176 lines
5.6 KiB
Java
176 lines
5.6 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.ByteArrayInputStream;
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import java.nio.charset.StandardCharsets;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.Objects;
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import java.util.Optional;
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import org.apache.commons.cli.*;
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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.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.sql.Dataset;
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import org.apache.spark.sql.Encoder;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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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.dhp.application.ArgumentApplicationParser;
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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 eu.dnetlib.message.Message;
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import eu.dnetlib.message.MessageManager;
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import eu.dnetlib.message.MessageType;
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public class GenerateNativeStoreSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GenerateNativeStoreSparkJob.class);
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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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if (invalidRecords != null)
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invalidRecords.add(1);
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e.printStackTrace();
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return null;
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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 Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class);
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final long dateOfCollection = new Long(parser.get("dateOfCollection"));
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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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final Map<String, String> ongoingMap = new HashMap<>();
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final Map<String, String> reportMap = new HashMap<>();
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final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
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SparkConf conf = new SparkConf();
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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(parser.get("input"), 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 MessageManager manager = new MessageManager(
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parser.get("rabbitHost"),
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parser.get("rabbitUser"),
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parser.get("rabbitPassword"),
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false,
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false,
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null);
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final JavaRDD<MetadataRecord> mappeRDD = 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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ongoingMap.put("ongoing", "0");
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if (!test) {
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manager
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.sendMessage(
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new Message(
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parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
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parser.get("rabbitOngoingQueue"),
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true,
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false);
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}
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final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
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final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
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final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
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mdStoreRecords.add(mdstore.count());
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ongoingMap.put("ongoing", "" + totalItems.value());
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if (!test) {
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manager
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.sendMessage(
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new Message(
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parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
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parser.get("rabbitOngoingQueue"),
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true,
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false);
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}
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mdstore.write().format("parquet").save(parser.get("output"));
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reportMap.put("inputItem", "" + totalItems.value());
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reportMap.put("invalidRecords", "" + invalidRecords.value());
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reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
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if (!test) {
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manager
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.sendMessage(
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new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
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parser.get("rabbitReportQueue"),
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true,
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false);
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manager.close();
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}
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});
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}
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}
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