDoc = collection.find(eq("i", 71)).first();
    System.out.println(myDoc.toJson());

    // now use a range query to get a larger subset
    cursor = collection.find(gt("i", 50)).iterator();

    try {
        while (cursor.hasNext()) {
            System.out.println(cursor.next().toJson());
        }
    } finally {
        cursor.close();
    }

    // range query with multiple constraints
    cursor = collection.find(and(gt("i", 50), lte("i", 100))).iterator();

    try {
        while (cursor.hasNext()) {
            System.out.println(cursor.next().toJson());
        }
    } finally {
        cursor.close();
    }

    // Query Filters
    myDoc = collection.find(eq("i", 71)).first();
    System.out.println(myDoc.toJson());

    // now use a range query to get a larger subset
    Block<Document> printBlock = new Block<Document>() {
        @Override
        public void apply(final Document document) {
            System.out.println(document.toJson());
        }
    };
    collection.find(gt("i", 50)).forEach(printBlock);

    // filter where; 50 < i <= 100
    collection.find(and(gt("i", 50), lte("i", 100))).forEach(printBlock);

    // Sorting
    myDoc = collection.find(exists("i")).sort(descending("i")).first();
    System.out.println(myDoc.toJson());

    // Projection
    myDoc = collection.find().projection(excludeId()).first();
    System.out.println(myDoc.toJson());

    // Update One
    collection.updateOne(eq("i", 10), new Document("$set", new Document("i", 110)));

    // Update Many
    UpdateResult updateResult = collection.updateMany(lt("i", 100),
            new Document("$inc", new Document("i", 100)));
    System.out.println(updateResult.getModifiedCount());

    // Delete One
    collection.deleteOne(eq("i", 110));

    // Delete Many
    DeleteResult deleteResult = collection.deleteMany(gte("i", 100));
    System.out.println(deleteResult.getDeletedCount());

    collection.drop();

    // ordered bulk writes
    List<WriteModel<Document>> writes = new ArrayList<WriteModel<Document>>();
    writes.add(new InsertOneModel<Document>(new Document("_id", 4)));
    writes.add(new InsertOneModel<Document>(new Document("_id", 5)));
    writes.add(new InsertOneModel<Document>(new Document("_id", 6)));
    writes.add(
            new UpdateOneModel<Document>(new Document("_id", 1), new Document("$set", new Document("x", 2))));
    writes.add(new DeleteOneModel<Document>(new Document("_id", 2)));
    writes.add(new ReplaceOneModel<Document>(new Document("_id", 3), new Document("_id", 3).append("x", 4)));

    collection.bulkWrite(writes);

    collection.drop();

    collection.bulkWrite(writes, new BulkWriteOptions().ordered(false));
    collection.find().forEach(printBlock);

    // Clean up
    //        database.drop();

    // release resources
    mongoClient.close();
}

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From source file:mongodbmanipulation.MongoDBManipulation.java

/**
 * @param args the command line arguments
 *//*www  .  j  av  a 2s .  c o m*/
public static void main(String[] args) {
    // TODO code application logic here
    UserInterface.main(args);
    try {
        MongoClient mongoClient = new MongoClient("localhost", 27017);
        MongoDatabase db = mongoClient.getDatabase("test");
        System.out.println("Connect to database successfully");
        //        boolean auth = db.authenticate(myUserName, myPassword);
        //        System.out.println("Authentication: "+auth);

        MongoCollection<Document> coll = db.getCollection("animals");

        FindIterable<Document> cursor = coll.find();
        int i = 0;
        for (Iterator iterator = cursor.iterator(); iterator.hasNext(); i++) {
            System.out.println(iterator.next());
            if (i == 100)
                break;
        }

    } catch (Exception e) {
        System.out.println("Failed!");
    }
}

---

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