List of usage examples for com.mongodb.client MongoCollection updateOne
UpdateResult updateOne(Bson filter, List<? extends Bson> update);
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("$set", doc));
}/* www . j a v a 2 s .co m*/
}
if (session.isOpen()) {
session.close();
}
sessionFactory.close();
mongoClient.close();
}
From source file:module.script.TransferExposure.java
License:Open Source License
@SuppressWarnings({ "unused", "unchecked" })
public TransferExposure() {
// ===== Session PostgreSQL =====
SessionFactory sessionFactory = HibernateUtil
.buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
Session session = sessionFactory.openSession();
// ===== Session Mongo =====
MongoClient mongoClient = MongoUtil.buildMongoClient();
MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
MongoCollection<Document> collection = db.getCollection("samples");
String sql = "select id_sample, main_gse_number, string_agg(id_substance, ', ') as list_substances from epimed_prod.om_sample "
+ "join epimed_prod.cl_biopatho using (id_biopatho) join epimed_prod.cl_patient using (id_patient) join epimed_prod.cl_exposure using (id_patient) "
+ "where exposed=true group by id_sample";
List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();
for (Object item : list) {
Map<String, Object> map = (HashMap<String, Object>) item;
String gsmNumber = (String) map.get("id_sample");
String gseNumber = (String) map.get("main_gse_number");
System.out.println("-----------------------------");
System.out.println(gseNumber + " " + gsmNumber);
Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();
if (doc != null) {
Document expGroup = (Document) doc.get("exp_group");
expGroup.put("exposure", map.get("list_substances"));
System.out.println(expGroup);
// Update Mongo document
doc.put("exp_group", expGroup);
doc.put("analyzed", true);
UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
new Document("$set", doc));
}//from w ww .j a v a 2 s . com
}
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 v a 2s. c om
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("$set", doc));
}
}
if (session.isOpen()) {
session.close();
}
sessionFactory.close();
mongoClient.close();
}
From source file:module.UpdateNumberSamples.java
License:Open Source License
public UpdateNumberSamples() { // ===== Connection ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionSeries = db.getCollection("series"); MongoCollection<Document> collectionSamples = db.getCollection("sample"); // String [] listIdSeries = {"TISSUE_SPECIFIC_GENES_MM"}; // List<Document> listSeries = collectionSeries.find(Filters.in("_id", listIdSeries)).into(new ArrayList<Document>()); List<Document> listSeries = collectionSeries.find().into(new ArrayList<Document>()); for (Document ser : listSeries) { System.out.println(ser);// www .j a v a 2 s. com String idSeries = ser.getString("_id"); Bson filter = Filters.in("series", idSeries); Long nbSamples = collectionSamples.count(filter); System.out.println(idSeries + " " + nbSamples); ser.append("nb_samples", nbSamples); collectionSeries.updateOne(Filters.eq("_id", idSeries), new Document("$set", ser)); } mongoClient.close(); }
From source file:module.UpdateTissueStatus.java
License:Open Source License
public UpdateTissueStatus() { // ===== Connection ===== 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>()); ;/*from www .j a va 2s .com*/ for (Document sample : samples) { Document expgroup = sample.get("exp_group", Document.class); Integer idTissueStatus = expgroup.getInteger("id_tissue_status"); if (idTissueStatus != null) { if (idTissueStatus.equals(1)) { expgroup.put("tissue_status", "normal"); } if (idTissueStatus.equals(2)) { expgroup.put("tissue_status", "pathological_non_tumoral"); } if (idTissueStatus.equals(3)) { expgroup.put("tissue_status", "tumoral"); } sample.put("exp_group", expgroup); System.out.println(sample.get("exp_group", Document.class)); collectionSample.updateOne(Filters.eq("_id", sample.getString("_id")), new Document("$set", sample)); } } mongoClient.close(); }
From source file:mongodb.QuickTour.java
License:Apache License
/** * Run this main method to see the output of this quick example. * * @param args takes an optional single argument for the connection string */// w ww .j av a 2 s. c o m public static void main(final String[] args) { //represents a pool of connections to the database MongoClient mongoClient = new MongoClient("10.9.17.105", 27017); // get handle to "mydb" database MongoDatabase database = mongoClient.getDatabase("test"); // get a handle to the "test" collection MongoCollection<Document> collection = database.getCollection("test"); // drop all the data in it collection.drop(); // make a document and insert it Document doc = new Document("name", "MongoDB").append("type", "database").append("count", 1).append("info", new Document("x", 203).append("y", 102)); collection.insertOne(doc); // get it (since it's the only one in there since we dropped the rest earlier on) Document myDoc = collection.find().first(); System.out.println(myDoc.toJson()); // now, lets add lots of little documents to the collection so we can explore queries and cursors List<Document> documents = new ArrayList<Document>(); for (int i = 0; i < 100; i++) { documents.add(new Document("i", i)); } collection.insertMany(documents); System.out.println( "total # of documents after inserting 100 small ones (should be 101) " + collection.count()); // find first myDoc = collection.find().first(); System.out.println(myDoc.toJson()); // lets get all the documents in the collection and print them out MongoCursor<Document> cursor = collection.find().iterator(); try { while (cursor.hasNext()) { System.out.println(cursor.next().toJson()); } } finally { cursor.close(); } for (Document cur : collection.find()) { System.out.println(cur.toJson()); } // now use a query to get 1 document out myDoc = collection.find(eq("i", 71)).first(); System.out.println(myDoc.toJson()); // now use a range query to get a larger subset cursor = collection.find(gt("i", 50)).iterator(); try { while (cursor.hasNext()) { System.out.println(cursor.next().toJson()); } } finally { cursor.close(); } // range query with multiple constraints cursor = collection.find(and(gt("i", 50), lte("i", 100))).iterator(); try { while (cursor.hasNext()) { System.out.println(cursor.next().toJson()); } } finally { cursor.close(); } // Query Filters myDoc = collection.find(eq("i", 71)).first(); System.out.println(myDoc.toJson()); // now use a range query to get a larger subset Block<Document> printBlock = new Block<Document>() { @Override public void apply(final Document document) { System.out.println(document.toJson()); } }; collection.find(gt("i", 50)).forEach(printBlock); // filter where; 50 < i <= 100 collection.find(and(gt("i", 50), lte("i", 100))).forEach(printBlock); // Sorting myDoc = collection.find(exists("i")).sort(descending("i")).first(); System.out.println(myDoc.toJson()); // Projection myDoc = collection.find().projection(excludeId()).first(); System.out.println(myDoc.toJson()); // Update One collection.updateOne(eq("i", 10), new Document("$set", new Document("i", 110))); // Update Many UpdateResult updateResult = collection.updateMany(lt("i", 100), new Document("$inc", new Document("i", 100))); System.out.println(updateResult.getModifiedCount()); // Delete One collection.deleteOne(eq("i", 110)); // Delete Many DeleteResult deleteResult = collection.deleteMany(gte("i", 100)); System.out.println(deleteResult.getDeletedCount()); collection.drop(); // ordered bulk writes List<WriteModel<Document>> writes = new ArrayList<WriteModel<Document>>(); writes.add(new InsertOneModel<Document>(new Document("_id", 4))); writes.add(new InsertOneModel<Document>(new Document("_id", 5))); writes.add(new InsertOneModel<Document>(new Document("_id", 6))); writes.add( new UpdateOneModel<Document>(new Document("_id", 1), new Document("$set", new Document("x", 2)))); writes.add(new DeleteOneModel<Document>(new Document("_id", 2))); writes.add(new ReplaceOneModel<Document>(new Document("_id", 3), new Document("_id", 3).append("x", 4))); collection.bulkWrite(writes); collection.drop(); collection.bulkWrite(writes, new BulkWriteOptions().ordered(false)); collection.find().forEach(printBlock); // Clean up // database.drop(); // release resources mongoClient.close(); }
From source file:mongoSample.MongoSample.java
License:Apache License
/** * Run this main method to see the output of this quick example. * * @param args//from w w w. java 2 s .c o m * takes an optional single argument for the connection string */ public static void main(final String[] args) { String mongoServer = args[0]; MongoClient mongoClient = new MongoClient(mongoServer); MongoDatabase database = mongoClient.getDatabase("sakila"); MongoCollection<Document> collection = database.getCollection("test"); // drop all the data in it collection.drop(); // make a document and insert it Document doc = new Document("name", "MongoDB").append("type", "database").append("count", 1).append("info", new Document("x", 203).append("y", 102)); collection.insertOne(doc); // get it (since it's the only one in there since we dropped the rest // earlier on) Document myDoc = collection.find().first(); System.out.println(myDoc.toJson()); // now, lets add lots of little documents to the collection so we can // explore queries and cursors List<Document> documents = new ArrayList<Document>(); for (int i = 0; i < 100; i++) { documents.add(new Document("i", i)); } collection.insertMany(documents); System.out.println( "total # of documents after inserting 100 small ones (should be 101) " + collection.count()); // find first myDoc = collection.find().first(); System.out.println(myDoc); System.out.println(myDoc.toJson()); // lets get all the documents in the collection and print them out MongoCursor<Document> cursor = collection.find().iterator(); try { while (cursor.hasNext()) { System.out.println(cursor.next().toJson()); } } finally { cursor.close(); } for (Document cur : collection.find()) { System.out.println(cur.toJson()); } // now use a query to get 1 document out myDoc = collection.find(eq("i", 71)).first(); System.out.println(myDoc.toJson()); // now use a range query to get a larger subset cursor = collection.find(gt("i", 50)).iterator(); try { while (cursor.hasNext()) { System.out.println(cursor.next().toJson()); } } finally { cursor.close(); } // range query with multiple constraints cursor = collection.find(and(gt("i", 50), lte("i", 100))).iterator(); try { while (cursor.hasNext()) { System.out.println(cursor.next().toJson()); } } finally { cursor.close(); } // Query Filters myDoc = collection.find(eq("i", 71)).first(); System.out.println(myDoc.toJson()); // now use a range query to get a larger subset Block<Document> printBlock = new Block<Document>() { @Override public void apply(final Document document) { System.out.println(document.toJson()); } }; collection.find(gt("i", 50)).forEach(printBlock); // filter where; 50 < i <= 100 collection.find(and(gt("i", 50), lte("i", 100))).forEach(printBlock); // Sorting myDoc = collection.find(exists("i")).sort(descending("i")).first(); System.out.println(myDoc.toJson()); // Projection myDoc = collection.find().projection(excludeId()).first(); System.out.println(myDoc.toJson()); // Update One collection.updateOne(eq("i", 10), new Document("$set", new Document("i", 110))); // Update Many UpdateResult updateResult = collection.updateMany(lt("i", 100), new Document("$inc", new Document("i", 100))); System.out.println(updateResult.getModifiedCount()); // Delete One collection.deleteOne(eq("i", 110)); // Delete Many DeleteResult deleteResult = collection.deleteMany(gte("i", 100)); System.out.println(deleteResult.getDeletedCount()); collection.drop(); // ordered bulk writes List<WriteModel<Document>> writes = new ArrayList<WriteModel<Document>>(); writes.add(new InsertOneModel<Document>(new Document("_id", 4))); writes.add(new InsertOneModel<Document>(new Document("_id", 5))); writes.add(new InsertOneModel<Document>(new Document("_id", 6))); writes.add( new UpdateOneModel<Document>(new Document("_id", 1), new Document("$set", new Document("x", 2)))); writes.add(new DeleteOneModel<Document>(new Document("_id", 2))); writes.add(new ReplaceOneModel<Document>(new Document("_id", 3), new Document("_id", 3).append("x", 4))); collection.bulkWrite(writes); collection.drop(); collection.bulkWrite(writes, new BulkWriteOptions().ordered(false)); // collection.find().forEach(printBlock); // Clean up //database.drop(); // release resources mongoClient.close(); }
From source file:net.acesinc.nifi.processors.mongodb.PartialUpdateMongo.java
protected UpdateResult performSingleUpdate(Document query, Document updateDocument, ProcessContext context, ProcessSession session) {/*from www .j a va 2 s .c o m*/ final ProcessorLog logger = getLogger(); StopWatch watch = new StopWatch(true); final String mode = context.getProperty(MODE).getValue(); final WriteConcern writeConcern = getWriteConcern(context); final MongoCollection<Document> collection = getCollection(context).withWriteConcern(writeConcern); UpdateResult result = null; if (!updateDocument.isEmpty()) { watch.start(); // logger.info("Running Mongo Update with query: " + query + " and document: " + updateDocument); switch (mode) { case MODE_SINGLE: result = collection.updateOne(query, updateDocument); break; case MODE_MANY: result = collection.updateMany(query, updateDocument); break; } watch.stop(); logger.info("Running Mongo Update with query: " + query + " and document: " + updateDocument + " took " + watch.getDuration(TimeUnit.MILLISECONDS) + "ms"); return result; } else { //nothing to do return null; } }
From source file:net.netzgut.integral.mongo.internal.services.MongoODMImplementation.java
License:Apache License
@Override public <T extends Serializable> UpdateResult update(Bson filter, T entity) { Class<? extends Serializable> entityClass = entity.getClass(); MongoCollection<Document> collection = this.mongo.getCollection(entityClass); Document document = this.converter.documentFrom(entity); Bson update = Filters.eq("$set", document); return collection.updateOne(filter, update); }
From source file:net.netzgut.integral.mongo.internal.services.MongoODMImplementation.java
License:Apache License
@Override public <T extends Serializable> UpdateResult update(Bson filter, Class<T> entityClass, Map<String, Object> updateMap) { MongoCollection<Document> collection = this.mongo.getCollection(entityClass); Bson update = Filters.eq("$set", new Document(updateMap)); return collection.updateOne(filter, update); }