[33634] | 1 | package org.greenstone.atea;
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| 2 |
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| 3 | import java.io.*;
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| 4 | import java.lang.ArrayIndexOutOfBoundsException;
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| 5 | import java.time.LocalDateTime;
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| 6 | import java.util.ArrayList;
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| 7 | import java.util.Arrays;
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| 8 |
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| 9 | import org.apache.commons.csv.*;
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| 10 | import org.apache.log4j.Logger;
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| 11 |
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[33652] | 12 | //import org.bson.types.ObjectId;
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| 13 |
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| 14 | import org.greenstone.atea.morphia.*;
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[33634] | 15 |
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[33652] | 16 |
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[33634] | 17 | /**
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| 18 | * Class to process the dump text files produced FOR EACH SITE (e.g. site "00001") that
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| 19 | * Nutch has finished crawling and whose text has been dumped out to a file called dump.txt.
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| 20 | * This reads in the dump.txt file contained in each site folder within the input folder.
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| 21 | * (e.g. input folder "crawled" could contain folders 00001 to 01465. Each contains a dump.txt)
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| 22 | * Each dump.txt could contain the text contents for an entire site, or for individual pages.
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| 23 | * This class then uses class TextDumpPage to parse each webpage within a dump.txt,
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| 24 | * which parses out the actual text body content of each webpage's section within a dump.txt.
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| 25 | * Finally, MaoriTextDetector is run over that to determine whether the full body text is
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| 26 | * likely to be in Maori or not.
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| 27 | *
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| 28 | * Potential issues: since a web page's text is dumped out by nutch with neither paragraph
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| 29 | * nor even newline separator, it's hard to be sure that the entire page is in language.
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| 30 | * If it's in multiple languages, there's no way to be sure there aren't promising Maori language
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| 31 | * paragraphs contained in a page, if the majority/the remainder happen to be in English.
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| 32 | *
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| 33 | * So if we're looking for any paragraphs in Maori to store in a DB, perhaps it's better to run
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| 34 | * the MaoriTextDetector.isTextInMaori(BufferedReader reader) over two "lines" at a time,
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| 35 | * instead of running it over the entire html body's text.
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| 36 | *
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| 37 | * TO COMPILE OR RUN, FIRST DO:
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| 38 | * cd maori-lang-detection/apache-opennlp-1.9.1
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| 39 | * export OPENNLP_HOME=`pwd`
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| 40 | * cd maori-lang-detection/src
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| 41 | *
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| 42 | * TO COMPILE:
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| 43 | * maori-lang-detection/src$
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| 44 | * javac -cp ".:../conf:../lib/*:$OPENNLP_HOME/lib/opennlp-tools-1.9.1.jar" org/greenstone/atea/NutchTextDumpToMongoDB.java
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| 45 | *
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| 46 | * TO RUN:
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| 47 | * maori-lang-detection/src$
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| 48 | * java -cp ".:../conf:../lib/*:$OPENNLP_HOME/lib/opennlp-tools-1.9.1.jar" org/greenstone/atea/NutchTextDumpToMongoDB ../crawled-small
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| 49 | *
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| 50 | * or:
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| 51 | * java -cp ".:../conf:../lib/*:$OPENNLP_HOME/lib/opennlp-tools-1.9.1.jar" org/greenstone/atea/NutchTextDumpToMongoDB ../crawled-small > ../crawled-small/bla.txt 2>&1
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| 52 | *
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| 53 | */
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| 54 | public class NutchTextDumpToMongoDB {
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| 55 | static Logger logger = Logger.getLogger(org.greenstone.atea.NutchTextDumpToMongoDB.class.getName());
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| 56 |
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[33810] | 57 | static boolean DEBUG_MODE = true; // this is set to false in main() at the end of this class
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[33634] | 58 |
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| 59 | /** Counter for number of sites.
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| 60 | * Should be equal to number of times NutchTextDumpToMongoDB constructor
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| 61 | * is called: once per site.
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| 62 | */
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| 63 | static private int SITE_COUNTER = 0;
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| 64 | static private long WEBPAGE_COUNTER = 0;
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| 65 |
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| 66 | private final MaoriTextDetector maoriTxtDetector;
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| 67 | private final MongoDBAccess mongodbAccess;
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| 68 |
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| 69 | public final String siteID;
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| 70 | public final boolean siteCrawlUnfinished;
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| 71 | public final long siteCrawledTimestamp; /** When the crawl of the site terminated */
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| 72 |
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| 73 | private int countOfWebPagesWithBodyText = 0;
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| 74 |
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| 75 | private String geoLocationCountryCode = null; /** 2 letter country code */
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[33811] | 76 | private boolean urlContainsLangCodeInPath = false; /** If any URL on this site contains a /mi(/) or http(s)://mi.* in its URL path */
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[33906] | 77 |
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[33634] | 78 | private String domainOfSite;
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[33909] | 79 | //private String baseSiteDomain; // domainOfSite stripped of any http(s)://www.
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[33634] | 80 | private int numPagesInMRI = 0;
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[33801] | 81 | private int numPagesContainingMRI = 0;
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[33634] | 82 |
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| 83 | /** keep a list to store the text of each page */
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| 84 | private ArrayList<TextDumpPage> pages;
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[33698] | 85 |
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| 86 |
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[33634] | 87 |
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[33698] | 88 | /** Number of language and confidence results to return for storing in MongoDB
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| 89 | * MongoDB runs out of space if storing too many, as we store this info per sentence
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[33801] | 90 | * and a long text document becomes a very large MongoDB document presumably */
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[33698] | 91 | private static final int NUM_TOP_LANGUAGES = 3; // 103 max, in current version of opennlp lang model
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| 92 |
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| 93 |
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[33634] | 94 | private boolean isStartOfNewWebPageRecord(String prevLine, String line) {
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| 95 | // The start of a new web page's record in nutch's text dump of an entire site
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| 96 | // is denoted by a newline followed by a URL (protocol)
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| 97 | // or the very start of the file with a URL (protocol)
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| 98 | return ((prevLine == null || prevLine.equals(""))
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| 99 | && (line.startsWith("http://") || line.startsWith("https://")));
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| 100 | }
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| 101 |
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| 102 | public void debugPageDump(StringBuilder pageDump) {
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| 103 | if(DEBUG_MODE) {
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| 104 | // START DEBUG
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| 105 | logger.debug("__________________________________________");
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| 106 | logger.debug("@@@ Found page entry: ");
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| 107 | logger.debug("__________________________________________");
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| 108 | logger.debug(pageDump.toString());
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| 109 | logger.debug("------------------------------------------");
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| 110 | // END DEBUG
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| 111 | }
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| 112 | }
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| 113 |
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| 114 | /** A NutchTextDumpToMongoDB processes the dump.txt for one site */
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| 115 | public NutchTextDumpToMongoDB(MongoDBAccess mongodbAccess,
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| 116 | MaoriTextDetector maoriTxtDetector, String siteID,
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| 117 | File txtDumpFile, long lastModified, boolean siteCrawlUnfinished)
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| 118 | throws IOException
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| 119 | {
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| 120 | // increment static counter of sites processed by a NutchTextDumpToMongoDB instance
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| 121 | SITE_COUNTER++;
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| 122 |
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| 123 | // siteID is of the form %5d (e.g. 00020) and is just the name of a site folder
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| 124 | this.siteID = siteID;
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| 125 | this.siteCrawlUnfinished = siteCrawlUnfinished;
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| 126 | this.siteCrawledTimestamp = lastModified;
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| 127 |
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| 128 | this.maoriTxtDetector = maoriTxtDetector;
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| 129 | this.mongodbAccess = mongodbAccess;
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| 130 |
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| 131 | pages = new ArrayList<TextDumpPage>();
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| 132 |
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| 133 | String line = null;
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| 134 | StringBuilder pageDump = null;
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| 135 | try (
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| 136 | BufferedReader reader = new BufferedReader(new FileReader(txtDumpFile));
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| 137 | ) {
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| 138 |
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| 139 | boolean readingText = false;
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| 140 | String prevLine = null;
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| 141 |
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| 142 | while((line = reader.readLine()) != null) { // readLine removes newline separator
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| 143 | line = line.trim();
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| 144 | // iff outside of a page's body text, then an empty line marks the end of a page
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| 145 | // in nutch's text dump of a site.
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| 146 | // But note, there can be an empty line (or more?) between the start and end
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| 147 | // markers of a page's text, though.
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| 148 |
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| 149 | if(isStartOfNewWebPageRecord(prevLine, line)) {
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| 150 |
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| 151 | if(pageDump != null) { // should also be the case then: if(prevLine != null)
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| 152 | // finish old pageDump and begin new one
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| 153 |
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| 154 | //debugPageDump(pageDump);
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| 155 |
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| 156 | TextDumpPage page = new TextDumpPage(siteID, pageDump.toString());
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| 157 | // parses the fields and body text of a webpage in nutch's txt dump of entire site
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| 158 | //page.parseFields();
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| 159 | //page.getText();
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| 160 | pages.add(page);
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[33810] | 161 | inspectPageURLPath(page);
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[33634] | 162 | pageDump = null;
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| 163 |
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| 164 | }
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| 165 |
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| 166 | // begin new webpage dump
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| 167 | pageDump = new StringBuilder();
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| 168 | pageDump.append(line);
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| 169 | pageDump.append("\n");
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| 170 |
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| 171 | }
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| 172 | else if(!line.equals("")) {
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| 173 | pageDump.append(line);
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| 174 | pageDump.append("\n");
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| 175 |
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| 176 | }
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| 177 | // can throw away any newlines between text start and end markers.
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| 178 |
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[33810] | 179 | prevLine = line;
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[33634] | 180 | }
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| 181 |
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| 182 | // process final webpage record:
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| 183 | //debugPageDump(pageDump);
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| 184 |
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[33657] | 185 | if(pageDump == null) {
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| 186 | logger.warn("siteID " + siteID + " had an empty dump.txt file. Reinspect site.");
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| 187 | } else {
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| 188 | TextDumpPage page = new TextDumpPage(siteID, pageDump.toString());
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| 189 | pages.add(page);
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[33810] | 190 | inspectPageURLPath(page);
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[33657] | 191 | pageDump = null;
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[33810] | 192 | }
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[33657] | 193 |
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[33634] | 194 |
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| 195 | } catch (IOException ioe) {
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| 196 | logger.error("@@@@@@@@@ Error reading in nutch txtdump file " + txtDumpFile, ioe);
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| 197 | }
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| 198 |
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| 199 | // Just do this once: get and store domain of site.
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| 200 | // Passing true to get domain with protocol prefix
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| 201 | if(pages.size() > 0) {
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| 202 | TextDumpPage firstPage = pages.get(0);
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| 203 | String url = firstPage.getPageURL();
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| 204 | this.domainOfSite = Utility.getDomainForURL(url, true);
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[33909] | 205 | //this.baseSiteDomain = Utility.stripProtocolAndWWWFromURL(this.domainOfSite);
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[33634] | 206 | }
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| 207 | else {
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| 208 | this.domainOfSite = "UNKNOWN";
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[33909] | 209 | //this.baseSiteDomain = "UNKNOWN";
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[33634] | 210 | }
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| 211 |
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[33811] | 212 | /* No need to loop again through all pages. Instead, just inspectPageURLPath() as each page is created above.
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| 213 | // For any site, we just need to work out if any of its pages contains /mi(/) or http(s)://mi.* in its URL path
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[33810] | 214 | for(TextDumpPage aPage : pages) {
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[33811] | 215 | inspectPageURLPath(aPage);
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[33810] | 216 | }
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| 217 | */
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[33634] | 218 | prepareSiteStats(mongodbAccess);
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| 219 | }
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| 220 |
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[33810] | 221 | /** for every site, we just need to work out if any of its pages contains /mi(/) or http(s)://mi. in its URL.
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| 222 | * This method is called on each page of a site as the page is created. */
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| 223 | private void inspectPageURLPath(TextDumpPage page) {
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| 224 | String url = page.getPageURL();
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| 225 | //logger.debug("@@@@ pageURL: " + url);
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| 226 |
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[33811] | 227 | if(!this.urlContainsLangCodeInPath) { // if not already set to true for any previous page in this site,
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| 228 | // check if this page of the site contains /mi(/) or http(s)://mi in its URL path
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| 229 | if(url.contains("/mi/") || url.endsWith("/mi") || url.startsWith("https://mi.") || url.startsWith("http://mi.")) {
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| 230 | this.urlContainsLangCodeInPath = true;
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| 231 | }
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[33810] | 232 | }
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| 233 | }
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[33634] | 234 |
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[33810] | 235 |
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[33634] | 236 | private void prepareSiteStats(MongoDBAccess mongodbAccess) throws IOException {
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| 237 |
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| 238 | TextDumpPage page = null;
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| 239 | for(int i = 0; i < pages.size(); i++) {
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| 240 |
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| 241 | page = pages.get(i);
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| 242 |
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| 243 | String text = page.getPageText();
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| 244 |
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| 245 | if(text.equals("")) {
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| 246 | // don't care about empty pages
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| 247 | continue;
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| 248 | }
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| 249 | else {
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| 250 | WEBPAGE_COUNTER++; // count of cumulative total of webpages for all sites
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| 251 | countOfWebPagesWithBodyText++; // of this site alone
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| 252 |
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| 253 | boolean isMRI = maoriTxtDetector.isTextInMaori(text);
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| 254 | if(isMRI) {
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| 255 | numPagesInMRI++;
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| 256 | }
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| 257 |
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| 258 | String[] sentences = maoriTxtDetector.getAllSentences(text);
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| 259 | int totalSentences = sentences.length;
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[33652] | 260 | int numSentencesInMRI = 0;
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[33698] | 261 | ArrayList<SentenceInfo> singleSentences = maoriTxtDetector.getAllSentencesInfo(sentences, NUM_TOP_LANGUAGES);
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| 262 | ArrayList<SentenceInfo> overlappingSentences = maoriTxtDetector.getAllOverlappingSentencesInfo(sentences, NUM_TOP_LANGUAGES);
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[33652] | 263 |
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| 264 | WebpageInfo webpage = page.convertStoredDataToWebpageInfo(WEBPAGE_COUNTER/*new ObjectId()*/,
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| 265 | this.siteID/*SITE_COUNTER*/,
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[33634] | 266 | isMRI,
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| 267 | totalSentences,
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| 268 | singleSentences,
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| 269 | overlappingSentences);
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| 270 |
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[33698] | 271 |
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[33652] | 272 | for(SentenceInfo si : singleSentences) {
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[33698] | 273 | //LanguageInfo bestLanguage = si.languagesInfo[0];
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| 274 | //if(bestLanguage.langCode.equals(MaoriTextDetector.MAORI_3LETTER_CODE)) {
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| 275 | if(si.bestLangCode.equals(MaoriTextDetector.MAORI_3LETTER_CODE)) {
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[33652] | 276 | numSentencesInMRI++;
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| 277 | }
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| 278 | }
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[33698] | 279 |
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| 280 |
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[33652] | 281 | webpage.setMRISentenceCount(numSentencesInMRI);
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| 282 | webpage.setContainsMRI((numSentencesInMRI > 0));
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[33801] | 283 | if(numSentencesInMRI > 0) { // if(numSentencesInMRI >= 5) {
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| 284 | // Not sure if we can trust that a single sentence detected as Maori on a page is really Maori
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| 285 | // But if at least 5 sentences are detected as Maori, it is more likely to be the case to be MRI?
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| 286 | numPagesContainingMRI++;
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| 287 | }
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| 288 |
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[33652] | 289 | //mongodbAccess.insertWebpageInfo(webpage);
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[33674] | 290 | // Uses morphia to save to mongodb, see https://www.baeldung.com/mongodb-morphia
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[33652] | 291 | mongodbAccess.datastore.save(webpage);
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[33634] | 292 | }
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| 293 | }
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| 294 | }
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| 295 |
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| 296 |
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| 297 | public void websiteDataToDB() {
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| 298 |
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| 299 |
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| 300 | // https://stackoverflow.com/questions/35183146/how-can-i-create-a-java-8-localdate-from-a-long-epoch-time-in-milliseconds
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| 301 | // LocalDateTime date =
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| 302 | // LocalDateTime.ofInstant(Instant.ofEpochMilli(this.siteCrawledTimestamp), ZoneId.systemDefault());
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| 303 | // String crawlTimestamp =
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| 304 | // date.format(DateTimeFormatter.ofPattern("yyyy-MM-dd")) + " " + date.format(DateTimeFormatter.ofPattern("HH:mm:ss"));
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| 305 |
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| 306 | boolean redoCrawl = false;
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| 307 |
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| 308 | if(this.siteCrawlUnfinished) {
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| 309 | // arbitrary decision, but need some indication that the MRI content was not close to one-off in the website
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| 310 | if(this.numPagesInMRI > 2) {
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| 311 | redoCrawl = true;
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| 312 | }
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| 313 | }
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| 314 |
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[33652] | 315 | File geoLiteCityDatFile = new File(this.getClass().getClassLoader().getResource("GeoLiteCity.dat").getFile());
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| 316 | try {
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[33800] | 317 | if(this.domainOfSite.equals("UNKNOWN")) { // for sites that had 0 webpages downloaded, we have no domain
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[33657] | 318 | this.geoLocationCountryCode = "UNKNOWN";
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| 319 | } else {
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| 320 | this.geoLocationCountryCode = Utility.getCountryCodeOfDomain(this.domainOfSite, geoLiteCityDatFile);
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| 321 | }
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| 322 | } catch(Exception e) {
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| 323 | logger.error("*** For SiteID " + siteID + ", got exception: " + e.getMessage(), e);
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[33801] | 324 |
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| 325 | //if(this.domainOfSite.endsWith(".nz")) { // nz TLDs are worth counting
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| 326 | //this.geoLocationCountryCode = "NZ";
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| 327 | //}
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| 328 |
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| 329 | // Help along identification of domain's country by construing TLDs if 2 letters after last period mark
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| 330 | int periodIndex = domainOfSite.length()-3;
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| 331 | // .com|org etc extensions that have 3 chars afte period mark will remain unknown
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| 332 | // 2 letter extensions will be considered TLD
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| 333 | if(periodIndex >=0 && domainOfSite.charAt(periodIndex) == '.' && ((periodIndex+1) < domainOfSite.length())) {
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| 334 | // has a 2 letter TLD. Make it uppercase to match return value of Utility.getCountryCodeOfDomain() above
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| 335 | String TLD = domainOfSite.substring(periodIndex+1);
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| 336 | this.geoLocationCountryCode = TLD.toUpperCase();
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| 337 | } else {
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| 338 | this.geoLocationCountryCode = "UNKNOWN"; // couldn't get the country code, so should also be UNKNOWN not null
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| 339 | }
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[33652] | 340 | }
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[33634] | 341 |
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| 342 | int totalPages = pages.size();
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| 343 |
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[33906] | 344 | WebsiteInfo website = new WebsiteInfo(/*SITE_COUNTER,*/ this.siteID,
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[33909] | 345 | this.domainOfSite, //this.baseSiteDomain,
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[33801] | 346 | totalPages, this.countOfWebPagesWithBodyText,
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| 347 | this.numPagesInMRI, this.numPagesContainingMRI,
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[33634] | 348 | this.siteCrawledTimestamp, this.siteCrawlUnfinished, redoCrawl,
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[33811] | 349 | this.geoLocationCountryCode, this.urlContainsLangCodeInPath);
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[33634] | 350 |
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[33652] | 351 | //mongodbAccess.insertWebsiteInfo(website);
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[33674] | 352 | // Uses morphia to save to mongodb, see https://www.baeldung.com/mongodb-morphia
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[33652] | 353 | mongodbAccess.datastore.save(website);
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[33634] | 354 | }
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| 355 |
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| 356 |
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| 357 | // --------------- STATIC METHODS AND INNER CLASSED USED BY MAIN -------------- //
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| 358 |
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| 359 | public static void printUsage() {
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| 360 | System.err.println("Run this program as:");
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| 361 | System.err.println("\tNutchTextDumpToMongoDB <path to 'crawled' folder>");
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| 362 | }
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| 363 |
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| 364 | public static void main(String[] args) {
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| 365 | if(args.length != 1) {
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| 366 | printUsage();
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| 367 | return;
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| 368 | }
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| 369 |
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| 370 | File sitesDir = new File(args[0]);
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| 371 | if(!sitesDir.exists() || !sitesDir.isDirectory()) {
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| 372 | logger.error("Error: " + args[0] + " does not exist or is not a directory");
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| 373 | return;
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| 374 | }
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| 375 |
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| 376 | NutchTextDumpToMongoDB.DEBUG_MODE = false;
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| 377 |
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| 378 |
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| 379 | try (
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| 380 | MongoDBAccess mongodb = new MongoDBAccess();
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| 381 | ) {
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| 382 |
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| 383 | mongodb.connectToDB();
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| 384 | //mongodb.showCollections();
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| 385 |
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| 386 | // print out the column headers for the websites csv file
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| 387 | // https://commons.apache.org/proper/commons-csv/apidocs/org/apache/commons/csv/CSVPrinter.html
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| 388 | // OPTIONAL TODO: creating collections can be done here if dropping and recreating
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| 389 |
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| 390 | MaoriTextDetector mriTxtDetector = new MaoriTextDetector(true); // true: run silent
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| 391 | File[] sites = sitesDir.listFiles();
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| 392 |
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| 393 | // sort site folders in alphabetical order
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| 394 | // https://stackoverflow.com/questions/7199911/how-to-file-listfiles-in-alphabetical-order
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| 395 | Arrays.sort(sites);
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| 396 |
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| 397 | for(File siteDir : sites) { // e.g. 00001
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| 398 | if(siteDir.isDirectory()) {
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| 399 | // look for dump.txt
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| 400 | File txtDumpFile = new File(siteDir, "dump.txt");
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| 401 | if(!txtDumpFile.exists()) {
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| 402 | logger.error("Text dump file " + txtDumpFile + " did not exist");
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| 403 | continue;
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| 404 | }
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| 405 |
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| 406 | else {
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[33656] | 407 | File UNFINISHED_FILE = new File(siteDir, "UNFINISHED");
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[33634] | 408 |
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| 409 | String siteID = siteDir.getName();
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[33656] | 410 | if(siteID.contains("_")) {
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| 411 | logger.warn("*** Skipping site " + siteID + " as its dir name indicates it wasn't crawled properly.");
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| 412 | continue;
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| 413 | }
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| 414 |
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[33634] | 415 | long lastModified = siteDir.lastModified();
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[33656] | 416 | logger.debug("@@@ Processing siteID: " + siteID);
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[33634] | 417 | NutchTextDumpToMongoDB nutchTxtDump = new NutchTextDumpToMongoDB(
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| 418 | mongodb, mriTxtDetector,
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| 419 | siteID, txtDumpFile, lastModified, UNFINISHED_FILE.exists());
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| 420 | // now it's parsed all the web pages in the site's text dump
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| 421 |
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| 422 | // Let's print stats on each web page's detected language being MRI or not
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| 423 | // and how many pages there were in the site in total.
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| 424 |
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| 425 | //nutchTxtDump.printSiteStats();
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| 426 |
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| 427 | nutchTxtDump.websiteDataToDB();
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| 428 | }
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| 429 | }
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| 430 |
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| 431 | }
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| 432 |
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| 433 | } catch(Exception e) {
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| 434 | // can get an exception when instantiating NutchTextDumpToMongoDB instance
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| 435 | // or with CSV file
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| 436 | logger.error(e.getMessage(), e);
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| 437 | }
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| 438 | }
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| 439 | }
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