List of usage examples for com.mongodb BulkWriteResult getModifiedCount
public abstract int getModifiedCount();
Returns the number of documents modified by the write operation.
From source file:org.lucee.mongodb.DBCollectionImpl.java
License:Open Source License
@Override public Object call(PageContext pc, Key methodName, Object[] args) throws PageException { // aggregate/*w w w .j av a2s. co m*/ if (methodName.equals("aggregate")) { boolean hasOptions = false; AggregationOptions options = null; int len = checkArgLength("aggregate", args, 1, -1); // no length limitation List<DBObject> pipeline = new ArrayList<DBObject>(); // Pipeline array as single argument if (len == 1 && decision.isArray(args[0])) { Array arr = caster.toArray(args[0]); if (arr.size() == 0) throw exp.createApplicationException( "the array passed to the function aggregate needs at least 1 element"); Iterator<Object> it = arr.valueIterator(); while (it.hasNext()) { pipeline.add(toDBObject(it.next())); } } else { // First argument is pipeline of operations, second argument is struct of options --> returns cursor! if (len == 2 && decision.isArray(args[0]) && decision.isStruct(args[1])) { Array arr = caster.toArray(args[0]); Iterator<Object> it = arr.valueIterator(); while (it.hasNext()) { pipeline.add(toDBObject(it.next())); } hasOptions = true; // options builder AggregationOptions.Builder optbuilder = AggregationOptions.builder() .outputMode(AggregationOptions.OutputMode.CURSOR); DBObject dboOpts = toDBObject(args[1]); if (dboOpts.containsField("allowDiskUse")) { if (!decision.isBoolean(dboOpts.get("allowDiskUse"))) throw exp.createApplicationException("allowDiskUse in options must be boolean value"); optbuilder = optbuilder.allowDiskUse(caster.toBooleanValue(dboOpts.get("allowDiskUse"))); } if (dboOpts.containsField("cursor")) { if (!decision.isStruct(dboOpts.get("cursor"))) throw exp.createApplicationException( "cursor in options must be struct with optional key batchSize"); DBObject cursoropts = toDBObject(dboOpts.get("cursor")); if (cursoropts.containsField("batchSize")) { if (!decision.isNumeric(cursoropts.get("batchSize"))) throw exp.createApplicationException("cursor.batchSize in options must be integer"); optbuilder = optbuilder.batchSize(caster.toIntValue(cursoropts.get("batchSize"))); } } options = optbuilder.build(); } // First argument is first operation, second argument is array of additional operations else if (len == 2 && decision.isArray(args[1])) { Array arr = caster.toArray(args[1]); pipeline.add(toDBObject(args[0])); Iterator<Object> it = arr.valueIterator(); while (it.hasNext()) { pipeline.add(toDBObject(it.next())); } } // N arguments of pipeline operations else { for (int i = 0; i < len; i++) { pipeline.add(toDBObject(args[i])); } } } if (hasOptions) { // returns Cursor - requires >= MongoDB 2.6 return toCFML(coll.aggregate(pipeline, options)); } else { // returns AggregationOutput return toCFML(coll.aggregate(pipeline)); } } // count if (methodName.equals("count")) { int len = checkArgLength("count", args, 0, 1); if (len == 0) { return toCFML(coll.count()); } else if (len == 1) { return toCFML(coll.count(toDBObject(args[0]))); } } // dataSize if (methodName.equals("dataSize")) { checkArgLength("dataSize", args, 0, 0); return toCFML(coll.getStats().get("size")); } // distinct if (methodName.equals("distinct")) { int len = checkArgLength("distinct", args, 1, 2); if (len == 1) { return toCFML(coll.distinct(caster.toString(args[0]))); } else if (len == 2) { return toCFML(coll.distinct(caster.toString(args[0]), toDBObject(args[1]))); } } // drop if (methodName.equals("drop")) { checkArgLength("drop", args, 0, 0); coll.drop(); return null; } // dropIndex if (methodName.equals("dropIndex")) { checkArgLength("dropIndex", args, 1, 1); DBObject dbo = toDBObject(args[0], null); if (dbo != null) coll.dropIndex(dbo); else coll.dropIndex(caster.toString(args[0])); return null; } // dropIndexes if (methodName.equals("dropIndexes")) { int len = checkArgLength("dropIndexes", args, 0, 1); if (len == 0) { coll.dropIndexes(); return null; } else if (len == 1) { coll.dropIndexes(caster.toString(args[0])); return null; } } // createIndex if (methodName.equals("createIndex") || methodName.equals("ensureIndex")) { int len = checkArgLength("createIndex", args, 1, 3); if (len == 1) { DBObject dbo = toDBObject(args[0], null); if (dbo != null) coll.createIndex(dbo); else coll.createIndex(caster.toString(args[0])); return null; } if (len == 2) { DBObject p1 = toDBObject(args[0]); DBObject p2 = toDBObject(args[1], null); if (p2 != null) coll.createIndex(p1, p2); else coll.createIndex(p1, caster.toString(args[1])); return null; } else if (len == 3) { coll.createIndex(toDBObject(args[0]), caster.toString(args[1]), caster.toBooleanValue(args[2])); return null; } } // getStats if (methodName.equals("getStats") || methodName.equals("stats")) { checkArgLength("getStats", args, 0, 0); return toCFML(coll.getStats()); } // getIndexes if (methodName.equals("getIndexes") || methodName.equals("getIndexInfo")) { checkArgLength(methodName.getString(), args, 0, 0); return toCFML(coll.getIndexInfo()); } // getWriteConcern if (methodName.equals("getWriteConcern")) { checkArgLength("getWriteConcern", args, 0, 0); return toCFML(coll.getWriteConcern()); } // find if (methodName.equals("find")) { int len = checkArgLength("find", args, 0, 3); DBCursor cursor = null; if (len == 0) { cursor = coll.find(); } else if (len == 1) { cursor = coll.find(toDBObject(args[0])); } else if (len == 2) { cursor = coll.find(toDBObject(args[0]), toDBObject(args[1])); } else if (len == 3) { cursor = coll.find(toDBObject(args[0]), toDBObject(args[1])).skip(caster.toIntValue(args[2])); } return toCFML(cursor); } // findOne else if (methodName.equals("findOne")) { int len = checkArgLength("findOne", args, 0, 3); DBObject obj = null; if (len == 0) { obj = coll.findOne(); } else if (len == 1) { DBObject arg1 = toDBObject(args[0], null); if (arg1 != null) obj = coll.findOne(arg1); else obj = coll.findOne(args[0]); } else if (len == 2) { DBObject arg1 = toDBObject(args[0], null); if (arg1 != null) obj = coll.findOne(arg1, toDBObject(args[1])); else obj = coll.findOne(args[0], toDBObject(args[1])); } else if (len == 3) { obj = coll.findOne(toDBObject(args[0]), toDBObject(args[1]), toDBObject(args[2])); } return toCFML(obj); } // findAndRemove if (methodName.equals("findAndRemove")) { checkArgLength("findAndRemove", args, 1, 1); DBObject obj = coll.findAndRemove(toDBObject(args[0])); return toCFML(obj); } // findAndModify if (methodName.equals("findAndModify")) { int len = args == null ? 0 : args.length; if (len != 2 && len != 3 && len != 7) { throw exp.createApplicationException( "the function findAndModify needs 2, 3 or 7 arguments, but you have defined only " + len); } DBObject obj = null; if (len == 2) { obj = coll.findAndModify(toDBObject(args[0]), toDBObject(args[1])); } else if (len == 3) { obj = coll.findAndModify(toDBObject(args[0]), toDBObject(args[1]), toDBObject(args[2])); } else if (len == 7) { obj = coll.findAndModify(toDBObject(args[0]), toDBObject(args[1]), toDBObject(args[2]), caster.toBooleanValue(args[3]), toDBObject(args[4]), caster.toBooleanValue(args[5]), caster.toBooleanValue(args[6])); } return toCFML(obj); } //group /* TODO: needs GroupCommand if(methodName.equals("group")) { int len=checkArgLength("group",args,1,1); if(len==1){ return toCFML(coll.group( toDBObject(args[0]) )); } }*/ // insert if (methodName.equals("insert")) { checkArgLength("insert", args, 1, 1); return toCFML(coll.insert(toDBObjectArray(args[0]))); } // insertMany(required array documents, struct options) valid options keys are string "writeconcern", boolean "ordered" if (methodName.equals("insertMany")) { int len = checkArgLength("insertMany", args, 1, 2); BulkWriteOperation bulk = coll.initializeOrderedBulkOperation(); WriteConcern wc = coll.getWriteConcern(); if (len == 2) { DBObject dboOpts = toDBObject(args[1]); if (dboOpts.containsField("ordered")) { if (!decision.isBoolean(dboOpts.get("ordered"))) throw exp.createApplicationException("ordered in options must be boolean value"); if (!caster.toBooleanValue(dboOpts.get("ordered"))) { bulk = coll.initializeUnorderedBulkOperation(); } } if (dboOpts.containsField("writeconcern")) { WriteConcern newWc = WriteConcern.valueOf(caster.toString(dboOpts.get("writeconcern"))); if (newWc != null) { wc = newWc; } } } Map<String, Object> result = new LinkedHashMap<String, Object>(); BulkWriteResult bulkResult; List<Map> writeErrors = new ArrayList<Map>(); Array arr = caster.toArray(args[0]); if (arr.size() == 0) { result.put("nInserted", 0); result.put("writeErrors", writeErrors); result.put("acknowledged", true); return toCFML(result); } Iterator<Object> it = arr.valueIterator(); while (it.hasNext()) { bulk.insert(toDBObject(it.next())); } try { bulkResult = bulk.execute(wc); } catch (BulkWriteException e) { Map<String, Object> bulkErrorItem; BulkWriteError bulkError; bulkResult = e.getWriteResult(); List<BulkWriteError> errors = e.getWriteErrors(); Iterator<BulkWriteError> jj = errors.iterator(); while (jj.hasNext()) { bulkErrorItem = new LinkedHashMap<String, Object>(); bulkError = jj.next(); bulkErrorItem.put("index", (bulkError.getIndex() + 1)); // +1 so we get index of item in CFML array bulkErrorItem.put("code", bulkError.getCode()); bulkErrorItem.put("errmsg", bulkError.getMessage()); bulkErrorItem.put("op", bulkError.getDetails()); writeErrors.add(bulkErrorItem); } } result.put("acknowledged", bulkResult.isAcknowledged()); if (bulkResult.isAcknowledged()) { result.put("nInserted", bulkResult.getInsertedCount()); result.put("writeErrors", writeErrors); } return toCFML(result); } // bulkWrite(required array operations, struct options) valid options keys are string "writeconcern", boolean "ordered", boolean "bypassDocumentValidation" // an operation is a struct with the following keys: { "operation":[insert|update|updateOne|remove|removeOne], "document":[(required if operation is insert) - a doc to insert], "query":[(optional) - the query to find for remove/update operations], "update":[(required for update/updateOne) - the update document] } // i.e. dbCollection.bulkWrite([ // {"operation":"insert", "document":{"test":"insert"}} // ,{"operation":"updateOne", "query":{"_id":"foo"}, "update":{"$set":{"updated":true}}} // ,{"operation":"removeOne", "query":{"_id":"goaway"}} // ],{"ordered":false}) if (methodName.equals("bulkWrite")) { int len = checkArgLength("bulkWrite", args, 1, 2); BulkWriteOperation bulk = coll.initializeOrderedBulkOperation(); WriteConcern wc = coll.getWriteConcern(); if (len == 2) { DBObject dboOpts = toDBObject(args[1]); if (dboOpts.containsField("ordered")) { if (!decision.isBoolean(dboOpts.get("ordered"))) throw exp.createApplicationException("ordered in options must be boolean value"); if (!caster.toBooleanValue(dboOpts.get("ordered"))) { bulk = coll.initializeUnorderedBulkOperation(); } } if (dboOpts.containsField("bypassDocumentValidation")) { if (!decision.isBoolean(dboOpts.get("bypassDocumentValidation"))) throw exp.createApplicationException( "bypassDocumentValidation in options must be boolean value"); bulk.setBypassDocumentValidation( caster.toBooleanValue(dboOpts.get("bypassDocumentValidation"))); } if (dboOpts.containsField("writeconcern")) { WriteConcern newWc = WriteConcern.valueOf(caster.toString(dboOpts.get("writeconcern"))); if (newWc != null) { wc = newWc; } } } Map<String, Object> result = new LinkedHashMap<String, Object>(); BulkWriteResult bulkResult; List<Map> writeErrors = new ArrayList<Map>(); Array arr = caster.toArray(args[0]); if (arr.size() == 0) { result.put("nInserted", 0); result.put("nMatched", 0); result.put("nModified", 0); result.put("nRemoved", 0); result.put("writeErrors", writeErrors); result.put("acknowledged", true); return toCFML(result); } Iterator<Object> it = arr.valueIterator(); while (it.hasNext()) { DBObject operation = toDBObject(it.next()); if (operation.get("operation") == "update") { // do stuff to add update operation bulk.find(toDBObject(operation.get("query"))).update(toDBObject(operation.get("update"))); } else if (operation.get("operation") == "updateOne") { // do stuff to add updateOne operation bulk.find(toDBObject(operation.get("query"))).updateOne(toDBObject(operation.get("update"))); } else if (operation.get("operation") == "remove") { // do stuff to add remove operation bulk.find(toDBObject(operation.get("query"))).remove(); } else if (operation.get("operation") == "removeOne") { // do stuff to add removeOne operation bulk.find(toDBObject(operation.get("query"))).removeOne(); } else if (operation.get("operation") == "insert") { bulk.insert(toDBObject(operation.get("document"))); } } try { bulkResult = bulk.execute(wc); } catch (BulkWriteException e) { Map<String, Object> bulkErrorItem; BulkWriteError bulkError; bulkResult = e.getWriteResult(); List<BulkWriteError> errors = e.getWriteErrors(); Iterator<BulkWriteError> jj = errors.iterator(); while (jj.hasNext()) { bulkErrorItem = new LinkedHashMap<String, Object>(); bulkError = jj.next(); bulkErrorItem.put("index", (bulkError.getIndex() + 1)); // +1 so we get index of item in CFML array bulkErrorItem.put("code", bulkError.getCode()); bulkErrorItem.put("errmsg", bulkError.getMessage()); bulkErrorItem.put("op", bulkError.getDetails()); writeErrors.add(bulkErrorItem); } } result.put("acknowledged", bulkResult.isAcknowledged()); if (bulkResult.isAcknowledged()) { result.put("nInserted", bulkResult.getInsertedCount()); result.put("nMatched", bulkResult.getMatchedCount()); result.put("nModified", bulkResult.getModifiedCount()); result.put("nRemoved", bulkResult.getRemovedCount()); result.put("writeErrors", writeErrors); } return toCFML(result); } //mapReduce if (methodName.equals("mapReduce")) { int len = checkArgLength("mapReduce", args, 4, 4); if (len == 4) { return toCFML(coll.mapReduce(caster.toString(args[0]), caster.toString(args[1]), caster.toString(args[2]), toDBObject(args[3]))); } } // remove if (methodName.equals("remove")) { checkArgLength("remove", args, 1, 1); return toCFML(coll.remove(toDBObject(args[0]))); } // rename if (methodName.equals("rename") || methodName.equals("renameCollection")) { int len = checkArgLength(methodName.getString(), args, 1, 2); if (len == 1) { return toCFML(coll.rename(caster.toString(args[0]))); } else if (len == 2) { return toCFML(coll.rename(caster.toString(args[0]), caster.toBooleanValue(args[1]))); } } // save if (methodName.equals("save")) { checkArgLength("save", args, 1, 1); return toCFML(coll.save(toDBObject(args[0]))); } // setWriteConcern if (methodName.equals("setWriteConcern")) { checkArgLength("setWriteConcern", args, 1, 1); WriteConcern wc = WriteConcern.valueOf(caster.toString(args[0])); if (wc != null) { coll.setWriteConcern(wc); } return null; } // storageSize if (methodName.equals("storageSize")) { checkArgLength("storageSize", args, 0, 0); return toCFML(coll.getStats().get("storageSize")); } // totalIndexSize if (methodName.equals("totalIndexSize")) { checkArgLength("totalIndexSize", args, 0, 0); return toCFML(coll.getStats().get("totalIndexSize")); } // update if (methodName.equals("update")) { int len = checkArgLength("update", args, 2, 4); if (len == 2) { return toCFML(coll.update(toDBObject(args[0]), toDBObject(args[1]))); } else if (len == 3) { return toCFML(coll.update(toDBObject(args[0]), toDBObject(args[1]), caster.toBooleanValue(args[2]), false)); } else if (len == 4) { return toCFML(coll.update(toDBObject(args[0]), toDBObject(args[1]), caster.toBooleanValue(args[2]), caster.toBooleanValue(args[3]))); } } String functionNames = "aggregate,count,dataSize,distinct,drop,dropIndex,dropIndexes,createIndex,stats,getIndexes,getWriteConcern,find,findOne,findAndRemove,findAndModify," + "group,insert,insertMany,bulkWrite,mapReduce,remove,rename,save,setWriteConcern,storageSize,totalIndexSize,update"; throw exp.createApplicationException( "function " + methodName + " does not exist existing functions are [" + functionNames + "]"); }
From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java
License:Apache License
@Override public QueryResult updateStats(List<VariantStatsWrapper> variantStatsWrappers, StudyConfiguration studyConfiguration, QueryOptions options) { DBCollection coll = db.getDb().getCollection(collectionName); BulkWriteOperation builder = coll.initializeUnorderedBulkOperation(); long start = System.nanoTime(); DBObjectToVariantStatsConverter statsConverter = new DBObjectToVariantStatsConverter( studyConfigurationManager);/* w w w . j a v a 2 s . c o m*/ // VariantSource variantSource = queryOptions.get(VariantStorageManager.VARIANT_SOURCE, VariantSource.class); DBObjectToVariantConverter variantConverter = getDbObjectToVariantConverter(new Query(), options); //TODO: Use the StudyConfiguration to change names to ids // TODO make unset of 'st' if already present? for (VariantStatsWrapper wrapper : variantStatsWrappers) { Map<String, VariantStats> cohortStats = wrapper.getCohortStats(); Iterator<VariantStats> iterator = cohortStats.values().iterator(); VariantStats variantStats = iterator.hasNext() ? iterator.next() : null; List<DBObject> cohorts = statsConverter.convertCohortsToStorageType(cohortStats, studyConfiguration.getStudyId()); // TODO remove when we remove fileId // List cohorts = statsConverter.convertCohortsToStorageType(cohortStats, variantSource.getStudyId()); // TODO use when we remove fileId // add cohorts, overwriting old values if that cid, fid and sid already exists: remove and then add // db.variants.update( // {_id:<id>}, // {$pull:{st:{cid:{$in:["Cohort 1","cohort 2"]}, fid:{$in:["file 1", "file 2"]}, sid:{$in:["study 1", "study 2"]}}}} // ) // db.variants.update( // {_id:<id>}, // {$push:{st:{$each: [{cid:"Cohort 1", fid:"file 1", ... , defaultValue:3},{cid:"Cohort 2", ... , defaultValue:3}] }}} // ) if (!cohorts.isEmpty()) { String id = variantConverter.buildStorageId(wrapper.getChromosome(), wrapper.getPosition(), variantStats.getRefAllele(), variantStats.getAltAllele()); List<Integer> cohortIds = new ArrayList<>(cohorts.size()); List<Integer> studyIds = new ArrayList<>(cohorts.size()); for (DBObject cohort : cohorts) { cohortIds.add((Integer) cohort.get(DBObjectToVariantStatsConverter.COHORT_ID)); studyIds.add((Integer) cohort.get(DBObjectToVariantStatsConverter.STUDY_ID)); } DBObject find = new BasicDBObject("_id", id); DBObject update = new BasicDBObject("$pull", new BasicDBObject(DBObjectToVariantConverter.STATS_FIELD, new BasicDBObject() .append(DBObjectToVariantStatsConverter.STUDY_ID, new BasicDBObject("$in", studyIds)) // .append( // DBObjectToVariantStatsConverter.FILE_ID, // new BasicDBObject("$in", fileIds)) .append(DBObjectToVariantStatsConverter.COHORT_ID, new BasicDBObject("$in", cohortIds)))); builder.find(find).updateOne(update); DBObject push = new BasicDBObject("$push", new BasicDBObject(DBObjectToVariantConverter.STATS_FIELD, new BasicDBObject("$each", cohorts))); builder.find(find).update(push); } } // TODO handle if the variant didn't had that studyId in the files array // TODO check the substitution is done right if the stats are already present BulkWriteResult writeResult = builder.execute(); int writes = writeResult.getModifiedCount(); return new QueryResult<>("", ((int) (System.nanoTime() - start)), writes, writes, "", "", Collections.singletonList(writeResult)); }
From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java
License:Apache License
@Override @Deprecated/*from ww w . ja va2 s .c o m*/ public QueryResult updateStats(List<VariantStatsWrapper> variantStatsWrappers, int studyId, QueryOptions queryOptions) { DBCollection coll = db.getDb().getCollection(collectionName); BulkWriteOperation builder = coll.initializeUnorderedBulkOperation(); long start = System.nanoTime(); DBObjectToVariantStatsConverter statsConverter = new DBObjectToVariantStatsConverter( studyConfigurationManager); // VariantSource variantSource = queryOptions.get(VariantStorageManager.VARIANT_SOURCE, VariantSource.class); int fileId = queryOptions.getInt(VariantStorageManager.Options.FILE_ID.key()); DBObjectToVariantConverter variantConverter = getDbObjectToVariantConverter(new Query(queryOptions), queryOptions); //TODO: Use the StudyConfiguration to change names to ids // TODO make unset of 'st' if already present? for (VariantStatsWrapper wrapper : variantStatsWrappers) { Map<String, VariantStats> cohortStats = wrapper.getCohortStats(); Iterator<VariantStats> iterator = cohortStats.values().iterator(); VariantStats variantStats = iterator.hasNext() ? iterator.next() : null; List<DBObject> cohorts = statsConverter.convertCohortsToStorageType(cohortStats, studyId); // TODO remove when we remove fileId // List cohorts = statsConverter.convertCohortsToStorageType(cohortStats, variantSource.getStudyId()); // TODO use when we remove fileId // add cohorts, overwriting old values if that cid, fid and sid already exists: remove and then add // db.variants.update( // {_id:<id>}, // {$pull:{st:{cid:{$in:["Cohort 1","cohort 2"]}, fid:{$in:["file 1", "file 2"]}, sid:{$in:["study 1", "study 2"]}}}} // ) // db.variants.update( // {_id:<id>}, // {$push:{st:{$each: [{cid:"Cohort 1", fid:"file 1", ... , defaultValue:3},{cid:"Cohort 2", ... , defaultValue:3}] }}} // ) if (!cohorts.isEmpty()) { String id = variantConverter.buildStorageId(wrapper.getChromosome(), wrapper.getPosition(), variantStats.getRefAllele(), variantStats.getAltAllele()); List<String> cohortIds = new ArrayList<>(cohorts.size()); List<Integer> fileIds = new ArrayList<>(cohorts.size()); List<Integer> studyIds = new ArrayList<>(cohorts.size()); for (DBObject cohort : cohorts) { cohortIds.add((String) cohort.get(DBObjectToVariantStatsConverter.COHORT_ID)); // fileIds.add((Integer) cohort.get(DBObjectToVariantStatsConverter.FILE_ID)); studyIds.add((Integer) cohort.get(DBObjectToVariantStatsConverter.STUDY_ID)); } DBObject find = new BasicDBObject("_id", id); DBObject update = new BasicDBObject("$pull", new BasicDBObject(DBObjectToVariantConverter.STATS_FIELD, new BasicDBObject() .append(DBObjectToVariantStatsConverter.STUDY_ID, new BasicDBObject("$in", studyIds)) // .append( // DBObjectToVariantStatsConverter.FILE_ID, // new BasicDBObject("$in", fileIds)) .append(DBObjectToVariantStatsConverter.COHORT_ID, new BasicDBObject("$in", cohortIds)))); builder.find(find).updateOne(update); DBObject push = new BasicDBObject("$push", new BasicDBObject(DBObjectToVariantConverter.STATS_FIELD, new BasicDBObject("$each", cohorts))); builder.find(find).update(push); } } // TODO handle if the variant didn't had that studyId in the files array // TODO check the substitution is done right if the stats are already present BulkWriteResult writeResult = builder.execute(); int writes = writeResult.getModifiedCount(); return new QueryResult<>("", ((int) (System.nanoTime() - start)), writes, writes, "", "", Collections.singletonList(writeResult)); }