Example usage for com.mongodb.client.model Filters in

List of usage examples for com.mongodb.client.model Filters in

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Introduction

In this page you can find the example usage for com.mongodb.client.model Filters in.

Prototype

public static <TItem> Bson in(final String fieldName, final Iterable<TItem> values)

Source Link

Document

Creates a filter that matches all documents where the value of a field equals any value in the list of specified values.

Usage

From source file:module.script.ImportSupplementaryGSE20711.java

License:Open Source License

public ImportSupplementaryGSE20711() {

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

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

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

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

    // ===== Excel data loader =====

    String inputfile = this.getInputDirectory() + this.getDirSeparator() + "GSE20711_emmm0003-0726-SD2.xlsx";
    System.out.println("LOADING \t " + inputfile);
    ExcelService excelService = new ExcelService();
    excelService.load(inputfile);/*from w  w w.  ja v  a 2 s.  c  o  m*/

    String gseNumber = "GSE20711";

    for (int i = 0; i < excelService.getData().size(); i++) {
        List<Object> dataLine = excelService.getData().get(i);

        String bcString = (String) dataLine.get(0);
        bcString = bcString.replaceAll("BC", "");

        Integer bcNumber = Integer.parseInt(bcString);

        Document docSample = collection
                .find(Filters
                        .and(Filters.in("series", gseNumber),
                                Filters.eq("exp_group.sample_title",
                                        "Breast tumor from patient P_" + bcNumber + " (expression data)")))
                .first();

        System.out.println("-------------------------------------------");
        System.out.println(dataLine);
        System.out.println(docSample);

    }

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

    mongoClient.close();
}

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  .ja v a 2  s.c  o  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();
}

From source file:module.test.SearchSeries.java

License:Open Source License

public SearchSeries() throws ParseException {

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

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

    String[] listSeries = { "E-MTAB-365", "GSE3156", "GSE3744", "GSE4922", "GSE5764", "GSE6367", "GSE6883",
            "GSE8977", "GSE9014", "GSE9195", "GSE10885", "GSE11078", "GSE11352", "GSE12080", "GSE12237",
            "GSE12276", "GSE14017", "GSE16391", "GSE17215", "GSE17907", "GSE19615", "GSE21653", "GSE28681",
            "GSE38867" };

    List<Document> list = collectionSamples.find(Filters.in("_id", listSeries)).into(new ArrayList<Document>());

    Set<String> setGse = new HashSet<String>();
    List<String> listGse = new ArrayList<String>();
    for (int i = 0; i < list.size(); i++) {
        Document doc = list.get(i);
        setGse.add(doc.getString("_id"));
    }/*from   ww  w. j  av  a  2  s.com*/
    listGse.addAll(setGse);
    Collections.sort(listGse);

    System.out.println("Found " + list.size() + " samples");
    System.out.println("List GSE " + listGse);

    mongoClient.close();

}

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 .  j ava  2s. c o  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.UpdatePlatformType.java

License:Open Source License

public UpdatePlatformType() {

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

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

    // ===== Platforms =====

    Bson filters = Filters.eq("type", "unknown");
    List<Document> listPlatforms = collectionPlatforms.find(filters).into(new ArrayList<Document>());

    for (Document platform : listPlatforms) {
        System.out.println("--------------------------------------------------------------");

        String idPlatform = platform.getString("_id");
        System.out.println(platform);
        List<Document> listSeries = collectionSeries.find(Filters.in("platforms", idPlatform))
                .into(new ArrayList<Document>());
        for (Document series : listSeries) {
            System.out.println(" \t -> " + series.getString("_id") + " " + series.getString("title"));
        }/*from   w ww  .j a v  a2s  .  c  o  m*/

        // platform.append("type", "expression array");
        // collectionPlatforms.updateOne(Filters.eq("_id", idPlatform), new Document("$set", platform));

    }

    mongoClient.close();
}

From source file:mongodb.clients.percunia.mongo.Restriction.java

License:Apache License

public static <T> Bson in(String field, List<T> value) {
    return Filters.in(field, value);
}

From source file:org.eclipse.ditto.services.thingsearch.persistence.read.criteria.visitors.CreateBsonPredicateVisitor.java

License:Open Source License

@Override
public Function<String, Bson> visitIn(final List<?> values) {
    return fieldName -> Filters.in(fieldName, values);
}

From source file:org.eclipse.ditto.services.thingsearch.persistence.read.expression.visitors.AbstractFieldBsonCreator.java

License:Open Source License

/**
 * Create filter BSON for global readability.
 *
 * @param authorizationSubjectIds authorization subject IDs for visibility restriction.
 * @return the BSON filter./*  w  ww . j  ava2s  . c  o m*/
 */
public static Bson getGlobalReadBson(final Iterable<String> authorizationSubjectIds) {
    return Filters.in(FIELD_GLOBAL_READ, authorizationSubjectIds);
}

From source file:org.eclipse.ditto.services.thingsearch.persistence.read.expression.visitors.AbstractFieldBsonCreator.java

License:Open Source License

Optional<Bson> getAuthorizationBson() {
    return Optional.ofNullable(authorizationSubjectIds)
            .map(subjectIds -> Filters.and(Filters.in(FIELD_GRANTED, authorizationSubjectIds),
                    Filters.nin(FIELD_REVOKED, authorizationSubjectIds)));
}

From source file:org.jnosql.diana.mongodb.document.DocumentQueryConversor.java

License:Open Source License

public static Bson convert(DocumentCondition condition) {
    Document document = condition.getDocument();
    Object value = document.getValue().get();
    switch (condition.getCondition()) {
    case EQUALS:/*  www  .  j  a v a2  s.  co  m*/
        return Filters.eq(document.getName(), value);
    case GREATER_THAN:
        return Filters.gt(document.getName(), value);
    case GREATER_EQUALS_THAN:
        return Filters.gte(document.getName(), value);
    case LESSER_THAN:
        return Filters.lt(document.getName(), value);
    case LESSER_EQUALS_THAN:
        return Filters.lte(document.getName(), value);
    case IN:
        return Filters.in(document.getName(), value);
    case LIKE:
        return Filters.regex(document.getName(), value.toString());
    case AND:
        List<Document> andList = condition.getDocument().getValue().get(new TypeReference<List<Document>>() {
        });
        return Filters.and(andList.stream().map(d -> new BasicDBObject(d.getName(), d.getValue().get()))
                .toArray(BasicDBObject[]::new));
    case OR:
        List<Document> orList = condition.getDocument().getValue().get(new TypeReference<List<Document>>() {
        });
        return Filters.or(orList.stream().map(d -> new BasicDBObject(d.getName(), d.getValue().get()))
                .toArray(BasicDBObject[]::new));
    default:
        throw new UnsupportedOperationException(
                "The condition " + condition.getCondition() + " is not supported from mongoDB diana driver");
    }
}