Java tutorial
/************************************************************************* * * * This file is part of the 20n/act project. * * 20n/act enables DNA prediction for synthetic biology/bioengineering. * * Copyright (C) 2017 20n Labs, Inc. * * * * Please direct all queries to act@20n.com. * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see <http://www.gnu.org/licenses/>. * * * *************************************************************************/ package act.server; import act.installer.bing.NameSearchResults; import act.installer.bing.SearchResult; import com.mongodb.BasicDBList; import com.mongodb.BasicDBObject; import com.mongodb.DB; import com.mongodb.DBCollection; import com.mongodb.MongoClient; import com.mongodb.MongoException; import java.net.UnknownHostException; import java.util.Scanner; import java.util.Set; public class BingCacheMongoDB { private DBCollection dbBingCache; // the Bing Search collection is located in a separate database private String hostname; private int port; private String database; private DB mongoDB; private static final String BING_CACHE_COLLECTION_NAME = "cache"; private static final String WARNING_MESSAGE = "\nWARNING!!!\n" + "No \"cache\" collection seems to exist in the \"bingsearch\" Mongo database.\n" + "Bing Cache queries should be found in a MongoDB instance running on Chimay on port 27777.\n" + "Please check that Chimay (Or your provided database) can be accessed from the host you are running the Bing Searcher on.\n" + "Note that it is possible to restore the Bing Search cache dump living on the NAS with " + "the \"mongorestore\" command.\n" + "If you don't take any action before continuing, all queries will be counted against our " + "monthly transaction quota.\n" + "Please enter [y] to continue, or [n] if you want to abort:"; public BingCacheMongoDB(String hostname, int port, String database) { this.hostname = hostname; this.port = port; this.database = database; init(); } public void init() { try { MongoClient mongo = new MongoClient(hostname, port); mongoDB = mongo.getDB(database); } catch (UnknownHostException e) { throw new IllegalArgumentException("Invalid host for Mongo Bing Cache server."); } catch (MongoException e) { throw new IllegalArgumentException("Could not initialize Mongo driver."); } if (!mongoDB.getCollectionNames().contains(BING_CACHE_COLLECTION_NAME) || mongoDB.getCollection(BING_CACHE_COLLECTION_NAME).count() == 0) { System.out.println(WARNING_MESSAGE); if (!askConfirmationWhenCacheEmpty()) { System.out.println("Aborting the run."); System.exit(1); } } this.dbBingCache = mongoDB.getCollection(BING_CACHE_COLLECTION_NAME); } private boolean askConfirmationWhenCacheEmpty() { try (Scanner reader = new Scanner(System.in)) { String userDecision = reader.next(); if (userDecision.equals("n")) { return false; } else if (userDecision.equals("y")) { return true; } } System.out.println("Incorrect input! Please enter either [y] or [n]. Asking again..."); return askConfirmationWhenCacheEmpty(); } public BasicDBObject getNameSearchResultDBObjectFromName(String formattedName) { BasicDBObject whereQuery = new BasicDBObject(); BasicDBObject allFields = new BasicDBObject(); whereQuery.put("name", formattedName); return (BasicDBObject) dbBingCache.findOne(whereQuery, allFields); } public void cacheNameSearchResult(NameSearchResults nameSearchResults) { BasicDBObject nameSearchResultDBObject = new BasicDBObject(); nameSearchResultDBObject.put("name", nameSearchResults.getName()); Long totalCountSearchResults = nameSearchResults.getTotalCountSearchResults(); if (totalCountSearchResults >= 0) { nameSearchResultDBObject.put("totalCountSearchResults", totalCountSearchResults); } Set<SearchResult> topSearchResults = nameSearchResults.getTopSearchResults(); if (topSearchResults != null) { BasicDBList topSearchResultsList = new BasicDBList(); for (SearchResult topSearchResult : topSearchResults) { topSearchResultsList.add(topSearchResult.getBasicDBObject()); } nameSearchResultDBObject.put("topSearchResults", topSearchResultsList); } dbBingCache.save(nameSearchResultDBObject); } public void updateTotalCountSearchResults(String formattedName, NameSearchResults nameSearchResults) { BasicDBObject whereQuery = new BasicDBObject(); whereQuery.put("name", formattedName); // Update the existing document in the cache BasicDBObject newTotalCountSearchResults = new BasicDBObject(); newTotalCountSearchResults.append("$set", new BasicDBObject().append("totalCountSearchResults", nameSearchResults.getTotalCountSearchResults())); dbBingCache.update(whereQuery, newTotalCountSearchResults); } public void updateTopSearchResults(String formattedName, NameSearchResults nameSearchResults) { BasicDBObject whereQuery = new BasicDBObject(); whereQuery.put("name", formattedName); // Transform Set into BasicDBList for storage BasicDBList topSearchResultsList = new BasicDBList(); for (SearchResult topSearchResult : nameSearchResults.getTopSearchResults()) { topSearchResultsList.add(topSearchResult.getBasicDBObject()); } // Update the existing document in the cache BasicDBObject newTopSearchResults = new BasicDBObject(); newTopSearchResults.append("$set", new BasicDBObject().append("topSearchResults", topSearchResultsList)); dbBingCache.update(whereQuery, newTopSearchResults); } }