source: other-projects/maori-lang-detection/src/org/greenstone/atea/NutchTextDumpToMongoDB.java

package org.greenstone.atea;

import java.io.*;
import java.lang.ArrayIndexOutOfBoundsException;
import java.time.LocalDateTime;
import java.util.ArrayList;
import java.util.Arrays;

import org.apache.commons.csv.*;
import org.apache.log4j.Logger;

//import org.bson.types.ObjectId;
    
import org.greenstone.atea.morphia.*;


/**
 * Class to process the dump text files produced FOR EACH SITE (e.g. site "00001") that
 * Nutch has finished crawling and whose text has been dumped out to a file called dump.txt.
 * This reads in the dump.txt file contained in each site folder within the input folder.
 * (e.g. input folder "crawled" could contain folders 00001 to 01465. Each contains a dump.txt)
 * Each dump.txt could contain the text contents for an entire site, or for individual pages.
 * This class then uses class TextDumpPage to parse each webpage within a dump.txt,
 * which parses out the actual text body content of each webpage's section within a dump.txt.
 * Finally, MaoriTextDetector is run over that to determine whether the full body text is
 * likely to be in Maori or not.
 *
 * Potential issues: since a web page's text is dumped out by nutch with neither paragraph
 * nor even newline separator, it's hard to be sure that the entire page is in language.
 * If it's in multiple languages, there's no way to be sure there aren't promising Maori language
 * paragraphs contained in a page, if the majority/the remainder happen to be in English.
 * 
 * So if we're looking for any paragraphs in Maori to store in a DB, perhaps it's better to run
 * the MaoriTextDetector.isTextInMaori(BufferedReader reader) over two "lines" at a time,
 * instead of running it over the entire html body's text.
 *
 * TO COMPILE OR RUN, FIRST DO:
 *    cd maori-lang-detection/apache-opennlp-1.9.1
 *    export OPENNLP_HOME=`pwd`
 *    cd maori-lang-detection/src
 *
 * MORE IMPORTANT PRELIMINARIES:
 * - Make sure the MongoDB is up and running and accessible.
 * - If you want to keep any existing MongoDB collections called Websites and Webpages, then
 * first renamed those collections in MongoDB (using Robo3T makes renaming easy) before
 * running this program.
 *
 * TO COMPILE:
 *    maori-lang-detection/src$
 *       javac -cp ".:../conf:../lib/*:$OPENNLP_HOME/lib/opennlp-tools-1.9.1.jar" org/greenstone/atea/NutchTextDumpToMongoDB.java
 *
 * TO RUN:
 *    maori-lang-detection/src$
 *       java -cp ".:../conf:../lib/*:$OPENNLP_HOME/lib/opennlp-tools-1.9.1.jar" org/greenstone/atea/NutchTextDumpToMongoDB ../crawled-small
 *
 * or:
 *       java -cp ".:../conf:../lib/*:$OPENNLP_HOME/lib/opennlp-tools-1.9.1.jar" org/greenstone/atea/NutchTextDumpToMongoDB ../crawled-small > ../crawled-small/bla.txt 2>&1
 *
*/
public class NutchTextDumpToMongoDB {
    static Logger logger = Logger.getLogger(org.greenstone.atea.NutchTextDumpToMongoDB.class.getName());

    static boolean DEBUG_MODE = true; // this is set to false in main() at the end of this class
       
    /** Counter for number of sites.
     * Should be equal to number of times NutchTextDumpToMongoDB constructor
     * is called: once per site.
     */
    static private int SITE_COUNTER = 0;
    static private long WEBPAGE_COUNTER = 0;
    
    private final MaoriTextDetector maoriTxtDetector;
    private final MongoDBAccess mongodbAccess;
    
    public final String siteID;
    public final boolean siteCrawlUnfinished;
    public final long siteCrawledTimestamp; /** When the crawl of the site terminated */

    // private handle to a csv writer
    private CSVPrinter emptyWebPageInfoCSVPrinter;
    
    private int countOfWebPagesWithBodyText = 0;
    
    private String geoLocationCountryCode = null; /** 2 letter country code */
    private boolean urlContainsLangCodeInPath = false; /** If any URL on this site contains a /mi(/) or http(s)://mi.* in its URL path */

    private String domainOfSite;
    //private String baseSiteDomain; // domainOfSite stripped of any http(s)://www.
    private int numPagesInMRI = 0;
    private int numPagesContainingMRI = 0;
    
    /** keep a list to store the text of each page */
    private ArrayList<TextDumpPage> pages;


    
    /** Number of language and confidence results to return for storing in MongoDB
     * MongoDB runs out of space if storing too many, as we store this info per sentence
     * and a long text document becomes a very large MongoDB document presumably */
    private static final int NUM_TOP_LANGUAGES = 3; // 103 max, in current version of opennlp lang model

    
    private boolean isStartOfNewWebPageRecord(String prevLine, String line) {
    // The start of a new web page's record in nutch's text dump of an entire site
    // is denoted by a newline followed by a URL (protocol)
    // or the very start of the file with a URL (protocol)
    return ((prevLine == null || prevLine.equals(""))
        && (line.startsWith("http://") || line.startsWith("https://")));
    }

    public void debugPageDump(StringBuilder pageDump) {
    if(DEBUG_MODE) {
        // START DEBUG
        logger.debug("__________________________________________");
        logger.debug("@@@ Found page entry: ");
        logger.debug("__________________________________________");
        logger.debug(pageDump.toString());
        logger.debug("------------------------------------------");
        // END DEBUG
    }
    }

    /** A NutchTextDumpToMongoDB processes the dump.txt for one site */
    public NutchTextDumpToMongoDB(MongoDBAccess mongodbAccess, CSVPrinter emptyWebPageInfoCSVPrinter,
                  MaoriTextDetector maoriTxtDetector, String siteID,
                  File txtDumpFile, long lastModified, boolean siteCrawlUnfinished)
    throws IOException
    {   
    // increment static counter of sites processed by a NutchTextDumpToMongoDB instance
    SITE_COUNTER++;

    // keep a handle to the csv file writer
    this.emptyWebPageInfoCSVPrinter = emptyWebPageInfoCSVPrinter;
    
    // siteID is of the form %5d (e.g. 00020) and is just the name of a site folder
    this.siteID = siteID;
    this.siteCrawlUnfinished = siteCrawlUnfinished;
    this.siteCrawledTimestamp = lastModified;
    
    this.maoriTxtDetector = maoriTxtDetector;
    this.mongodbAccess = mongodbAccess;
    
    pages = new ArrayList<TextDumpPage>();

    String line = null;
    StringBuilder pageDump = null;
    try (
         BufferedReader reader = new BufferedReader(new FileReader(txtDumpFile));
         ) {

        boolean readingText = false;
        String prevLine = null;
        
        while((line = reader.readLine()) != null) { // readLine removes newline separator
        line = line.trim();
        // iff outside of a page's body text, then an empty line marks the end of a page
        // in nutch's text dump of a site.
        // But note, there can be an empty line (or more?) between the start and end
        // markers of a page's text, though.

        if(isStartOfNewWebPageRecord(prevLine, line)) {

            if(pageDump != null) { // should also be the case then: if(prevLine != null)
            // finish old pageDump and begin new one            

            //debugPageDump(pageDump);
                
            TextDumpPage page = new TextDumpPage(siteID, pageDump.toString());
            // parses the fields and body text of a webpage in nutch's txt dump of entire site
            //page.parseFields();
            //page.getText();
            pages.add(page);
            inspectPageURLPath(page);
            pageDump = null;

            }           

            // begin new webpage dump
            pageDump = new StringBuilder();
            pageDump.append(line);
            pageDump.append("\n");
            
        }
        else if(!line.equals("")) {
            pageDump.append(line);
            pageDump.append("\n");

        }
        // can throw away any newlines between text start and end markers.
        
        prevLine = line;
        }

        // process final webpage record:
        //debugPageDump(pageDump);

        if(pageDump == null) {
        logger.warn("siteID " + siteID + " had an empty dump.txt file. Reinspect site.");
        } else {
        TextDumpPage page = new TextDumpPage(siteID, pageDump.toString());
        pages.add(page);
        inspectPageURLPath(page);
        pageDump = null;
        }   

        
    } catch (IOException ioe) {
        logger.error("@@@@@@@@@ Error reading in nutch txtdump file " + txtDumpFile, ioe);
    }

    // Just do this once: get and store domain of site.
    // Passing true to get domain with protocol prefix
    if(pages.size() > 0) {
        TextDumpPage firstPage = pages.get(0);
        String url = firstPage.getPageURL();
        this.domainOfSite = Utility.getDomainForURL(url, true);
        //this.baseSiteDomain = Utility.stripProtocolAndWWWFromURL(this.domainOfSite);
    }
    else {
        this.domainOfSite = "UNKNOWN";
        //this.baseSiteDomain = "UNKNOWN";
    }
    
    /* No need to loop again through all pages. Instead, just inspectPageURLPath() as each page is created above.
    // For any site, we just need to work out if any of its pages contains /mi(/) or http(s)://mi.* in its URL path
    for(TextDumpPage aPage : pages) {
        inspectPageURLPath(aPage);
    }
    */
    webPageDataToMongoDB(mongodbAccess);
    }
    

    /** for every site, we just need to work out if any of its pages contains /mi(/) or http(s)://mi. in its URL.
      * This method is called on each page of a site as the page is created. */
    private void inspectPageURLPath(TextDumpPage page) {
    String url = page.getPageURL();
    //logger.debug("@@@@ pageURL: " + url);
    
    if(!this.urlContainsLangCodeInPath) { // if not already set to true for any previous page in this site,
        // check if this page of the site contains /mi(/) or http(s)://mi in its URL path
        if(url.contains("/mi/") || url.endsWith("/mi") || url.startsWith("https://mi.") || url.startsWith("http://mi.")) {
        this.urlContainsLangCodeInPath = true;
        }
    }
    }
    
    
    private void webPageDataToMongoDB(MongoDBAccess mongodbAccess) throws IOException {
    
    TextDumpPage page = null;
    for(int i = 0; i < pages.size(); i++) {
        
        page = pages.get(i);
        
        String text = page.getPageText();
        
        if(text.equals("")) {
        System.err.println(siteID + ",Empty page " + i + "," + page.getPageURL()
                   + "," + page.get("status")
                   + "," + page.get("protocolStatus")
                   + "," + page.get("parseStatus"));
        // write information about any empty web page into the emptyPage csv file
        emptyWebPageInfoCSVPrinter.printRecord(siteID, i, page.getPageURL(),
               page.get("status"), page.get("protocolStatus"),page.get("parseStatus"));
        
        // don't care about empty pages
        continue;
        }
        else {
        WEBPAGE_COUNTER++; // count of cumulative total of webpages for all sites
        countOfWebPagesWithBodyText++; // of this site alone                
        
        boolean isMRI = maoriTxtDetector.isTextInMaori(text);
        if(isMRI) {
            numPagesInMRI++;
        }
        
        String[] sentences = maoriTxtDetector.getAllSentences(text);
        int totalSentences = sentences.length;
        int numSentencesInMRI = 0;
        ArrayList<SentenceInfo> singleSentences = maoriTxtDetector.getAllSentencesInfo(sentences, NUM_TOP_LANGUAGES);
        ArrayList<SentenceInfo> overlappingSentences = maoriTxtDetector.getAllOverlappingSentencesInfo(sentences, NUM_TOP_LANGUAGES);

        WebpageInfo webpage = page.convertStoredDataToWebpageInfo(WEBPAGE_COUNTER/*new ObjectId()*/,
                                     this.siteID/*SITE_COUNTER*/,
                                     isMRI,
                                     totalSentences,
                                     singleSentences,
                                     overlappingSentences);

        
        for(SentenceInfo si : singleSentences) {
            //LanguageInfo bestLanguage = si.languagesInfo[0];
            //if(bestLanguage.langCode.equals(MaoriTextDetector.MAORI_3LETTER_CODE)) {
            if(si.bestLangCode.equals(MaoriTextDetector.MAORI_3LETTER_CODE)) {
            numSentencesInMRI++;
            }
        }
        
        
        webpage.setMRISentenceCount(numSentencesInMRI);
        webpage.setContainsMRI((numSentencesInMRI > 0));
        if(numSentencesInMRI > 0) { // if(numSentencesInMRI >= 5) {
            // Not sure if we can trust that a single sentence detected as Maori on a page is really Maori
            // But if at least 5 sentences are detected as Maori, it is more likely to be the case to be MRI?
            numPagesContainingMRI++;
        }
            
        //mongodbAccess.insertWebpageInfo(webpage);
        // Uses morphia to save to mongodb, see https://www.baeldung.com/mongodb-morphia
        mongodbAccess.datastore.save(webpage);
        }
    }
    }
    

    public void websiteDataToDB() {
    
    
    // https://stackoverflow.com/questions/35183146/how-can-i-create-a-java-8-localdate-from-a-long-epoch-time-in-milliseconds
    // LocalDateTime date =
    //     LocalDateTime.ofInstant(Instant.ofEpochMilli(this.siteCrawledTimestamp), ZoneId.systemDefault());
    // String crawlTimestamp =
    //     date.format(DateTimeFormatter.ofPattern("yyyy-MM-dd")) + " " + date.format(DateTimeFormatter.ofPattern("HH:mm:ss"));

    boolean redoCrawl = false;

    if(this.siteCrawlUnfinished) {
        // arbitrary decision, but need some indication that the MRI content was not close to one-off in the website
        if(this.numPagesInMRI > 2) { 
        redoCrawl = true;
        }
    }
    
    File geoLiteCityDatFile = new File(this.getClass().getClassLoader().getResource("GeoLiteCity.dat").getFile());
    try {
        if(this.domainOfSite.equals("UNKNOWN")) { // for sites that had 0 webpages downloaded, we have no domain
        this.geoLocationCountryCode = "UNKNOWN";
        } else {
        this.geoLocationCountryCode = Utility.getCountryCodeOfDomain(this.domainOfSite, geoLiteCityDatFile);
        }
    } catch(Exception e) {      
        logger.error("*** For SiteID " + siteID + ", got exception: "  + e.getMessage(), e);

        //if(this.domainOfSite.endsWith(".nz")) { // nz TLDs are worth counting
        //this.geoLocationCountryCode = "NZ"; 
        //}

        // Help along identification of domain's country by construing TLDs if 2 letters after last period mark
        int periodIndex = domainOfSite.length()-3;
        // .com|org etc extensions that have 3 chars afte period mark will remain unknown
        // 2 letter extensions will be considered TLD
        if(periodIndex >=0 && domainOfSite.charAt(periodIndex) == '.' && ((periodIndex+1) < domainOfSite.length())) {
        // has a 2 letter TLD. Make it uppercase to match return value of Utility.getCountryCodeOfDomain() above
        String TLD = domainOfSite.substring(periodIndex+1);
        this.geoLocationCountryCode = TLD.toUpperCase();
        } else {
        this.geoLocationCountryCode = "UNKNOWN"; // couldn't get the country code, so should also be UNKNOWN not null
        }
    }

    int totalPages = pages.size();  

    WebsiteInfo website = new WebsiteInfo(/*SITE_COUNTER,*/ this.siteID,
          this.domainOfSite, //this.baseSiteDomain,
          totalPages, this.countOfWebPagesWithBodyText,
          this.numPagesInMRI, this.numPagesContainingMRI,
          this.siteCrawledTimestamp, this.siteCrawlUnfinished, redoCrawl,
          this.geoLocationCountryCode, this.urlContainsLangCodeInPath);

    //mongodbAccess.insertWebsiteInfo(website);
    // Uses morphia to save to mongodb, see https://www.baeldung.com/mongodb-morphia
    mongodbAccess.datastore.save(website);
    }

    
    // --------------- STATIC METHODS AND INNER CLASSED USED BY MAIN -------------- //
   
    public static void printUsage() {
    System.err.println("Run this program as:");
    System.err.println("\tNutchTextDumpToMongoDB <path to 'crawled' folder>");
    }
    
    public static void main(String[] args) {
    if(args.length != 1) {
        printUsage();
        return;
    }

    File sitesDir = new File(args[0]);
    if(!sitesDir.exists() || !sitesDir.isDirectory()) {
        logger.error("Error: " + args[0] + " does not exist or is not a directory");
        return;
    }

    NutchTextDumpToMongoDB.DEBUG_MODE = false;
    
    try (
         MongoDBAccess mongodb = new MongoDBAccess();
         CSVPrinter emptyWebPageInfoCSVPrinter = new CSVPrinter(new FileWriter("InfoOnEmptyPagesNotInMongoDB.csv"), CSVFormat.DEFAULT.withQuoteMode(QuoteMode.MINIMAL));
         ) {
        
        mongodb.connectToDB();
        //mongodb.showCollections();

        // write out csv column headings into the csv file on empty web pages
        emptyWebPageInfoCSVPrinter.printRecord("siteID","pagenum","URL","(fetch)status","protocolStatus","parseStatus");
        
        // print out the column headers for the websites csv file
        // https://commons.apache.org/proper/commons-csv/apidocs/org/apache/commons/csv/CSVPrinter.html
        // OPTIONAL TODO: creating collections can be done here if dropping and recreating
        
        MaoriTextDetector mriTxtDetector = new MaoriTextDetector(true); // true: run silent
        File[] sites = sitesDir.listFiles();

        // sort site folders in alphabetical order
        // https://stackoverflow.com/questions/7199911/how-to-file-listfiles-in-alphabetical-order
        Arrays.sort(sites);
        
        for(File siteDir : sites) { // e.g. 00001
        if(siteDir.isDirectory()) {
            // look for dump.txt
            File txtDumpFile = new File(siteDir, "dump.txt");
            if(!txtDumpFile.exists()) {
            logger.error("Text dump file " + txtDumpFile + " did not exist");
            continue;
            }
            
            else {
            File UNFINISHED_FILE = new File(siteDir, "UNFINISHED");
            
            String siteID = siteDir.getName();
            if(siteID.contains("_")) {
                logger.warn("*** Skipping site " + siteID + " as its dir name indicates it wasn't crawled properly.");
                continue;
            }
            
            long lastModified = siteDir.lastModified();
            logger.debug("@@@ Processing siteID: " + siteID);           
            NutchTextDumpToMongoDB nutchTxtDump = new NutchTextDumpToMongoDB(
                 mongodb, emptyWebPageInfoCSVPrinter, mriTxtDetector,
                 siteID, txtDumpFile, lastModified, UNFINISHED_FILE.exists());
            // now it's parsed all the web pages in the site's text dump

            // Let's print stats on each web page's detected language being MRI or not
            // and how many pages there were in the site in total.
            
            //nutchTxtDump.printSiteStats();
            
            nutchTxtDump.websiteDataToDB();
            }
        }
        
        }
        
    } catch(Exception e) {
        // can get an exception when instantiating NutchTextDumpToMongoDB instance
        // or with CSV file
        logger.error(e.getMessage(), e);
    }
    }
}