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

Introduction

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

Prototype

public static <TItem> Bson eq(final String fieldName, @Nullable final TItem value) 

Source Link

Document

Creates a filter that matches all documents where the value of the field name equals the specified value.

Usage

From source file:module.script.TransferFromEpimedProd.java

License:Open Source License

@SuppressWarnings({ "unused", "unchecked" })
public TransferFromEpimedProd() {

    // ===== 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");

    String sql = "select * from epimed_prod.view_exp_group order by main_gse_number, id_sample";
    List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

    String[] commonAttributes = { "pathology", "tnm_stage", "id_topology_group", "histology_subtype",
            "tissue_stage", "dead", "dfs_months", "age_max", "morphology", "id_tissue_stage", "topology", "sex",
            "age_min", "m", "topology_group", "n", "t", "collection_method", "id_morphology", "relapsed",
            "histology_type", "os_months", "id_topology" };

    List<ClPathology> listPathology = session.createCriteria(ClPathology.class).list();
    Map<String, ClPathology> mapPathology = new HashMap<String, ClPathology>();
    for (ClPathology p : listPathology) {
        mapPathology.put(p.getName(), p);
    }// w w w  .j a va2s  .com

    List<ClTissueStatus> listTissueStatus = session.createCriteria(ClTissueStatus.class).list();
    Map<Integer, ClTissueStatus> mapTissueStatus = new HashMap<Integer, ClTissueStatus>();
    for (ClTissueStatus t : listTissueStatus) {
        mapTissueStatus.put(t.getIdTissueStatus(), t);
    }

    System.out.println(listTissueStatus);

    for (Object item : list) {

        Map<String, Object> map = (HashMap<String, Object>) item;

        String gsmNumber = (String) map.get("id_sample");
        String gseNumber = (String) map.get("main_gse_number");

        System.out.println("-----------------------------");
        System.out.println(gseNumber + " " + gsmNumber);

        Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();

        if (doc != null) {
            Document expGroup = (Document) doc.get("exp_group");
            for (int j = 0; j < commonAttributes.length; j++) {
                String attr = commonAttributes[j];
                expGroup.put(attr, map.get(attr));
            }

            // Treatment
            expGroup.put("treatment", map.get("treatment_type"));

            // Pathology
            String pathoString = (String) map.get("pathology");
            ClPathology pathology = mapPathology.get(pathoString);
            if (pathology != null) {
                expGroup.put("id_pathology", pathology.getIdPathology());
                expGroup.put("pathology", pathology.getName());
            }

            // Tissue status
            Integer idTissueStatus = (Integer) map.get("id_tissue_status");
            if (idTissueStatus != null && idTissueStatus > 3) {
                idTissueStatus = 3;
            }
            ClTissueStatus tissueStatus = mapTissueStatus.get(idTissueStatus);
            if (tissueStatus != null) {
                expGroup.put("id_tissue_status", tissueStatus.getIdTissueStatus());
                expGroup.put("tissue_status", tissueStatus.getName());
            }

            System.out.println("idTissueStatus=" + tissueStatus + ", pathology=" + pathology);
            System.out.println(expGroup);

            // Update Mongo document
            doc.put("exp_group", expGroup);
            doc.put("analyzed", true);
            UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
                    new Document("$set", doc));
        }

    }

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

    mongoClient.close();
}

---

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 ===
    /*/*from ww  w . j av  a 2 s .com*/
    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: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 w  w .  ja  v a 2s. c o  m

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

    mongoClient.close();

}

---

From source file:module.test.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");

    List<Document> list = collectionSamples.find(Filters.and(Filters.eq("exp_group.id_tissue_stage", 4),
            Filters.ne("exp_group.main_gse_number", "GSE30654"))).into(new ArrayList<Document>());

    for (Document document : list) {
        System.out.println(document);
    }/*from  w ww .  j  av a  2s  . c  o m*/

    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 ww w.ja  va  2 s  .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"));
        }/* ww w.  ja va  2  s. c  o m*/

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

    }

    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  ww w . ja v  a 2 s . co  m*/

    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();

}

---

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

License:Apache License

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

---

From source file:mongodbmanipulation.UserInterface.java

private void jButtonAddColumnActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonAddColumnActionPerformed
    // TODO add your handling code here:
    String colName = JOptionPane.showInputDialog(this, "Enter New Column Name:", "New Column Info",
            QUESTION_MESSAGE);// w  w w  .  j av a  2  s  . c om
    if (colName == null) {
        return;
    }
    String idName = JOptionPane.showInputDialog(this,
            "Enter _id of the document in which you want to add this column:", "New Column Info",
            QUESTION_MESSAGE);
    if (colName == null) {
        return;
    }
    String value = JOptionPane.showInputDialog(this, "Enter the value of _id = " + idName + ":",
            "New Column Info", QUESTION_MESSAGE);
    if (colName == null) {
        return;
    }
    columnUpdating = true;
    Document where = new Document("_id", new ObjectId(idName));
    Document what = new Document("$set", new Document((String) colName, value));
    collections.updateOne(Filters.eq("_id", where.get("_id")), what);
    refreshTable();
    columnUpdating = false;
}

---

From source file:my.beesyn.MongoConn.java

public void insert_or_update(Identifier idf, MongoCollection coll) {
    Document dc;// ww  w . j  a  v a 2s  . c o  m
    FindOneAndReplaceOptions op = new FindOneAndReplaceOptions();
    op.upsert(true);

    dc = Document.parse(idf.get_fetched());
    dc.append("u_id", idf.get_id());
    dc.append("chsum", dc.hashCode());
    coll.findOneAndReplace(Filters.and(Filters.eq("u_id", idf.get_id()), Filters.ne("chsum", idf.get_chk())),
            dc, op);

}

---

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