dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java

package eu.dnetlib.dhp.collection;

import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;

import java.io.ByteArrayInputStream;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;

import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.fasterxml.jackson.databind.ObjectMapper;

import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;

public class GenerateNativeStoreSparkJob {

	private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class);

	public static void main(String[] args) throws Exception {

		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
				IOUtils
						.toString(
								GenerateNativeStoreSparkJob.class
										.getResourceAsStream(
												"/eu/dnetlib/dhp/collection/collection_input_parameters.json")));
		parser.parseArgument(args);
		final ObjectMapper jsonMapper = new ObjectMapper();
		final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class);
		final long dateOfCollection = new Long(parser.get("dateOfCollection"));

		Boolean isSparkSessionManaged = Optional
				.ofNullable(parser.get("isSparkSessionManaged"))
				.map(Boolean::valueOf)
				.orElse(Boolean.TRUE);
		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);

		final Map<String, String> ongoingMap = new HashMap<>();
		final Map<String, String> reportMap = new HashMap<>();

		final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));

		SparkConf conf = new SparkConf();
		runWithSparkSession(
				conf,
				isSparkSessionManaged,
				spark -> {
					final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());

					final JavaPairRDD<IntWritable, Text> inputRDD = sc
							.sequenceFile(parser.get("input"), IntWritable.class, Text.class);

					final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
					final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");

					final MessageManager manager = new MessageManager(
							parser.get("rabbitHost"),
							parser.get("rabbitUser"),
							parser.get("rabbitPassword"),
							false,
							false,
							null);

					final JavaRDD<MetadataRecord> mappeRDD = inputRDD
							.map(
									item -> parseRecord(
											item._2().toString(),
											parser.get("xpath"),
											parser.get("encoding"),
											provenance,
											dateOfCollection,
											totalItems,
											invalidRecords))
							.filter(Objects::nonNull)
							.distinct();

					ongoingMap.put("ongoing", "0");
					if (!test) {
						manager
								.sendMessage(
										new Message(
												parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
										parser.get("rabbitOngoingQueue"),
										true,
										false);
					}

					final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
					final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
					final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
					mdStoreRecords.add(mdstore.count());
					ongoingMap.put("ongoing", "" + totalItems.value());
					if (!test) {
						manager
								.sendMessage(
										new Message(
												parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
										parser.get("rabbitOngoingQueue"),
										true,
										false);
					}
					mdstore.write().format("parquet").save(parser.get("output"));
					reportMap.put("inputItem", "" + totalItems.value());
					reportMap.put("invalidRecords", "" + invalidRecords.value());
					reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
					if (!test) {
						manager
								.sendMessage(
										new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
										parser.get("rabbitReportQueue"),
										true,
										false);
						manager.close();
					}
				});

	}

	public static MetadataRecord parseRecord(
		final String input,
		final String xpath,
		final String encoding,
		final Provenance provenance,
		final Long dateOfCollection,
		final LongAccumulator totalItems,
		final LongAccumulator invalidRecords) {

		if (totalItems != null)
			totalItems.add(1);
		try {
			SAXReader reader = new SAXReader();
			Document document = reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
			Node node = document.selectSingleNode(xpath);
			final String originalIdentifier = node.getText();
			if (StringUtils.isBlank(originalIdentifier)) {
				if (invalidRecords != null)
					invalidRecords.add(1);
				return null;
			}
			return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection);
		} catch (Throwable e) {
			if (invalidRecords != null)
				invalidRecords.add(1);
			e.printStackTrace();
			return null;
		}
	}


}