222 lines
7.1 KiB
Java
222 lines
7.1 KiB
Java
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package eu.dnetlib.dhp.collection;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.*;
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import java.nio.charset.StandardCharsets;
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import java.util.Collections;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.IntWritable;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.expressions.Aggregator;
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import org.apache.spark.util.LongAccumulator;
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import org.dom4j.Document;
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import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion;
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import eu.dnetlib.dhp.aggregation.common.AggregationUtility;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.collection.worker.CollectorWorkerApplication;
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import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
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import eu.dnetlib.dhp.model.mdstore.Provenance;
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import scala.Tuple2;
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public class GenerateNativeStoreSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class);
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private static final String DATASET_NAME = "/store";
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public static class MDStoreAggregator extends Aggregator<MetadataRecord, MetadataRecord, MetadataRecord> {
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@Override
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public MetadataRecord zero() {
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return new MetadataRecord();
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}
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@Override
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public MetadataRecord reduce(MetadataRecord b, MetadataRecord a) {
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return getLatestRecord(b, a);
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}
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private MetadataRecord getLatestRecord(MetadataRecord b, MetadataRecord a) {
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if (b == null)
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return a;
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if (a == null)
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return b;
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return (a.getDateOfCollection() > b.getDateOfCollection()) ? a : b;
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}
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@Override
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public MetadataRecord merge(MetadataRecord b, MetadataRecord a) {
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return getLatestRecord(b, a);
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}
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@Override
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public MetadataRecord finish(MetadataRecord j) {
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return j;
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}
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@Override
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public Encoder<MetadataRecord> bufferEncoder() {
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return Encoders.kryo(MetadataRecord.class);
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}
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@Override
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public Encoder<MetadataRecord> outputEncoder() {
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return Encoders.kryo(MetadataRecord.class);
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}
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}
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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GenerateNativeStoreSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/collection/collection_input_parameters.json")));
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parser.parseArgument(args);
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final ObjectMapper jsonMapper = new ObjectMapper();
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final String provenanceArgument = parser.get("provenance");
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log.info("Provenance is {}", provenanceArgument);
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final Provenance provenance = jsonMapper.readValue(provenanceArgument, Provenance.class);
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final String dateOfCollectionArgs = parser.get("dateOfCollection");
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log.info("dateOfCollection is {}", dateOfCollectionArgs);
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final long dateOfCollection = new Long(dateOfCollectionArgs);
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String mdStoreVersion = parser.get("mdStoreVersion");
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log.info("mdStoreVersion is {}", mdStoreVersion);
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final MDStoreVersion currentVersion = jsonMapper.readValue(mdStoreVersion, MDStoreVersion.class);
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String readMdStoreVersionParam = parser.get("readMdStoreVersion");
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log.info("readMdStoreVersion is {}", readMdStoreVersionParam);
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final MDStoreVersion readMdStoreVersion = StringUtils.isBlank(readMdStoreVersionParam) ? null
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: jsonMapper.readValue(readMdStoreVersionParam, MDStoreVersion.class);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(Collections.singleton(MetadataRecord.class).toArray(new Class[] {}));
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final JavaPairRDD<IntWritable, Text> inputRDD = sc
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.sequenceFile(
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currentVersion.getHdfsPath() + CollectorWorkerApplication.SEQUENTIAL_FILE_NAME,
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IntWritable.class, Text.class);
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final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
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final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
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final JavaRDD<MetadataRecord> nativeStore = inputRDD
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.map(
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item -> parseRecord(
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item._2().toString(),
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parser.get("xpath"),
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parser.get("encoding"),
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provenance,
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dateOfCollection,
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totalItems,
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invalidRecords))
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.filter(Objects::nonNull)
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.distinct();
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final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
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Dataset<MetadataRecord> mdstore = spark.createDataset(nativeStore.rdd(), encoder);
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if (readMdStoreVersion != null) {
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// INCREMENTAL MODE
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Dataset<MetadataRecord> currentMdStoreVersion = spark
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.read()
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.load(readMdStoreVersion.getHdfsPath() + DATASET_NAME)
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.as(encoder);
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TypedColumn<MetadataRecord, MetadataRecord> aggregator = new MDStoreAggregator().toColumn();
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mdstore = currentMdStoreVersion
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.union(mdstore)
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.groupByKey(
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(MapFunction<MetadataRecord, String>) MetadataRecord::getId,
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Encoders.STRING())
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.agg(aggregator)
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.map((MapFunction<Tuple2<String, MetadataRecord>, MetadataRecord>) Tuple2::_2, encoder);
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}
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mdstore
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.write()
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.mode(SaveMode.Overwrite)
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.format("parquet")
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.save(currentVersion.getHdfsPath() + DATASET_NAME);
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mdstore = spark.read().load(currentVersion.getHdfsPath() + DATASET_NAME).as(encoder);
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final Long total = mdstore.count();
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AggregationUtility.writeTotalSizeOnHDFS(spark, total, currentVersion.getHdfsPath() + "/size");
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});
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}
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public static MetadataRecord parseRecord(
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final String input,
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final String xpath,
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final String encoding,
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final Provenance provenance,
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final Long dateOfCollection,
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final LongAccumulator totalItems,
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final LongAccumulator invalidRecords) {
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if (totalItems != null)
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totalItems.add(1);
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try {
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SAXReader reader = new SAXReader();
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Document document = reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
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Node node = document.selectSingleNode(xpath);
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final String originalIdentifier = node.getText();
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if (StringUtils.isBlank(originalIdentifier)) {
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if (invalidRecords != null)
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invalidRecords.add(1);
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return null;
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}
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return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection);
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} catch (Throwable e) {
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invalidRecords.add(1);
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return null;
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}
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}
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}
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