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

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:io.mandrel.metrics.impl.MongoMetricsRepository.java

License:Apache License

@Override
public Timeserie serie(String name) {
    Set<Data> results = StreamSupport.stream(timeseries.find(Filters.eq("type", name))
            .sort(Sorts.ascending("timestamp_hour")).limit(3).map(doc -> {
                LocalDateTime hour = LocalDateTime
                        .ofEpochSecond(((Date) doc.get("timestamp_hour")).getTime() / 1000, 0, ZoneOffset.UTC);
                Map<String, Long> values = (Map<String, Long>) doc.get("values");

                List<Data> mapped = values.entrySet().stream()
                        .map(elt -> Data.of(hour.plusMinutes(Long.valueOf(elt.getKey())), elt.getValue()))
                        .collect(Collectors.toList());
                return mapped;
            }).spliterator(), true).flatMap(elts -> elts.stream())
            .collect(TreeSet::new, Set::add, (left, right) -> {
                left.addAll(right);//w  w w. ja va 2 s.co  m
            });

    Timeserie timeserie = new Timeserie();
    timeserie.addAll(results);
    return timeserie;
}

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From source file:io.mandrel.spider.impl.MongoSpiderRepository.java

License:Apache License

public void delete(long id) {
    collection.deleteOne(Filters.eq("_id", id));
}

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From source file:io.mandrel.spider.impl.MongoSpiderRepository.java

License:Apache License

public Optional<Spider> get(long id) {
    Document doc = collection.find(Filters.eq("_id", id)).first();
    return doc == null ? Optional.empty() : Optional.of(JsonBsonCodec.fromBson(mapper, doc, Spider.class));
}

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From source file:io.mandrel.spider.impl.MongoSpiderRepository.java

License:Apache License

protected Bson activeFilter() {
    return Filters.or(Filters.eq("status", SpiderStatuses.STARTED), Filters.eq("status", SpiderStatuses.PAUSED),
            Filters.eq("status", SpiderStatuses.INITIATED));
}

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From source file:io.sip3.tapir.twig.mongo.query.SipSearchQuery.java

License:Apache License

private Bson filter(String field, String value) {
    if (isBlank(value)) {
        return null;
    }/*from   w w w  .  j  a  va2  s.c  o m*/
    if (isRegex(value)) {
        return Filters.regex(field, value.replaceAll("\\*", "\\.\\*"));
    }
    return Filters.eq(field, value);
}

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From source file:it.av.fac.webserver.handlers.WikiPageFetcher.java

/**
 * TODO: Add more query functionalities.
 *
 * @param page/*from   w w w  . java  2  s .  co  m*/
 * @return
 */
public JSONArray fetchPage(String page) {
    JSONArray ret = new JSONArray();

    List<Bson> filters = new ArrayList<>();
    filters.add(Filters.eq("_id", page));

    FindIterable<Document> documents = this.collection.find(Filters.and(filters));

    documents.forEach(new Consumer<Document>() {
        @Override
        public void accept(Document doc) {
            ret.put(new JSONObject(doc.toJson()));
        }
    });
    return ret;
}

---

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 a  2  s .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  .j a  va  2 s .  co 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 ava2s  .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);
    }

}

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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}]+\\]";
    ;/*w  w  w. j a  va2s.  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();

}

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