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 ongoingMap = new HashMap<>(); final Map 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 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 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 encoder = Encoders.bean(MetadataRecord.class); final Dataset 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; } } }