D-Net

package eu.dnetlib.data.mapreduce.hbase.oai;

import java.io.IOException;

import java.net.UnknownHostException;

import java.time.LocalDateTime;

import java.time.ZoneId;

import java.time.format.DateTimeFormatter;

import java.util.Collection;

import java.util.Date;

import java.util.Map;

import java.util.zip.ZipEntry;

import java.util.zip.ZipOutputStream;

import com.google.common.base.Splitter;

import com.google.common.collect.Iterables;

import com.google.common.collect.Lists;

import com.google.common.collect.Maps;

import com.google.common.collect.Multimap;

import com.mongodb.BasicDBObject;

import com.mongodb.DBObject;

import com.mongodb.MongoClient;

import com.mongodb.WriteConcern;

import com.mongodb.client.MongoCollection;

import com.mongodb.client.MongoDatabase;

import eu.dnetlib.data.mapreduce.JobParams;

import eu.dnetlib.data.mapreduce.hbase.oai.config.OAIConfiguration;

import eu.dnetlib.data.mapreduce.hbase.oai.config.OAIConfigurationReader;

import eu.dnetlib.data.mapreduce.hbase.oai.config.OAIConfigurationStringReader;

import eu.dnetlib.data.mapreduce.hbase.oai.utils.MongoSetCollection;

import eu.dnetlib.data.mapreduce.hbase.oai.utils.PublisherField;

import eu.dnetlib.data.mapreduce.hbase.oai.utils.RecordFieldsExtractor;

import eu.dnetlib.miscutils.functional.xml.IndentXmlString;

import org.apache.commons.io.output.ByteArrayOutputStream;

import org.apache.commons.lang.StringUtils;

import org.apache.hadoop.io.NullWritable;

import org.apache.hadoop.io.Text;

import org.apache.hadoop.mapreduce.Mapper;

import org.bson.types.Binary;

public class OaiFeedMapper extends Mapper<Text, Text, NullWritable, NullWritable> {

	enum RecordStatus {

		NEW, UPDATED, UNCHANGED;

	}

	private MongoCollection<DBObject> collection;

	private MongoCollection<DBObject> discardedCollection;

	private OAIConfigurationStringReader oaiConfigurationReader;

	private OAIConfiguration oaiConfiguration;

	private Date feedDate;

	private MongoSetCollection mongoSetCollection;

	private RecordFieldsExtractor extractor;

	// these are set in the setup

	private String format;

	private String interpretation;

	private String layout;

	private Map<String, PublisherField> fieldsToIndex = Maps.newHashMap();

	private String duplicateXPath;

	private boolean skipDuplicates;

	private MongoClient mongo;

	private Collection<String> enrichmentXPaths;

	private String[] parseDatePatterns;

	@Override

	protected void setup(final Context context) throws UnknownHostException {

		String host = context.getConfiguration().get("services.publisher.oai.host");

		String port = context.getConfiguration().get("services.publisher.oai.port");

		String db = context.getConfiguration().get("services.publisher.oai.db");

		String collectionName = context.getConfiguration().get("services.publisher.oai.collection");

		String patterns = context.getConfiguration().get("services.publisher.oai.datepatterns");

		this.parseDatePatterns = Lists.newArrayList(Splitter.on(',')

				.trimResults()

				.omitEmptyStrings().split(patterns)).toArray(new String[0]);

		System.out.println("Mongodb client params");

		System.out.println("host: " + host);

		System.out.println("port: " + port);

		System.out.println("db: " + db);

		System.out.println("collection: " + collectionName);

		System.out.println("split date patterns: " + patterns);

		String[] formatLayoutInterp = collectionName.split("-");

		format = formatLayoutInterp[0];

		layout = formatLayoutInterp[1];

		interpretation = formatLayoutInterp[2];

		String oaiConfigurationProfile = context.getConfiguration().get("oaiConfiguration");

		System.out.println("oaiConfiguration:\n" + IndentXmlString.apply(oaiConfigurationProfile));

		oaiConfigurationReader = new OAIConfigurationStringReader(oaiConfigurationProfile);

		oaiConfiguration = oaiConfigurationReader.getOaiConfiguration();

		System.out.println("parsed configuration:" + oaiConfiguration.toString());

		mongo = new MongoClient(host, Integer.parseInt(port));

		MongoDatabase mongoDB = mongo.getDatabase(db);

		collection = mongoDB.getCollection(collectionName, DBObject.class).withWriteConcern(WriteConcern.UNACKNOWLEDGED);

		discardedCollection = mongoDB.getCollection("discarded-" + collectionName, DBObject.class).withWriteConcern(WriteConcern.UNACKNOWLEDGED);

		mongoSetCollection = new MongoSetCollection(mongo);

		duplicateXPath = context.getConfiguration().get("services.publisher.oai.duplicateXPath");

		skipDuplicates = Boolean.parseBoolean(context.getConfiguration().get("services.publisher.oai.skipDuplicates"));

		enrichmentXPaths = oaiConfiguration.getEnrichmentXPathsFor(format, layout, interpretation);

		Collection<PublisherField> indexFields = oaiConfiguration.getFieldsFor(format, layout, interpretation);

		extractor = new RecordFieldsExtractor(Lists.newArrayList(indexFields));

		extractor.setDuplicateXPath(duplicateXPath);

		extractor.setSkipDuplicates(skipDuplicates);

		for (PublisherField field : indexFields) {

			fieldsToIndex.put(field.getFieldName(), field);

		}

		String feedDateString = context.getConfiguration().get(JobParams.OAI_FEED_DATE);

		feedDate = parseDate(feedDateString);

	}

	@Override

	protected void map(final Text key, final Text value, final Context context) throws IOException, InterruptedException {

		String recordKey = key.toString();

		String recordBody = value.toString();

		if (StringUtils.isBlank(recordBody)) {

			discard(context, recordKey, recordBody, "blank body");

		} else {

			Multimap<String, String> recordFields = extractor.extractFields(recordBody, enrichmentXPaths);

			String id;

			String oaiID;

			if (checkRecordFields(recordFields, context, recordKey, recordBody)) {

				id = recordFields.get(OAIConfigurationReader.ID_FIELD).iterator().next();

				oaiID = getOAIIdentifier(id);

				handleRecord(context, oaiID, recordBody, recordFields);

			}

		}

	}

	public boolean checkRecordFields(final Multimap<String, String> recordFields, final Context context, final String recordKey, final String recordBody) {

		if ((recordFields == null)) {

			context.getCounter("oai", "invalid").increment(1);

			return false;

		}

		if (recordFields.containsEntry("duplicate", "true")) {

			if (skipDuplicates) {

				context.getCounter("oai", "discardedDuplicate").increment(1);

				return false;

			} else return true;

		}

		if (!recordFields.containsKey(OAIConfigurationReader.ID_FIELD)) {

			discard(context, recordKey, recordBody, "missing " + OAIConfigurationReader.ID_FIELD);

			return false;

		}

		return true;

	}

	private void handleRecord(final Context context, final String oaiID, final String record, final Multimap<String, String> recordProperties) {

		DBObject obj = this.createBasicObject(oaiID, record, recordProperties,context);

		if (obj != null) { // it can be null if the compression did not succeeded: counter is updated in the compress method in that case

			//let's use the date of collection and transformation for those records that have them.

			//for the rest, we'll keep the feedDate...

			Collection<String> collectionDates = recordProperties.get("dateOfCollection");

			Collection<String> transDates = recordProperties.get("dateOfTransformation");

			Date collDate = feedDate;

			if(collectionDates != null && !collectionDates.isEmpty()){

				String collDateString = collectionDates.iterator().next();

				if(StringUtils.isNotBlank(collDateString))

					collDate = parseDate(collDateString);

			}

			else{

				context.getCounter("oai", "missing dateOfCollection").increment(1);

			}

			obj.put(OAIConfigurationReader.LAST_COLLECTION_DATE_FIELD, collDate);

			Date timestamp = feedDate;

			if(transDates != null && !transDates.isEmpty()){

				String transDateString = transDates.iterator().next();

				if(StringUtils.isNotBlank(transDateString))

					timestamp = parseDate(transDateString);

			}

			else{

				context.getCounter("oai", "missing dateOfTransformation").increment(1);

			}

			obj.put(OAIConfigurationReader.DATESTAMP_FIELD, timestamp);

			//the updated_field must stay false, as the oai store is empty.

			obj.put(OAIConfigurationReader.UPDATED_FIELD, false);

			collection.insertOne(obj);

			context.getCounter("oai", "total").increment(1);

		}

	}

	protected Date parseDate(final String date) {

		// date should be in the form: 2017-12-18 or 2017-12-18T12:00:04+00:00 or 2014-10-12T15:54:02.43Z or 2014-10-12T15:54:02.432Z or 2014-10-12T15:54:02.4Z

		try {

			LocalDateTime d = LocalDateTime.parse(date, DateTimeFormatter.ISO_ZONED_DATE_TIME);

			return Date.from(d.atZone(ZoneId.systemDefault()).toInstant());

		}catch(Exception dateException){

			try {

				return org.apache.commons.lang.time.DateUtils.parseDate(

						date,

						parseDatePatterns);

			}catch(Exception dateException2){

				dateException2.printStackTrace(System.err);

				throw new RuntimeException(dateException2);

			}

		}

	}

	private void discard(final Context context, final String recordKey, final String recordBody, final String reason) {

		context.getCounter("oai", reason).increment(1);

		discardedCollection.insertOne(new BasicDBObject("id", recordKey).append(OAIConfigurationReader.BODY_FIELD, recordBody));

	}

	private String getOAIIdentifier(final String id) {

		return oaiConfiguration.getIdScheme() + ":" + oaiConfiguration.getIdNamespace() + ":" + id;

	}

	protected DBObject createBasicObject(final String oaiID, final String record, final Multimap<String, String> recordProperties, final Context context) {

		DBObject obj = new BasicDBObject();

		for (final String key : recordProperties.keySet()) {

			if (key.equals(OAIConfigurationReader.ID_FIELD)) {

				obj.put(key, oaiID);

			} else {

				Collection<String> values = recordProperties.get(key);

				if (key.equals(OAIConfigurationReader.SET_FIELD)) {

					Iterable<String> setSpecs = Iterables.transform(values, s -> mongoSetCollection.normalizeSetSpec(s));

					obj.put(key, setSpecs);

				} else {

					PublisherField keyField = fieldsToIndex.get(key);

					//Skipping record properties that are not listed as fields to index (e.g. date of transformation and collection)

					if (keyField != null) {

						// let's check if the key is the name of a repeatable field or not

						if ((keyField != null) && !keyField.isRepeatable()) {

							if ((values != null) && !values.isEmpty()) {

								obj.put(key, values.iterator().next());

							}

						} else {

							obj.put(key, values);

						}

					}

				}

			}

		}

		Binary compressedRecordBody = createCompressRecord(context, oaiID, record);

		if (compressedRecordBody != null) {

			obj.put(OAIConfigurationReader.BODY_FIELD, compressedRecordBody);

			obj.put(OAIConfigurationReader.DELETED_FIELD, false);

			return obj;

		} else return null;

	}

	public Binary createCompressRecord(final Context context, final String recordKey, final String recordBody) {

		try {

			ByteArrayOutputStream os = new ByteArrayOutputStream();

			ZipOutputStream zos = new ZipOutputStream(os);

			ZipEntry entry = new ZipEntry(OAIConfigurationReader.BODY_FIELD);

			zos.putNextEntry(entry);

			zos.write(recordBody.getBytes());

			zos.closeEntry();

			zos.flush();

			zos.close();

			return new Binary(os.toByteArray());

		} catch (IOException e) {

			discard(context, recordKey, recordBody, "cannot compress");

			return null;

		}

	}

	@Override

	protected void cleanup(final Context context) throws IOException, InterruptedException {

		super.cleanup(context);

	}

	public MongoCollection<DBObject> getCollection() {

		return collection;

	}

	public void setCollection(final MongoCollection<DBObject> collection) {

		this.collection = collection;

	}

	public MongoCollection<DBObject> getDiscardedCollection() {

		return discardedCollection;

	}

	public void setDiscardedCollection(final MongoCollection<DBObject> discardedCollection) {

		this.discardedCollection = discardedCollection;

	}

	public OAIConfigurationStringReader getOaiConfigurationReader() {

		return oaiConfigurationReader;

	}

	public void setOaiConfigurationReader(final OAIConfigurationStringReader oaiConfigurationReader) {

		this.oaiConfigurationReader = oaiConfigurationReader;

	}

	public OAIConfiguration getOaiConfiguration() {

		return oaiConfiguration;

	}

	public void setOaiConfiguration(final OAIConfiguration oaiConfiguration) {

		this.oaiConfiguration = oaiConfiguration;

	}

	public Date getFeedDate() {

		return feedDate;

	}

	public void setFeedDate(final Date feedDate) {

		this.feedDate = feedDate;

	}

	public MongoSetCollection getMongoSetCollection() {

		return mongoSetCollection;

	}

	public void setMongoSetCollection(final MongoSetCollection mongoSetCollection) {

		this.mongoSetCollection = mongoSetCollection;

	}

	public String getDuplicateXPath() {

		return duplicateXPath;

	}

	public void setDuplicateXPath(final String duplicateXPath) {

		this.duplicateXPath = duplicateXPath;

	}

	public boolean isSkipDuplicates() {

		return skipDuplicates;

	}

	public void setSkipDuplicates(final boolean skipDuplicates) {

		this.skipDuplicates = skipDuplicates;

	}

	public String[] getParseDatePatterns() {

		return parseDatePatterns;

	}

	public void setParseDatePatterns(final String[] parseDatePatterns) {

		this.parseDatePatterns = parseDatePatterns;

	}

}