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WriteConcern ACKNOWLEDGED
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From source file:fr.cirad.web.controller.gigwa.base.AbstractVariantController.java
License:Open Source License
/** * This method returns the number of variants that match provided parameters. * * @param request the request//from ww w . jav a2s.c o m * @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 processID the process id * @return the long * @throws Exception the exception */ @RequestMapping(variantCountURL) protected @ResponseBody long countVariants(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") Integer genotypeQualityThreshold, @RequestParam("readDepthThreshold") Integer readDepthThreshold, @RequestParam("missingData") Double missingData, @RequestParam(value = "minmaf", required = false) Float minmaf, @RequestParam(value = "maxmaf", required = false) Float maxmaf, @RequestParam("minposition") Long minposition, @RequestParam("maxposition") Long maxposition, @RequestParam("alleleCount") String alleleCount, @RequestParam("geneName") String geneName, @RequestParam("variantEffects") String variantEffects, @RequestParam("processID") final String processID) throws Exception { final ProgressIndicator progress = new ProgressIndicator(processID.substring(1 + processID.indexOf('|')), new String[0]); ProgressIndicator.registerProgressIndicator(progress); DBCollection tmpVarColl = getTemporaryVariantCollection(sModule, progress.getProcessId(), true /*empty it*/); try { 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); // cachedCountcollection.drop(); DBCursor countCursor = cachedCountcollection.find(new BasicDBObject("_id", queryKey)); Long count = null; if (countCursor.hasNext()) { count = 0l; for (Object aPartialCount : ((BasicDBList) countCursor.next() .get(MgdbDao.FIELD_NAME_CACHED_COUNT_VALUE)).toArray()) count += (Long) aPartialCount; } LOG.debug((count == null ? "new" : "existing") + " queryKey hash: " + queryKey); if (count == null) { long before = System.currentTimeMillis(); progress.addStep("Counting matching variants"); String sRegexOrAggregationOperator = GenotypingDataQueryBuilder.getGenotypePatternToQueryMap() .get(gtPattern); List<String> alleleCountList = alleleCount.length() == 0 ? null : Arrays.asList(alleleCount.split(";")); GenotypingProject genotypingProject = mongoTemplate.findById(projId, GenotypingProject.class); if (genotypingProject.getAlleleCounts().size() != 1 || genotypingProject.getAlleleCounts().iterator().next() != 2) { // Project does not only have bi-allelic data: make sure we can apply MAF filter on selection boolean fExactlyOneNumberOfAllelesSelected = alleleCountList != null && alleleCountList.size() == 1; boolean fBiAllelicSelected = fExactlyOneNumberOfAllelesSelected && "2".equals(alleleCountList.get(0)); boolean fMafRequested = (maxmaf != null && maxmaf < 50) || (minmaf != null && minmaf > 0); if (fMafRequested && !fBiAllelicSelected) { progress.setError("MAF is only supported on biallelic data!"); return 0l; } } String actualSequenceSelection = selectedSequences; if (actualSequenceSelection.length() == 0) { ArrayList<String> externallySelectedSeqs = getSequenceIDsBeingFilteredOn(request, sModule); if (externallySelectedSeqs != null) actualSequenceSelection = StringUtils.join(externallySelectedSeqs, ";"); } boolean fNeedToFilterOnGenotypingData = needToFilterOnGenotypingData(sModule, projId, sRegexOrAggregationOperator, genotypeQualityThreshold, readDepthThreshold, missingData, minmaf, maxmaf, geneName, variantEffects); BasicDBList variantQueryDBList = buildVariantDataQuery(sModule, projId, selectedVariantTypes.length() == 0 ? null : Arrays.asList(selectedVariantTypes.split(";")), actualSequenceSelection.length() == 0 ? null : Arrays.asList(actualSequenceSelection.split(";")), minposition, maxposition, alleleCountList); if (variantQueryDBList.isEmpty()) { if (!fNeedToFilterOnGenotypingData && mongoTemplate.count(null, GenotypingProject.class) == 1) count = mongoTemplate.count(new Query(), VariantData.class); // no filter whatsoever } else { if (!fNeedToFilterOnGenotypingData) { // filtering on variant features only: we just need a count count = mongoTemplate.getCollection(mongoTemplate.getCollectionName(VariantData.class)) .count(new BasicDBObject("$and", variantQueryDBList)); } else { // filtering on variant features and genotyping data: we need a list of variant IDs to restrict the genotyping data search to long beforeAggQuery = System.currentTimeMillis(); progress.setProgressDescription("Filtering variants for count..."); DBCollection variantColl = mongoTemplate .getCollection(mongoTemplate.getCollectionName(VariantData.class)); List<DBObject> pipeline = new ArrayList<DBObject>(); pipeline.add(new BasicDBObject("$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_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); mongoTemplate.getDb().setWriteConcern(WriteConcern.ACKNOWLEDGED); LOG.debug("Variant preliminary query found " + tmpVarColl.count() + " results in " + (System.currentTimeMillis() - beforeAggQuery) / 1000f + "s"); progress.setProgressDescription(null); if (tmpVarColl.count() == 0) count = 0l; // no need to search any further } } if (count != null) { BasicDBObject dbo = new BasicDBObject("_id", queryKey); dbo.append(MgdbDao.FIELD_NAME_CACHED_COUNT_VALUE, new Long[] { count }); cachedCountcollection.save(dbo); } else { // now filter on genotyping data List<String> selectedIndividualList = selectedIndividuals.length() == 0 ? null : Arrays.asList(selectedIndividuals.split(";")); if (selectedIndividualList == null) selectedIndividualList = getIndividualsInDbOrder(sModule, projId); 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(selectedIndividualList); GenotypingDataQueryBuilder genotypingDataQueryBuilder = new GenotypingDataQueryBuilder(gsvr, tmpVarColl); try { final int nChunkCount = genotypingDataQueryBuilder.getNumberOfQueries(); if (nChunkCount > 1) LOG.debug("Query split into " + nChunkCount); final Long[] partialCountArray = new Long[nChunkCount]; final Builder aggOpts = AggregationOptions.builder().allowDiskUse(false); final ArrayList<Thread> threadsToWaitFor = new ArrayList<Thread>(); final AtomicInteger finishedThreadCount = new AtomicInteger(0); 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()/*/2*/; i++) { final List<DBObject> genotypingDataPipeline = genotypingDataPipelines .get(chunkIndices.get(i)); // Now the $group operation, used for counting DBObject groupFields = new BasicDBObject("_id", null); groupFields.put("count", new BasicDBObject("$sum", 1)); genotypingDataPipeline.add(new BasicDBObject("$group", groupFields)); if (i == 0 && tmpVarColl.count() <= 5) LOG.debug(genotypingDataPipeline); if (progress.hasAborted()) { genotypingDataQueryBuilder.cleanup(); // otherwise a pending db-cursor will remain return 0l; } final int chunkIndex = i; Thread t = new Thread() { public void run() { // long b4 = System.currentTimeMillis(); Cursor it = mongoTemplate .getCollection(MongoTemplateManager .getMongoCollectionName(VariantRunData.class)) .aggregate(genotypingDataPipeline, aggOpts.build()); partialCountArray[chunkIndex] = it.hasNext() ? ((Number) it.next().get("count")).longValue() : 0; progress.setCurrentStepProgress( (short) (finishedThreadCount.incrementAndGet() * 100 / nChunkCount)); // System.out.println("chunk " + chunkIndex + " took " + (System.currentTimeMillis() - b4)); genotypingDataPipeline.clear(); // release memory (VERY IMPORTANT) } }; if (i % NUMBER_OF_SIMULTANEOUS_QUERY_THREADS == (NUMBER_OF_SIMULTANEOUS_QUERY_THREADS - 1)) { t.run(); // run synchronously } else { threadsToWaitFor.add(t); t.start(); // run asynchronously for better speed } } for (Thread t : threadsToWaitFor) // wait for all threads before moving to next phase t.join(); progress.setCurrentStepProgress(100); count = 0l; for (Long partialCount : partialCountArray) count += partialCount; BasicDBObject dbo = new BasicDBObject("_id", queryKey); dbo.append(MgdbDao.FIELD_NAME_CACHED_COUNT_VALUE, partialCountArray); cachedCountcollection.save(dbo); } catch (Exception e) { genotypingDataQueryBuilder.cleanup(); // otherwise a pending db-cursor will remain throw e; } } LOG.info("countVariants found " + count + " results in " + (System.currentTimeMillis() - before) / 1000d + "s"); } progress.markAsComplete(); if (progress.hasAborted()) return 0l; return count; } finally { // getTemporaryVariantCollection(sModule, progress.getProcessId(), true); // always empty it } }
From source file:fr.cirad.web.controller.gigwa.base.AbstractVariantController.java
License:Open Source License
/** * Find variants./*from w w w. j a v a2 s .c o 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:geojson.sof20181050.ConvertToGeoJSON.java
License:Apache License
/** * Performs the document updates using the legacy driver. * <p>//from w w w . j a v a2s. c om * The main draw back here (other than those discussed in * {@link #doSynchronously()}) is the difficulty creating the GeoJSON * documents. * </p> * * @throws UnknownHostException * On an invalid URI. */ protected static void doLegacy() throws UnknownHostException { // Execute the query to find all of the documents and then // update them. final com.mongodb.MongoClient legacyClient = new com.mongodb.MongoClient(new MongoClientURI(URI)); final com.mongodb.DBCollection legacyCollection = legacyClient.getDB(theCollection.getDatabaseName()) .getCollection(theCollection.getName()); try { int count = 0; for (final DBObject doc : legacyCollection.find()) { final Object id = doc.get("_id"); final Number lat = (Number) doc.get("latitude_deg"); final Number lon = (Number) doc.get("longitude_deg"); final BasicDBObject query = new BasicDBObject(); query.append("_id", id); final ArrayList<Double> coordinates = new ArrayList<>(); coordinates.add(lon.doubleValue()); coordinates.add(lat.doubleValue()); final BasicDBObject geojson = new BasicDBObject("type", "Point"); geojson.append("coordinates", coordinates); final BasicDBObject set = new BasicDBObject("loc", geojson); final BasicDBObject update = new BasicDBObject("$set", set); legacyCollection.update(query, update, /* upsert= */false, /* multi= */false, WriteConcern.ACKNOWLEDGED); count += 1; } System.out.printf("Updated %d documents via the legacy driver.%n", count); } finally { // Always close the client. legacyClient.close(); } }
From source file:io.github.microcks.config.MongoConfiguration.java
License:Apache License
@Bean public WriteConcernResolver writeConcernResolver() { return action -> { log.info("Using Write Concern of Acknowledged"); return WriteConcern.ACKNOWLEDGED; };//from w w w .j av a 2 s .com }
From source file:io.gravitee.am.repository.mongodb.common.MongoFactory.java
License:Apache License
@Override public MongoClient getObject() throws Exception { // Client settings MongoClientSettings.Builder builder = MongoClientSettings.builder(); builder.writeConcern(WriteConcern.ACKNOWLEDGED); // codec configuration for pojo mapping CodecRegistry pojoCodecRegistry = fromRegistries(MongoClients.getDefaultCodecRegistry(), fromProviders(PojoCodecProvider.builder().automatic(true).build())); builder.codecRegistry(pojoCodecRegistry); // Trying to get the MongoClientURI if uri property is defined String uri = readPropertyValue(propertyPrefix + "uri"); if (uri != null && !uri.isEmpty()) { // The builder can be configured with default options, which may be overridden by options specified in // the URI string. MongoClientSettings settings = builder.codecRegistry(pojoCodecRegistry) .applyConnectionString(new ConnectionString(uri)).build(); return MongoClients.create(settings); } else {//from w w w . ja v a2s . c o m // Advanced configuration SocketSettings.Builder socketBuilder = SocketSettings.builder(); ClusterSettings.Builder clusterBuilder = ClusterSettings.builder(); ConnectionPoolSettings.Builder connectionPoolBuilder = ConnectionPoolSettings.builder(); ServerSettings.Builder serverBuilder = ServerSettings.builder(); SslSettings.Builder sslBuilder = SslSettings.builder(); Integer connectTimeout = readPropertyValue(propertyPrefix + "connectTimeout", Integer.class, 1000); Integer maxWaitTime = readPropertyValue(propertyPrefix + "maxWaitTime", Integer.class); Integer socketTimeout = readPropertyValue(propertyPrefix + "socketTimeout", Integer.class, 1000); Boolean socketKeepAlive = readPropertyValue(propertyPrefix + "socketKeepAlive", Boolean.class, true); Integer maxConnectionLifeTime = readPropertyValue(propertyPrefix + "maxConnectionLifeTime", Integer.class); Integer maxConnectionIdleTime = readPropertyValue(propertyPrefix + "maxConnectionIdleTime", Integer.class); // We do not want to wait for a server Integer serverSelectionTimeout = readPropertyValue(propertyPrefix + "serverSelectionTimeout", Integer.class, 1000); Integer minHeartbeatFrequency = readPropertyValue(propertyPrefix + "minHeartbeatFrequency", Integer.class); String description = readPropertyValue(propertyPrefix + "description", String.class, "gravitee.io"); Integer heartbeatFrequency = readPropertyValue(propertyPrefix + "heartbeatFrequency", Integer.class); Boolean sslEnabled = readPropertyValue(propertyPrefix + "sslEnabled", Boolean.class); if (maxWaitTime != null) connectionPoolBuilder.maxWaitTime(maxWaitTime, TimeUnit.MILLISECONDS); if (connectTimeout != null) socketBuilder.connectTimeout(connectTimeout, TimeUnit.MILLISECONDS); if (socketTimeout != null) socketBuilder.readTimeout(socketTimeout, TimeUnit.MILLISECONDS); if (socketKeepAlive != null) socketBuilder.keepAlive(socketKeepAlive); if (maxConnectionLifeTime != null) connectionPoolBuilder.maxConnectionLifeTime(maxConnectionLifeTime, TimeUnit.MILLISECONDS); if (maxConnectionIdleTime != null) connectionPoolBuilder.maxConnectionIdleTime(maxConnectionIdleTime, TimeUnit.MILLISECONDS); if (minHeartbeatFrequency != null) serverBuilder.minHeartbeatFrequency(minHeartbeatFrequency, TimeUnit.MILLISECONDS); if (description != null) clusterBuilder.description(description); if (heartbeatFrequency != null) serverBuilder.heartbeatFrequency(heartbeatFrequency, TimeUnit.MILLISECONDS); if (sslEnabled != null) sslBuilder.enabled(sslEnabled); if (serverSelectionTimeout != null) clusterBuilder.serverSelectionTimeout(serverSelectionTimeout, TimeUnit.MILLISECONDS); // credentials option String username = readPropertyValue(propertyPrefix + "username"); String password = readPropertyValue(propertyPrefix + "password"); MongoCredential credentials = null; if (username != null || password != null) { String authSource = readPropertyValue(propertyPrefix + "authSource", String.class, "gravitee-am"); credentials = MongoCredential.createCredential(username, authSource, password.toCharArray()); builder.credential(credentials); } // clustering option List<ServerAddress> seeds; int serversCount = getServersCount(); if (serversCount == 0) { String host = readPropertyValue(propertyPrefix + "host", String.class, "localhost"); int port = readPropertyValue(propertyPrefix + "port", int.class, 27017); seeds = Collections.singletonList(new ServerAddress(host, port)); } else { seeds = new ArrayList<>(serversCount); for (int i = 0; i < serversCount; i++) { seeds.add(buildServerAddress(i)); } } clusterBuilder.hosts(seeds); SocketSettings socketSettings = socketBuilder.build(); ClusterSettings clusterSettings = clusterBuilder.build(); ConnectionPoolSettings connectionPoolSettings = connectionPoolBuilder.build(); ServerSettings serverSettings = serverBuilder.build(); SslSettings sslSettings = sslBuilder.build(); MongoClientSettings settings = builder .applyToClusterSettings(builder1 -> builder1.applySettings(clusterSettings)) .applyToSocketSettings(builder1 -> builder1.applySettings(socketSettings)) .applyToConnectionPoolSettings(builder1 -> builder1.applySettings(connectionPoolSettings)) .applyToServerSettings(builder1 -> builder1.applySettings(serverSettings)) .applyToSslSettings(builder1 -> builder1.applySettings(sslSettings)).build(); return MongoClients.create(settings); } }
From source file:io.gravitee.am.repository.mongodb.management.ManagementRepositoryTestConfiguration.java
License:Apache License
@Bean(name = "managementMongo") public MongoClient mongo() { // cluster configuration ClusterSettings clusterSettings = ClusterSettings.builder() .hosts(Collections.singletonList(new ServerAddress("localhost", 12345))).build(); // codec configuration CodecRegistry pojoCodecRegistry = fromRegistries(MongoClients.getDefaultCodecRegistry(), fromProviders(PojoCodecProvider.builder().automatic(true).build())); MongoClientSettings settings = MongoClientSettings.builder().clusterSettings(clusterSettings) .codecRegistry(pojoCodecRegistry).writeConcern(WriteConcern.ACKNOWLEDGED).build(); return MongoClients.create(settings); }
From source file:io.gravitee.am.repository.mongodb.oauth2.OAuth2RepositoryTestConfiguration.java
License:Apache License
@Bean(name = "oauth2Mongo") public MongoClient mongo() { // cluster configuration ClusterSettings clusterSettings = ClusterSettings.builder() .hosts(Collections.singletonList(new ServerAddress("localhost", 12346))).build(); // codec configuration CodecRegistry pojoCodecRegistry = fromRegistries(MongoClients.getDefaultCodecRegistry(), fromProviders(PojoCodecProvider.builder().automatic(true).build())); MongoClientSettings settings = MongoClientSettings.builder().clusterSettings(clusterSettings) .codecRegistry(pojoCodecRegistry).writeConcern(WriteConcern.ACKNOWLEDGED).build(); return MongoClients.create(settings); }
From source file:net.acesinc.nifi.processors.mongodb.PartialUpdateMongo.java
protected WriteConcern getWriteConcern(final ProcessContext context) { final String writeConcernProperty = context.getProperty(WRITE_CONCERN).getValue(); WriteConcern writeConcern = null;//from w ww. j av a2 s . c om switch (writeConcernProperty) { case WRITE_CONCERN_ACKNOWLEDGED: writeConcern = WriteConcern.ACKNOWLEDGED; break; case WRITE_CONCERN_UNACKNOWLEDGED: writeConcern = WriteConcern.UNACKNOWLEDGED; break; case WRITE_CONCERN_FSYNCED: writeConcern = WriteConcern.FSYNCED; break; case WRITE_CONCERN_JOURNALED: writeConcern = WriteConcern.JOURNALED; break; case WRITE_CONCERN_REPLICA_ACKNOWLEDGED: writeConcern = WriteConcern.REPLICA_ACKNOWLEDGED; break; case WRITE_CONCERN_MAJORITY: writeConcern = WriteConcern.MAJORITY; break; default: writeConcern = WriteConcern.ACKNOWLEDGED; } return writeConcern; }
From source file:org.alfresco.cacheserver.dao.mongo.MongoWebSocketDAO.java
License:Open Source License
private void init() { if (db == null) { throw new RuntimeException("Mongo DB must not be null"); }/*ww w . j av a 2 s . co m*/ this.registrationData = getCollection(db, registrationDataCollectionName, WriteConcern.ACKNOWLEDGED); { DBObject keys = BasicDBObjectBuilder.start("u", 1).get(); this.registrationData.ensureIndex(keys, "byUserName", false); } }
From source file:org.alfresco.contentstore.dao.mongo.MongoContentDAO.java
License:Open Source License
private void init() { if (db == null) { throw new RuntimeException("Mongo DB must not be null"); }/* ww w . j a va 2s . co m*/ this.contentData = getCollection(db, contentCollectionName, WriteConcern.ACKNOWLEDGED); { DBObject keys = BasicDBObjectBuilder.start("e", 1).add("n", 1).add("v", 1).add("pri", 1).get(); this.contentData.ensureIndex(keys, "byNodeId", false); } { DBObject keys = BasicDBObjectBuilder.start("e", 1).add("n", 1).add("p", 1).get(); this.contentData.ensureIndex(keys, "byNodePath", false); } }