Example usage for com.mongodb.client MongoCollection aggregate

Introduction

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

Prototype

AggregateIterable<TDocument> aggregate(List<? extends Bson> pipeline);

Source Link

Document

Aggregates documents according to the specified aggregation pipeline.

Usage

From source file:data.ProjectPhase.java

License:Open Source License

public static ProjectPhase getByProjectAndPhaseName(String projectName, String projectPhaseName,
        DBManagerMongo manager) throws Exception {
    MongoCollection<Document> coll = manager.getDb().getCollection("project_phase");
    Bson lookup = new Document("$lookup",
            new Document("from", "project").append("localField", "project_id").append("foreignField", "id") //local field, remote field
                    .append("as", "project"));

    Bson match = new Document("$match", new Document("$and",
            Arrays.asList(new Document("project.name", projectName), new Document("name", projectPhaseName))));

    List<Bson> filters = new ArrayList<>();
    filters.add(lookup);//w w w.ja  v  a  2  s.c  om
    filters.add(match);
    AggregateIterable<Document> it = coll.aggregate(filters);
    return extractPhase(it.first(), manager);
}

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From source file:data.User.java

License:Open Source License

public static ArrayList<User> getAvailableUsersFor(int projectId, DBManagerMongo manager) throws Exception {
    ArrayList<User> list = new ArrayList<>();
    MongoCollection<Document> coll = manager.getDb().getCollection("user");
    Bson lookup = new Document("$lookup",
            new Document("from", "project_member").append("localField", "login_name")
                    .append("foreignField", "user_login_name") //local field, remote field
                    .append("as", "project_member"));

    List<Bson> filters = new ArrayList<>();
    filters.add(lookup);/* w  w w  . ja va 2 s . c om*/

    AggregateIterable<Document> it = coll.aggregate(filters);

    for (Document row : it) {
        boolean add = true;
        ArrayList<Document> members = (ArrayList<Document>) row.get("project_member");
        for (Document doc : members) {
            if (doc.getInteger("project_id") == projectId) {
                add = false;
                break;
            }
        }

        if (add)
            list.add(extractUser(row));

    }

    return list;
}

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From source file:examples.tour.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
 *//*www  . jav  a2s .c o  m*/
public static void main(final String[] args) {
    MongoClient mongoClient;

    if (args.length == 0) {
        // connect to the local database server
        mongoClient = new MongoClient();
    } else {
        mongoClient = new MongoClient(new MongoClientURI(args[0]));
    }

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

    // 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>() {

        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());

    // Aggregation
    collection
            .aggregate(
                    asList(match(gt("i", 0)), project(Document.parse("{ITimes10: {$multiply: ['$i', 10]}}"))))
            .forEach(printBlock);

    myDoc = collection.aggregate(singletonList(group(null, sum("total", "$i")))).first();
    System.out.println(myDoc.toJson());

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

    // Update Many
    UpdateResult updateResult = collection.updateMany(lt("i", 100), inc("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:module.script.epilung.SearchSamples.java

License:Open Source License

public SearchSamples() {

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

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
    MongoCollection<Document> collectionSamples = db.getCollection("samples");
    MongoCollection<Document> collectionPlatforms = db.getCollection("platforms");

    Bson filters = Filters.and(//from   w  w w.  ja  v  a2s  .  c om
            Filters.in("exp_group.id_platform", new String[] { "GPL13534", "GPL8490", "GPL21145" }),
            Filters.eq("exp_group.id_tissue_status", 1), Filters.ne("exp_group.id_topology", null));

    /*
    List<Document> list = collectionSamples
    .find(filters)
    .into(new ArrayList<Document>());
    */

    List<Document> list = collectionSamples.aggregate(Arrays.asList(Aggregates.match(filters),
            Aggregates.group("$exp_group.topology", Accumulators.sum("total", 1)),
            Aggregates.sort(Sorts.orderBy(Sorts.descending("total"))))).into(new ArrayList<Document>());

    for (int i = 0; i < list.size(); i++) {
        System.out.println((i + 1) + " " + list.get(i));
    }

    collectionPlatforms.find(Filters.regex("title", ".*ethyl.*")).forEach(printBlock);

    mongoClient.close();

}

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From source file:module.script.QueryAvailableData.java

License:Open Source License

public QueryAvailableData() {

    // ===== Service =====
    FormatService formatService = new FormatService();

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

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

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

    // ===== Print block =====
    Block<Document> printBlock = new Block<Document>() {
        public void apply(final Document document) {
            System.out.println(document.toJson());
        }//from w  ww.  j  ava  2s.co  m
    };

    // ===== Group by topology =====
    // db.getCollection('samples').aggregate({ $group: { "_id" : "$exp_group.topology", "total" : {$sum : 1} }}, {$sort : {total : -1}} )
    /*
    List<Document> listDocuments = collectionSamples.aggregate(
    Arrays.asList(
          Aggregates.group("$exp_group.topology", Accumulators.sum("total", 1)),
          Aggregates.sort(Sorts.orderBy(Sorts.descending("total")))
          ))
    .into(new ArrayList<Document>());
     */

    // ===== Group by sample =====
    /*
    List<Document> listSeries = collectionSeries
    .find()
    .projection(Projections.fields(Projections.include("title")))
    .sort(Sorts.ascending("_id"))
    .into(new ArrayList<Document>());
            
    for (Document doc : listSeries) {
            
       String idSeries = doc.getString("_id");
       Long nbSamples = collectionSamples.count((Filters.eq("series", idSeries)));
       doc.append("nbSamples", nbSamples);
    } 
    display(listSeries);
    */

    // === Export Geo for a list of idSeries ===

    // String[] listIdSeries = {"GSE11092","GSE13309", "GSE13159"};

    /*
    List<Document> docExpGroup = collectionSamples
    .find(Filters.in("series", listIdSeries))
    .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId()))
    .into(new ArrayList<Document>());
    // display(docExpGroup);
            
    List<String> header = formatService.extractHeader(docExpGroup, "exp_group");
    List<Object> data = formatService.extractData(docExpGroup, header, "exp_group");
    System.out.println(header);
    displayMatrix(data);
            
    */
    // List<Object> listObjects = formatService.convertHeterogeneousMongoDocuments(docExpGroup, "exp_group");
    // displayMatrix(listObjects);

    // List<Object> listObjects = formatService.convertHomogeneousMongoDocuments(listDocuments);

    // === Find series ===

    String[] listIdSamples = { "GSM80908", "GSM274639", "GSM274638", "GSM280213" };
    List<Document> listDocuments = collectionSamples
            .aggregate(Arrays.asList(Aggregates.match(Filters.in("_id", listIdSamples)),
                    Aggregates.group("$main_gse_number"),
                    Aggregates.sort(Sorts.orderBy(Sorts.ascending("main_gse_numbe")))))
            .into(new ArrayList<Document>());
    List<Object> listObjects = formatService.convertHomogeneousMongoDocuments(listDocuments);
    displayMatrix(listObjects);

    mongoClient.close();
}

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From source file:module.test.SearchPlatforms.java

License:Open Source License

public SearchPlatforms() {

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

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

    List<Document> list = collectionSamples
            .aggregate(Arrays.asList(Aggregates.group("$exp_group.id_platform", Accumulators.sum("total", 1)),
                    Aggregates.sort(Sorts.orderBy(Sorts.descending("total")))))
            .into(new ArrayList<Document>());

    for (int i = 0; i < list.size(); i++) {
        System.out.println((i + 1) + " " + list.get(i));
    }//from  w ww .  j a  va  2s.c o  m

    // collectionPlatforms.find(Filters.regex("title", ".*ethyl.*")).forEach(printBlock);
    collectionPlatforms.find(Filters.eq("id_organism", "9606")).forEach(printBlock);

    mongoClient.close();

}

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From source file:org.apache.beam.sdk.io.mongodb.AggregationQuery.java

License:Apache License

@Override
public MongoCursor<Document> apply(MongoCollection<Document> collection) {
    if (bucket() != null) {
        if (mongoDbPipeline().size() == 1) {
            mongoDbPipeline().add(bucket());
        } else {//  w w w.java 2s  .c  o m
            mongoDbPipeline().set(mongoDbPipeline().size() - 1, bucket());
        }
    }
    return collection.aggregate(mongoDbPipeline()).iterator();
}

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From source file:org.apache.nifi.processors.mongodb.RunMongoAggregation.java

License:Apache License

@Override
public void onTrigger(ProcessContext context, ProcessSession session) throws ProcessException {
    FlowFile flowFile = null;//from  w  w  w . ja  va2  s  .co m
    if (context.hasIncomingConnection()) {
        flowFile = session.get();

        if (flowFile == null && context.hasNonLoopConnection()) {
            return;
        }
    }

    final String query = context.getProperty(QUERY).evaluateAttributeExpressions(flowFile).getValue();
    final Boolean allowDiskUse = context.getProperty(ALLOW_DISK_USE).asBoolean();
    final String queryAttr = context.getProperty(QUERY_ATTRIBUTE).evaluateAttributeExpressions(flowFile)
            .getValue();
    final Integer batchSize = context.getProperty(BATCH_SIZE).asInteger();
    final Integer resultsPerFlowfile = context.getProperty(RESULTS_PER_FLOWFILE).asInteger();
    final String jsonTypeSetting = context.getProperty(JSON_TYPE).getValue();
    final String dateFormat = context.getProperty(DATE_FORMAT).evaluateAttributeExpressions(flowFile)
            .getValue();

    configureMapper(jsonTypeSetting, dateFormat);

    Map<String, String> attrs = new HashMap<>();
    if (queryAttr != null && queryAttr.trim().length() > 0) {
        attrs.put(queryAttr, query);
    }

    MongoCursor<Document> iter = null;

    try {
        MongoCollection<Document> collection = getCollection(context, flowFile);
        List<Bson> aggQuery = buildAggregationQuery(query);
        AggregateIterable<Document> it = collection.aggregate(aggQuery).allowDiskUse(allowDiskUse);
        ;
        it.batchSize(batchSize != null ? batchSize : 1);

        iter = it.iterator();
        List<Document> batch = new ArrayList<>();

        while (iter.hasNext()) {
            batch.add(iter.next());
            if (batch.size() == resultsPerFlowfile) {
                writeBatch(buildBatch(batch), flowFile, context, session, attrs, REL_RESULTS);
                batch = new ArrayList<>();
            }
        }

        if (batch.size() > 0) {
            writeBatch(buildBatch(batch), flowFile, context, session, attrs, REL_RESULTS);
        }

        if (flowFile != null) {
            session.transfer(flowFile, REL_ORIGINAL);
        }
    } catch (Exception e) {
        getLogger().error("Error running MongoDB aggregation query.", e);
        if (flowFile != null) {
            session.transfer(flowFile, REL_FAILURE);
        }
    } finally {
        if (iter != null) {
            iter.close();
        }
    }
}

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From source file:org.cleaner.mongo.FindDuplicatesByMd5.java

License:Open Source License

public void find(MongoCollection<Document> collection) {

    writeOutDuplicates(collection.aggregate(getPipeline()));

}

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From source file:org.codinjutsu.tools.nosql.mongo.logic.SingleMongoClient.java

License:Apache License

private MongoResult aggregate(MongoQueryOptions mongoQueryOptions, MongoResult mongoResult,
        MongoCollection<Document> collection) {
    AggregateIterable<Document> aggregate = collection.aggregate(mongoQueryOptions.getOperations());
    aggregate.useCursor(true);/*from ww w .  j  a  v a 2  s.  co  m*/

    int index = 0;
    MongoCursor<Document> iterator = aggregate.iterator();
    while (iterator.hasNext() && index < mongoQueryOptions.getResultLimit()) {
        mongoResult.add(iterator.next());
    }
    return mongoResult;
}

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