Example usage for com.mongodb.client MongoCollection updateOne

List of usage examples for com.mongodb.client MongoCollection updateOne

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Introduction

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

Prototype

UpdateResult updateOne(Bson filter, List<? extends Bson> update);

Source Link

Document

Update a single document in the collection according to the specified arguments.

Usage

From source file:module.script.emtab365.ImportSamplesEMTAB365.java

License:Open Source License

public ImportSamplesEMTAB365() {

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

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

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

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

    String inputfile = this.getInputDirectory() + this.getDirSeparator() + "E-MTAB-365.sdrf.xlsx";
    System.out.println("LOADING \t " + inputfile);
    excelService.load(inputfile);/*from  w ww.  j  a  v  a  2  s. c o m*/

    // ===== Init values ======

    String idSeries = "E-MTAB-365";
    List<String> listSeries = new ArrayList<String>();
    listSeries.add(idSeries);
    Document docSeries = collectionSeries.find(Filters.eq("_id", idSeries)).first();
    String organism = "Homo sapiens";

    // ==== Header processing ====

    Map<Integer, String> mapHeader = new HashMap<Integer, String>();
    for (int i = 0; i < excelService.getHeader().size(); i++) {
        String headerItem = (String) excelService.getHeader().get(i);
        if (headerItem != null && headerItem.contains("[")) {
            String[] parts = headerItem.split("[\\[\\]]");
            headerItem = parts[1];
            headerItem = headerItem.replaceAll("[:_\\.]", " ");
        }
        mapHeader.put(i, headerItem.trim());
    }
    System.out.println(mapHeader);

    for (int i = 0; i < excelService.getData().size(); i++) {
        // for (int i=0; i<1; i++) {

        List<Object> dataline = excelService.getData().get(i);
        String idSample = (String) dataline.get(0);

        if (!idSample.equals("pool XX")) {

            String idPlatform = ((String) dataline.get(54)).trim();
            if (idPlatform.contains("A-AFFY-44")) {
                idPlatform = "GPL570";
            } else {
                Document docPlatform = mongoService.createPlatform(idPlatform, null, "9606", "Homo sapiens",
                        null, null, null, null);
                UpdateResult res = collectionPlatforms.updateOne(
                        Filters.eq("_id", docPlatform.getString("_id")), new Document("$set", docPlatform));
                if (res.getMatchedCount() == 0) {
                    collectionPlatforms.insertOne(docPlatform);
                }
            }

            Document docSample = mongoService.createSample(idSample, idSeries, listSeries, organism,
                    (Date) docSeries.get("submission_date"), (Date) docSeries.get("last_update"), false);

            // === exp_group ===

            Document expgroup = mongoService.createExpGroup(docSample, idPlatform, null, null, organism);
            docSample.append("exp_group", expgroup);

            // === parameters ===

            Map<String, Object> mapParameters = new HashMap<String, Object>();

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

                String key = mapHeader.get(j);
                Object value = dataline.get(j);

                if (value instanceof String) {
                    String valueString = ((String) value).trim();
                    if (valueString != null && !valueString.isEmpty() && !valueString.equals("NA")
                            && !valueString.equals("ND")) {
                        value = valueString;
                    } else {
                        value = null;
                    }
                }

                if (key != null && value != null) {
                    mapParameters.put(key, value);
                    // System.out.println(key + "='" + value+"'");
                }
            }

            Document parameters = mongoService.createParameters(docSample, mapParameters);
            docSample.append("parameters", parameters);

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

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

            System.out.println(docSample);

        }
    }

    mongoClient.close();
}

From source file:module.script.emtab365.UpdateSamplesEMTAB365.java

License:Open Source License

public UpdateSamplesEMTAB365() {

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

    // ===== INIT =====

    ClMorphology ductal = session.get(ClMorphology.class, "8500/3"); // 8500/3   Infiltrating duct carcinoma, NOS (C50._)
    ClMorphology lobular = session.get(ClMorphology.class, "8520/3"); // 8520/3   Lobular carcinoma, NOS (C50._)
    ClMorphology morphology = session.get(ClMorphology.class, "8010/3"); // Carcinoma

    ClTopology breast = session.get(ClTopology.class, "C50.9"); // Breast
    ClTopology blood = session.get(ClTopology.class, "C42.0"); // Blood
    ClTopology lymphNode = session.get(ClTopology.class, "C77.9"); // Lymph node

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

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

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

    List<Document> listDocuments = collection.find(Filters.in("series", gseNumber))
            .into(new ArrayList<Document>());

    for (int i = 0; i < listDocuments.size(); i++) {
        Document doc = listDocuments.get(i);
        Document expgroup = (Document) doc.get("exp_group");
        Document parameters = (Document) doc.get("parameters");

        String histoType = parameters.getString("Histology");
        String histoSubtype = parameters.getString("CIT classification");

        expgroup.put("histology_subtype", histoSubtype);

        if (histoType != null && histoType.toLowerCase().equals("lobular")) {
            morphology = lobular;//from w  w w. j  a va2 s . co  m
        }
        if (histoType != null && histoType.toLowerCase().equals("ductal")) {
            morphology = ductal;
        }

        expgroup.put("id_morphology", morphology.getIdMorphology());
        expgroup.put("morphology", morphology.getName());

        expgroup.put("sample_source", parameters.getString("Source Name"));

        String organismPart = parameters.getString("OrgansimPart");

        ClTopology topology = null;
        if (organismPart != null) {

            if (organismPart.toLowerCase().contains("breast")) {
                topology = breast;
            }

            if (organismPart.toLowerCase().contains("blood")) {
                topology = blood;
            }
            if (organismPart.toLowerCase().contains("lymph")) {
                topology = lymphNode;
            }

        } else {
            topology = breast;
        }

        expgroup.put("id_topology", topology.getIdTopology());
        expgroup.put("topology", topology.getName());
        expgroup.put("id_topology_group", topology.getClTopologyGroup().getIdGroup());
        expgroup.put("topology_group", topology.getClTopologyGroup().getName());

        // ==== Survival =====

        Object dfs_months = parameters.get("Delay Metastasis Free Survival months");
        if (dfs_months != null) {
            expgroup.put("dfs_months", dfs_months);
        }

        Object os_months = parameters.get("Delay Overall Survival months");
        if (os_months != null) {
            expgroup.put("os_months", os_months);
        }

        Double os = (Double) expgroup.get("os_months");
        Double dfs = (Double) expgroup.get("dfs_months");
        if (os != null && dfs != null && dfs.equals(os)) {
            expgroup.put("relapsed", false);
        }

        if (os != null && dfs != null && dfs < os) {
            expgroup.put("relapsed", true);
        }

        if (os != null && dfs != null && dfs > os) {
            expgroup.put("relapsed", null);
        }

        Object relapseDate = parameters.get("Relapse  Metastasis Date");
        if (relapseDate != null) {
            expgroup.put("relapsed", true);
        }

        // ==== Grade ====
        expgroup.put("tnm_grade", parameters.get("Grade  Scarff Bloom Richardson"));

        // ==== Files =====

        expgroup.put("ftp", parameters.getString("ArrayExpress FTP file"));
        expgroup.put("file_name", parameters.getString("Array Data File"));

        expgroup.remove("individual");
        if (parameters.getString("Individual") != null) {
            expgroup.put("individual", parameters.getString("Individual"));
        }

        // ==== Biomarkers ====
        /*
        String p53 = parameters.getString("Phenotype - TP53  Gene mutation  Status");
        expgroup.put("p53", value)
                
        String pr = parameters.getString("PGR  Protein expression");
        String er = parameters.getString("ESR1  Protein expression");
        String her2 = parameters.getString("ERBB2  Protein expression");
         */

        doc.put("exp_group", expgroup);

        System.out.println(i + " " + doc.get("_id") + " " + doc.get("analyzed") + " " + expgroup);

        if (commit) {
            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.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 . ja va 2  s. c  o m*/

    }

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

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

    mongoClient.close();
}

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 ww .  jav a2  s .  co 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}]+\\]";
    ;/*  w w w  . ja  v  a 2s  . co 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.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 www. j  a va2  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.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  w w  w  .  jav a2  s.  c om*/

    }

    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 ww w.  j a va 2  s  .c  o  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.probcp.UpdateSamplesProbcp.java

License:Open Source License

public UpdateSamplesProbcp() {

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

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

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

    String[] studies = { "tya16" };
    List<String> series = new ArrayList<String>();

    for (int l = 0; l < studies.length; l++) {

        String idStudy = studies[l];
        String studyName = idStudy.toUpperCase();

        series.clear();/*from  w  w w.j ava 2  s  .  c o m*/
        series.add(studyName);
        series.add("PROBCP");

        String sql = "select * from st_bcp." + idStudy + "_sample order by id_sample";

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

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

            Object[] lineSample = (Object[]) listSamples.get(i);

            String idSample = (String) lineSample[0];
            String clinicalClassification = (String) lineSample[1];
            String tnmStage = (String) lineSample[2];
            Integer grade = (Integer) lineSample[3];
            String type = (String) lineSample[4];

            System.out.println(Arrays.toString(lineSample));

            String id = studyName + "_" + idSample;

            Document docSample = collectionSamples.find(Filters.eq("_id", id)).first();
            Document expgroup = (Document) docSample.get("exp_group");
            expgroup.append("tnm_grade", grade);
            expgroup.append("tnm_stage", null);
            docSample.append("exp_group", expgroup);

            UpdateResult updateResult = collectionSamples.updateOne(Filters.eq("_id", id),
                    new Document("$set", docSample));

            System.out.println(docSample);

        }

    }

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

    mongoClient.close();

}

From source file:module.script.TransferBrbAnnotations.java

License:Open Source License

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

    // ===== 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, main_gse_number, string_agg(id_substance, ', ') as list_substances from epimed_prod.om_sample "
            + "join epimed_prod.cl_biopatho using (id_biopatho) join epimed_prod.cl_patient using (id_patient) join epimed_prod.cl_exposure using (id_patient) "
            + "where exposed=true group by id_sample";

    List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

    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");
            expGroup.put("exposure", map.get("list_substances"));
            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));
        }// ww  w  .j  ava  2  s  .  c om

    }

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

    mongoClient.close();
}