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

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

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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.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
    );//from w ww  . jav a 2 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}]+\\]";
    ;/*from w  w w.  j  a va  2s .com*/
    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);//  www .ja va 2s.  c om

    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);// ww w.  ja  v  a  2  s  .  co 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 ww.j  av a  2  s  .c o m

    }

    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 w ww.ja  v  a  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();/*w  w w. ja v  a2  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));
        }/*  w  w  w  .  j  ava  2  s . c  o m*/

    }

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

    mongoClient.close();
}

From source file:module.script.TransferBrbHistologyCodes.java

License:Open Source License

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

    // ===== 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, index_histology_code, histology_code, ordered_histology_code from db_brb_lung.view_exp_group";

    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("index_histology_code", map.get("index_histology_code"));
            expGroup.put("histology_code", map.get("histology_code"));
            expGroup.put("ordered_histology_code", map.get("ordered_histology_code"));
            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));
        }/*from  w w  w  .  j ava  2  s  .c o m*/

    }

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

    mongoClient.close();
}

From source file:module.script.TransferExposure.java

License:Open Source License

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

    // ===== 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));
        }//from  ww  w.j  av a  2s.c  o m

    }

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

    mongoClient.close();
}