package eu.dnetlib.dhp.collection; 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; import java.io.ByteArrayInputStream; import java.nio.charset.StandardCharsets; import java.util.HashMap; import java.util.Map; import java.util.Objects; 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.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; public class GenerateNativeStoreSparkJob { 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; } } 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")); final SparkSession spark = SparkSession.builder() .appName("GenerateNativeStoreSparkJob") .master(parser.get("master")) .getOrCreate(); final Map ongoingMap = new HashMap<>(); final Map reportMap = new HashMap<>(); final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest")); final JavaSparkContext sc = new JavaSparkContext(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(); } } }