List of usage examples for org.hibernate SessionFactory close
void close() throws HibernateException;
From source file:model.ConnectionBD.java
public static void main(String args[]) { SessionFactory sf = HibernateUtil.getSessionFactory(); Session session = sf.openSession();/* w w w . jav a 2 s. c om*/ sf.close(); }
From source file:Modelos.Clases.Pruebas.java
public static void main(String[] args) { Configuration configuracion = new Configuration(); configuracion.configure(); // lee el archivo de hibernate ServiceRegistry serviceRegistry = new ServiceRegistryBuilder().applySettings(configuracion.getProperties()) .buildServiceRegistry();// w w w. j a v a 2s . c o m SessionFactory sessionFactory = configuracion.buildSessionFactory(serviceRegistry); Session session = sessionFactory.openSession(); LoginDAO login = new LoginDAO("root", "root"); ClienteDAO cliente = new ClienteDAO("nombre", "apellido", "telefono", "dni"); VehiculoDAO vehiculo = new VehiculoDAO("marca", "modelo", "color", "matricula", "descripcion"); MecanicoDAO mecanico = new MecanicoDAO("nombre", "apellido"); cliente.setVehiculo(vehiculo); vehiculo.setCliente(cliente); vehiculo.setMecanico(mecanico); mecanico.setVehiculo(vehiculo); session.beginTransaction(); session.saveOrUpdate(login); session.saveOrUpdate(cliente); session.saveOrUpdate(vehiculo); session.saveOrUpdate(mecanico); session.getTransaction().commit(); session.close(); sessionFactory.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 w w .j a va2 s .co 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.ExportTissueOntology.java
License:Open Source License
public ExportTissueOntology() { // === Output matrix === List<Object> data = new ArrayList<Object>(); List<String> header = new ArrayList<String>(); header.add("id_topology"); header.add("topology"); header.add("id_topology_group"); header.add("topology_group"); // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); // ===== Begin transaction ===== session.beginTransaction();//from w w w . j a v a 2s.c o m ClTopologyDao topologyDao = new ClTopologyDao(session); List<ClTopology> listTopologies = topologyDao.findAll(); for (ClTopology t : listTopologies) { System.out.println(t); Object[] dataline = new Object[header.size()]; int j = 0; dataline[j] = t.getIdTopology(); dataline[++j] = t.getName(); dataline[++j] = t.getClTopologyGroup().getIdGroup(); dataline[++j] = t.getClTopologyGroup().getName(); data.add(dataline); System.out.println(Arrays.toString(dataline)); } // === Output file === String fileName = this.getOutputDirectory() + this.getDirSeparator() + "EpiMed_tissue_ontology" + "_" + dateFormat.format(new Date()) + ".xlsx"; fileService.writeExcelFile(fileName, header, data); System.out.println(fileName); // === Commit transaction === // session.getTransaction().commit(); session.getTransaction().rollback(); if (session.isOpen()) { session.close(); } sessionFactory.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 w ww.j ava 2s . 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.emtab365.UpdateSamplesEMTAB365.java
License:Open Source License
public UpdateSamplesEMTAB365() { // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); // ===== INIT ===== ClMorphology ductal = session.get(ClMorphology.class, "8500/3"); // 8500/3 Infiltrating duct carcinoma, NOS (C50._) ClMorphology lobular = session.get(ClMorphology.class, "8520/3"); // 8520/3 Lobular carcinoma, NOS (C50._) ClMorphology morphology = session.get(ClMorphology.class, "8010/3"); // Carcinoma ClTopology breast = session.get(ClTopology.class, "C50.9"); // Breast ClTopology blood = session.get(ClTopology.class, "C42.0"); // Blood ClTopology lymphNode = session.get(ClTopology.class, "C77.9"); // Lymph node // ===== 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>()); for (int i = 0; i < listDocuments.size(); i++) { Document doc = listDocuments.get(i); Document expgroup = (Document) doc.get("exp_group"); Document parameters = (Document) doc.get("parameters"); String histoType = parameters.getString("Histology"); String histoSubtype = parameters.getString("CIT classification"); expgroup.put("histology_subtype", histoSubtype); if (histoType != null && histoType.toLowerCase().equals("lobular")) { morphology = lobular;/*from w ww. j a v a2 s .co m*/ } if (histoType != null && histoType.toLowerCase().equals("ductal")) { morphology = ductal; } expgroup.put("id_morphology", morphology.getIdMorphology()); expgroup.put("morphology", morphology.getName()); expgroup.put("sample_source", parameters.getString("Source Name")); String organismPart = parameters.getString("OrgansimPart"); ClTopology topology = null; if (organismPart != null) { if (organismPart.toLowerCase().contains("breast")) { topology = breast; } if (organismPart.toLowerCase().contains("blood")) { topology = blood; } if (organismPart.toLowerCase().contains("lymph")) { topology = lymphNode; } } else { topology = breast; } expgroup.put("id_topology", topology.getIdTopology()); expgroup.put("topology", topology.getName()); expgroup.put("id_topology_group", topology.getClTopologyGroup().getIdGroup()); expgroup.put("topology_group", topology.getClTopologyGroup().getName()); // ==== Survival ===== Object dfs_months = parameters.get("Delay Metastasis Free Survival months"); if (dfs_months != null) { expgroup.put("dfs_months", dfs_months); } Object os_months = parameters.get("Delay Overall Survival months"); if (os_months != null) { expgroup.put("os_months", os_months); } Double os = (Double) expgroup.get("os_months"); Double dfs = (Double) expgroup.get("dfs_months"); if (os != null && dfs != null && dfs.equals(os)) { expgroup.put("relapsed", false); } if (os != null && dfs != null && dfs < os) { expgroup.put("relapsed", true); } if (os != null && dfs != null && dfs > os) { expgroup.put("relapsed", null); } Object relapseDate = parameters.get("Relapse Metastasis Date"); if (relapseDate != null) { expgroup.put("relapsed", true); } // ==== Grade ==== expgroup.put("tnm_grade", parameters.get("Grade Scarff Bloom Richardson")); // ==== Files ===== expgroup.put("ftp", parameters.getString("ArrayExpress FTP file")); expgroup.put("file_name", parameters.getString("Array Data File")); expgroup.remove("individual"); if (parameters.getString("Individual") != null) { expgroup.put("individual", parameters.getString("Individual")); } // ==== Biomarkers ==== /* String p53 = parameters.getString("Phenotype - TP53 Gene mutation Status"); expgroup.put("p53", value) String pr = parameters.getString("PGR Protein expression"); String er = parameters.getString("ESR1 Protein expression"); String her2 = parameters.getString("ERBB2 Protein expression"); */ doc.put("exp_group", expgroup); System.out.println(i + " " + doc.get("_id") + " " + doc.get("analyzed") + " " + expgroup); if (commit) { UpdateResult updateResult = collection.updateOne(Filters.eq("_id", doc.get("_id")), new Document("$set", doc)); } } if (session.isOpen()) { session.close(); } sessionFactory.close(); mongoClient.close(); }
From source file:module.script.epimed_ontology.AddEpimedGroupToSamples.java
License:Open Source License
public AddEpimedGroupToSamples() { // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); ClTopologyDao topologyDao = new ClTopologyDao(session); // ===== Session Mongo ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionSample = db.getCollection("sample"); List<Document> samples = collectionSample.find().into(new ArrayList<Document>()); for (int i = 0; i < samples.size(); i++) { Document sample = samples.get(i); Document expgroup = sample.get("exp_group", Document.class); String idTopology = expgroup.getString("id_topology"); if (idTopology != null && !idTopology.isEmpty()) { ClTopology topology = topologyDao.find(idTopology); ClEpimedGroup grp1 = topology.getClEpimedGroup(); ClEpimedGroup grp2 = grp1.getParent(); ClEpimedGroup grp3 = grp2.getParent(); expgroup.append("tissue_group_level1", grp1.getName()); expgroup.append("tissue_group_level2", grp2.getName()); expgroup.append("tissue_group_level3", grp3.getName()); System.out.println((i + 1) + "/" + samples.size() + " " + expgroup); sample.append("exp_group", expgroup); collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")), new Document("$set", sample)); }// ww w . ja v a 2 s .com } // === Commit transaction === // session.getTransaction().commit(); session.getTransaction().rollback(); if (session.isOpen()) { session.close(); } sessionFactory.close(); mongoClient.close(); }
From source file:module.script.epimed_ontology.UpdateFetalAdultOvary.java
License:Open Source License
public UpdateFetalAdultOvary() { // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); ClTopologyDao topologyDao = new ClTopologyDao(session); ClTopology adultOvary = topologyDao.find("C56.9"); ClTopology fetalOvary = topologyDao.find("E56.9"); // ===== Session Mongo ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionSample = db.getCollection("sample"); Bson filters = Filters.and(Filters.eq("exp_group.id_topology", "C56.9"), // ovary Filters.eq("exp_group.id_tissue_stage", 1) // adult );//from w w w .j a v a 2s . c o m List<Document> samples = collectionSample.find(filters).into(new ArrayList<Document>()); for (Document sample : samples) { Document expgroup = sample.get("exp_group", Document.class); expgroup.append("id_topology", adultOvary.getIdTopology()); expgroup.append("topology", adultOvary.getName()); sample.append("exp_group", expgroup); collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")), new Document("$set", sample)); } System.out.println(samples.size()); // === Commit transaction === // session.getTransaction().commit(); session.getTransaction().rollback(); if (session.isOpen()) { session.close(); } sessionFactory.close(); mongoClient.close(); }
From source file:module.script.ImportSupplementaryGSE20711.java
License:Open Source License
public ImportSupplementaryGSE20711() { // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); // ===== Session Mongo ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collection = db.getCollection("samples"); // ===== Excel data loader ===== String inputfile = this.getInputDirectory() + this.getDirSeparator() + "GSE20711_emmm0003-0726-SD2.xlsx"; System.out.println("LOADING \t " + inputfile); ExcelService excelService = new ExcelService(); excelService.load(inputfile);/*from w w w. jav a 2s .com*/ String gseNumber = "GSE20711"; for (int i = 0; i < excelService.getData().size(); i++) { List<Object> dataLine = excelService.getData().get(i); String bcString = (String) dataLine.get(0); bcString = bcString.replaceAll("BC", ""); Integer bcNumber = Integer.parseInt(bcString); Document docSample = collection .find(Filters .and(Filters.in("series", gseNumber), Filters.eq("exp_group.sample_title", "Breast tumor from patient P_" + bcNumber + " (expression data)"))) .first(); System.out.println("-------------------------------------------"); System.out.println(dataLine); System.out.println(docSample); } if (session.isOpen()) { session.close(); } sessionFactory.close(); mongoClient.close(); }
From source file:module.script.ImportSupplementaryGSE25219.java
License:Open Source License
@SuppressWarnings({ "unused", "unchecked" })
public ImportSupplementaryGSE25219() {
// ===== Session PostgreSQL =====
SessionFactory sessionFactory = HibernateUtil
.buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
Session session = sessionFactory.openSession();
// ===== Session Mongo =====
MongoClient mongoClient = MongoUtil.buildMongoClient();
MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
MongoCollection<Document> collection = db.getCollection("samples");
// ===== Excel data loader =====
String inputfile = this.getInputDirectory() + this.getDirSeparator() + "NIHMS321722-supplement-7.xlsx";
System.out.println("LOADING \t " + inputfile);
ExcelService excelService = new ExcelService();
excelService.load(inputfile);/* w w w. ja v a 2 s . c o m*/
// ===== Format raw data into data structures ======
List<Map<String, String>> listMap = new ArrayList<Map<String, String>>();
List<String> headerMap = new ArrayList<String>();
Map<String, String> mapBrain = new HashMap<String, String>();
for (int i = 0; i < excelService.getData().size(); i++) {
List<Object> dataLine = excelService.getData().get(i);
String brainCode = (String) dataLine.get(0);
if (brainCode != null) {
mapBrain = new HashMap<String, String>();
}
// Existing brain code
if (dataLine != null && dataLine.size() > 2 && dataLine.get(1) != null && dataLine.get(2) != null) {
// System.out.println(dataLine.get(1) + " = " + dataLine.get(2));
mapBrain.put(dataLine.get(1).toString().trim(), dataLine.get(2).toString().trim());
}
if (brainCode != null) {
// New Brain code
// System.out.println("brain code " + brainCode);
headerMap.add(brainCode);
listMap.add(mapBrain);
}
}
// ===== Recognize data =====
for (int i = 0; i < headerMap.size(); i++) {
System.out.println("----------------------------");
String code = headerMap.get(i);
System.out.println(i + " " + code);
Map<String, String> map = listMap.get(i);
Map<String, String> updatedMap = new HashMap<String, String>();
for (Map.Entry<String, String> entry : map.entrySet()) {
String key = entry.getKey();
String value = entry.getValue();
if (!key.toLowerCase().equals("age")
// && !key.toLowerCase().equals("ethnicity")
// && !key.toLowerCase().equals("sex")
&& !value.toLowerCase().equals("no data")) {
updatedMap.put(key, value);
}
// System.out.println(key + " -> " + value);
}
List<Document> listDocuments = collection
.find(Filters.and(Filters.eq("exp_group.main_gse_number", "GSE25219"),
Filters.eq("parameters.brain code", code)))
.into(new ArrayList<Document>());
System.out.println("Number of corresponding Mongo documents " + listDocuments.size());
System.out.println(updatedMap);
for (int j = 0; j < listDocuments.size(); j++) {
Document doc = listDocuments.get(j);
Document parameters = (Document) doc.get("parameters");
parameters.putAll(updatedMap);
System.out.println("\t" + parameters);
// Update Mongo document
doc.put("parameters", parameters);
doc.put("analyzed", true);
UpdateResult updateResult = collection.updateOne(Filters.eq("_id", doc.get("_id")),
new Document("$set", doc));
}
}
if (session.isOpen()) {
session.close();
}
sessionFactory.close();
mongoClient.close();
}