List of usage examples for com.mongodb DBCollection remove
public WriteResult remove(final DBObject query)
From source file:eu.eubrazilcc.lvl.storage.mongodb.MongoDBConnector.java
License:EUPL
/** * Removes an object from a collection.//from w w w. j av a 2 s .c o m * @param query - statement that is used to find the object in the collection * @param collection - collection from which the object is removed */ public void remove(final DBObject query, final String collection) { checkArgument(query != null, "Uninitialized query"); checkArgument(isNotBlank(collection), "Uninitialized or invalid collection"); final DB db = client().getDB(CONFIG_MANAGER.getDbName()); final DBCollection dbcol = db.getCollection(collection); dbcol.remove(query); }
From source file:ezbake.locksmith.db.MongoDBService.java
License:Apache License
public void removeDocumentFromCollection(String collection, BasicDBObject obj) { DBCollection coll = db.getCollection(collection); coll.remove(obj); }
From source file:fr.cirad.web.controller.gigwa.base.AbstractVariantController.java
License:Open Source License
/** * Find variants.//w ww .ja va 2 s .co m * * @param request the request * @param sModule the module * @param projId the proj id * @param selectedVariantTypes the selected variant types * @param selectedSequences the selected sequences * @param selectedIndividuals the selected individuals * @param gtPattern the gt code * @param genotypeQualityThreshold the genotype quality threshold * @param readDepthThreshold the read depth threshold * @param missingData the missing data * @param minmaf the minmaf * @param maxmaf the maxmaf * @param minposition the minposition * @param maxposition the maxposition * @param alleleCount the allele count * @param geneName the gene name * @param variantEffects the variant effects * @param wantedFields the wanted fields * @param page the page * @param size the size * @param sortBy the sort by * @param sortDir the sort dir * @param processID the process id * @return true, if successful * @throws Exception the exception */ @RequestMapping(variantFindURL) /** * This method build a list of variants in a temporary collection, that may be used later for browsing or exporting results */ protected @ResponseBody boolean findVariants(HttpServletRequest request, @RequestParam("module") String sModule, @RequestParam("project") int projId, @RequestParam("variantTypes") String selectedVariantTypes, @RequestParam("sequences") String selectedSequences, @RequestParam("individuals") String selectedIndividuals, @RequestParam("gtPattern") String gtPattern, @RequestParam("genotypeQualityThreshold") int genotypeQualityThreshold, @RequestParam("readDepthThreshold") int readDepthThreshold, @RequestParam("missingData") double missingData, @RequestParam("minmaf") Float minmaf, @RequestParam("maxmaf") Float maxmaf, @RequestParam("minposition") Long minposition, @RequestParam("maxposition") Long maxposition, @RequestParam("alleleCount") String alleleCount, @RequestParam("geneName") String geneName, @RequestParam("variantEffects") String variantEffects, @RequestParam("wantedFields") String wantedFields, @RequestParam("page") int page, @RequestParam("size") int size, @RequestParam("sortBy") String sortBy, @RequestParam("sortDir") String sortDir, @RequestParam("processID") String processID) throws Exception { long before = System.currentTimeMillis(); String token = processID.substring(1 + processID.indexOf('|')); final ProgressIndicator progress = new ProgressIndicator(token, new String[0]); ProgressIndicator.registerProgressIndicator(progress); progress.addStep("Loading results"); String actualSequenceSelection = selectedSequences; if (actualSequenceSelection.length() == 0) { ArrayList<String> externallySelectedSeqs = getSequenceIDsBeingFilteredOn(request, sModule); if (externallySelectedSeqs != null) actualSequenceSelection = StringUtils.join(externallySelectedSeqs, ";"); } List<String> selectedSequenceList = actualSequenceSelection.length() == 0 ? null : Arrays.asList(actualSequenceSelection.split(";")); String queryKey = getQueryKey(request, sModule, projId, selectedVariantTypes, selectedSequences, selectedIndividuals, gtPattern, genotypeQualityThreshold, readDepthThreshold, missingData, minmaf, maxmaf, minposition, maxposition, alleleCount, geneName, variantEffects); final MongoTemplate mongoTemplate = MongoTemplateManager.get(sModule); DBCollection cachedCountCollection = mongoTemplate.getCollection(MgdbDao.COLLECTION_NAME_CACHED_COUNTS); DBCursor countCursor = cachedCountCollection.find(new BasicDBObject("_id", queryKey)); final DBCollection variantColl = mongoTemplate .getCollection(mongoTemplate.getCollectionName(VariantData.class)); final Object[] partialCountArray = !countCursor.hasNext() ? null : ((BasicDBList) countCursor.next().get(MgdbDao.FIELD_NAME_CACHED_COUNT_VALUE)).toArray(); final DBCollection tmpVarColl = getTemporaryVariantCollection(sModule, progress.getProcessId(), false); String sRegexOrAggregationOperator = GenotypingDataQueryBuilder.getGenotypePatternToQueryMap() .get(gtPattern); boolean fNeedToFilterOnGenotypingData = needToFilterOnGenotypingData(sModule, projId, sRegexOrAggregationOperator, genotypeQualityThreshold, readDepthThreshold, missingData, minmaf, maxmaf, geneName, variantEffects); final BasicDBList variantQueryDBList = buildVariantDataQuery(sModule, projId, selectedVariantTypes.length() == 0 ? null : Arrays.asList(selectedVariantTypes.split(";")), selectedSequenceList, minposition, maxposition, alleleCount.length() == 0 ? null : Arrays.asList(alleleCount.split(";"))); if (!variantQueryDBList.isEmpty() && tmpVarColl.count() == 0 /* otherwise we kept the preliminary list from the count procedure */) { // apply filter on variant features progress.setProgressDescription("Filtering variants for display..."); long beforeAggQuery = System.currentTimeMillis(); List<DBObject> pipeline = new ArrayList<DBObject>(); pipeline.add(new BasicDBObject("$match", new BasicDBObject("$and", variantQueryDBList))); BasicDBObject projectObject = new BasicDBObject("_id", "$_id"); projectObject.put(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_SEQUENCE, "$" + VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_SEQUENCE); projectObject.put( VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_START_SITE, "$" + VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_START_SITE); projectObject.put(VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_END_SITE, "$" + VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_END_SITE); projectObject.put(VariantData.FIELDNAME_TYPE, "$" + VariantData.FIELDNAME_TYPE); projectObject.put(VariantData.FIELDNAME_KNOWN_ALLELE_LIST, "$" + VariantData.FIELDNAME_KNOWN_ALLELE_LIST); pipeline.add(new BasicDBObject("$project", projectObject)); pipeline.add(new BasicDBObject("$out", tmpVarColl.getName())); variantColl.aggregate(pipeline); LOG.debug("Variant preliminary query found " + tmpVarColl.count() + " results in " + (System.currentTimeMillis() - beforeAggQuery) / 1000f + "s"); progress.setProgressDescription(null); } else if (fNeedToFilterOnGenotypingData && tmpVarColl.count() > 0) LOG.debug( "Re-using " + tmpVarColl.count() + " results from count procedure's variant preliminary query"); if (progress.hasAborted()) return false; if (fNeedToFilterOnGenotypingData) { // now filter on genotyping data final ConcurrentLinkedQueue<Thread> queryThreadsToWaitFor = new ConcurrentLinkedQueue<Thread>(), removalThreadsToWaitFor = new ConcurrentLinkedQueue<Thread>(); final AtomicInteger finishedThreadCount = new AtomicInteger(0); final ConcurrentSkipListSet<Comparable> allVariantsThatPassRunFilter = new ConcurrentSkipListSet<Comparable>(); GigwaSearchVariantsExportRequest gsvr = new GigwaSearchVariantsExportRequest(); gsvr.setAlleleCount(alleleCount); if (minposition != null) gsvr.setStart(minposition); if (maxposition != null) gsvr.setEnd(maxposition); gsvr.setGeneName(geneName); gsvr.setReferenceName(selectedSequences); gsvr.setSelectedVariantTypes(selectedVariantTypes); gsvr.setVariantEffect(variantEffects); gsvr.setVariantSetId(sModule + ServiceInterface.ID_SEPARATOR + projId); gsvr.setMissingData(missingData); gsvr.setMinmaf(minmaf); gsvr.setMaxmaf(maxmaf); gsvr.setGtPattern(gtPattern); HashMap<String, Integer> annotationFieldThresholds = new HashMap<String, Integer>(); annotationFieldThresholds.put(VCFConstants.GENOTYPE_QUALITY_KEY, genotypeQualityThreshold); annotationFieldThresholds.put(VCFConstants.DEPTH_KEY, readDepthThreshold); gsvr.setAnnotationFieldThresholds(annotationFieldThresholds); gsvr.setCallSetIds(selectedIndividuals == null || selectedIndividuals.length() == 0 ? getIndividualsInDbOrder(sModule, projId) : Arrays.asList(selectedIndividuals.split(";"))); final GenotypingDataQueryBuilder genotypingDataQueryBuilder = new GenotypingDataQueryBuilder(gsvr, tmpVarColl); genotypingDataQueryBuilder.keepTrackOfPreFilters(!variantQueryDBList.isEmpty()); try { final int nChunkCount = genotypingDataQueryBuilder.getNumberOfQueries(); if (nChunkCount != partialCountArray.length) { LOG.error("Different number of chunks between counting and listing variant rows!"); progress.setError("Different number of chunks between counting and listing variant rows!"); return false; } if (nChunkCount > 1) LOG.debug("Query split into " + nChunkCount); ArrayList<List<DBObject>> genotypingDataPipelines = new ArrayList(); while (genotypingDataQueryBuilder.hasNext()) genotypingDataPipelines.add(genotypingDataQueryBuilder.next()); ArrayList<Integer> chunkIndices = new ArrayList<Integer>(); for (int i = 0; i < genotypingDataPipelines.size(); i++) chunkIndices.add(i); Collections.shuffle(chunkIndices); for (int i = 0; i < chunkIndices.size(); i++) { final int chunkIndex = chunkIndices.get(i); final List<DBObject> genotypingDataPipeline = genotypingDataPipelines.get(chunkIndex); if (progress.hasAborted()) { genotypingDataQueryBuilder.cleanup(); // otherwise a pending db-cursor will remain return false; } Thread t = new Thread() { public void run() { Cursor genotypingDataCursor = mongoTemplate .getCollection( MongoTemplateManager.getMongoCollectionName(VariantRunData.class)) .aggregate(genotypingDataPipeline, AggregationOptions.builder().allowDiskUse(true).build()); final ArrayList<Comparable> variantsThatPassedRunFilter = new ArrayList<Comparable>(); while (genotypingDataCursor.hasNext()) variantsThatPassedRunFilter .add((Comparable) genotypingDataCursor.next().get("_id")); if (variantQueryDBList.isEmpty()) // otherwise we won't need it allVariantsThatPassRunFilter.addAll(variantsThatPassedRunFilter); else { // mark the results we want to keep final List<Comparable> lastUsedPreFilter = genotypingDataQueryBuilder .getPreFilteredIDsForChunk(chunkIndex); Thread removalThread = new Thread() { public void run() { genotypingDataPipeline.clear(); // release memory (VERY IMPORTANT) long beforeTempCollUpdate = System.currentTimeMillis(); if (variantsThatPassedRunFilter.size() == lastUsedPreFilter.size()) return; // none to remove Collection<Comparable> filteredOutVariants = variantsThatPassedRunFilter .size() == 0 ? lastUsedPreFilter : CollectionUtils.subtract(lastUsedPreFilter, variantsThatPassedRunFilter); BasicDBObject removalQuery = GenotypingDataQueryBuilder .tryAndShrinkIdList("_id", filteredOutVariants, 4); WriteResult wr = tmpVarColl.remove(removalQuery); LOG.debug("Chunk N." + (chunkIndex) + ": " + wr.getN() + " filtered-out temp records removed in " + (System.currentTimeMillis() - beforeTempCollUpdate) / 1000d + "s"); progress.setCurrentStepProgress( (short) (finishedThreadCount.incrementAndGet() * 100 / nChunkCount)); } }; removalThreadsToWaitFor.add(removalThread); removalThread.start(); } } }; if (i % NUMBER_OF_SIMULTANEOUS_QUERY_THREADS == (NUMBER_OF_SIMULTANEOUS_QUERY_THREADS - 1)) t.run(); // sometimes run synchronously so that all queries are not sent at the same time (also helps smooth progress display) else { queryThreadsToWaitFor.add(t); t.start(); // run asynchronously for better speed } } // wait for all threads before moving to next phase for (Thread t : queryThreadsToWaitFor) t.join(); for (Thread t : removalThreadsToWaitFor) t.join(); } catch (Exception e) { genotypingDataQueryBuilder.cleanup(); // otherwise a pending db-cursor will remain throw e; } if (progress.hasAborted()) return false; progress.addStep("Updating temporary results"); progress.moveToNextStep(); final long beforeTempCollUpdate = System.currentTimeMillis(); mongoTemplate.getDb().setWriteConcern(WriteConcern.ACKNOWLEDGED); if (variantQueryDBList.isEmpty()) { // we filtered on runs only: keep track of the final dataset List<BasicDBObject> pipeline = new ArrayList<>(); pipeline.add(new BasicDBObject("$match", GenotypingDataQueryBuilder.tryAndShrinkIdList("_id", allVariantsThatPassRunFilter, 4))); BasicDBObject projectObject = new BasicDBObject("_id", "$_id"); projectObject.put( VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_SEQUENCE, "$" + VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_SEQUENCE); projectObject.put( VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_START_SITE, "$" + VariantData.FIELDNAME_REFERENCE_POSITION + "." + ReferencePosition.FIELDNAME_START_SITE); projectObject.put(VariantData.FIELDNAME_TYPE, "$" + VariantData.FIELDNAME_TYPE); projectObject.put(VariantData.FIELDNAME_KNOWN_ALLELE_LIST, "$" + VariantData.FIELDNAME_KNOWN_ALLELE_LIST); projectObject.put(VariantData.FIELDNAME_VERSION, "$" + VariantData.FIELDNAME_VERSION); pipeline.add(new BasicDBObject("$project", projectObject)); pipeline.add(new BasicDBObject("$out", tmpVarColl.getName())); variantColl.aggregate(pipeline); LOG.debug(tmpVarColl.count() + " temp records created in " + (System.currentTimeMillis() - beforeTempCollUpdate) / 1000d + "s"); } } progress.markAsComplete(); LOG.info("findVariants took " + (System.currentTimeMillis() - before) / 1000d + "s"); return true; }
From source file:framework.modules.users.client.Model.DAO.DAO_client_MG.java
/** * Function to delete client in db/*from ww w. ja va 2 s . c o m*/ * @param db * @param table * @param nombre */ public static void delete_client(client_class client) { DBCollection table = singleton.collection; table.remove(new BasicDBObject().append("dni", client.getDni())); }
From source file:github.macrohuang.orm.mongo.core.MongoDBTemplate.java
License:Apache License
/** * Delete documents match the given <code>entry</code> with manual specify * <code>DBChooser</code>//w w w . j a v a2s . com * * @param <T> * @param dbChooser * The <code>DBChoose</code> configure with the DB name and * collection name. * @param entry * The document to be deleted. Any documents match this entry * query will be deleted. * @return <code>true</code> if the deletion is success, or * <code>false</code> while fail. * @throws MongoDataAccessException */ public <T> boolean delete(DBChooser dbChooser, T entry) throws MongoDataAccessException { Assert.assertNotNull(entry); if (Constants.coreLogEnable) LOGGER.info("delete request received: " + dbChooser + entry); DBCollection collection = getCollection(dbChooser); boolean result = isOperateSuccess(collection.remove(DBObjectUtil.convertPO2DBObject(entry))); if (Constants.coreLogEnable) LOGGER.info("delete result: " + result); return result; }
From source file:io.github.apfelcreme.LitePortals.Bungee.Database.MongoController.java
License:Open Source License
/** * deletes a portal and resets the target of all portals it was connected to * * @param portal a portal/*from w w w. jav a 2s . c o m*/ */ public void deletePortal(Portal portal) { DBCollection collection = MongoConnector.getInstance().getCollection(); // find all portals who have this portal as target BasicDBObject query = new BasicDBObject("target", portal.getId().toString()); DBCursor dbCursor = collection.find(query); while (dbCursor.hasNext()) { DBObject portalObject = dbCursor.next(); portalObject.removeField("target"); UUID targetId = UUID.fromString((String) portalObject.get("portal_id")); collection.update(query, portalObject); Portal p = PortalManager.getInstance().getPortal(targetId); if (p != null) { p.setTarget(null); } } // remove the object itself BasicDBObject portalObject = new BasicDBObject("portal_id", portal.getId().toString()); collection.remove(portalObject); PortalManager.getInstance().getPortals().remove(portal); }
From source file:it.sayservice.platform.smartplanner.otp.OTPStorage.java
License:Apache License
public void bulkDelete(MongoTemplate template, String key, Collection<Object> values, String collectionName) { DBCollection collection = template.getCollection(collectionName); QueryBuilder qb = QueryBuilder.start(key).notIn(values); collection.remove(qb.get()); }
From source file:me.yyam.mongodbutils.MongoDbOperater.java
public void remove(String dbName, String sql) throws JSQLParserException { QueryInfo query = sql2QueryInfo(dbName, sql); DB db = mongoClient.getDB(dbName);//from ww w . j av a 2 s. com DBCollection coll = db.getCollection(query.collName); coll.remove(query.query); }
From source file:me.yyam.mongodbutils.MongoDbOperater.java
public void remove(String dbName, String colName, Map query) { DB db = mongoClient.getDB(dbName);/*from ww w. j a v a 2 s. c om*/ DBCollection coll = db.getCollection(colName); coll.remove(new BasicDBObject(query)); }
From source file:mini_mirc_server.miniIRCHandler.java
/** * Delete a user from a channel (used in leave method) * @param Channel//from ww w . ja va2 s . c om * @param Username * @return code */ private int DeleteChannelUser(String Channel, String Username) { int ret = 0; try { MongoClient mongoClient = new MongoClient(); DB db = mongoClient.getDB("mirc"); DBCollection coll = db.getCollection("channelCollection"); BasicDBObject query = new BasicDBObject("username", Username).append("channel", Channel); DBCursor cursor = coll.find(query); try { while (cursor.hasNext()) { coll.remove(cursor.next()); } } finally { cursor.close(); } } catch (UnknownHostException ex) { Logger.getLogger(miniIRCHandler.class.getName()).log(Level.SEVERE, null, ex); } System.out.println(Username + " has leaved Channel : " + Channel); return ret; }