List of usage examples for com.mongodb MongoClient close
public void close()
From source file:gov.wa.wsdot.cms.templates.ProjectTemplate.java
License:Open Source License
@Override public ChannelsAndPostingsBase build(ChannelsAndPostingsBase item, HashMap<String, String> controlsMap, HashMap<String, String> genericPropertiesMap) { StringBuilder leftNav = new StringBuilder(); StringBuilder update = new StringBuilder(); StringBuilder pageContent = new StringBuilder(); StringBuilder contact = new StringBuilder(); StringBuilder map = new StringBuilder(); List<String> fundingList = new ArrayList<String>(); MongoClient mongo = null; try {/*from ww w . j a v a 2s . c om*/ mongo = new MongoClient("localhost"); } catch (UnknownHostException e) { // TODO Auto-generated catch block e.printStackTrace(); } DB db = mongo.getDB("projects"); DBCollection projectsCollection = db.getCollection("posts"); BasicDBObject query = new BasicDBObject("Link", "/" + item.getLocation().replace(">>", "/") + "/"); DBCursor cursor = projectsCollection.find(query); try { while (cursor.hasNext()) { DBObject dbObject = cursor.next(); item.setProjectId(dbObject.get("ID").toString()); item.setCounties(dbObject.get("County").toString()); item.setRegions(dbObject.get("Region").toString()); item.setHighways(getHighwayTaxonomy(dbObject.get("Highway").toString())); if (!dbObject.get("Nickel").toString().equalsIgnoreCase("0")) { fundingList.add("Nickel"); } else if (!dbObject.get("Partner").toString().equalsIgnoreCase("0")) { fundingList.add("TPA"); } else if (!dbObject.get("FedStim").toString().equalsIgnoreCase("0")) { fundingList.add("ARRA"); } } String[] fundingArray = fundingList.toArray(new String[fundingList.size()]); item.setFunding(Arrays.toString(fundingArray).replace("[", "").replace("]", "").replace(",", ";")); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } finally { cursor.close(); mongo.close(); } // This can be concatenated into the leftNav field leftNav.append(""); if (controlsMap.get("LeftNav") != null) { leftNav.append(controlsMap.get("LeftNav")); } if (controlsMap.get("LeftNavPlaceholderDefinition2") != null) { leftNav.append(controlsMap.get("LeftNavPlaceholderDefinition2")); } item.setLeftNav(leftNav.toString()); // All this can be concatenated into the projectUpdate field update.append("<p>"); update.append("<strong>" + controlsMap.get("ProjectUpdateDate") + "</strong>"); update.append("</p>"); update.append(controlsMap.get("ProjectUpdate")); item.setUpdate(update.toString()); // All this can be concatenated into the pageContent field if (controlsMap.get("OverviewDefinition") != null) { pageContent.append("<p>"); pageContent.append(controlsMap.get("OverviewDefinition")); pageContent.append("</p>"); } if (controlsMap.get("What") != null) { pageContent.append("<p>"); pageContent.append("<strong>Why is WSDOT " + controlsMap.get("What") + "</strong>"); pageContent.append("<br />"); pageContent.append(controlsMap.get("Why")); pageContent.append("</p>"); } if (controlsMap.get("EndResult") != null) { pageContent.append("<p>"); pageContent.append("<strong>The End Result</strong>"); pageContent.append("<br />"); pageContent.append(controlsMap.get("EndResult")); pageContent.append("</p>"); } if (controlsMap.get("ProjectBenefits") != null) { pageContent.append("<p>"); pageContent.append("<strong>Project Benefits</strong>"); pageContent.append("<br />"); pageContent.append(controlsMap.get("ProjectBenefits")); pageContent.append("</p>"); } if (controlsMap.get("ProjectTimelines") != null) { pageContent.append("<p>"); pageContent.append("<strong>What is the project timeline?</strong>"); pageContent.append("<br />"); pageContent.append(controlsMap.get("ProjectTimelines")); pageContent.append("</p>"); } if (controlsMap.get("Financial") != null) { pageContent.append("<p>"); pageContent.append("<strong>Financial Information</strong>"); pageContent.append("<br />"); pageContent.append(controlsMap.get("Financial")); pageContent.append("</p>"); } item.setPageContent(pageContent.toString()); // This will be separate and go into contact field if (controlsMap.get("Contact") != null) { contact.append("<p>"); contact.append("<strong>How can I get more information?<br />Contact:</strong><br />"); contact.append(controlsMap.get("Contact")); contact.append("</p>"); } item.setContact(contact.toString()); item.setPhase(getProjectPhaseTaxonomy(controlsMap.get("PhaseImage"))); // This can be concatenated into the projectMap field if (controlsMap.get("MapPlaceholder") != null) { map.append(controlsMap.get("MapPlaceholder")); } // FlickrLightbox <- Ignore for now // This appears under Map -> [Flickr Photos] -> RightPlaceHolder if (controlsMap.get("RightPlaceHolder") != null) { map.append(controlsMap.get("RightPlaceHolder")); } item.setLegacyMap(map.toString()); // Process GenericProperties item.setShowSignageDisclaimer(genericPropertiesMap.get("ShowCostEscalation")); item.setShowFinancialTable(genericPropertiesMap.get("ShowFinancialTable")); item.setShowMonthlyUpdateLeftNav(genericPropertiesMap.get("ShowMonthlyUpdateLeftNav")); item.setShowFlickrLightbox(genericPropertiesMap.get("ShowFlickrLightbox")); try { Pattern pattern = Pattern.compile("([\\d+]{10,})"); Matcher matcher = pattern.matcher(genericPropertiesMap.get("FlickrFeedURL")); if (matcher.find()) { item.setFlickrAlbumId(matcher.group(1)); } } catch (NullPointerException e) { } return item; }
From source file:localdomain.localhost.MyServlet.java
License:Apache License
@Override protected void service(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { PrintWriter writer = resp.getWriter(); writer.println("<html>"); writer.println("<head><title>MyServlet</title></head>"); writer.println("<body><h1>MyServlet</h1>"); writer.println("<h2>MongoDB</h2>"); String uriAsString = System.getProperty("MONGOHQ_URL_MYDB", "mongodb://localhost/local"); MongoClient mongoClient = null; try {//from ww w . j a va2 s. c o m writer.println("<h4>MongoClientURI</h4>"); MongoClientURI uri = new MongoClientURI(uriAsString); writer.println("<p>" + "host=" + uri.getHosts() + ",username=" + uri.getUsername() + ",database=" + uri.getDatabase() + ",collection=" + uri.getCollection() + "</p>"); writer.println("<h4>MongoClient</h4>"); mongoClient = new MongoClient(uri); writer.println("<p>" + mongoClient + "</p>"); writer.println("<h4>Databases</h4>"); try { List<String> databaseNames = mongoClient.getDatabaseNames(); writer.println("<ul>"); for (String databaseName : databaseNames) { writer.println("<li>" + databaseName + (databaseName.equals(uri.getDatabase()) ? " - default database" : "")); } writer.println("</ul>"); } catch (Exception e) { writer.println("<p>Could not list the databases of the MongoDB instance: <code>" + e.getMessage() + "</code></p>"); } writer.println("<h4>Database</h4>"); DB db = mongoClient.getDB(uri.getDatabase()); writer.println("<p>DB: " + db.getName() + "</p>"); writer.println("<h4>Collections</h4>"); Set<String> myCollections = db.getCollectionNames(); if (myCollections.isEmpty()) { writer.println("<p>NO COLLECTIONS!</p>"); } else { writer.println("<ul>"); for (String collection : myCollections) { DBCollection dbCollection = db.getCollection(collection); writer.println( "<li>" + dbCollection.getName() + " - " + dbCollection.getCount() + " entries</li>"); } writer.println("</ul>"); } writer.println("<h4>Success!</h4>"); writer.println("SUCCESS to access the mongodb database"); } catch (Exception e) { writer.println("<code><pre>"); e.printStackTrace(writer); writer.println("</pre></code>"); e.printStackTrace(); } finally { if (mongoClient != null) { try { mongoClient.close(); } catch (Exception e) { e.printStackTrace(); } } } writer.println("</body></html>"); }
From source file:models.util.DbUtil.java
License:Open Source License
public static void closeQuietly(MongoClient mongoClient) { mongoClient.close(); }
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 ww . ja v a 2 s.c o m*/ // ===== 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)); }/*w ww. j a v a 2 s. c o m*/ } mongoClient.close(); }
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(); // ===== 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()); }// ww w .j av a2 s . c o m 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}]+\\]"; ;// w ww. ja v a 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}]+\\]"; ;//from w w w . j a v a 2 s. c o 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 w ww. j a v a 2 s. 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(); }
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 a v a 2 s. c o m*/ } mongoClient.close(); }