Example usage for com.mongodb.client MongoDatabase getCollection

List of usage examples for com.mongodb.client MongoDatabase getCollection

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Introduction

In this page you can find the example usage for com.mongodb.client MongoDatabase getCollection.

Prototype

MongoCollection<Document> getCollection(String collectionName);

Source Link

Document

Gets a collection.

Usage

From source file:module.AnalyseGeo.java

License:Open Source License

public AnalyseGeo() {

    // ===== 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("sample");
    List<Document> listDocuments = collection.find(Filters.in("series", gseNumber))
            // .find(Filters.and(Filters.in("series", gseNumber), Filters.eq("analyzed", false)))
            .into(new ArrayList<Document>());

    // ===== Service =====
    OntologyService ontologyService = new OntologyService(session);
    DispatcherFactory dispatcherFactory = new DispatcherFactory(session);

    // ===== Begin transaction =====
    session.beginTransaction();/*from  w  w w .j  a  v a2s  .c om*/

    // ===== Analyse ======

    for (int i = 0; i < listDocuments.size(); i++) {
        // for (int i=0; i<1; i++) {
        Document doc = listDocuments.get(i);
        Document expGroup = (Document) doc.get("exp_group");

        String gsmNumber = doc.getString("_id");

        List<String> listEntries = new ArrayList<String>();
        List<String> parameters = new ArrayList<String>();

        String title = (String) expGroup.get("sample_title");
        String source = (String) expGroup.get("sample_source");
        listEntries.add(title);
        listEntries.add(source);

        Map<String, Object> mapParameters = (Map<String, Object>) doc.get("parameters");
        parameters.addAll(mapParameters.keySet());
        parameters.remove("id_sample");
        parameters.remove("extract_protocol");

        // To remove
        parameters.remove("lab description");

        for (int j = 0; j < parameters.size(); j++) {
            listEntries.add(parameters.get(j) + ": " + mapParameters.get(parameters.get(j)));
        }

        // === Clear already filled fields (only if necessary) ===
        // this.clear(expGroup);

        Map<String, List<Object>> mapOntologyObjects = ontologyService.recognizeOntologyObjects(listEntries);
        // Map <ClOntologyCategory, Set<String>> mapOntologyCategories = ontologyService.getMapOntologyCategories();
        // this.generateSummary(ontologyService, mapOntologyCategories, mapOntologyObjects);

        System.out.println("------------------------------------------------------------");
        System.out.println(i + " " + gsmNumber + " " + listEntries);
        System.out.println(ontologyService.toString());

        // ===== Create mapping objects and making links =====

        try {

            // === Dispatcher ===
            for (int j = 0; j < categories.length; j++) {

                dispatcherFactory.getObject(expGroup, mapOntologyObjects, categories[j]);

                System.out.print(categories[j]);
                if (expGroup.getString(categories[j]) != null) {
                    System.out.print(" " + expGroup.getString(categories[j]) + "\n");
                } else {
                    System.out.print("\n");
                }

            }

            System.out.println(expGroup);

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

            }

        } catch (DispatcherException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }

    }

    if (commit) {
        MongoCollection<Document> collectionSeries = db.getCollection("series");
        Document series = collectionSeries.find(Filters.eq("_id", gseNumber)).first();
        series.put("status", "analyzed");
        collectionSeries.updateOne(Filters.eq("_id", gseNumber), new Document("$set", series));
    }

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

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

    mongoClient.close();
}

From source file:module.ClearGeoExpGroup.java

License:Open Source License

public ClearGeoExpGroup() {

    // ===== 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>());

    // ===== Analyse ======

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

        Document doc = listDocuments.get(i);
        String id = doc.getString("_id");
        Document expGroup = (Document) doc.get("exp_group");
        this.clear(expGroup);
        expGroup.remove("er");
        expGroup.remove("pr");
        expGroup.remove("her2");
        expGroup.remove("triple_negative");

        // Update Mongo document
        doc.put("exp_group", expGroup);
        doc.put("analyzed", false);
        if (commit) {
            UpdateResult updateResult = collection.updateOne(Filters.eq("_id", id), new Document("$set", doc));

        }//from w  w  w  . ja v  a  2  s  . c o m

    }

    mongoClient.close();
}

From source file:module.CreateStudy.java

License:Open Source License

@SuppressWarnings("unchecked")
public CreateStudy() {

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

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

    // === Excel data loader ===

    String inputfile = this.getInputDirectory() + this.getDirSeparator() + "prolung2_expgrp4.xlsx";
    System.out.println("LOADING \t " + inputfile);
    ExcelService excelService = new ExcelService();
    excelService.load(inputfile);/*from   w ww . j ava 2 s . c o  m*/
    List<Object> listCel = excelService.extractColumn(0);

    Integer indCel = excelService.getHeaderMap().get("gse8894_sample_cel");

    // ===  New Series === 
    MongoCollection<Document> collectionSeries = db.getCollection("series");
    Document docSeries = new Document();
    docSeries.append("_id", "PROLUNG").append("title", "Lung cancerous and non-cancerous samples")
            .append("platforms", null).append("submission_date", today).append("last_update", today)
            .append("import_date", today);

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

    // === Add samples to new series ===
    MongoCollection<Document> collectionSamples = db.getCollection("samples");
    for (int i = 0; i < listCel.size(); i++) {

        String gsm = this.getGsm(listCel.get(i));

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

        if (docSample == null) {
            System.err.println("ERROR! Sample " + gsm + "doesn't exist. Try another column.");

            gsm = this.getGsm(excelService.getData().get(i).get(indCel));
            docSample = collectionSamples.find(Filters.eq("_id", gsm)).first();

            if (docSample == null) {
                System.err.println("ERROR! Sample " + gsm + " doesn't exist. Exit.");
                System.exit(0);
            } else {
                System.err.println("Found " + gsm);
            }
        }

        Document expGroup = (Document) docSample.get("exp_group");
        setGpl.add(expGroup.get("id_platform").toString());

        List<String> listSeries = (List<String>) docSample.get("series");
        listSeries.add(docSeries.getString("_id"));
        docSample.put("series", listSeries);

        System.out.println(docSample);
        // updateResult = collectionSamples.updateOne(Filters.eq("_id", docSample.get("_id")), new Document("$set", docSample));
    }

    // === Update platforms of the series ===

    System.out.println(setGpl);

    docSeries.put("platforms", setGpl);
    updateResult = collectionSeries.updateOne(Filters.eq("_id", docSeries.get("_id")),
            new Document("$set", docSeries));
    if (updateResult.getMatchedCount() == 0) {
        collectionSeries.insertOne(docSeries);
    }

}

From source file:module.ExportGeo.java

License:Open Source License

public ExportGeo() {

    String gseNumber = "GSE2109";

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

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

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

    // ===== Find exp_group in the database =====

    List<Document> docExpGroup = collection.find(Filters.in("series", gseNumber))
            .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId()))
            .into(new ArrayList<Document>());

    List<Document> docParam = collection.find(Filters.in("series", gseNumber))
            .projection(Projections.fields(Projections.include("parameters"), Projections.excludeId()))
            .into(new ArrayList<Document>());

    mongoClient.close();/*from   www  . j  a  va2s . c o  m*/

    // ===== 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());
        }

        String[] dataLine = new String[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");
        String[] dataLine = new String[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() + "Export_Mongo_" + gseNumber + "_"
            + 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.ImportArrayExpress.java

License:Open Source License

public ImportArrayExpress() {

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

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

    // ===== Pattern =====
    String patternText = "\\[[\\p{Print}\\p{Space}]+\\]";
    ;//from   w w  w .ja  va  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 (commit) {
                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 = accession + "-" + 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;

                boolean analysed = false;

                if (docAlreadyExist) {
                    analysed = (Boolean) docSampleExist.get("analyzed");
                }

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

                Document docSample = mongoService.createSample(idSample, (String) docSeries.get("_id"),
                        accessionAsList, organism, (Date) docSeries.get("submission_date"),
                        (Date) docSeries.get("last_update"), analysed);

                Document expGroup = null;
                Document parameters = null;

                // System.out.println("------------------------------------------------------------------");

                if (docAlreadyExist) {
                    // === ID sample alredy exists ===
                    System.out.println(i + "/" + nbSamples + "\t " + docSeries.get("_id") + "\t " + idSample
                            + ":  already exists in the database, analyzed=" + analysed);
                    expGroup = docSampleExist.get("exp_group", Document.class);
                    parameters = mongoService.updateParameters(docSampleExist, mapParameters);
                } else {
                    // === New sample ===
                    System.out.println(i + "/" + nbSamples + "\t " + docSeries.get("_id") + "\t " + idSample);
                    expGroup = mongoService.createExpGroup(docSample, platform, null, null, organism);
                    parameters = mongoService.createParameters(docSample, mapParameters);
                    nbImportedSamples++;
                }

                // === Update sample_title, sample_source, layout ===
                expGroup.put("sample_title", parameters.getString("organism part"));
                expGroup.put("sample_source", parameters.getString("Source Name"));
                expGroup.put("layout", parameters.getString("LIBRARY_LAYOUT"));

                docSample.append("exp_group", expGroup);
                docSample.append("parameters", parameters);

                if (commit) {

                    // === Update old if already exist ===
                    if (docAlreadyExist) {
                        // collectionSamples.deleteOne(eq("_id", idSample));
                        collectionSamples.updateOne(Filters.eq("_id", idSample),
                                new Document("$set", docSample));
                    } else {
                        // ===== Insert data =====
                        collectionSamples.insertOne(docSample);
                    }

                    // ===== Update series for platforms =====
                    List<String> listPlatforms = collectionSamples
                            .distinct("exp_group.id_platform", Filters.in("series", accession), String.class)
                            .into(new ArrayList<String>());
                    docSeries.append("platforms", listPlatforms);
                    collectionSeries.updateOne(Filters.eq("_id", accession), new Document("$set", docSeries));
                }

            }

        } 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.ImportArrayExpressInit.java

License:Open Source License

public ImportArrayExpressInit() {

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

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

    // ===== Pattern =====
    String patternText = "\\[[\\p{Print}\\p{Space}]+\\]";
    ;/* w w w.j  ava 2  s. c  om*/
    Pattern pattern = Pattern.compile(patternText);

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

    for (String accession : listAccessions) {

        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;
                // System.out.println("GEO accession " +  gseNumber + " found: " + isGseFound);
            }
        }

        if (!isGseFound) {

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

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

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

            if (series.getListAccessions() != null && !series.getListAccessions().isEmpty()) {
                listSeriesAcc.addAll(series.getListAccessions());
            }

            docSeries.put("accessions", listSeriesAcc);

            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));

            // ===== 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.createParameters(data.get(i), header);
                String idSample = this.createIdSample(mapParameters);

                if (idSample == null) {
                    System.err.println("idSample is not recongnized for " + mapParameters);
                    mongoClient.close();
                    System.exit(0);
                }

                String organism = (String) mapParameters.get("organism");
                if (organism == null || organism.isEmpty()) {
                    organism = "Homo sapiens";
                }
                String platform = (String) mapParameters.get("LIBRARY_STRATEGY");
                if (platform != null && !platform.isEmpty()) {
                    platform = platform.toLowerCase().trim();
                } else {
                    platform = "rna-seq";
                }
                String layout = (String) mapParameters.get("LIBRARY_LAYOUT");
                if (layout != null && !layout.isEmpty()) {
                    layout = layout.toLowerCase().trim();
                }

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

                boolean analysed = false;

                if (docAlreadyExist) {
                    analysed = (Boolean) docSampleExist.get("analyzed");
                    System.out.println(i + "/" + nbSamples + "\t " + docSeries.get("_id") + "\t " + idSample
                            + ":  already exists in the database, analyzed=" + analysed);
                } else {
                    System.out.println(i + "/" + nbSamples + "\t " + docSeries.get("_id") + "\t " + idSample);
                }

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

                Document docSample = mongoService.createSample(idSample, (String) docSeries.get("_id"),
                        listSeriesAcc, organism, (Date) docSeries.get("submission_date"),
                        (Date) docSeries.get("last_update"), analysed);

                // ===== Mandatory parameters =====

                // Preserve "exp_group" if the document exists already

                Document expGroup = null;
                if (docAlreadyExist) {
                    expGroup = (Document) docSampleExist.get("exp_group");
                } else {
                    expGroup = mongoService.createExpGroup(docSample, platform,
                            (String) mapParameters.get("organism part"),
                            (String) mapParameters.get("Source Name"), organism);
                    if (layout != null) {
                        expGroup.append("layout", layout);

                        // run_name
                        int j = 0;
                        boolean isFound = false;
                        String runName = null;
                        while (!isFound && j < listRunNameParameters.length) {
                            runName = (String) mapParameters.get(listRunNameParameters[j]);
                            isFound = runName != null;
                            j++;
                        }
                        if (runName != null) {
                            expGroup.append("run_name", runName);
                        }

                    }
                }

                docSample.append("exp_group", expGroup);

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

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

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

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

                // ===== Update series for platforms =====
                List<String> listPlatforms = collectionSamples
                        .distinct("exp_group.id_platform", Filters.in("series", accession), String.class)
                        .into(new ArrayList<String>());
                docSeries.append("platforms", listPlatforms);
                collectionSeries.updateOne(Filters.eq("_id", accession), new Document("$set", docSeries));

            }

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

    mongoClient.close();

}

From source file:module.ImportGeo.java

License:Open Source License

public ImportGeo() {

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

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

    // ===== Insert data =====

    for (int k = 0; k < listGseNumber.length; k++) {

        String gseNumber = listGseNumber[k];

        System.out.println("------------------------------------------");
        System.out.println(k + " Import " + gseNumber);

        // ===== Load GSE =====

        NcbiGeoGse gse = new NcbiGeoGse(webService.loadGeo(gseNumber));
        System.out.println(gse);/*from   w  w  w .  j  a  v  a2  s .c o m*/

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

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

        Document docSeries = mongoService.createSeries(gse.getGseNumber(), gse.getTitle(), gse.getListGpl(),
                gse.getSubmissionDate(), gse.getLastUpdate());

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

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

        MongoCollection<Document> collectionPlatforms = db.getCollection("platform");

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

            NcbiGeoGpl gpl = new NcbiGeoGpl(webService.loadGeo(gse.getListGpl().get(i)));

            System.out.println("\t Import platform " + gpl.getGplNumber());

            Document docPlatforms = mongoService.createPlatform(gpl.getGplNumber(), gpl.getTitle(),
                    gpl.getTaxid(), gpl.getOrganism(), gpl.getManufacturer(), gpl.getSubmissionDate(),
                    gpl.getLastUpdate(), gpl.getTechnology());

            UpdateResult res = collectionPlatforms.updateOne(Filters.eq("_id", gpl.getGplNumber()),
                    new Document("$set", docPlatforms));
            if (res.getMatchedCount() == 0) {
                collectionPlatforms.insertOne(docPlatforms);
            }
        }

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

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

        // for (int i=0; i<1; i++) {
        for (int i = 0; i < gse.getListGsm().size(); i++) {

            NcbiGeoGsm gsm = new NcbiGeoGsm(webService.loadGeo(gse.getListGsm().get(i)));

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

            boolean analysed = false;

            if (docAlreadyExist) {
                analysed = (Boolean) docSampleExist.get("analyzed");
                System.out.println(i + "/" + gse.getListGsm().size() + "\t " + gse.getGseNumber() + "\t "
                        + gsm.getGsmNumber() + ":  already exists in the database, analyzed=" + analysed);
            } else {
                System.out.println(i + "/" + gse.getListGsm().size() + "\t " + gse.getGseNumber() + "\t "
                        + gsm.getGsmNumber());
            }

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

            Document docSample = mongoService.createSample(gsm.getGsmNumber(), gse.getGseNumber(),
                    gsm.getListGse(), gsm.getOrganism(), gsm.getSubmissionDate(), gsm.getLastUpdate(),
                    analysed);

            // ===== Mandatory parameters =====

            // Preserve "exp_group" if the document exists already

            Document expGroup = null;
            if (docAlreadyExist) {
                expGroup = (Document) docSampleExist.get("exp_group");
            } else {
                expGroup = mongoService.createExpGroup(docSample, gsm.getGplNumber(), gsm.getTitle(),
                        gsm.getSourceName(), gsm.getOrganism());

            }
            docSample.append("exp_group", expGroup);

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

            Document parameters = generateParameters(gsm);
            docSample.append("parameters", parameters);

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

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

        }

    }

    mongoClient.close();
}

From source file:module.ImportPlatform.java

License:Open Source License

public ImportPlatform() {

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

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

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

    List<String> listGpl = collectionSamples.distinct("exp_group.id_platform", String.class)
            .into(new ArrayList<String>());

    for (String idPlatform : listGpl) {
        Document doc = collectionPlatforms.find(Filters.in("_id", idPlatform)).first();
        if (doc.getString("type") == null) {
            System.out.println(idPlatform + ": " + doc);
        }/*w w  w .j av a  2s  . c  o m*/
    }

    mongoClient.close();
}

From source file:module.ImportPlatformFromFile.java

License:Open Source License

public ImportPlatformFromFile() {

    // === Display ===
    System.out.println("\n================ BEGIN Module " + this.getClass().getName() + "================");

    // === INPUT ===
    String idPlatform = "GPL97";
    String inputfile = this.getInputDirectory() + this.getDirSeparator() + "GPL97-17394.txt";
    String gpl = idPlatform.toLowerCase().trim();

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

    // ===== DAO =====
    OmGeneDao geneDao = new OmGeneDao(session);

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

    try {//from  www. j  a  v  a2s .  c o  m
        // === Begin transaction ===
        session.beginTransaction();

        // ===== Load file =====
        System.out.println("ID Platform " + gpl);
        System.out.println("LOADING \t " + inputfile);
        System.out.println("Please wait... ");
        List<String> listRows = fileService.loadTextFile(inputfile);
        // List<String> listRows = webService.loadGeoData(idPlatform);
        System.out.println("File sucessfully LOADED");

        // ===== Recognize header =====

        List<String> header = fileService.readHeader(listRows, "\t");

        if (header == null || header.isEmpty()) {
            throw new ImportDataException("The header is empty");
        } else {
            System.out.println("Header " + header);
        }

        Integer indId = fileService.findIndex(header, "ID");
        Integer indGbacc = fileService.findIndex(header, "GB_ACC");
        Integer indEntrez = fileService.findIndex(header, "ENTREZ");

        if (indId == null || indGbacc == null || indEntrez == null) {
            throw new ImportDataException("Header not recognized: " + "ID index=" + indId + ", GB_ACC index="
                    + indGbacc + ", ENTREZ index=" + indEntrez);
        } else {
            System.out.println("The following header items are recognized:");
            System.out.println("\t ID index=" + indId + ": " + header.get(indId));
            System.out.println("\t GB_ACC index=" + indGbacc + ": " + header.get(indGbacc));
            System.out.println("\t ENTREZ index=" + indEntrez + ": " + header.get(indEntrez));
        }

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

        List<List<String>> data = fileService.readData(listRows, "\t");

        if (data == null || data.isEmpty()) {
            throw new ImportDataException("The data are empty");
        } else {
            System.out.println(
                    "The data are sucessfully loaded: rows " + data.size() + ", columns " + data.get(0).size());
        }

        // ===== Create specific tables =====

        String sqlCheckTableProbe = "select * from information_schema.tables WHERE table_schema = 'hs' and table_name='om_probe_"
                + gpl + "'";

        List<Object> result = session.createNativeQuery(sqlCheckTableProbe).getResultList();

        String tableProbe = "hs.om_probe_" + gpl;
        String tableGP = "hs.om_gp_" + gpl;

        if (result == null || result.isEmpty()) {
            // Table probe
            String sqlCreateTableProbe = "create table " + tableProbe
                    + "(id_probe             VARCHAR(50)          not null,"
                    + " genbank_acc          VARCHAR(50)          null," + " constraint pk_om_probe_" + gpl
                    + " primary key (id_probe))";
            session.createNativeQuery(sqlCreateTableProbe).executeUpdate();

            // Table gp
            String sqlCreateTableGP = "create table " + tableGP
                    + "(id_probe             VARCHAR(50)          not null,"
                    + " id_gene              INT4                 not null," + " constraint pk_om_gp_" + gpl
                    + " primary key (id_probe, id_gene))";
            session.createNativeQuery(sqlCreateTableGP).executeUpdate();

            // Foregn keys

            String sqlAlterTableProbe = "alter table " + tableGP + " add constraint fk_gp_probe_" + gpl
                    + " foreign key (id_probe)" + "  references " + tableProbe
                    + " (id_probe) on delete restrict on update restrict";
            session.createNativeQuery(sqlAlterTableProbe).executeUpdate();

            String sqlAlterTableGene = "alter table " + tableGP + " add constraint fk_gp_gene_" + gpl
                    + " foreign key (id_gene)"
                    + "  references hs.om_gene (id_gene) on delete restrict on update restrict";
            session.createNativeQuery(sqlAlterTableGene).executeUpdate();
        }

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

        for (int i = 0; i < data.size(); i++) {
            // for (int i=0; i<10; i++) {

            List<String> dataline = data.get(i);

            String idProbe = dataline.get(indId).trim();
            String genbankAcc = dataline.get(indGbacc).trim();

            String sqlInsertProbe = "insert into " + tableProbe + " values('" + idProbe + "',  null)";
            if (genbankAcc != null && !genbankAcc.isEmpty()) {
                sqlInsertProbe = "insert into " + tableProbe + " values('" + idProbe + "', '" + genbankAcc
                        + "')";
            }
            session.createNativeQuery(sqlInsertProbe).executeUpdate();

            OmGenbankUnigene gu = session.get(OmGenbankUnigene.class, genbankAcc);
            if (gu == null && genbankAcc != null && !genbankAcc.isEmpty()) {
                gu = new OmGenbankUnigene();
                gu.setGenbankAcc(genbankAcc);
                session.save(gu);
            }

            String listEntrez = null;
            String[] parts = null;
            if (indEntrez < dataline.size()) {
                listEntrez = dataline.get(indEntrez).trim();
                parts = listEntrez.split("[///\\p{Space}]");

                for (String entrezString : parts) {

                    Integer entrez = null;

                    try {
                        entrez = Integer.parseInt(entrezString);
                    } catch (NumberFormatException e) {
                        // nothing to do
                    }

                    if (entrez != null) {

                        OmGene gene = geneDao.find(entrez);
                        if (gene == null) {
                            gene = geneDao.createGene(entrez, null);
                        }

                        String sqlInsertGP = "insert into " + tableGP + " values('" + idProbe + "', " + entrez
                                + ")";
                        session.createNativeQuery(sqlInsertGP).executeUpdate();

                    }
                }
            }

            if (i % 1000 == 0) {
                System.out.println(i + "\t" + idProbe + "\t" + genbankAcc + "\t" + listEntrez + "\t"
                        + Arrays.toString(parts));
            }

            if (i % 20 == 0) {
                session.flush();
            }
        }

        // ===== Subscribe platform =====

        OmPlatform platform = session.get(OmPlatform.class, idPlatform);
        if (platform != null) {
            platform.setEnabled(true);
            session.update(platform);
        } else {
            MongoCollection<Document> collection = db.getCollection("platforms");
            Document docPlatform = collection.find(Filters.eq("_id", idPlatform)).first();
            String title = docPlatform.getString("title");
            String manufacturer = docPlatform.getString("manufacturer");
            platform = new OmPlatform();
            platform.setIdPlatform(idPlatform);
            platform.setTitle(title);
            platform.setManufacturer(manufacturer);
            platform.setEnabled(true);
            session.save(platform);
        }

        // ===== Rights =====
        String sqlRights;
        String[] users = { "epimed_prod", "epimed_web", "epimed_script" };
        for (String user : users) {
            sqlRights = "GRANT SELECT ON ALL TABLES IN SCHEMA hs TO " + user;
            session.createNativeQuery(sqlRights).executeUpdate();
        }
        sqlRights = "GRANT ALL ON ALL TABLES IN SCHEMA hs TO epimed_admin";
        session.createNativeQuery(sqlRights).executeUpdate();

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

    } catch (Exception e) {
        session.getTransaction().rollback();
        System.out.println("ROLLBACK in module " + this.getClass().getName());
        e.printStackTrace();
    } finally {
        if (session.isOpen()) {
            session.close();
        }
        sessionFactory.close();
        mongoClient.close();
    }

    // === Display ===
    System.out.println("================ END Module " + this.getClass().getName() + "================");

}

From source file:module.script.AddSeriesToSamples.java

License:Open Source License

public AddSeriesToSamples() {

    // ===== Service =====
    FormatService formatService = new FormatService();

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

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

    Set<String> setProjects = new HashSet<String>();

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

    Bson filters = Filters.and(Filters.in("series", "PRJNA270632"));

    List<Document> listDocuments = collection.find(filters).into(new ArrayList<Document>());

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

        Document doc = listDocuments.get(i);
        Document expgroup = doc.get("exp_group", Document.class);

        if (expgroup.get("exp_Mcount") != null) {

            List<String> projects = doc.get("series", ArrayList.class);
            setProjects.clear();//from  w w  w .  j  a  v  a  2 s .c  o  m
            setProjects.addAll(projects);
            setProjects.add("TISSUE_SPECIFIC_GENES_HS");
            doc.put("series", setProjects);
            System.out.println(doc.getString("_id") + " " + projects + " -> " + setProjects);

            collection.updateOne(Filters.eq("_id", doc.getString("_id")), new Document("$set", doc));
        }

    }

    mongoClient.close();
}