List of usage examples for com.mongodb MongoClient close
public void close()
From source file:module.script.probcp.UpdateSamplesProbcp.java
License:Open Source License
public UpdateSamplesProbcp() { // ===== Connection ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionSamples = db.getCollection("samples"); // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); String[] studies = { "tya16" }; List<String> series = new ArrayList<String>(); for (int l = 0; l < studies.length; l++) { String idStudy = studies[l]; String studyName = idStudy.toUpperCase(); series.clear();//from w w w . j a v a 2s . c o m series.add(studyName); series.add("PROBCP"); String sql = "select * from st_bcp." + idStudy + "_sample order by id_sample"; List<Object> listSamples = session.createSQLQuery(sql).list(); for (int i = 0; i < listSamples.size(); i++) { Object[] lineSample = (Object[]) listSamples.get(i); String idSample = (String) lineSample[0]; String clinicalClassification = (String) lineSample[1]; String tnmStage = (String) lineSample[2]; Integer grade = (Integer) lineSample[3]; String type = (String) lineSample[4]; System.out.println(Arrays.toString(lineSample)); String id = studyName + "_" + idSample; Document docSample = collectionSamples.find(Filters.eq("_id", id)).first(); Document expgroup = (Document) docSample.get("exp_group"); expgroup.append("tnm_grade", grade); expgroup.append("tnm_stage", null); docSample.append("exp_group", expgroup); UpdateResult updateResult = collectionSamples.updateOne(Filters.eq("_id", id), new Document("$set", docSample)); System.out.println(docSample); } } if (session.isOpen()) { session.close(); } sessionFactory.close(); mongoClient.close(); }
From source file:module.script.QueryAvailableData.java
License:Open Source License
public QueryAvailableData() { // ===== Service ===== FormatService formatService = new FormatService(); // ===== Session Mongo ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionSeries = db.getCollection("series"); MongoCollection<Document> collectionSamples = db.getCollection("samples"); // ===== Print block ===== Block<Document> printBlock = new Block<Document>() { public void apply(final Document document) { System.out.println(document.toJson()); }//w ww . j a v a2s . com }; // ===== Group by topology ===== // db.getCollection('samples').aggregate({ $group: { "_id" : "$exp_group.topology", "total" : {$sum : 1} }}, {$sort : {total : -1}} ) /* List<Document> listDocuments = collectionSamples.aggregate( Arrays.asList( Aggregates.group("$exp_group.topology", Accumulators.sum("total", 1)), Aggregates.sort(Sorts.orderBy(Sorts.descending("total"))) )) .into(new ArrayList<Document>()); */ // ===== Group by sample ===== /* List<Document> listSeries = collectionSeries .find() .projection(Projections.fields(Projections.include("title"))) .sort(Sorts.ascending("_id")) .into(new ArrayList<Document>()); for (Document doc : listSeries) { String idSeries = doc.getString("_id"); Long nbSamples = collectionSamples.count((Filters.eq("series", idSeries))); doc.append("nbSamples", nbSamples); } display(listSeries); */ // === Export Geo for a list of idSeries === // String[] listIdSeries = {"GSE11092","GSE13309", "GSE13159"}; /* List<Document> docExpGroup = collectionSamples .find(Filters.in("series", listIdSeries)) .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId())) .into(new ArrayList<Document>()); // display(docExpGroup); List<String> header = formatService.extractHeader(docExpGroup, "exp_group"); List<Object> data = formatService.extractData(docExpGroup, header, "exp_group"); System.out.println(header); displayMatrix(data); */ // List<Object> listObjects = formatService.convertHeterogeneousMongoDocuments(docExpGroup, "exp_group"); // displayMatrix(listObjects); // List<Object> listObjects = formatService.convertHomogeneousMongoDocuments(listDocuments); // === Find series === String[] listIdSamples = { "GSM80908", "GSM274639", "GSM274638", "GSM280213" }; List<Document> listDocuments = collectionSamples .aggregate(Arrays.asList(Aggregates.match(Filters.in("_id", listIdSamples)), Aggregates.group("$main_gse_number"), Aggregates.sort(Sorts.orderBy(Sorts.ascending("main_gse_numbe"))))) .into(new ArrayList<Document>()); List<Object> listObjects = formatService.convertHomogeneousMongoDocuments(listDocuments); displayMatrix(listObjects); mongoClient.close(); }
From source file:module.script.TransferBrbAnnotations.java
License:Open Source License
@SuppressWarnings({ "unused", "unchecked" })
public TransferBrbAnnotations() {
// ===== 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");
String sql = "select id_sample, main_gse_number, string_agg(id_substance, ', ') as list_substances from epimed_prod.om_sample "
+ "join epimed_prod.cl_biopatho using (id_biopatho) join epimed_prod.cl_patient using (id_patient) join epimed_prod.cl_exposure using (id_patient) "
+ "where exposed=true group by id_sample";
List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();
for (Object item : list) {
Map<String, Object> map = (HashMap<String, Object>) item;
String gsmNumber = (String) map.get("id_sample");
String gseNumber = (String) map.get("main_gse_number");
System.out.println("-----------------------------");
System.out.println(gseNumber + " " + gsmNumber);
Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();
if (doc != null) {
Document expGroup = (Document) doc.get("exp_group");
expGroup.put("exposure", map.get("list_substances"));
System.out.println(expGroup);
// Update Mongo document
doc.put("exp_group", expGroup);
doc.put("analyzed", true);
UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
new Document("$set", doc));
}//from w ww .ja v a 2 s . co m
}
if (session.isOpen()) {
session.close();
}
sessionFactory.close();
mongoClient.close();
}
From source file:module.script.TransferBrbHistologyCodes.java
License:Open Source License
@SuppressWarnings({ "unused", "unchecked" })
public TransferBrbHistologyCodes() {
// ===== Session PostgreSQL =====
SessionFactory sessionFactory = HibernateUtil
.buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
Session session = sessionFactory.openSession();
// ===== Session Mongo =====
MongoClient mongoClient = MongoUtil.buildMongoClient();
MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
MongoCollection<Document> collection = db.getCollection("samples");
String sql = "select id_sample, main_gse_number, index_histology_code, histology_code, ordered_histology_code from db_brb_lung.view_exp_group";
List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();
for (Object item : list) {
Map<String, Object> map = (HashMap<String, Object>) item;
String gsmNumber = (String) map.get("id_sample");
String gseNumber = (String) map.get("main_gse_number");
System.out.println("-----------------------------");
System.out.println(gseNumber + " " + gsmNumber);
Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();
if (doc != null) {
Document expGroup = (Document) doc.get("exp_group");
expGroup.put("index_histology_code", map.get("index_histology_code"));
expGroup.put("histology_code", map.get("histology_code"));
expGroup.put("ordered_histology_code", map.get("ordered_histology_code"));
System.out.println(expGroup);
// Update Mongo document
doc.put("exp_group", expGroup);
doc.put("analyzed", true);
UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
new Document("$set", doc));
}//from w w w. j a v a 2s . co m
}
if (session.isOpen()) {
session.close();
}
sessionFactory.close();
mongoClient.close();
}
From source file:module.script.TransferExposure.java
License:Open Source License
@SuppressWarnings({ "unused", "unchecked" })
public TransferExposure() {
// ===== 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");
String sql = "select id_sample, main_gse_number, string_agg(id_substance, ', ') as list_substances from epimed_prod.om_sample "
+ "join epimed_prod.cl_biopatho using (id_biopatho) join epimed_prod.cl_patient using (id_patient) join epimed_prod.cl_exposure using (id_patient) "
+ "where exposed=true group by id_sample";
List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();
for (Object item : list) {
Map<String, Object> map = (HashMap<String, Object>) item;
String gsmNumber = (String) map.get("id_sample");
String gseNumber = (String) map.get("main_gse_number");
System.out.println("-----------------------------");
System.out.println(gseNumber + " " + gsmNumber);
Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();
if (doc != null) {
Document expGroup = (Document) doc.get("exp_group");
expGroup.put("exposure", map.get("list_substances"));
System.out.println(expGroup);
// Update Mongo document
doc.put("exp_group", expGroup);
doc.put("analyzed", true);
UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
new Document("$set", doc));
}//w w w .ja v a 2 s . c om
}
if (session.isOpen()) {
session.close();
}
sessionFactory.close();
mongoClient.close();
}
From source file:module.script.TransferFromEpimedProd.java
License:Open Source License
@SuppressWarnings({ "unused", "unchecked" })
public TransferFromEpimedProd() {
// ===== 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");
String sql = "select * from epimed_prod.view_exp_group order by main_gse_number, id_sample";
List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();
String[] commonAttributes = { "pathology", "tnm_stage", "id_topology_group", "histology_subtype",
"tissue_stage", "dead", "dfs_months", "age_max", "morphology", "id_tissue_stage", "topology", "sex",
"age_min", "m", "topology_group", "n", "t", "collection_method", "id_morphology", "relapsed",
"histology_type", "os_months", "id_topology" };
List<ClPathology> listPathology = session.createCriteria(ClPathology.class).list();
Map<String, ClPathology> mapPathology = new HashMap<String, ClPathology>();
for (ClPathology p : listPathology) {
mapPathology.put(p.getName(), p);
}//from w w w. j a va 2 s . c o m
List<ClTissueStatus> listTissueStatus = session.createCriteria(ClTissueStatus.class).list();
Map<Integer, ClTissueStatus> mapTissueStatus = new HashMap<Integer, ClTissueStatus>();
for (ClTissueStatus t : listTissueStatus) {
mapTissueStatus.put(t.getIdTissueStatus(), t);
}
System.out.println(listTissueStatus);
for (Object item : list) {
Map<String, Object> map = (HashMap<String, Object>) item;
String gsmNumber = (String) map.get("id_sample");
String gseNumber = (String) map.get("main_gse_number");
System.out.println("-----------------------------");
System.out.println(gseNumber + " " + gsmNumber);
Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();
if (doc != null) {
Document expGroup = (Document) doc.get("exp_group");
for (int j = 0; j < commonAttributes.length; j++) {
String attr = commonAttributes[j];
expGroup.put(attr, map.get(attr));
}
// Treatment
expGroup.put("treatment", map.get("treatment_type"));
// Pathology
String pathoString = (String) map.get("pathology");
ClPathology pathology = mapPathology.get(pathoString);
if (pathology != null) {
expGroup.put("id_pathology", pathology.getIdPathology());
expGroup.put("pathology", pathology.getName());
}
// Tissue status
Integer idTissueStatus = (Integer) map.get("id_tissue_status");
if (idTissueStatus != null && idTissueStatus > 3) {
idTissueStatus = 3;
}
ClTissueStatus tissueStatus = mapTissueStatus.get(idTissueStatus);
if (tissueStatus != null) {
expGroup.put("id_tissue_status", tissueStatus.getIdTissueStatus());
expGroup.put("tissue_status", tissueStatus.getName());
}
System.out.println("idTissueStatus=" + tissueStatus + ", pathology=" + pathology);
System.out.println(expGroup);
// Update Mongo document
doc.put("exp_group", expGroup);
doc.put("analyzed", true);
UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
new Document("$set", doc));
}
}
if (session.isOpen()) {
session.close();
}
sessionFactory.close();
mongoClient.close();
}
From source file:module.test.CreateProbesets.java
License:Open Source License
public CreateProbesets() { // ===== Connection ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionProbesets = db.getCollection("probesets"); Document docProbeset = mongoService.createProbeset("GPL570", "1007_s_at"); collectionProbesets.insertOne(docProbeset); mongoClient.close(); }
From source file:module.test.CustomExport.java
License:Open Source License
public CustomExport() { // ===== Connection ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collection = db.getCollection("samples"); // ===== Find exp_group in the database ===== // === Query 1 === /*/*from www . j a va 2s . c om*/ String queryName = "breast_cancer_GPL570"; List<Bson> filters = new ArrayList<Bson>(); filters.add(Filters.eq("exp_group.id_platform", "GPL570")); filters.add(Filters.eq("exp_group.id_topology_group", "C50")); filters.add(Filters.eq("exp_group.id_tissue_status", 3)); // tumoral */ // === Query 2 === /* String queryName = "breast_normal_GPL570"; List<Bson> filters = new ArrayList<Bson>(); filters.add(Filters.eq("exp_group.id_platform", "GPL570")); filters.add(Filters.eq("exp_group.id_topology_group", "C50")); filters.add(Filters.eq("exp_group.id_tissue_status", 1)); // normal */ // === Query 3 === String queryName = "breast_cancer_with_survival_GPL570"; List<Bson> filters = new ArrayList<Bson>(); filters.add(Filters.eq("exp_group.id_platform", "GPL570")); filters.add(Filters.eq("exp_group.id_topology_group", "C50")); filters.add(Filters.eq("exp_group.id_tissue_status", 3)); // tumoral filters.add(Filters.or(Filters.ne("exp_group.os_months", null), Filters.ne("exp_group.dfss_months", null), Filters.ne("exp_group.relapsed", null), Filters.ne("exp_group.dead", null))); Bson filter = Filters.and(filters); Long nbSamples = collection.count(filter); List<String> listSeries = collection.distinct("exp_group.main_gse_number", filter, String.class) .into(new ArrayList<String>()); queryName = queryName + "_" + nbSamples + "_samples_" + listSeries.size() + "_series"; List<Document> docExpGroup = collection.find(filter) .projection(Projections.fields(Projections.include("exp_group"), Projections.excludeId())) .into(new ArrayList<Document>()); List<Document> docParam = collection.find(filter) .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()); } Object[] dataLine = new Object[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"); Object[] dataLine = new Object[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() + "EpiMed_database_" + queryName + "_" + 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.test.ImportProbesets.java
License:Open Source License
public ImportProbesets() { // === Display === System.out.println("\n================ BEGIN Module " + this.getClass().getName() + "================"); // ===== Connection ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionProbesets = db.getCollection("probesets"); // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); String idPlatform = "GPL570"; String gpl = idPlatform.toLowerCase(); // ===== Load file ===== String inputfile = this.getInputDirectory() + this.getDirSeparator() + "HG-U133_Plus_2.na36.annot.csv"; System.out.println("ID Platform " + gpl); System.out.println("LOADING \t " + inputfile); System.out.println("Please wait... "); List<String> listRows = fileService.loadTextFile(inputfile); System.out.println("File sucessfully LOADED"); // ===== Recognize header ===== List<String> header = fileService.readHeader(listRows, "\",\""); System.out.println("Header " + header); List<List<String>> data = fileService.readData(listRows, "\",\""); System.out.println(//from w w w.java2 s .c o m "The data are sucessfully loaded: rows " + data.size() + ", columns " + data.get(0).size()); Integer indProbeset = fileService.findIndex(header, "Probe Set ID"); Integer indGenes = fileService.findIndex(header, "Entrez Gene"); Integer indUnigenes = fileService.findIndex(header, "UniGene ID"); Integer indTranscripts = fileService.findIndex(header, "RefSeq Transcript ID"); Integer indGb = fileService.findIndex(header, "Representative Public ID"); for (int i = 0; i < 5; i++) { List<String> dataline = data.get(i); String probeset = dataline.get(indProbeset); String genes = dataline.get(indGenes); String unigenes = dataline.get(indUnigenes); String transcripts = dataline.get(indTranscripts); String gb = dataline.get(indGb); System.out.println(probeset + "\t" + genes + "\t" + formatService.splitInArray(unigenes, "///") + "\t" + gb + "\t" + transcripts); Document docProbeset = mongoService.createProbeset(idPlatform, probeset); docProbeset.put("genes", formatService.splitInArray(genes, "///")); docProbeset.put("unigenes", formatService.splitInArray(unigenes, "///")); List<String> listTranscripts = formatService.splitInArray(transcripts, "///"); listTranscripts.addAll(formatService.splitInArray(gb, "///")); docProbeset.put("transcripts", listTranscripts); collectionProbesets.insertOne(docProbeset); /* for (int j=0; j<dataline.size(); j++) { String key = header.get(j); String value = dataline.get(j); System.out.println(key + ": " + value); } */ } /* String tableProbe = "hs.om_probe_" + gpl; String tableGP = "hs.om_gp_" + gpl; List<Object []> listProbesets = session.createNativeQuery("select * from " + tableProbe + " order by id_probe").getResultList(); for (int i=0; i<10; i++) { Object[] line = listProbesets.get(i); System.out.println(Arrays.toString(line)); // Document docProbeset = mongoService.createProbeset(idPlatform, "1007_s_at"); // collectionProbesets.insertOne(docProbeset); } */ // === Close connections === if (session.isOpen()) { session.close(); } sessionFactory.close(); mongoClient.close(); // === Display === System.out.println("================ END Module " + this.getClass().getName() + "================"); }
From source file:module.test.SearchPlatforms.java
License:Open Source License
public SearchPlatforms() { // ===== Connection ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionSamples = db.getCollection("sample"); MongoCollection<Document> collectionPlatforms = db.getCollection("platform"); List<Document> list = collectionSamples .aggregate(Arrays.asList(Aggregates.group("$exp_group.id_platform", Accumulators.sum("total", 1)), Aggregates.sort(Sorts.orderBy(Sorts.descending("total"))))) .into(new ArrayList<Document>()); for (int i = 0; i < list.size(); i++) { System.out.println((i + 1) + " " + list.get(i)); }/*from w w w. ja va2 s . co m*/ // collectionPlatforms.find(Filters.regex("title", ".*ethyl.*")).forEach(printBlock); collectionPlatforms.find(Filters.eq("id_organism", "9606")).forEach(printBlock); mongoClient.close(); }