Example usage for com.mongodb MongoClient getDatabase

Introduction

In this page you can find the example usage for com.mongodb MongoClient getDatabase.

Prototype

public MongoDatabase getDatabase(final String databaseName) 

Source Link

Usage

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

License:Open Source License

public UpdateFetalAdultOvary() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();
    ClTopologyDao topologyDao = new ClTopologyDao(session);
    ClTopology adultOvary = topologyDao.find("C56.9");
    ClTopology fetalOvary = topologyDao.find("E56.9");

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

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

    Bson filters = Filters.and(Filters.eq("exp_group.id_topology", "C56.9"), // ovary
            Filters.eq("exp_group.id_tissue_stage", 1) // adult
    );// w  w w .j a  v  a  2s  .c  o m

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

    for (Document sample : samples) {
        Document expgroup = sample.get("exp_group", Document.class);
        expgroup.append("id_topology", adultOvary.getIdTopology());
        expgroup.append("topology", adultOvary.getName());
        sample.append("exp_group", expgroup);
        collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")), new Document("$set", sample));
    }
    System.out.println(samples.size());

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

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

    mongoClient.close();
}

---

From source file:module.script.ImportArrayExpress1733.java

License:Open Source License

public ImportArrayExpress1733() {

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

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

    // ===== Pattern =====
    String patternText = "\\[[\\p{Print}\\p{Space}]+\\]";
    ;//from  w w w  .  j  a  v  a  2  s .  c  o m
    Pattern pattern = Pattern.compile(patternText);

    // ===== Series =====

    for (String accession : listAccessions) {

        List<String> accessionAsList = new ArrayList<String>();
        accessionAsList.add(accession);

        String urlString = "https://www.ebi.ac.uk/arrayexpress/files/" + accession + "/" + accession
                + ".idf.txt";
        System.out.println(urlString);
        String text = webService.loadUrl(urlString);

        String[] parts = text.split(lineSeparator);
        List<String> dataSeries = new ArrayList<String>(Arrays.asList(parts));

        AESeries series = new AESeries(dataSeries);
        System.out.println(series);

        // ===== Check if already imported as a GSE ===== 
        boolean isGseFound = false;
        String gseNumber = null;
        for (String secondaryAccession : series.getListAccessions()) {
            if (secondaryAccession.startsWith("GSE")) {
                gseNumber = secondaryAccession;
                Document gse = db.getCollection("series").find(Filters.eq("_id", secondaryAccession)).first();
                isGseFound = gse != null;

            }
        }

        int nbImportedSamples = 0;

        if (!isGseFound) {

            // ===== Create Mongo series =====

            Document docSeries = mongoService.createSeries(accession, series.getTitle(), null,
                    series.getSubmissionDate(), series.getSubmissionDate());

            if (series.getListAccessions() != null && !series.getListAccessions().isEmpty()) {
                docSeries.put("secondary_accessions", series.getListAccessions());
            }

            if (false) {
                UpdateResult updateResult = collectionSeries.updateOne(Filters.eq("_id", accession),
                        new Document("$set", docSeries));
                if (updateResult.getMatchedCount() == 0) {
                    collectionSeries.insertOne(docSeries);
                }
            }

            System.out.println(docSeries);

            // ===== Import clinical data =====

            String url = "https://www.ebi.ac.uk/arrayexpress/files/" + accession + "/" + series.getSdrf();
            System.out.println(url);
            String clindata = webService.loadUrl(url);

            String[] clinparts = clindata.split(lineSeparator);
            List<String> data = new ArrayList<String>(Arrays.asList(clinparts));

            // ===== Recognize samples =====

            List<String> header = this.createHeader(data.get(0), pattern);
            System.out.println(header);

            for (int i = 1; i < data.size(); i++) {

                Integer nbSamples = data.size() - 1;

                Map<String, Object> mapParameters = this.createMapParameters(data.get(i), header);
                String idSample = this.createIdSample(mapParameters);

                if (idSample == null) {
                    System.err.println("ERROR: idSample is not recongnized for " + accession);
                    System.out.println("Line " + i);
                    System.out.println(mapParameters);
                    mongoClient.close();
                    System.exit(0);
                } else {
                    if (formatIdSample) {
                        idSample = "E-MTAB-2836" + "-" + idSample;
                        idSample = idSample.trim().replaceAll(" ", "-");
                    }
                }
                idSample = idSample.split(" ")[0].trim();

                // === Organism ===
                String organism = (String) mapParameters.get("organism");
                if (organism == null || organism.isEmpty()) {
                    organism = defaultOrganism;
                }

                // === Platform ===
                String platform = (String) mapParameters.get("LIBRARY_STRATEGY");
                if (platform != null && !platform.isEmpty()) {
                    platform = platform.toLowerCase().trim();
                } else {
                    platform = defaultPlatform;
                }

                Document docSampleExist = collectionSamples.find(Filters.eq("_id", idSample)).first();
                boolean docAlreadyExist = docSampleExist != null;

                System.out.println("docAlreadyExist " + docAlreadyExist);

                // === Delete old if already exist ===
                if (docAlreadyExist) {
                    List<String> listSeries = (List<String>) docSampleExist.get("series");
                    Set<String> setSeries = new HashSet<String>();
                    listSeries.add(accession);
                    setSeries.addAll(listSeries);
                    listSeries.clear();
                    listSeries.addAll(setSeries);
                    docSampleExist.append("series", listSeries);

                    System.out.println(docSampleExist);

                    if (commit) {
                        collectionSamples.deleteOne(eq("_id", docSampleExist.get("_id")));
                        collectionSamples.insertOne(docSampleExist);
                    }

                }

            }

        } else {
            System.out.println("GEO accession " + gseNumber + " corresponding to  " + accession
                    + " exists already. Skip import.");
        }

        System.out.println("Number of imported samples: " + nbImportedSamples);

    }

    mongoClient.close();

}

---

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  www .j  a  v a2s  . 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.ImportSupplementaryGSE25219.java

License:Open Source License

@SuppressWarnings({ "unused", "unchecked" })
public ImportSupplementaryGSE25219() {

    // ===== 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() + "NIHMS321722-supplement-7.xlsx";
    System.out.println("LOADING \t " + inputfile);
    ExcelService excelService = new ExcelService();
    excelService.load(inputfile);/*from   w  w w  . j  a  va 2  s.  c  o m*/

    // ===== Format raw data into data structures ======

    List<Map<String, String>> listMap = new ArrayList<Map<String, String>>();
    List<String> headerMap = new ArrayList<String>();
    Map<String, String> mapBrain = new HashMap<String, String>();

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

        String brainCode = (String) dataLine.get(0);
        if (brainCode != null) {
            mapBrain = new HashMap<String, String>();
        }

        // Existing brain code
        if (dataLine != null && dataLine.size() > 2 && dataLine.get(1) != null && dataLine.get(2) != null) {
            // System.out.println(dataLine.get(1) + " = " + dataLine.get(2));
            mapBrain.put(dataLine.get(1).toString().trim(), dataLine.get(2).toString().trim());
        }

        if (brainCode != null) {
            // New Brain code

            // System.out.println("brain code " + brainCode);
            headerMap.add(brainCode);
            listMap.add(mapBrain);
        }
    }

    // ===== Recognize data =====

    for (int i = 0; i < headerMap.size(); i++) {
        System.out.println("----------------------------");
        String code = headerMap.get(i);
        System.out.println(i + " " + code);
        Map<String, String> map = listMap.get(i);

        Map<String, String> updatedMap = new HashMap<String, String>();

        for (Map.Entry<String, String> entry : map.entrySet()) {
            String key = entry.getKey();
            String value = entry.getValue();

            if (!key.toLowerCase().equals("age")
                    // && !key.toLowerCase().equals("ethnicity")
                    // && !key.toLowerCase().equals("sex")
                    && !value.toLowerCase().equals("no data")) {
                updatedMap.put(key, value);
            }

            // System.out.println(key + " -> " + value);
        }

        List<Document> listDocuments = collection
                .find(Filters.and(Filters.eq("exp_group.main_gse_number", "GSE25219"),
                        Filters.eq("parameters.brain code", code)))
                .into(new ArrayList<Document>());
        System.out.println("Number of corresponding Mongo documents " + listDocuments.size());
        System.out.println(updatedMap);

        for (int j = 0; j < listDocuments.size(); j++) {
            Document doc = listDocuments.get(j);

            Document parameters = (Document) doc.get("parameters");
            parameters.putAll(updatedMap);
            System.out.println("\t" + parameters);

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

        }

    }

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

    mongoClient.close();
}

---

From source file:module.script.pro12.CreatePro12.java

License:Open Source License

@SuppressWarnings({ "unchecked" })
public CreatePro12() {

    // ===== 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");
    // MongoDatabase db = mongoClient.getDatabase("geo");

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

    Date submissionDate = null;//from   w ww. jav  a 2 s.  c  o m
    try {
        submissionDate = dateFormat.parse("2010-01-01");
    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    List<String> platforms = new ArrayList<String>();
    platforms.add("GPL570");

    Document docSeries = new Document();
    docSeries.append("_id", "PRO12").append("title", "Project 12: Reference tissues and cell lines")
            .append("platforms", platforms).append("submission_date", submissionDate)
            .append("last_update", submissionDate).append("import_date", new Date());

    System.out.println(docSeries);
    collectionSeries.insertOne(docSeries);

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

    mongoClient.close();
}

---

From source file:module.script.pro12.TransferPro12.java

License:Open Source License

@SuppressWarnings({ "unchecked" })
public TransferPro12() {

    // ===== 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 id_sample from epimed_prod.om_sample join epimed_prod.om_sample_series using (id_sample) "
            + "join epimed_prod.om_series using (id_series) where id_series='PRO12'";

    List<String> list = session.createSQLQuery(sql).list();

    Document pro12 = new Document();
    pro12.append("series", "PRO12");

    for (String gsmNumber : list) {

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

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

        if (doc != null) {
            // Update Mongo document
            collection.updateOne(Filters.eq("_id", gsmNumber), new Document("$push", pro12));
        }//from  ww  w .ja  v  a 2  s  . c  o  m

    }

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

    mongoClient.close();
}

---

From source file:module.script.proallchen.CreateProallChen.java

License:Open Source License

public CreateProallChen() {

    // ===== 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");
    // MongoDatabase db = mongoClient.getDatabase("geo");

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

    Date submissionDate = null;//from   w ww  . j  a v a 2 s .c o  m
    try {
        submissionDate = dateFormat.parse("2016-05-13");
    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // List<String> platforms = new ArrayList<String>();
    // platforms.add("GPL570");

    Document docSeries = new Document();
    docSeries.append("_id", "PROALL_CHEN")
            .append("title", "Genomic Profiling of Adult and Pediatric B-cell Acute Lymphoblastic Leukemia")
            .append("platforms", null).append("submission_date", submissionDate)
            .append("last_update", submissionDate).append("import_date", new Date());

    System.out.println(docSeries);
    collectionSeries.insertOne(docSeries);

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

    mongoClient.close();
}

---

From source file:module.script.proallchen.ImportProallChenOriginal.java

License:Open Source License

public ImportProallChenOriginal() {

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

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

    // ===== Samples ======

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

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

    String inputfile = this.getInputDirectory() + this.getDirSeparator() + "PROALL_CHEN_clinical.xlsx";
    System.out.println("LOADING \t " + inputfile);
    ExcelService excelService = new ExcelService();
    excelService.load(inputfile);//from www. j  a  v a2  s  . co  m

    System.out.println(excelService.getHeader());

    String idSeries = "PROALL_CHEN";
    List<String> listSeries = new ArrayList<String>();
    listSeries.add(idSeries);

    for (int i = 0; i < excelService.getData().size(); i++) {

        List<Object> line = excelService.getData().get(i);

        String idSample = "ESM" + line.get(0);

        System.out.println(idSample + " " + line);

        Document docSample = collectionSamples.find(Filters.eq("_id", idSample.trim())).first();

        System.out.println(docSample);

        Document parameters = (Document) docSample.get("parameters");

        for (int j = 0; j < excelService.getHeader().size(); j++) {

            String header = (String) excelService.getHeader().get(j);
            Object value = line.get(j);
            // System.out.println(header + " = " + value);

            parameters.append(header, value);

        }

        System.out.println(parameters);

        // Update Mongo document
        docSample.put("parameters", parameters);
        UpdateResult updateResult = collectionSamples.updateOne(Filters.eq("_id", docSample.get("_id")),
                new Document("$set", docSample));
    }

    mongoClient.close();
}

---

From source file:module.script.proallchen.ImportProallChenSupplementary.java

License:Open Source License

public ImportProallChenSupplementary() {

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

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

    // ===== Samples ======

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

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

    String inputfile = this.getInputDirectory() + this.getDirSeparator()
            + "DB_ALL_JIN_RNASEC_clinical_data_supplementary.xlsx";
    System.out.println("LOADING \t " + inputfile);
    ExcelService excelService = new ExcelService();
    excelService.load(inputfile);/*w  ww.  jav  a  2 s .co  m*/

    System.out.println(excelService.getHeader());

    String idSeries = "PROALL_CHEN";
    List<String> listSeries = new ArrayList<String>();
    listSeries.add(idSeries);

    for (int i = 0; i < excelService.getData().size(); i++) {

        List<Object> line = excelService.getData().get(i);

        String idSample = "ESM" + line.get(0);

        System.out.println(idSample + " " + line);

        // ===== Sample Document =====

        Document docSample = new Document();

        docSample.append("_id", idSample).append("main_gse_number", idSeries).append("series", listSeries)
                .append("organism", "Homo sapiens").append("submission_date", today)
                .append("last_update", today).append("import_date", today).append("analyzed", false);

        // ===== Mandatory parameters =====
        Document expGroup = generateExpGroup(idSeries, idSample);
        docSample.append("exp_group", expGroup);

        // ===== Supplementary parameters =====

        Document parameters = new Document();
        parameters.append("id_sample", idSample);

        // === Attributes ===

        for (int j = 0; j < excelService.getHeader().size(); j++) {

            String header = (String) excelService.getHeader().get(j);
            Object value = line.get(j);
            // System.out.println(header + " = " + value);

            parameters.append(header, value);

        }
        docSample.append("parameters", parameters);

        System.out.println(docSample);

        // === Delete if already exist ===
        collectionSamples.deleteOne(eq("_id", idSample));

        // ===== Insert data =====
        collectionSamples.insertOne(docSample);

    }

    mongoClient.close();
}

---

From source file:module.script.probcp.CreateProbcp.java

License:Open Source License

@SuppressWarnings({ "unchecked" })
public CreateProbcp() {

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

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

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

    Date submissionDate = null;/*from ww w.ja  v a 2 s .c  om*/
    try {
        submissionDate = dateFormat.parse("2017-03-20");
    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    List<String> platforms = new ArrayList<String>();
    platforms.add("proteomics");

    Document docSeries = new Document();
    docSeries.append("_id", "PROBCP").append("title", "Breast cancer proteomics").append("platforms", platforms)
            .append("submission_date", submissionDate).append("last_update", submissionDate)
            .append("import_date", new Date());

    System.out.println(docSeries);
    collectionSeries.insertOne(docSeries);

    mongoClient.close();
}

---

• «
• 1
• 2
• 3
• 4
• 5
• 6
• 7
• 8
• 9
• 10
• 11
• 12
• 13
• 14
• 15
• 16
• 17
• 18
• 19
• 20
• 21
• 22
• 23
• 24
• 25
• 26
• 27
• 28
• 29
• 30
• 31
• 32
• 33
• 34
• 35
• 36
• 37
• 38
• »