package eu.dnetlib.dhp.oa.provision; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; import java.util.List; import java.util.Map; import java.util.Optional; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.SparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Maps; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.provision.model.*; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; import scala.collection.JavaConverters; import scala.collection.Seq; /** * XmlConverterJob converts the JoinedEntities as XML records */ public class XmlConverterJob { private static final Logger log = LoggerFactory.getLogger(XmlConverterJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static final String schemaLocation = "https://www.openaire.eu/schema/1.0/oaf-1.0.xsd"; public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( XmlConverterJob.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json"))); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); String otherDsTypeId = parser.get("otherDsTypeId"); log.info("otherDsTypeId: {}", otherDsTypeId); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ProvisionModelSupport.getModelClasses()); runWithSparkSession( conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); convertToXml( spark, inputPath, outputPath, ContextMapper.fromIS(isLookupUrl), otherDsTypeId); }); } private static void convertToXml( SparkSession spark, String inputPath, String outputPath, ContextMapper contextMapper, String otherDsTypeId) { final XmlRecordFactory recordFactory = new XmlRecordFactory( prepareAccumulators(spark.sparkContext()), contextMapper, false, schemaLocation, otherDsTypeId); final List paths = HdfsSupport .listFiles(inputPath, spark.sparkContext().hadoopConfiguration()); log.info("Found paths: {}", String.join(",", paths)); spark .read() .load(toSeq(paths)) .as(Encoders.kryo(JoinedEntity.class)) .map( (MapFunction>) je -> new Tuple2<>( je.getEntity().getId(), recordFactory.build(je)), Encoders.tuple(Encoders.STRING(), Encoders.STRING())) .javaRDD() .mapToPair( (PairFunction, Text, Text>) t -> new Tuple2<>(new Text(t._1()), new Text(t._2()))) .saveAsHadoopFile( outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); } private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } private static Seq toSeq(List list) { return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq(); } private static Map prepareAccumulators(SparkContext sc) { Map accumulators = Maps.newHashMap(); accumulators .put( "resultResult_similarity_isAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_isAmongTopNSimilarDocuments")); accumulators .put( "resultResult_similarity_hasAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_hasAmongTopNSimilarDocuments")); accumulators .put( "resultResult_supplement_isSupplementTo", sc.longAccumulator("resultResult_supplement_isSupplementTo")); accumulators .put( "resultResult_supplement_isSupplementedBy", sc.longAccumulator("resultResult_supplement_isSupplementedBy")); accumulators .put( "resultResult_dedup_isMergedIn", sc.longAccumulator("resultResult_dedup_isMergedIn")); accumulators.put("resultResult_dedup_merges", sc.longAccumulator("resultResult_dedup_merges")); accumulators .put( "resultResult_publicationDataset_isRelatedTo", sc.longAccumulator("resultResult_publicationDataset_isRelatedTo")); accumulators .put( "resultResult_relationship_isRelatedTo", sc.longAccumulator("resultResult_relationship_isRelatedTo")); accumulators .put( "resultProject_outcome_isProducedBy", sc.longAccumulator("resultProject_outcome_isProducedBy")); accumulators .put( "resultProject_outcome_produces", sc.longAccumulator("resultProject_outcome_produces")); accumulators .put( "resultOrganization_affiliation_isAuthorInstitutionOf", sc.longAccumulator("resultOrganization_affiliation_isAuthorInstitutionOf")); accumulators .put( "resultOrganization_affiliation_hasAuthorInstitution", sc.longAccumulator("resultOrganization_affiliation_hasAuthorInstitution")); accumulators .put( "projectOrganization_participation_hasParticipant", sc.longAccumulator("projectOrganization_participation_hasParticipant")); accumulators .put( "projectOrganization_participation_isParticipant", sc.longAccumulator("projectOrganization_participation_isParticipant")); accumulators .put( "organizationOrganization_dedup_isMergedIn", sc.longAccumulator("organizationOrganization_dedup_isMergedIn")); accumulators .put( "organizationOrganization_dedup_merges", sc.longAccumulator("resultProject_outcome_produces")); accumulators .put( "datasourceOrganization_provision_isProvidedBy", sc.longAccumulator("datasourceOrganization_provision_isProvidedBy")); accumulators .put( "datasourceOrganization_provision_provides", sc.longAccumulator("datasourceOrganization_provision_provides")); return accumulators; } }