1 | package org.greenstone.atea;
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2 |
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3 | //import org.bson.BSONObject;
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4 |
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5 | import com.mongodb.client.AggregateIterable;
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6 | import com.mongodb.client.MongoCollection;
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7 | import com.mongodb.client.MongoDatabase;
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8 | //import com.mongodb.client.MongoIterable;
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9 |
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10 | // to use collection.find() filters like eq(), regex() etc
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11 | import static com.mongodb.client.model.Filters.*;
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12 | // to use collection.find().projection() filters like include() etc
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13 | import static com.mongodb.client.model.Projections.*;
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14 | // to use aggregation functions like unwind(), match(), sort() etc
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15 | import static com.mongodb.client.model.Aggregates.*;
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16 | // to use functions like sum() and addToSet() within aggregation functions
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17 | import static com.mongodb.client.model.Accumulators.*;
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18 |
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19 | //import org.bson.conversions.Bson;
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20 | import com.mongodb.BasicDBObject;
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21 | import com.mongodb.MongoClient;
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22 | import com.mongodb.MongoCredential;
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23 | import com.mongodb.ServerAddress;
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24 | import com.mongodb.MongoClientOptions;
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25 |
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26 | import com.mongodb.Block;
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27 |
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28 | import org.bson.Document;
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29 | import org.bson.conversions.Bson;
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30 |
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31 | import com.mongodb.util.JSON;
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32 | //import com.mongodb.DBObject;
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33 |
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34 | import java.io.BufferedReader;
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35 | import java.io.File;
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36 | import java.io.FileReader;
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37 | import java.util.Arrays;
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38 | import java.util.ArrayList;
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39 | import java.util.List;
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40 | import java.util.Properties;
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41 | import java.util.regex.Pattern;
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42 |
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43 | import org.apache.log4j.Logger;
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44 |
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45 | import org.greenstone.atea.morphia.*;
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46 | import dev.morphia.*;
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47 |
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48 | /**
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49 | * https://www.tutorialspoint.com/mongodb/mongodb_java.htm
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50 | *
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51 | * TO COMPILE:
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52 | * maori-lang-detection/src$
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53 | * javac -cp ".:../conf:../lib/*" org/greenstone/atea/MongoDBAccess.java
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54 | *
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55 | * TO RUN:
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56 | * java -cp ".:../conf:../lib/*" org.greenstone.atea.MongoDBAccess
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57 | *
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58 | * Manually connecting to mongodb from client:
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59 | * mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u USERNAME -p
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60 | * Then after connecting with pwd, type:
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61 | * use DBNAME
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62 | *
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63 | * Or connect to mongodb and specify db in one statement:
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64 | * mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017/DBNAME?authSource=admin' -u USERNAME -p
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65 | *
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66 | * Some links:
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67 | * - https://stackoverflow.com/questions/19938153/do-i-need-to-explicitly-close-connection
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68 | * - https://docs.mongodb.com/manual/reference/glossary/ (particularly "collection")
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69 | * - https://tecadmin.net/tutorial/mongodb/drop-collection/
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70 | * IMPORTANT LINK:
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71 | * - https://www.mongodb.com/blog/post/6-rules-of-thumb-for-mongodb-schema-design-part-1
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72 | *
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73 | */
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74 | public class MongoDBAccess implements AutoCloseable {
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75 |
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76 | private static Logger logger = Logger.getLogger(org.greenstone.atea.MongoDBAccess.class.getName());
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77 |
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78 | static final String PROPS_FILENAME = "config.properties";
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79 | public static final String WEBPAGES_COLLECTION = "Webpages";
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80 | public static final String WEBSITES_COLLECTION = "Websites";
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81 |
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82 | /** mongodb filter types to execute */
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83 | public static final int IS_MRI = 0;
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84 | public static final int CONTAINS_MRI = 1;
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85 |
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86 | // configuration details, some with fallback values
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87 | private String HOST = "localhost";
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88 | private int PORT = 27017; // mongodb port
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89 | private String USERNAME;
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90 | private String PASSWORD;
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91 | private String DB_NAME ="ateacrawldata";
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92 |
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93 | private MongoClient mongo = null;
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94 | private MongoDatabase database = null;
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95 |
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96 | /**
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97 | * Mongodb Client handle via morphia, which handles the ODM (object document mapper)
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98 | * for MongoDB
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99 | */
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100 | public Datastore datastore = null;
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101 |
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102 | public MongoDBAccess() throws Exception {
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103 | boolean success = false;
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104 |
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105 | // Read in the username and password from our props file
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106 | Properties props = new Properties();
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107 |
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108 | //File propsFile = new File(PROPS_FILENAME);
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109 | //logger.debug("*** Conf props filename: " + propsFile.getAbsolutePath());
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110 | try {
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111 | props.load(getClass().getClassLoader().getResourceAsStream(PROPS_FILENAME));
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112 | } catch(Exception e) {
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113 | logger.error(e);
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114 | }
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115 |
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116 |
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117 | USERNAME = props.getProperty("mongodb.user", "");
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118 | if(USERNAME.equals("")) {
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119 | USERNAME = "root";
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120 | logger.warn("WARNING: No sensible value for mongodb.user specified in " + PROPS_FILENAME + ". Attempting to use: " + USERNAME);
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121 | }
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122 | PASSWORD = props.getProperty("mongodb.pwd");
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123 |
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124 | logger.debug("Got pwd: " + PASSWORD);
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125 |
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126 | if(PASSWORD != null && PASSWORD.equals("CHANGEME")) {
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127 |
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128 | success = false;
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129 | throw new Exception("************ FATAL ERROR: Change DB password in properties file " + PROPS_FILENAME);
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130 | }
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131 |
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132 | HOST = props.getProperty("mongodb.host", HOST);
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133 | String port = props.getProperty("mongodb.port", Integer.toString(PORT));
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134 | PORT = Integer.parseInt(port);
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135 | DB_NAME = props.getProperty("mongodb.dbname", DB_NAME);
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136 |
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137 | logger.info("Connecting to mongodb with:");
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138 | logger.info(" - host: " + HOST);
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139 | logger.info(" - port: " + PORT);
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140 | logger.info(" - user: " + USERNAME);
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141 | logger.info(" - db name: " + DB_NAME);
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142 | }
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143 |
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144 | /**
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145 | * Since we have only a single MongoClient, don't need to call close/disconnect on it as per
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146 | * https://stackoverflow.com/questions/19938153/do-i-need-to-explicitly-close-connection
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147 | */
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148 | public void connectToDB() throws Exception {
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149 |
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150 | // Creating a Mongo client
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151 | mongo = new MongoClient( HOST, PORT );
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152 |
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153 | // Creating Credentials
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154 | MongoCredential credential;
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155 | credential = MongoCredential.createCredential(USERNAME, DB_NAME, PASSWORD.toCharArray());
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156 | System.out.println("Connected to the database successfully");
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157 |
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158 | // Accessing the database
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159 | this.database = mongo.getDatabase(DB_NAME);
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160 | logger.info("Credentials: "+ credential);
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161 |
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162 | /*
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163 | MongoCredential credential;
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164 | credential = MongoCredential.createCredential(USERNAME, DB_NAME, PASSWORD.toCharArray());
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165 | logger.info("Credentials: "+ credential);
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166 |
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167 | // Create our Mongo client
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168 | mongo = new MongoClient( new ServerAddress(HOST, PORT), credential, new MongoClientOptions.Builder().build());
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169 | System.out.println("Connected to the database successfully");
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170 |
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171 | this.database = mongo.getDatabase(DB_NAME);
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172 | */
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173 |
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174 | Morphia morphia = new Morphia();
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175 | morphia.mapPackage("com.greenstone.atea.morphia");
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176 | datastore = morphia.createDatastore(mongo, DB_NAME);
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177 | datastore.ensureIndexes();
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178 |
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179 | }
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180 |
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181 | // TODO: which fields should be indexed?
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182 |
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183 | public void showCollections() {
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184 | //MongoIterable<String> colls = this.database.listCollectionNames();
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185 | for(String coll : this.database.listCollectionNames()) {
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186 | System.err.println("coll: " + coll);
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187 | }
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188 | }
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189 |
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190 | /*
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191 | public void insertWebsiteInfo(WebsiteInfo website)
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192 | {
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193 | MongoCollection<Document> collection = this.database.getCollection(WEBSITES_COLLECTION);
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194 | Document document = new Document("_id", website.id)
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195 | .append("siteFolderName", website.siteFolderName)
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196 | .append("domain", website.domain)
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197 | .append("totalPages", website.totalPages)
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198 | .append("numPagesWithBodyText", website.countOfWebPagesWithBodyText)
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199 | .append("numPagesInMRI", website.numPagesInMRI)
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200 | .append("siteCrawledTimestamp", website.siteCrawledTimestamp)
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201 | .append("siteCrawlUnfinished", website.siteCrawlUnfinished)
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202 | .append("redoCrawl", website.redoCrawl);
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203 |
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204 | document.put("urlContainsLangCodeInpath", website.urlContainsLangCodeInpath);
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205 | if(website.geoLocationCountryCode != null && !website.geoLocationCountryCode.equals("")) {
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206 | document.put("countryCode", website.geoLocationCountryCode);
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207 | }
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208 |
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209 | collection.insertOne(document);
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210 | logger.debug("Website info for " + website.id + "(" + website.siteFolderName + ")"
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211 | + " inserted successfully into " + WEBSITES_COLLECTION);
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212 | }
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213 | */
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214 |
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215 | /**
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216 | * Inserts a web page into the mongodb. Besides page related metadata and full body text
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217 | * the language information per sentence and per 2 adjacent sentences also get stored
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218 | * into the mongodb.
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219 | */
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220 | /*
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221 | public void insertWebpageInfo(WebpageInfo webpage)
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222 | {
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223 | int mri_sentence_count = 0;
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224 |
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225 | // load the webpages db 'table'
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226 | // in mongodb, the equivalent of db tables are called 'collections'
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227 | MongoCollection<Document> collection = this.database.getCollection(WEBPAGES_COLLECTION);
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228 |
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229 | Document document = new Document("_id", webpage.webpageID)
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230 | .append("siteid", webpage.websiteID)
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231 | .append("url", webpage.URL)
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232 | .append("isMRI", webpage.isMRI)
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233 | .append("totalSentences", webpage.totalSentences)
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234 | .append("charEncoding", webpage.charEncoding)
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235 | .append("modTime", webpage.modifiedTime)
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236 | .append("fetchTime", webpage.fetchTime);
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237 |
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238 | // INSTEAD, ARRAY OF OBJECTS TO BE INSERTED AS PER:
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239 | // https://stackoverflow.com/questions/15371839/how-to-add-an-array-to-a-mongodb-document-using-java
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240 | List<BasicDBObject> sentencesList = new ArrayList<>();
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241 | for(SentenceInfo sentenceInfo : webpage.singleSentences) {
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242 |
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243 | BasicDBObject bsonRecord = new BasicDBObject("langCode", sentenceInfo.langCode);
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244 |
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245 | bsonRecord.put("confidence", sentenceInfo.confidenceLevel);
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246 | bsonRecord.put("sentence", sentenceInfo.sentence);
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247 |
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248 | sentencesList.add(bsonRecord);
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249 |
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250 | if(sentenceInfo.langCode.equals(MaoriTextDetector.MAORI_3LETTER_CODE)) {
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251 | mri_sentence_count++;
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252 | }
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253 |
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254 | }
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255 | document.put("singleSentences", sentencesList);
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256 |
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257 | List<BasicDBObject> overlappingSentencesList = new ArrayList<>();
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258 | for(SentenceInfo sentenceInfo : webpage.overlappingSentences) {
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259 |
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260 | BasicDBObject bsonRecord = new BasicDBObject("langCode", sentenceInfo.langCode);
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261 | bsonRecord.put("confidence", sentenceInfo.confidenceLevel);
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262 | bsonRecord.put("sentence", sentenceInfo.sentence);
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263 |
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264 | overlappingSentencesList.add(bsonRecord);
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265 | }
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266 | document.put("overlappingSentences", overlappingSentencesList);
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267 |
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268 | // also put the full text in there
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269 | document.put("text", webpage.text);
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270 |
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271 | // also store the count of sentences in MRI
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272 | webpage.setMRISentenceCount(mri_sentence_count);
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273 | document.put("mriSentenceCount", mri_sentence_count);
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274 |
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275 |
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276 | collection.insertOne(document);
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277 | logger.debug("\nwebpage info for " + webpage.webpageID + " inserted successfully into " + WEBPAGES_COLLECTION);
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278 | }
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279 | */
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280 |
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281 | public ArrayList<String> queryAllMatchingIsMRIURLs(String domain) {
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282 | return queryAllMatchingURLsFilteredBy(domain, IS_MRI);
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283 | }
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284 | public ArrayList<String> queryAllMatchingcontainsMRIURLs(String domain) {
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285 | return queryAllMatchingURLsFilteredBy(domain, CONTAINS_MRI);
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286 | }
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287 |
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288 | /**
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289 | * Java mongodb find: https://mongodb.github.io/mongo-java-driver/3.4/driver/getting-started/quick-start/
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290 | * Java mongodb find filters: https://mongodb.github.io/mongo-java-driver/3.4/javadoc/?com/mongodb/client/model/Filters.html
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291 | * Java mongodb projection: https://stackoverflow.com/questions/44894497/retrieving-data-with-mongodb-java-driver-3-4-using-find-method-with-projection
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292 | * mongodb projection: https://docs.mongodb.com/v3.2/reference/method/db.collection.find/#db.collection.find
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293 | *
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294 | * Parse MongoDB query into Java: https://stackoverflow.com/questions/17326747/parsing-strings-to-mongodb-query-documents-with-operators-in-java
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295 | * Maybe also https://stackoverflow.com/questions/48000891/parse-mongodb-json-query-in-java-with-multiple-criteria
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296 | * https://stackoverflow.com/questions/55029222/parse-mongodb-query-to-java
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297 | * http://pingax.com/trick-convert-mongo-shell-query-equivalent-java-objects/
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298 | */
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299 | public ArrayList<String> queryAllMatchingURLsFilteredBy(String domain, int filterType) {
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300 |
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301 | final ArrayList<String> urlsList = new ArrayList<String>();
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302 |
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303 | // remove any http(s)://(www.) from the start of URL first
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304 | // since it goes into a regex
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305 | domain = Utility.stripProtocolAndWWWFromURL(domain);
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306 |
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307 | // load the "webpages" db table
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308 | // in mongodb, the equivalent of db tables are called 'collections'
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309 | MongoCollection<Document> collection = this.database.getCollection(WEBPAGES_COLLECTION);
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310 |
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311 | // code we'll execute in Iterable.forEach() below
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312 | Block<Document> storeURL = new Block<Document>() {
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313 | @Override
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314 | public void apply(final Document document) {
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315 | //System.out.println(document.toJson());
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316 | String url = document.getString("URL");
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317 | // add to our urlsList
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318 | //System.out.println(url);
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319 | urlsList.add(url);
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320 | }
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321 | };
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322 |
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323 |
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324 | // Run the following mongodb query:
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325 | // db.getCollection('Webpages').find({URL: /domain/, isMRI: true}, {URL: 1, _id: 0})
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326 |
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327 | // 1. One way that works:
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328 | //collection.find(and(eq("isMRI", true), regex("URL", pattern))).projection(fields(include("URL"), excludeId())).forEach(storeURL);
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329 |
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330 | // 2. Another way:
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331 | //String query = "{URL: /DOMAIN/, isMRI: true}";
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332 | String query = "{URL: /DOMAIN/, ";
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333 | if(filterType == IS_MRI) {
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334 | query += "isMRI: true}";
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335 | } else if(filterType == CONTAINS_MRI) {
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336 | query += "containsMRI: true}";
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337 | }
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338 |
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339 | domain = domain.replace(".", "\\."); // escape dots in domain for regex
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340 | query = query.replace("DOMAIN", domain);
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341 |
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342 | //System.err.println("Executing find query: " + query);
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343 |
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344 | BasicDBObject findObj = BasicDBObject.parse(query);
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345 | BasicDBObject projectionObj = BasicDBObject.parse("{URL: 1, _id: 0}");
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346 |
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347 |
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348 | collection.find(findObj).projection(projectionObj).forEach(storeURL);
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349 |
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350 | return urlsList;
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351 | }
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352 |
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353 | /**
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354 | RUNNING A MONGODB COLLECTION.AGGREGATE() in JAVA:
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355 |
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356 | https://stackoverflow.com/questions/31643109/mongodb-aggregation-with-java-driver
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357 | https://stackoverflow.com/questions/48000891/parse-mongodb-json-query-in-java-with-multiple-criteria
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358 | Not Java: https://stackoverflow.com/questions/39060221/a-pipeline-stage-specification-object-must-contain-exactly-one-field-with-php-mo
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359 |
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360 | (https://stackoverflow.com/questions/55029222/parse-mongodb-query-to-java)
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361 | https://www.programcreek.com/java-api-examples/?api=com.mongodb.client.model.Aggregates
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362 | On using group(TExpression) inside collection.aggregate().
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363 |
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364 |
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365 | The aggregate() we want to run:
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366 |
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367 | db.Websites.aggregate([
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368 | {
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369 | $match: {
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370 | $and: [
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371 | {geoLocationCountryCode: {$ne: "NZ"}},
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372 | {domain: {$not: /\.nz/}},
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373 | {numPagesContainingMRI: {$gt: 0}},
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374 | {$or: [{geoLocationCountryCode: "AU"}, {urlContainsLangCodeInPath: false}]}
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375 | ]
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376 | }
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377 | },
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378 | { $unwind: "$geoLocationCountryCode" },
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379 | {
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380 | $group: {
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381 | _id: {$toLower: '$geoLocationCountryCode'},
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382 | count: { $sum: 1 },
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383 | domain: { $addToSet: '$domain' }
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384 | }
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385 | },
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386 | { $sort : { count : -1} }
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387 | ]);
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388 |
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389 | */
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390 | public String aggregateContainsMRIForOverseas() {
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391 | // working with the WebSites collection, not WebPages collection!
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392 | MongoCollection<Document> collection = this.database.getCollection(WEBSITES_COLLECTION);
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393 |
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394 | /*String matchQuery =
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395 | "$and: ["
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396 | + "{geoLocationCountryCode: {$ne: \"NZ\"}},"
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397 | + "{domain: {$not: /\\.nz/}},"
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398 | + "{numPagesContainingMRI: {$gt: 0}},"
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399 | + "{$or: [{geoLocationCountryCode: \"AU\"}, {urlContainsLangCodeInPath: false}]}"
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400 | + "]";*/
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401 |
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402 |
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403 |
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404 |
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405 | Bson orQuery = or(
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406 | BasicDBObject.parse("{geoLocationCountryCode: \"AU\"}"),
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407 | BasicDBObject.parse("{urlContainsLangCodeInPath: false}")
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408 | );
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409 | Bson andQuery = and(
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410 | BasicDBObject.parse("{geoLocationCountryCode: {$ne: \"NZ\"}}"),
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411 | BasicDBObject.parse("{domain: {$not: /\\.nz/}}"),
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412 | BasicDBObject.parse("{numPagesContainingMRI: {$gt: 0}}"),
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413 | orQuery);
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414 |
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415 | AggregateIterable<Document> output
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416 | = collection.aggregate(Arrays.asList(
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417 | match(andQuery), //match(BasicDBObject.parse(matchQuery))
|
---|
418 | // match((List<DBObject>)JSON.parse(matchQuery)),
|
---|
419 | unwind("$geoLocationCountryCode"),
|
---|
420 | group("$geoLocationCountryCode", Arrays.asList(sum("count", 1), addToSet("domain", "$domain"))),
|
---|
421 | sort(BasicDBObject.parse("{count : -1}"))
|
---|
422 | ));
|
---|
423 |
|
---|
424 | for (Document doc : output) {
|
---|
425 | //System.out.println(doc);
|
---|
426 | System.out.println(doc.toJson());
|
---|
427 | }
|
---|
428 |
|
---|
429 | return "";
|
---|
430 | }
|
---|
431 |
|
---|
432 |
|
---|
433 | /**
|
---|
434 | The mongodb aggregate() we want to run this time:
|
---|
435 |
|
---|
436 | db.Websites.aggregate([
|
---|
437 | {
|
---|
438 | $match: {
|
---|
439 | $and: [
|
---|
440 | {numPagesContainingMRI: {$gt: 0}},
|
---|
441 | {$or: [{geoLocationCountryCode:"NZ"},{domain: /\.nz/}]}
|
---|
442 | ]
|
---|
443 | }
|
---|
444 | },
|
---|
445 | { $unwind: "$geoLocationCountryCode" },
|
---|
446 | {
|
---|
447 | $group: {
|
---|
448 | _id: "nz",
|
---|
449 | count: { $sum: 1 },
|
---|
450 | domain: { $addToSet: '$domain' }
|
---|
451 | }
|
---|
452 | },
|
---|
453 | { $sort : { count : -1} }
|
---|
454 | ]);
|
---|
455 | */
|
---|
456 | public String aggregateContainsMRIForNZ() {
|
---|
457 | // working with the WebSites collection, not WebPages collection!
|
---|
458 | MongoCollection<Document> collection = this.database.getCollection(WEBSITES_COLLECTION);
|
---|
459 |
|
---|
460 |
|
---|
461 | //String isMRI_filter =
|
---|
462 |
|
---|
463 | Bson orQuery = or(
|
---|
464 | BasicDBObject.parse("{geoLocationCountryCode: \"NZ\"}"),
|
---|
465 | BasicDBObject.parse("{domain: /\\.nz/}")
|
---|
466 | );
|
---|
467 | Bson andQuery = and(
|
---|
468 | BasicDBObject.parse("{numPagesContainingMRI: {$gt: 0}}"),
|
---|
469 | orQuery);
|
---|
470 |
|
---|
471 | AggregateIterable<Document> output
|
---|
472 | = collection.aggregate(Arrays.asList(
|
---|
473 | match(andQuery),
|
---|
474 | unwind("$geoLocationCountryCode"),
|
---|
475 | group("NZ", Arrays.asList(sum("count", 1), addToSet("domain", "$domain"))),
|
---|
476 | sort(BasicDBObject.parse("{count : -1}"))
|
---|
477 | ));
|
---|
478 |
|
---|
479 | // should only have one doc
|
---|
480 | for (Document doc : output) {
|
---|
481 | //System.out.println(doc);
|
---|
482 | System.out.println(doc.toJson());
|
---|
483 | }
|
---|
484 |
|
---|
485 | return "";
|
---|
486 | }
|
---|
487 |
|
---|
488 | public void writeToFile(boolean append, String filename, AggregateIterable<Document> output) {
|
---|
489 |
|
---|
490 | // should only have one doc
|
---|
491 | for (Document doc : output) {
|
---|
492 | //System.out.println(doc);
|
---|
493 | System.out.println(doc.toJson());
|
---|
494 | }
|
---|
495 | }
|
---|
496 |
|
---|
497 |
|
---|
498 | /** https://stackoverflow.com/questions/19938153/do-i-need-to-explicitly-close-connection */
|
---|
499 | public void close() {}
|
---|
500 |
|
---|
501 |
|
---|
502 | // TODO:
|
---|
503 | // In the database, need to ensure we have else
|
---|
504 | // create collection (table in RDBMS) websites, create collection webpages.
|
---|
505 | // The webpages collection will have sentences embedded based on my decisions from
|
---|
506 | // reading the series
|
---|
507 | // https://www.mongodb.com/blog/post/6-rules-of-thumb-for-mongodb-schema-design-part-1
|
---|
508 | // Then need functions:
|
---|
509 | // insertWebsiteDocument()
|
---|
510 | // insertWebpageDocument()
|
---|
511 |
|
---|
512 | public static void main(String args[]) {
|
---|
513 | try {
|
---|
514 | MongoDBAccess mongodbCon = new MongoDBAccess();
|
---|
515 | mongodbCon.connectToDB();
|
---|
516 | mongodbCon.showCollections();
|
---|
517 |
|
---|
518 | } catch(Exception e) {
|
---|
519 | e.printStackTrace();
|
---|
520 | }
|
---|
521 | }
|
---|
522 | }
|
---|