Example usage for com.mongodb.client MongoCollection deleteOne

Introduction

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

Prototype

DeleteResult deleteOne(Bson filter);

Source Link

Document

Removes at most one document from the collection that matches the given filter.

Usage

From source file:me.lucko.luckperms.common.storage.backing.MongoDBBacking.java

License:Open Source License

@Override
public boolean saveUser(User user) {
    if (!GenericUserManager.shouldSave(user)) {
        user.getIoLock().lock();//from   w ww .ja  v a2  s  .  c  o m
        try {
            return call(() -> {
                MongoCollection<Document> c = database.getCollection("users");
                return c.deleteOne(new Document("_id", user.getUuid())).wasAcknowledged();
            }, false);
        } finally {
            user.getIoLock().unlock();
        }
    }

    user.getIoLock().lock();
    try {
        return call(() -> {
            MongoCollection<Document> c = database.getCollection("users");
            try (MongoCursor<Document> cursor = c.find(new Document("_id", user.getUuid())).iterator()) {
                if (!cursor.hasNext()) {
                    c.insertOne(fromUser(user));
                } else {
                    c.replaceOne(new Document("_id", user.getUuid()), fromUser(user));
                }
            }
            return true;
        }, false);
    } finally {
        user.getIoLock().unlock();
    }
}

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From source file:me.lucko.luckperms.common.storage.backing.MongoDBBacking.java

License:Open Source License

@Override
public boolean deleteGroup(Group group) {
    group.getIoLock().lock();//ww w  .ja  v a  2 s  .  c o  m
    boolean success;
    try {
        success = call(() -> {
            MongoCollection<Document> c = database.getCollection("groups");
            return c.deleteOne(new Document("_id", group.getName())).wasAcknowledged();
        }, false);
    } finally {
        group.getIoLock().unlock();
    }

    if (success)
        plugin.getGroupManager().unload(group);
    return success;
}

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From source file:me.lucko.luckperms.common.storage.backing.MongoDBBacking.java

License:Open Source License

@Override
public boolean deleteTrack(Track track) {
    track.getIoLock().lock();//from ww w  .  j  a  va  2s  .c om
    boolean success;
    try {
        success = call(() -> {
            MongoCollection<Document> c = database.getCollection("tracks");
            return c.deleteOne(new Document("_id", track.getName())).wasAcknowledged();
        }, false);
    } finally {
        track.getIoLock().unlock();
    }

    if (success)
        plugin.getTrackManager().unload(track);
    return success;
}

---

From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public boolean saveUser(User user) {
    user.getIoLock().lock();//from   www  .j a  v a2s .  co m
    try {
        MongoCollection<Document> c = database.getCollection(prefix + "users");
        if (!GenericUserManager.shouldSave(user)) {
            return c.deleteOne(new Document("_id", user.getUuid())).wasAcknowledged();
        } else {
            return c.replaceOne(new Document("_id", user.getUuid()), userToDoc(user),
                    new UpdateOptions().upsert(true)).wasAcknowledged();
        }
    } finally {
        user.getIoLock().unlock();
    }
}

---

From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public boolean deleteGroup(Group group) {
    group.getIoLock().lock();// w w w.j  av  a2s. co  m
    try {
        MongoCollection<Document> c = database.getCollection(prefix + "groups");
        return c.deleteOne(new Document("_id", group.getName())).wasAcknowledged();
    } finally {
        group.getIoLock().unlock();
    }
}

---

From source file:me.lucko.luckperms.common.storage.dao.mongodb.MongoDao.java

License:MIT License

@Override
public boolean deleteTrack(Track track) {
    track.getIoLock().lock();/*from   w w  w. j a v  a 2 s.  c  o  m*/
    try {
        MongoCollection<Document> c = database.getCollection(prefix + "tracks");
        return c.deleteOne(new Document("_id", track.getName())).wasAcknowledged();
    } finally {
        track.getIoLock().unlock();
    }
}

---

From source file:me.lucko.luckperms.storage.methods.MongoDBDatastore.java

License:Open Source License

@Override
public boolean saveUser(User user) {
    if (!plugin.getUserManager().shouldSave(user)) {
        user.getIoLock().lock();//from w  w w .  j a va 2s.  c om
        try {
            return call(() -> {
                MongoCollection<Document> c = database.getCollection("users");
                return c.deleteOne(new Document("_id", user.getUuid())).wasAcknowledged();
            }, false);
        } finally {
            user.getIoLock().unlock();
        }
    }

    user.getIoLock().lock();
    try {
        return call(() -> {
            MongoCollection<Document> c = database.getCollection("users");
            try (MongoCursor<Document> cursor = c.find(new Document("_id", user.getUuid())).iterator()) {
                if (!cursor.hasNext()) {
                    c.insertOne(fromUser(user));
                } else {
                    c.replaceOne(new Document("_id", user.getUuid()), fromUser(user));
                }
            }
            return true;
        }, false);
    } finally {
        user.getIoLock().unlock();
    }
}

---

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  a v  a 2s .co m*/
    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   ww w.jav  a2s. co  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();
}

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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);/*w  ww  .  j  a  v a  2 s  .c  om*/

    // ===== 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();
}

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