package eu.dnetlib.dhp.oa.graph.raw; import com.clearspring.analytics.util.Lists; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.util.*; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; public class CopyHdfsOafApplication extends AbstractMigrationApplication { private static final Logger log = LoggerFactory.getLogger(CopyHdfsOafApplication.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( CopyHdfsOafApplication.class .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json"))); parser.parseArgument(args); final Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl"); log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl); final String mdFormat = parser.get("mdFormat"); log.info("mdFormat: {}", mdFormat); final String mdLayout = parser.get("mdLayout"); log.info("mdLayout: {}", mdLayout); final String mdInterpretation = parser.get("mdInterpretation"); log.info("mdInterpretation: {}", mdInterpretation); final String hdfsPath = parser.get("hdfsPath"); log.info("hdfsPath: {}", hdfsPath); final String isLookupUrl = parser.get("isLookupUrl"); log.info("isLookupUrl: {}", isLookupUrl); final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); final Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); final SparkConf conf = new SparkConf(); runWithSparkSession(conf, isSparkSessionManaged, spark -> processPaths(spark, vocs, hdfsPath, paths)); } public static void processPaths(final SparkSession spark, final VocabularyGroup vocs, final String outputPath, final Set paths) { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); log.info("Found {} mdstores", paths.size()); paths.forEach(log::info); final String[] validPaths = paths .stream() .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) .toArray(String[]::new); log.info("Non empty mdstores {}", validPaths.length); if (validPaths.length > 0) { // load the dataset Dataset oaf = spark .read() .load(validPaths) .as(Encoders.kryo(Oaf.class)); // dispatch each entity type individually in the respective graph subdirectory in append mode for(Map.Entry e : ModelSupport.oafTypes.entrySet()) { oaf .filter((FilterFunction) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey())) .map((MapFunction) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue())) .write() .option("compression", "gzip") .mode(SaveMode.Append) .text(outputPath + "/" + e.getKey()); } } } private static Relation getInverse(Relation rel, VocabularyGroup vocs) { final Relation inverse = new Relation(); inverse.setProperties(rel.getProperties()); inverse.setValidated(rel.getValidated()); inverse.setValidationDate(rel.getValidationDate()); inverse.setCollectedfrom(rel.getCollectedfrom()); inverse.setDataInfo(rel.getDataInfo()); inverse.setLastupdatetimestamp(rel.getLastupdatetimestamp()); inverse.setSource(rel.getTarget()); inverse.setTarget(rel.getSource()); inverse.setRelType(rel.getRelType()); inverse.setSubRelType(rel.getSubRelType()); return inverse; } }