package eu.dnetlib.dhp.transformation; import static eu.dnetlib.dhp.common.Constants.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.utils.DHPUtils.*; import java.io.IOException; import java.util.Map; import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; 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.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.data.mdstore.manager.common.model.MDStoreVersion; import eu.dnetlib.dhp.aggregation.common.AggregationCounter; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class TransformSparkJobNode { private static final Logger log = LoggerFactory.getLogger(TransformSparkJobNode.class); public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( TransformSparkJobNode.class .getResourceAsStream( "/eu/dnetlib/dhp/transformation/transformation_input_parameters.json"))); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String mdstoreInputVersion = parser.get("mdstoreInputVersion"); final String mdstoreOutputVersion = parser.get("mdstoreOutputVersion"); final MDStoreVersion nativeMdStoreVersion = MAPPER.readValue(mdstoreInputVersion, MDStoreVersion.class); final String inputPath = nativeMdStoreVersion.getHdfsPath() + MDSTORE_DATA_PATH; log.info("inputPath: {}", inputPath); final MDStoreVersion cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, MDStoreVersion.class); final String outputBasePath = cleanedMdStoreVersion.getHdfsPath(); log.info("outputBasePath: {}", outputBasePath); final String isLookupUrl = parser.get("isLookupUrl"); log.info(String.format("isLookupUrl: %s", isLookupUrl)); final String dateOfTransformation = parser.get("dateOfTransformation"); log.info(String.format("dateOfTransformation: %s", dateOfTransformation)); final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService); log.info("Retrieved {} vocabularies", vocabularies.vocabularyNames().size()); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { transformRecords( parser.getObjectMap(), isLookupService, spark, inputPath, outputBasePath); }); } public static void transformRecords(final Map args, final ISLookUpService isLookUpService, final SparkSession spark, final String inputPath, final String outputBasePath) throws DnetTransformationException, IOException { final LongAccumulator totalItems = spark.sparkContext().longAccumulator(CONTENT_TOTALITEMS); final LongAccumulator errorItems = spark.sparkContext().longAccumulator(CONTENT_INVALIDRECORDS); final LongAccumulator transformedItems = spark.sparkContext().longAccumulator(CONTENT_TRANSFORMEDRECORDS); final AggregationCounter ct = new AggregationCounter(totalItems, errorItems, transformedItems); final Encoder encoder = Encoders.bean(MetadataRecord.class); final Dataset mdstore = spark .read() .format("parquet") .load(inputPath) .as(encoder) .map( TransformationFactory.getTransformationPlugin(args, ct, isLookUpService), encoder); saveDataset(mdstore, outputBasePath + MDSTORE_DATA_PATH); log.info("Transformed item " + ct.getProcessedItems().count()); log.info("Total item " + ct.getTotalItems().count()); log.info("Transformation Error item " + ct.getErrorItems().count()); writeHdfsFile( spark.sparkContext().hadoopConfiguration(), "" + spark.read().load(outputBasePath + MDSTORE_DATA_PATH).count(), outputBasePath + MDSTORE_SIZE_PATH); } }